bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Aquifer Simulation Program for Micro‐Based Processors
Authors: Briz‐Kishore B. H. , Avadhanulu R.V.S.S. 
Published: July 2006

ABSTRACTA generalized aquifer simulation program is designed and developed to handle problems connected with different kinds of complex ground‐water systems on microprocessors. The characteristic aspect of this program, involving the “Strongly Implicit Procedure” is that it requires only 10K bytes of memory for the generated code.Using this program, the effect of pumping on an aquifer can be studied for multiple pumping periods and predictions or observations can be scrutinized at various time steps within each pumping period. The program can also handle conversion problems between confined and water‐table aquifers under leaky or nonleaky states along with the effects of evapotranspiration, constant recharge or discharge boundaries. The utility and precision of the program have been tested using a sample problem quoted by Trescott et al. (1976).
Geohydrologic Models of the Houston District, Texas
Authors: Jorgensen Donald G. 
Published: July 2006

ABSTRACTThe major water‐bearing units in the Houston district are the Chicot and Evangeline aquifer systems. Both systems consist of discontinuous layers of unconsolidated sand (aquifers) separated by clay layers.Extensive pumping has caused large declines of potentiometric surfaces in and around Houston. The declines have caused both the compaction of clay layers, which has resulted in land‐surface subsidence, and the movement of salt water towards Houston.During the early 1960's, an electric analog model of the district was made. The model simulated water‐level declines; but more importantly, the model indicated that the available data and conceptual model of the hydrologic system, consisting of two aquifers, were not totally adequate to allow simulation of the ground‐water systems.During the early 1970's, a second electric analog was built. The second model used new data and a conceptual model consisting of two aquifer systems simulated water‐level declines quite accurately, but the model was unable to accurately simulate the spatial distribution of water yielded from clay storage.A digital model was then developed during 1979 to simulate the hydrology of the district. The digital model used five layers and accurately simulated the hydraulic heads in both aquifer systems and land‐surface subsidence.
Characterization of a Contaminant Plume in Ground Water, Meredosia, Illinois
Authors: Naymik Thomas G. , Barcelona Michael J. 
Published: July 2006

ABSTRACTAspects of a nine‐month characterization of the physical‐chemical dynamics of a dissolved inorganic fertilizer plume in a shallow sand and gravel aquifer are reported. The work was undertaken to establish the extent of ground‐water contamination due to extremely high levels of total ammonia (>2,000 mg L−1) and to provide a basis for remedial action.The results from a numerical solute transport model showed the plume of contaminated ground water persisted at steady‐state conditions within the study site. This conclusion is supported by a comparison of the time of source emplacement (three years) to the calculated requirement of approximately one year for the plume at the field location to achieve a steady‐state configuration. Simulations suggested once the source was removed, about 420 days would be required to naturally flush the contaminant plume from the site.Chemical equilibrium calculations demonstrate that phosphate and carbonate mineral equilibria control calcium solubility in contaminated ground water. The most probable natural sink for ammonia removal from the plume is by the activity of nitrifying microorganisms, presumably well‐acclimated to the extreme conditions.
Well Vulnerability: A Quantitative Approach for Source Water Protection
Authors: Frind E.O. , Molson J.W. , Rudolph D.L. 
Published: July 2006

AbstractThe concept of vulnerability of drinking water sources is reviewed, and a quantitative approach for assessing well vulnerability for complex three‐dimensional ground water systems is developed. The approach focuses on the relative expected impact of potential contaminant sources at unknown locations within a well capture zone, providing relative measures of intrinsic well vulnerability, including the expected times of arrival of a contaminant, the dispersion‐related reduction in concentration, the time taken to breach a certain quality objective, and the corresponding exposure times. Thus, the result of the analysis includes the usual advective travel time information used in conventional wellhead protection analysis, plus a set of selected quantitative measures expressing the expected impact. The technique is based on adjoint theory and combines forward‐ and backward‐in‐time transport modeling using a standard numerical flow and transport code. The methodology is demonstrated using the case study of a complex glacial multiaquifer system in Ontario. The new approach will be useful in helping water managers develop more physically based and quantitative wellhead protection strategies.
An Assessment of Aquifer Storage Recovery Using Ground Water Flow Models
Authors: Lowry Christopher S. , Anderson Mary P. 
Published: July 2006

AbstractOwing to increased demands on ground water accompanied by increased drawdowns, technologies that use recharge options, such as aquifer storage recovery (ASR), are being used to optimize available water resources and reduce adverse effects of pumping. In this paper, three representative ground water flow models were created to assess the impact of hydrogeologic and operational parameters/factors on recovery efficiency of ASR systems. Flow/particle tracking and solute transport models were used to track the movement of water during injection, storage, and recovery. Results from particle tracking models consistently produced higher recovery efficiency than the solute transport models for the parameters/properties examined because the particle tracking models neglected mixing of the injected and ambient water. Mixing between injected and ambient water affected recovery efficiency. Results from this study demonstrate the interactions between hydrogeologic and operational parameters on predictions of recovery efficiency. These interactions are best simulated using coupled numerical ground water flow and transport models that include the effects of mixing of injected water and ambient ground water.
Reducing Long‐Term Remedial Costs by Transport Modeling Optimization
Authors: Becker David , Minsker Barbara , Greenwald Robert , Zhang Yan , Harre Karla , Yager Kathleen , Zheng Chunmiao , Peralta Richard 
Published: July 2006

AbstractThe Department of Defense (DoD) Environmental Security Technology Certification Program and the Environmental Protection Agency sponsored a project to evaluate the benefits and utility of contaminant transport simulation‐optimization algorithms against traditional (trial and error) modeling approaches. Three pump‐and‐treat facilities operated by the DoD were selected for inclusion in the project. Three optimization formulations were developed for each facility and solved independently by three modeling teams (two using simulation‐optimization algorithms and one applying trial‐and‐error methods). The results clearly indicate that simulation‐optimization methods are able to search a wider range of well locations and flow rates and identify better solutions than current trial‐and‐error approaches. The solutions found were 5% to 50% better than those obtained using trial‐and‐error (measured using optimal objective function values), with an average improvement of ∼20%. This translated into potential savings ranging from $600,000 to $10,000,000 for the three sites. In nearly all cases, the cost savings easily outweighed the costs of the optimization. To reduce computational requirements, in some cases the simulation‐optimization groups applied multiple mathematical algorithms, solved a series of modified subproblems, and/or fit “meta‐models” such as neural networks or regression models to replace time‐consuming simulation models in the optimization algorithm. The optimal solutions did not account for the uncertainties inherent in the modeling process. This project illustrates that transport simulation‐optimization techniques are practical for real problems. However, applying the techniques in an efficient manner requires expertise and should involve iterative modification to the formulations based on interim results.
Induction of Multiple Prophages from a Marine Bacterium: a Genomic Approach
Authors: Chen Feng , Wang Kui , Stewart Jeneen , Belas Robert 
Published: July 2006

ABSTRACT

Approximately 70% of sequenced bacterial genomes contain prophage-like structures, yet little effort has been made to use this information to determine the functions of these elements. The recent genomic sequencing of the marine bacterium
Silicibacter
sp. strain TM1040 revealed five prophage-like elements in its genome. The genomes of these prophages (named prophages 1 to 5) are approximately 74, 30, 39, 36, and 15 kb long, respectively. To understand the function of these prophages, cultures of TM1040 were treated with mitomycin C to induce the production of viral particles. A significant increase in viral counts and a decrease in bacterial counts when treated with mitomycin C suggested that prophages were induced from TM1040. Transmission electron microscopy revealed one dominant type of siphovirus, while pulsed-field gel electrophoresis demonstrated two major DNA bands, equivalent to 35 and 75 kb, in the lysate. PCR amplification with primer sets specific to each prophage detected the presence of prophages 1, 3, and 4 in the viral lysate, suggesting that these prophages are inducible, but not necessarily to the same level, while prophages 2 and 5 are likely defective or non-mitomycin C-inducible phages. The combination of traditional phage assays and modern microbial genomics provides a quick and efficient way to investigate the functions and inducibility of prophages, particularly for a host harboring multiple prophages with similar sizes and morphological features.
Effect of Drug Transporter Genes on Cysteine Export and Overproduction in
Escherichia coli
Authors: Yamada Satoshi , Awano Naoki , Inubushi Kyoko , Maeda Eri , Nakamori Shigeru , Nishino Kunihiko , Yamaguchi Akihito , Takagi Hiroshi 
Published: July 2006

ABSTRACT

l
-Cysteine is an important amino acid in terms of its industrial applications. We previously found a marked production of
l
-cysteine from glucose in recombinant
Escherichia coli
cells expressing an altered
cysE
gene encoding feedback inhibition-insensitive serine acetyltransferase. Also, a lower level of cysteine desulfhydrase (CD) activity, which is involved in
l
-cysteine degradation, increased
l
-cysteine productivity in
E. coli
. The use of an
l
-cysteine efflux system could be promising for breeding
l
-cysteine overproducers. In addition to YdeD and YfiK, which have been reported previously as
l
-cysteine exporter proteins in
E. coli
, we analyzed the effects of 33 putative drug transporter genes in
E. coli
on
l
-cysteine export and overproduction. Overexpression of the
acrD
,
acrEF
,
bcr
,
cusA
,
emrAB
,
emrKY
,
ybjYZ
, and
yojIH
genes reversed the growth inhibition of
tnaA
(the major CD gene)-disrupted
E. coli
cells by
l
-cysteine. We also found that overexpression of these eight genes reduces intracellular
l
-cysteine levels after cultivation in the presence of
l
-cysteine. Amino acid transport assays showed that Bcr overexpression conferring bicyclomycin and tetracycline resistance specifically promotes
l
-cysteine export driven by energy derived from the proton gradient. When a
tnaA
-disrupted
E. coli
strain expressing the altered
cysE
gene was transformed with a plasmid carrying the
bcr
gene, the transformant exhibited more
l
-cysteine production than cells carrying the vector only. A reporter gene assay suggested that the
bcr
gene is constitutively expressed at a substantial level. These results indicate that the multidrug transporter Bcr in the major facilitator family is involved in
l
-cysteine export and overproduction in genetically engineered
E. coli
cells.
The 3′ CCACCA Sequence of tRNA
Ala
(UGC) Is the Motif That Is Important in Inducing Th1-Like Immune Response, and This Motif Can Be Recognized by Toll-Like Receptor 3
Authors: Wang Zhijun , Xiang Li , Shao Junjie , Yuan Zhenghong 
Published: July 2006

ABSTRACT

In this article, the immunogenicity of tRNA and the recognition of tRNA by Toll-like receptors (TLRs) are analyzed. Analyses of the effects of different tRNA
Ala
(UGC) fragments (tRNA
Ala
1-76 [corresponding to positions 1 through 76], tRNA
Ala
26-76, tRNA
Ala
40-76, tRNA
Ala
62-76, tRNA
Ala
1-70, tRNA
Ala
26-70, tRNA
Ala
40-70, and tRNA
Ala
62-70) on the immune responses of hepatitis B surface antigen (HBsAg) were performed with BALB/c mice. Results show that tRNA
Ala
1-76, tRNA
Ala
26-76, tRNA
Ala
40-76, and tRNA
Ala
62-76 adjuvants not only induced stronger T helper (Th) 1 immune responses but also cytotoxic-T-lymphocyte (CTL) responses relative to tRNA
Ala
1-70, tRNA
Ala
26-70, tRNA
Ala
40-70, and tRNA
Ala
62-70 adjuvants in HBsAg immunization. A deletion of the D loop (tRNA
Ala
26-76), anticodon loop (tRNA
Ala
40-76), or TψC (tRNA
Ala
62-76) loop of tRNA
Ala
(UGC) does not significantly decrease the adjuvant characteristic of tRNA
Ala
(UGC). However a deletion of the 3′-end CCACCA sequence (tRNA
Ala
1-70, tRNA
Ala
26-70, tRNA
Ala
40-70, and tRNA
Ala
62-70) of tRNA
Ala
(UGC) significantly decreased the adjuvant characteristic in Th1 and CTL immune responses. Moreover, the recognitions of different tRNA
Ala
(UGC) fragments by TLR3, TLR7, TLR8, and TLR9 were analyzed. Results show that a deletion of the 3′ CCACCA sequence of tRNA
Ala
(UGC) significantly decreased the recognition by TLR3. We concluded that the 3′ CCACCA sequence of tRNA
Ala
(UGC) is the important motif to induce Th1 and CTL responses and this motif can be effectively recognized by TLR3.
Tuberculin Skin Test Conversion and Reactivity Rates among Adults with and without Human Immunodeficiency Virus in Urban Settings in Ethiopia
Authors: Tegbaru Belete , Wolday Dawit , Messele Tsehaynesh , Legesse Mengistu , Mekonnen Yared , Miedema Frank , van Baarle Debbie 
Published: July 2006

ABSTRACT

To investigate whether low CD4
+
T-cell counts in healthy and human immunodeficiency virus (HIV)-infected Ethiopians influence tuberculosis (TB) immunological memory, tuberculin skin test (TST) conversion and reactivity rates were investigated among adults with and without HIV infection in urban settings in Ethiopia. Reaction to the TST was analyzed with purified protein derivative by the Mantoux technique. A total of 1,286 individuals with TST results of ≥5-mm (
n
= 851) and ≤4-mm (
n
= 435) induration diameters were included. Individuals with ≤4-mm induration sizes were followed up for 21.4 ± 9.5 months (mean ± standard deviation) to observe skin test conversion. The overall TST reactivity (≥5-mm induration diameter) was 66.2% (
n
= 851). Reactivity was significantly lower among HIV-positive persons (40.5%) than among HIV-negative persons (68.7%) (
P
< 0.001). Of the above persons, 32 incident TB patients were checked for their TST status 13.05 ± 11.1 months before diagnosis and reactivity was found among 22 (68.7%) of them. Of the TST-negative persons with 0- to 4-mm indurations who were followed up for 3 years, the conversion rate to positivity was 17.9/100 person-years of observation (PYO) (14.4/100 PYO and 18.3/100 PYO in HIV-positive and -negative persons, respectively). Despite lower absolute CD4
+
T-cell numbers in Ethiopians, higher TST conversion and reactivity rates show the presence of a higher rate of latent TB infection and/or transmission. The lower TST positivity rate before a diagnosis of TB disease showed the lower sensitivity of the test. This indicates the need for other sensitive and specific diagnostic and screening methods to detect TB infection, particularly among HIV-positive persons, so that they can be given prophylactic isoniazid therapy.
Antibody Response to
Cryptococcus neoformans
Capsular Polysaccharide Glucuronoxylomannan in Patients after Solid-Organ Transplantation
Authors: Jalali Ziba , Ng Lucky , Singh Nina , Pirofski Liise-anne 
Published: July 2006

ABSTRACT

Cryptococcosis is an important complication of solid-organ transplantation, but the risk factors for disease are poorly understood. The goal of this study was to investigate whether specific or nonspecific serum immunoglobulin levels determined in samples obtained before and after solid-organ transplantation differed in patients who did or did not develop cryptococcosis after transplantation. We analyzed pretransplantation sera from 25 subjects, 15 who subsequently developed cryptococcosis and 10 who did not, and posttransplantation sera from 24 subjects, 13 who developed cryptococcosis and 11 who did not. All subjects received a tacrolimus-based immunosuppressive regimen. Total immunoglobulin levels were measured by immunodiffusion, and
Cryptococcus neoformans
capsular polysaccharide glucuronoxylomannan (GXM)-specific serum antibody levels were determined by enzyme-linked immunosorbent assays. The results showed that solid-organ transplantation had a significant effect on total immunoglobulin and GXM-reactive antibody levels. GXM-reactive antibody levels differed in subjects who did and did not develop cryptococcosis. In pretransplant serum samples, the levels of GXM-reactive immunoglobulin M (IgM) were significantly lower in subjects who developed cryptococcosis after transplantation than in those who did not. For posttransplant serum samples, the levels of GXM-reactive IgM and IgG were significantly higher among the subjects who developed cryptococcosis than among those who did not. These findings suggest that perturbations in the preexisting antibody or B-cell repertoire and/or related to treatment of rejection, transplantation, or immunosuppressive therapy could translate into an increased risk for transplant-associated cryptococcosis.
Macrorestriction Analysis of Clinical and Environmental Isolates of
Sporothrix schenckii
Authors: O'Reilly L. C. , Altman S. A. 
Published: July 2006

ABSTRACT

Sporothrix schenckii
causes sporotrichosis, a disease that most commonly presents as a subacute or chronic skin infection. An unusually high incidence of clinical cases of sporotrichosis occurred in the southwest of Western Australia over the last 5 years. Anecdotal accounts from patients implicated contact with hay prior to infection. Isolates of
S. schenckii
from hay and clinical cases were investigated by traditional phenotypic methods and pulsed-field gel electrophoresis (PFGE). The phenotypic evaluation separated
S. schenckii
from
Ophiostoma
spp. A DNA macrorestriction method using SfiI and NotI macrorestriction digestion by PFGE was developed to investigate the epidemiological connections. BioNumerics software was used to analyze the results. DNA macrorestriction digestion patterns for the recent Western Australian clinical isolates and four hay isolates were indistinguishable. Eastern state clinical isolates, national Quality Assurance Program isolates, and other environmental isolates gave different macrorestriction patterns. Clinical isolates from the southwest of Western Australia collected in the 1980s and 1990s were also characterized using PFGE. The patterns generated were indistinguishable from those of the recent clinical isolates. PFGE showed that the dominant strain of
S. schenckii
causing sporotrichosis in Western Australia is present in hay, has caused sporotrichosis for at least 15 years, and is a different strain from the strains found in other parts of Australia.
Sternal Wound Infection byTrichosporon inkinfollowing Cardiac Surgery
Authors: Davies Frances , Logan Sarah , Johnson Elizabeth , Klein John L. 
Published: July 2006

ABSTRACTWound infection following cardiac surgery is well described but is rarely due to fungal infection. We describe a case of sternal wound infection caused byTrichosporon inkinwith a fatal outcome, in an immunocompetent patient following aortic root surgery.
Toxin Gene Content of the Lyon Methicillin-Resistant
Staphylococcus aureus
Clone Compared with That of Other Pandemic Clones
Authors: Ferry Tristan , Bes Michèle , Dauwalder Olivier , Meugnier Hélène , Lina Gerard , Forey Françoise , Vandenesch François , Etienne Jerome 
Published: July 2006

ABSTRACT

The methicillin-resistant
Staphylococcus aureus
(MRSA) Lyon clone, detected throughout France, contains the enterotoxin A gene (
sea
), like other pandemic clones of clonal complex 8 (CC8). The
egc
locus was detected in MRSA pandemic clones of CC5, CC22, and CC45, occasionally with the toxic shock syndrome toxin 1 gene. The representative strain of the EMRSA-16 clone (CC30) harbored both
sea
and the
egc
locus.
Culture-Independent Molecular Subtyping of
Mycoplasma pneumoniae
in Clinical Samples
Authors: Dumke Roger , Lück Paul Christian , Noppen Christoph , Schaefer Christoph , von Baum Heike , Marre Reinhard , Jacobs Enno 
Published: July 2006

ABSTRACT

A new molecular subtyping approach was developed which is based on the amplification and sequencing of a repetitive region of the P1 gene of
Mycoplasma pneumoniae
. It allows the differentiation of all known subtypes and variants of
M. pneumoniae
as well as the identification of new subtypes directly in clinical samples to characterize endemic and epidemic
M. pneumoniae
infections.
Sequence Analysis of
Enterococcus faecium
Strain 10/96A (VanD4), the Original Vancomycin-Resistant
E. faecium
Strain in Brazil
Authors: Camargo Ilana L. B. C. , Dalla Costa Libera M. , Woodford Neil , Gilmore Michael S. , Darini Ana L. C. 
Published: July 2006

ABSTRACT

Enterococcus faecium
strain 10/96A (VanD4) was the first vancomycin-resistant enterococcus (VRE) isolated in Brazil. Subsequent Brazilian VRE strains have all had the VanA phenotype. Multilocus sequence typing showed that strain 10/96A was isolated sporadically, has a unique sequence type (ST 281), and was not the progenitor of the VRE strains isolated from hospital outbreaks in Brazil.
Hospital-Acquired
Bordetella bronchiseptica
Infection following Hematopoietic Stem Cell Transplantation
Authors: Huebner Elizabeth S. , Christman Brian , Dummer Stephen , Tang Yi-Wei , Goodman Stacey 
Published: July 2006

ABSTRACT

Two patients who had undergone nonmyeloablative allogeneic stem cell transplantation 53 and 112 days earlier and were being monitored at the same transplant center developed severe
Bordetella bronchiseptica
infections within 3 days of each other. Pulsed-field gel electrophoresis analysis indicated that the isolates from the two cases were identical. Neither patient had had direct contact with animals since transplantation. These findings strongly support nosocomial transmission of
B. bronchiseptica.