bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pesticides in Ground Water of the United States, 1992–1996
Authors: Kolpin Dana W. , Barbash Jack E. , Gilliom Robert J. 
Published: August 2005

AbstractDuring the first cycle of the National Water Quality Assessment (1992–1996), ground water in 20 of the nation's major hydro‐logic basins was analyzed for 90 pesticide compounds (pesticides and degradates). One or more of the pesticide compounds examined were detected at 48.4% of the 2485 ground water sites sampled. However, approximately 70% of the sites where pesticides were detected, two or more pesticide compounds analyzed were present–documenting the prevalence of pesticide mixtures in ground water. The pesticide concentrations encountered were generally low, with the median total concentration (summation of concentrations for the 90 pesticide compounds) being 0.046 μg/L. Pesticides were commonly detected in shallow ground water beneath both agricultural (60.4%) and urban (48.5%) areas. This is an important finding because, although agricultural activities have long been associated with pesticide contamination, urban areas have only recently been recognized as a potential source of these types of compounds. Pesticides with higher frequencies of detection were generally those with more extensive use, greater environmental persistence, and greater mobility in ground water (lower soil‐water partition coefficients).
Fingering in Unsaturated Zone Flow: A Qualitative Review with Laboratory Experiments on Heterogeneous Systems
Authors: Sililo Oliver T.N. , Tellam John H. 
Published: August 2005

AbstractUnstable unsaturated zone flow (fingering) is a potentially important process in recharge, pollution, and surface water/ground water body interactions. Extending previous workers' studies on homogeneous systems, sand tank experiments have been carried out on heterogeneous systems. The experiments on initially dry silica sands suggest that (1) stratification will tend to enhance rather than dissipate fingering; (2) in discontinuously layered systems, funneling influences the location of fingers; (3) in multilayered systems, lateral flow on top of fine‐grained layers promotes greater flux (and more fingers) in the down‐dip direction; (4) in systems where a top fine‐grained layer has a variable thickness, finger frequency and, hence, amount of flow will be greatest where the fine‐grained layer is thinnest; (5) surface depressions in an upper fine‐grained layer will concentrate flow, with fingers forming below such areas; and (6) in systems where an upper fine‐grained layer has macropores, the latter will concentrate water flow and fingers will form directly below these zones. The experiments also confirmed that fingers can persist in the same locations from one recharge event to another, and that in initially moist sands, fingers are widened. It is clear that a complex interplay between fingering and funneling processes can occur and that finger behavior is sensitive to heterogeneity.
Anomalous Fresh Water Lens Morphology on a Strip Barrier Island
Authors: Ruppel C. , Schultz G. , Kruse S. 
Published: August 2005

AbstractElectromagnetic surveys of a young, wholly sedimentary, strip barrier island (St. George Island) on Florida's Gulf Coast reveal a Dupuit‐Ghyben‐Herzberg fresh water lens with the thickest part located close to the ocean side of the island at both undeveloped and developed sites. This result is at odds with those obtained on other barrier beaches, where the lens is either approximately symmetric or skewed toward the lagoon side due to higher sea level and greater upper beach storage on the ocean side. The inferred morphology of the fresh water lens on St. George Island can be attributed to variations in hydrogeologic (e.g., hydraulic conductivity, presence of semipermeable confining layer) and/or boundary conditions (e.g., recharge, higher sea level on the lagoon side), but the effects of variations in these factors on the shape of the lens are not separable. We therefore use independent constraints on hydraulic conductivity (from tidal pumping analyses), hydrofacies distribution, and recharge patterns to assess the plausibility that lateral variations in various physical parameters produce the observed lens shape. Dune ridge topography, which may constitute a significant portion of the width of a narrow island, perturbs recharge and shallow ground water flow patterns and may contribute to the development of a thick fresh water lens on an island's ocean side. However, topographic variations alone cannot account for the anomalous form of the island's fresh water lens.
Reducing the Influence of Skin Effects on Hydraulic Conductivity Determinations in Multilevel Samplers Installed with Direct Push Methods
Authors: Henebry Brent J. , Robbins Gary A. 
Published: August 2005

AbstractField tests were conducted to investigate skin effects in multilevel ground water samplers installed with direct push methods. Tests consisted of determining hydraulic conductivity values using slug tests in five multilevel samplers before, during, and after development. Development was conducted using a minisurge block tool designed for this study. Post‐development hydraulic conductivity values were found to be 3.2 to 9.6 times greater than predevelopment values. The largest differences were observed in multilevel samplers positioned in low permeable materials that were installed in preprobed holes advanced by hydraulic hammering and pushing as opposed to probes situated in higher permeable materials that were installed in cored holes. The presence and magnitude of the skin effects, as well as the reduction of these effects by rigorous development, were confirmed through comparisons with steady‐state pumping tests conducted in multilevel samplers and previously conducted slug tests in conventional monitoring wells. These results indicate the need for rigorous development prior to hydraulic conductivity testing in ground water samplers installed with direct push methods.
Systematic Makings of Early Stage Hydrogeologic Conceptual Models
Authors: LeGrand Harry E. , Rosen Lars 
Published: August 2005

AbstractTechniques to obtain optimal value from existing hydrogeological information are neglected in many ground water contamination studies, resulting in great costs to the public. Data collection and routine interpretations should not be good enough for hydrogeologists, who should be inherently adept at keen early perspectives and applying useful generalizations. Techniques are available to obtain and explain expanded knowledge from piecemeal and imprecise information at the early stages of site studies. Scarcity of precise data should not be a deterrent. This needed mindset should precede the prevailing mindset of initial collection of extensive new data, followed by data interpretation and mathematical modeling. The existing mindset is often guided by rigid regulations.The procedure of interlocking the past with the present to predict the future through the systematic use of generalizations and retrodictive inferences builds a prior conceptual model explanation (PCME). This early PCME is an organized, mental picture or discernment of a hydrogeological setting displaying three‐dimensional hydrogeologic features, the discernment being capable of explaining in narrative form the general fluid mechanics and contaminant behavior within imprecise but reasonable bounds. This characterization is logically followed by possible cause‐and‐effect relations and predictions of extended consequences of natural and human actions. A site PCME has sound support from the cross‐checking of interrelated factors that leads to almost interlocking proofs.
Transient‐State History Matching of a Karst Aquifer Ground Water Flow Model
Authors: Larocque M. , Banton O. , Razack M. 
Published: August 2005

AbstractGround water flow modeling in a karst aquifer presents many difficulties. In particular, the hydrodynamic properties and the flow behavior can vary over time. History matching of transient‐state conditions is required to test the accuracy of the model under varying hydrodynamic conditions. The objective of this study was to illustrate how transient‐state conditions can be used to history match a ground water flow model of a large aquifer, the La Rochefoucauld karst (Charente, France). The model used a porous medium equivalent and was based on a steady‐state calibration of hydraulic conductivities. The history match consisted of studying the simulated heads and spring flow rates to test the capacity of the model to reproduce different aspects of the aquifer behavior. The simulated heads and flow rates were analyzed as new data using correlation and spectral analyses to compare the temporal structures of the measured and simulated time series. The analyses provided information on the storage capacity of the aquifer, the input‐output delays, the degree of correlation between input and output, and the length of the impulse response of the aquifer. These data were used to study the impact of the hypotheses underlying the model (hydraulic conductivities, storage coefficient, representation of rivers, use of a porous medium equivalent). The results show that the model adequately simulates the overall behavior of the studied aquifer. The model can be used under variable hydrodynamic conditions to simulate ground water flow on a regional scale. This case study illustrates how a complete history match of a simplified representation of reality can lead to an adequate mathematical tool.
Water Resource Implications of 18O and 2H Distributions in a Basalt Aquifer System
Authors: Larson Kathryn R. , Keller C. Kent , Larson Peter B. , Allen‐King Richelle M. 
Published: August 2005

AbstractOngoing decline of water levels in the confined basalt aquifers of the Pullman‐Moscow Basin of Washington and Idaho has prompted study of the timing, amount and distribution of recharge to the system. Previous radiocarbon ages indicate residence times on the order of 103 years and greater and suggest a low rate of recharge to the lower basalt aquifer since the end of Pleistocene time. By contrast, more recent hydrodynamic flow modeling studies invoke a larger Holocene recharge rate through the unconfined loess unit to the upper and lower basalt aquifers, which implies relatively short residence times (102 years). Stable isotopes were used to independently assess contrasting recharge models by comparing 18O/16O and D/H ratios of late‐Holocene shallow ground water and deep ground water. Linear regression of local precipitation ratios yields δD = 6.9 δ18O −18.5. There is no evidence of fractionation of ground water ratios by recharge processes or water‐rock interactions. Deep basalt ground water δ18O values are depleted by 0.4 to 4.9 per mil relative to shallow, recently recharged ground waters and have δ18O values statistically distinct from waters sampled from other stratigraphic units. These findings suggest that the deep waters in the basin were not precipitated under current climate conditions and that aquifer recharge rates to the deep basalt aquifer are substantially lower than have been recently estimated. This in turn suggests that a sustainable ground water exploitation scheme must reduce reliance on the deep ground water resource.
Use of a Suspension Array for Rapid Identification of the Varieties and Genotypes of the
Cryptococcus neoformans
Species Complex
Authors: Diaz Mara R. , Fell Jack W. 
Published: August 2005

ABSTRACT

Cryptococcus neoformans
is an encapsulated fungal pathogen known to cause severe disease in immunocompromised patients. The disease, cryptococcosis, is mostly acquired by inhalation and can result in a chronic meningoencephalitis, which can be fatal. Here, we describe a molecular method to identify the varieties and genotypic groups within the
C. neoformans
species complex from culture-based assays. The method employs a novel flow cytometer with a dual laser system that allows the simultaneous detection of different target sequences in a multiplex and high-throughput format. The assay uses a liquid suspension hybridization format with specific oligonucleotide probes that are covalently bound to the surface of fluorescent color-coded microspheres. Biotinylated target amplicons, which hybridized to their complementary probe sequences, are quantified by the addition of the conjugate, streptavidin R-phycoerythrin. In this study we developed and validated eight probes derived from sequence analysis of the intergenic spacer region of the rRNA gene region. The assay proved to be specific and sensitive, allowed discrimination of a 1-bp mismatch with no apparent cross-reactivity, and detected 10
1
to 10
3
genome copies. The described protocol, which can be used directly with yeast cells or isolated DNA, can be undertaken in less than 1 h following PCR amplification and permits identification of species in a multiplex format. In addition to a multiplex capability, the assay allows the simultaneous detection of target sequences in a single reaction. The accuracy, speed, flexibility, and sensitivity of this technology are a few of the advantages that will make this assay useful for the diagnosis of human cryptococcal infections and other pathogenic diseases.
Development of a New Oligonucleotide Array To Identify Staphylococcal Strains at Species Level
Authors: Giammarinaro Philippe , Leroy Sabine , Chacornac Jean-Paul , Delmas Julien , Talon Regine 
Published: August 2005

ABSTRACT

The genus
Staphylococcus
is made up of 36 validated species which contain strains that are pathogenic, saprophytic, or used as starter cultures for the food industry. An oligonucleotide array targeting the manganese-dependent superoxide dismutase (
sodA
) gene was developed to overcome the drawbacks of the conventional methods of identification. Divergences of the
sodA
gene were used to design oligonucleotide probes, and we showed that each of the 36 species had a characteristic pattern of hybridization. To evaluate the array, we analyzed 38 clinical and 38 food or food plant
Staphylococcus
isolates identified by the phenotype-based system VITEK 2 (bioMérieux). This commercial kit failed to identify 8 (21%) of the clinical isolates and 32 (84%) of the food and food plant isolates. In contrast, the oligonucleotide array we designed provided an accurate and rapid method for the identification of staphylococcal strains, isolated from clinical, environmental, or food samples, at species level.
Multilocus Sequence Typing of Swedish Invasive Group B Streptococcus Isolates Indicates a Neonatally Associated Genetic Lineage and Capsule Switching
Authors: Luan Shi-Lu , Granlund Margareta , Sellin Mats , Lagergård Teresa , Spratt Brian G. , Norgren Mari 
Published: August 2005

ABSTRACT

Streptococcus agalactiae
, also designated group B streptococcus (GBS), is an important pathogen in neonates, pregnant women, and nonpregnant adults with predisposing conditions. We used multilocus sequence typing (MLST) to characterize 158 GBS isolates that were associated with neonatal and adult invasive disease and that were collected in northern and western Sweden from 1988 to 1997. Five major genetic lineages (sequence type [ST] 19, ST-17, ST-1, ST-23, and ST-9 complexes) were identified among the isolates, including serotype Ia, Ib, and II to V isolates, indicating a highly clonal population structure among invasive GBS isolates. A number of STs were found to contain isolates of different serotypes, which indicates that capsule switching occurred rather frequently. Two distantly related genetic lineages were identified among isolates of serotype III, namely, clonal complex 19 (CC19), and CC17. CC19 was equally common among isolates from adult and neonatal disease (accounting for 10.3% of GBS isolates from adult disease and 18.7% from neonatal disease), whereas CC17 significantly appeared to be associated with neonatal invasive disease (isolated from 21.9% of neonatal isolates but only 2.6% of adult isolates). The distribution of the mobile elements GBSi1 and IS
1548
reveals that they can act as genetic markers for lineages CC17 and CC19, respectively.
Ability of the Vector Tick
Boophilus microplus
To Acquire and Transmit
Babesia equi
following Feeding on Chronically Infected Horses with Low-Level Parasitemia
Authors: Ueti Massaro W. , Palmer Guy H. , Kappmeyer Lowell S. , Statdfield Mary , Scoles Glen A. , Knowles Donald P. 
Published: August 2005

ABSTRACT

The protozoan parasite
Babesia equi
replicates within erythrocytes. During the acute phase of infection,
B. equi
can reach high levels of parasitemia, resulting in a hemolytic crisis. Horses that recover from the acute phase of the disease remain chronically infected. Subsequent transmission is dependent upon the ability of vector ticks to acquire
B. equi
and, following development and replication, establishment of
B. equi
in the salivary glands. Although restriction of the movement of chronically infected horses with
B. equi
is based on the presumption that ticks can acquire and transmit the parasite at low levels of long-term infection, parasitemia levels during the chronic phase of infection have never been quantified, nor has transmission been demonstrated. To address these epidemiologically significant questions, we established long-term
B. equi
infections (>1 year), measured parasitemia levels over time, and tested whether nymphal
Boophilus microplus
ticks could acquire and, after molting to the adult stage, transmit
B. equi
to naive horses.
B. equi
levels during the chronic phase of infection ranged from 10
3.3
to 10
6.0
/ml of blood, with fluctuation over time within individual horses.
B. microplus
ticks fed on chronically infected horses with mean parasite levels of 10
5.5
± 10
0.48
/ml of blood acquired
B. equi
, with detection of
B. equi
in the salivary glands of 7 to 50% of fed ticks, a range encompassing the percentage of positive ticks that had been identically fed on a horse in the acute phase of infection with high parasitemia levels. Ticks that acquired
B. equi
from chronically infected horses, as well as those fed during the acute phase of infection, successfully transmitted the parasite to naive horses. The results unequivocally demonstrated that chronically infected horses with low-level parasitemia are competent mammalian reservoirs for tick transmission of
B. equi
.
Identification of Medically Important Molds by an Oligonucleotide Array
Authors: Hsiao Chen Ren , Huang Liyin , Bouchara Jean-Philippe , Barton Richard , Li Hsin Chieh , Chang Tsung Chain 
Published: August 2005

ABSTRACT
Infections caused by fungi have increased in recent years. Accurate and rapid identification of fungal pathogens is important for appropriate treatment with antifungal agents. On the basis of the internal transcribed spacer 1 (ITS 1) and ITS 2 sequences of the rRNA genes, an oligonucleotide array was developed to identify 64 species (32 genera) of clinically important filamentous (or dimorphic) fungi. These 64 species included fungi causing superficial, cutaneous, subcutaneous, and invasive infections. The method consisted of PCR amplification of the ITS regions using a pair of universal primers, followed by hybridization of the digoxigenin-labeled PCR products to a panel of species- or group-specific oligonucleotides immobilized on a nylon membrane. Of 397 fungal strains (290 target and 107 nontarget strains) tested, the sensitivity and specificity of the array was 98.3% (285/290) and 98.1% (105/107), respectively. Misidentified strains were usually those belonging to the same genus of the target species or having partial homology with oligonucleotide probes on the membrane. The whole procedure can be finished within 24 h starting from isolated colonies; reproductive structures, which are essential for the conventional identification methods, are not needed. In conclusion, the present array is a powerful tool for identification of clinically important filamentous fungi and may have the potential to be continually extended by adding further oligonucleotides to the array without significantly increasing the cost or complexity.
Broadly Reactive Nested Reverse Transcription-PCR Using an Internal RNA Standard Control for Detection of Noroviruses in Stool Samples
Authors: Medici Maria Cristina , Martinelli Monica , Ruggeri Franco Maria , Abelli Laura Anna , Bosco Simona , Arcangeletti Maria Cristina , Pinardi Federica , De Conto Flora , Calderaro Adriana , Chezzi Carlo , Dettori Giuseppe 
Published: August 2005

ABSTRACT

We developed a nested reverse transcription-PCR (nRT-PCR) for the detection of noroviruses in stools, using random primers for RT, the JV12/JV13 primer pair in the first round of nPCR, and a set of nine inner primers for the second, comprising the reverse sequences of primers SR46, SR48, SR50, and SR52, and five novel oligonucleotide sequences (113-1, 113-2, 115-1, 115-2, and 115-3). The specificity of the nRT-PCR was confirmed by testing 61 stools containing enteric viruses other than noroviruses. In comparative assays on either stools or RNA dilutions from two genogroup I and three genogroup II (GII) norovirus-positive samples, nRT-PCR was always at least as sensitive as RT-PCR and Southern hybridization. With some of the samples tested, the increase in sensitivity was 10-fold or higher. For GII viruses, the detectable range of nRT-PCR was estimated to be 8.4 × 10
4
to 2 RNA viral particles. When used on 85 stools from pediatric patients with acute gastroenteritis negative for viruses by electron microscopy and cell culture, the nRT-PCR detected norovirus in 19 samples (22.3%), while it failed to detect one reference RT-PCR-positive sample containing a Desert Shield strain. Sixteen of the 19 nRT-PCR-positive samples gave concordant results with reference RT-PCR and Southern hybridization, and all with sequence analysis. Partial sequencing of the polymerase region revealed that from January to April 2000 all GII strains except two (Rotterdam- and Leeds-like viruses) formed a tight cluster related to Hawaii virus. The nRT-PCR described could prove suitable for large epidemiological studies and for specialized clinical laboratories performing routine molecular testing.
DNA Probe Array for the Simultaneous Identification of Herpesviruses, Enteroviruses, and Flaviviruses
Authors: Korimbocus Jehanara , Scaramozzino Noël , Lacroix Bruno , Crance Jean Marc , Garin Daniel , Vernet Guy 
Published: August 2005

ABSTRACT

Viral infections of the central nervous system (CNS) are caused by a variety of viruses, namely, herpesviruses, enteroviruses, and flaviviruses. The similar clinical signs provoked by these viruses make the diagnosis difficult. We report on the simultaneous detection of these major CNS pathogens using amplification by PCR and detection of amplified products using DNA microarray technology. Consensus primers were used for the amplification of all members of each genus. Sequences specific for the identification of each virus species were selected from the sequence alignments of each target gene and were synthesized on a high-density microarray. The amplified products were pooled, labeled, and cleaved, followed by hybridization on a single array. This method was successfully used to identify herpesviruses, namely, herpes simplex virus type 1 (HSV-1), HSV-2, and cytomegalovirus; all serotypes of human enteroviruses; and five flaviviruses (West Nile virus, dengue viruses, and Langat virus). This approach, which used highly conserved consensus primers for amplification and specific sequences for identification, would be extremely useful for the detection of variants and would probably help solve some unexplained cases of encephalitis. The analytical sensitivity of the method was shown to be 500 genome equivalents ml
−1
for HSV-1, 0.3 50% tissue culture infectious doses (TCID
50
s) ml
−1
for the enterovirus coxsackievirus A9, and 200 TCID
50
s ml
−1
for West Nile virus. The clinical sensitivity of this method must now be evaluated.