bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transition Probability/Markov Chain Analyses of DNAPL Source Zones and Plumes
Authors: Maji R. , Sudicky E.A. , Panday S. , Teutsch G. 
Published: March 2006

AbstractAt sites where a dense nonaqueous phase liquid (DNAPL) was spilled or released into the subsurface, estimates of the mass of DNAPL contained in the subsurface from core or monitoring well data, either in the nonaqueous or aqueous phase, can be highly uncertain because of the erratic distribution of the DNAPL due to geologic heterogeneity. In this paper, a multiphase compositional model is applied to simulate, in detail, the DNAPL saturations and aqueous‐phase plume migration in a highly characterized, heterogeneous glaciofluvial aquifer, the permeability and porosity data of which were collected by researchers at the University of Tübingen, Germany. The DNAPL saturation distribution and the aqueous‐phase contaminant mole fractions are then reconstructed by sampling the data from the forward simulation results using two alternate approaches, each with different degrees of sampling conditioning. To reconstruct the DNAPL source zone architecture, the aqueous‐phase plume configuration, and the contaminant mass in each phase, one method employs the novel transition probability/Markov chain approach (TP/MC), while the other involves a traditional variogram analysis of the sampled data followed by ordinary kriging. The TP/MC method is typically used for facies and/or hydraulic conductivity reconstruction, but here we explore the applicability of the TP/MC method for the reconstruction of DNAPL source zones and aqueous‐phase plumes. The reconstructed geometry of the DNAPL source zone, the dissolved contaminant plume, and the estimated mass in each phase are compared using the two different geostatistical modeling approaches and for various degrees of data sampling from the results of the forward simulation. It is demonstrated that the TP/MC modeling technique is robust and accurate and is a preferable alternative compared to ordinary kriging for the reconstruction of DNAPL saturation patterns and dissolved‐phase contaminant plumes.
Karst Spring Responses Examined by Process‐Based Modeling
Authors: Birk Steffen , Liedl Rudolf , Sauter Martin 
Published: March 2006

AbstractGround water in karst terrains is highly vulnerable to contamination due to the rapid transport of contaminants through the highly conductive conduit system. For contamination risk assessment purposes, information about hydraulic and geometric characteristics of the conduits and their hydraulic interaction with the fissured porous rock is an important prerequisite. The relationship between aquifer characteristics and short‐term responses to recharge events of both spring discharge and physicochemical parameters of the discharged water was examined using a process‐based flow and transport model. In the respective software, a pipe‐network model, representing fast conduit flow, is coupled to MODFLOW, which simulates flow in the fissured porous rock. This hybrid flow model was extended to include modules simulating heat and reactive solute transport in conduits. The application of this modeling tool demonstrates that variations of physicochemical parameters, such as solute concentration and water temperature, depend to a large extent on the intensity and duration of recharge events and provide information about the structure and geometry of the conduit system as well as about the interaction between conduits and fissured porous rock. Moreover, the responses of solute concentration and temperature of spring discharge appear to reflect different processes, thus complementing each other in the aquifer characterization.
Aquifer Responses to El Niño–Southern Oscillation, Southwest British Columbia
Authors: Fleming Sean W. , Quilty Edward J. 
Published: March 2006

AbstractWe used climatological composite analysis to investigate El Niño–Southern Oscillation (ENSO) signals in long‐term shallow ground water level observations from four wells in the lower Fraser Valley of British Columbia. Significance of differences between warm‐phase, cold‐phase, and neutral climate states was assessed with a Monte Carlo bootstrap technique. We also considered time series of local precipitation and streamflow for comparison. Composite annual hyetographs suggest that ENSO precipitation impacts are largely limited to winter and spring, with higher and lower rainfall occurring, respectively, under cold‐phase and warm‐phase episodes. This is consistent with prior work in the region and is found to be directly reflected in both streamflow and ground water level data. The mean magnitude of ENSO terrestrial hydrologic anomalies can be up to ∼50% of the average seasonal cycle amplitude. ENSO does not appear to systematically affect annual hydrometeorological cycle timing in this study area. However, relative to the surface hydrologic systems considered, aquifers are observed to retain a stronger memory of seasonal ENSO‐related precipitation anomalies, with changes potentially extending through the following summer, presumably reflecting storage effects. Most responses appear to be somewhat nonlinear.
The Role of Hand Calculations in Ground Water Flow Modeling
Authors: Haitjema Henk 
Published: March 2006

AbstractMost ground water modeling courses focus on the use of computer models and pay little or no attention to traditional analytic solutions to ground water flow problems. This shift in education seems logical. Why waste time to learn about the method of images, or why study analytic solutions to one‐dimensional or radial flow problems? Computer models solve much more realistic problems and offer sophisticated graphical output, such as contour plots of potentiometric levels and ground water path lines. However, analytic solutions to elementary ground water flow problems do have something to offer over computer models: insight. For instance, an analytic one‐dimensional or radial flow solution, in terms of a mathematical expression, may reveal which parameters affect the success of calibrating a computer model and what to expect when changing parameter values. Similarly, solutions for periodic forcing of one‐dimensional or radial flow systems have resulted in a simple decision criterion to assess whether or not transient flow modeling is needed. Basic water balance calculations may offer a useful check on computer‐generated capture zones for wellhead protection or aquifer remediation. An easily calculated “characteristic leakage length” provides critical insight into surface water and ground water interactions and flow in multi‐aquifer systems. The list goes on. Familiarity with elementary analytic solutions and the capability of performing some simple hand calculations can promote appropriate (computer) modeling techniques, avoids unnecessary complexity, improves reliability, and is likely to save time and money. Training in basic hand calculations should be an important part of the curriculum of ground water modeling courses.
River‐Aquifer Interactions, Geologic Heterogeneity, and Low‐Flow Management
Authors: Fleckenstein Jan H. , Niswonger Richard G. , Fogg Graham E. 
Published: March 2006

AbstractLow river flows are commonly controlled by river‐aquifer exchange, the magnitude of which is governed by hydraulic properties of both aquifer and aquitard materials beneath the river. Low flows are often important ecologically. Numerical simulations were used to assess how textural heterogeneity of an alluvial system influences river seepage and low flows. The Cosumnes River in California was used as a test case. Declining fall flows in the Cosumnes River have threatened Chinook salmon runs. A ground water–surface water model for the lower river basin was developed, which incorporates detailed geostatistical simulations of aquifer heterogeneity. Six different realizations of heterogeneity and a homogenous model were run for a 3‐year period. Net annual seepage from the river was found to be similar among the models. However, spatial distribution of seepage along the channel, water table configuration and the level of local connection, and disconnection between the river and aquifer showed strong variations among the different heterogeneous models. Most importantly, the heterogeneous models suggest that river seepage losses can be reduced by local reconnections, even when the regional water table remains well below the riverbed. The percentage of river channel responsible for 50% of total river seepage ranged from 10% to 26% in the heterogeneous models as opposed to 23% in the homogeneous model. Differences in seepage between the models resulted in up to 13 d difference in the number of days the river was open for salmon migration during the critical fall months in one given year.
Breastfeeding by Aboriginal mothers in Perth
Authors: BINNS Colin W. , GILCHRIST Dawn , WOODS Beth , GRACEY Michael , SCOTT Jane , SMITH Hannah , ZHANG Min , ROBERMAN Brian 
Published: March 2006

AbstractObjective:  To document the breastfeeding practices of Aboriginal mothers delivering in Perth.Design and methods:  A cohort of mothers was followed from the time of delivery for six months to obtain details of infant feeding practices.Subjects:  A total of 455 mothers delivered during the study period and were asked to participate. A total of 425 mothers completed the initial questionnaire.Setting:  The study was undertaken in six public hospitals in Perth, Western Australia.Data analyses:  The data were analysed using spss. Breastfeeding duration was calculated using Kaplan–Meier survival analysis.Main outcome measures:  Breastfeeding initiation and duration.Results:  The mean age of the Aboriginal mothers was 21.8 years (range 14–39 years, SD 5.32) and the average gestational age was 38.3 weeks. Almost 50% of the mothers in the study delivered by Caesarean section. At discharge from hospital 89.4% (CI 86.6–92.1) of mothers were breastfeeding, declining to 58.8% (CI 53.5–64.1) at six months. When compared with non‐Aboriginal mothers, the Aboriginal breastfeeding rates were higher than the non‐Aboriginal average breastfeeding rates, but lower than the highest socioeconomic group.Conclusions:  The breastfeeding rates of Aboriginal mothers are higher than for other Australians. This is despite the low maternal age and level of education and the high rates of low‐birth‐weight infants and Caesarean section among this population. The World Health Organization recommendation for infant feeding is exclusive breastfeeding until six months, but less than one‐third of Aboriginal mothers achieved this recommendation.
Household factors associated with older Australian's purchasing a varied diet: Results from household expenditure data
Authors: TEMPLE Jeromey B. 
Published: March 2006

AbstractObjective:  To examine the household factors associated with older Australian's (aged 55 years and over) purchasing a varied diet.Design and methods:  National cross‐sectional survey.Setting:  All states and territories of Australia.Subjects:  A total of 1898 households headed by adults aged 55 years and over.Main outcome measures:  Food diversity was measured using the Dietary Variety Score (DVS). The DVS is the total number of food items purchased within a two‐week period, from a possible 110 individual food expenditure items.Data analysis:  Negative binomial regression was used to examine the association between the respondent's individual and household characteristics with the DVS, after controlling for all factors in the model.Results:  Among the demographic factors, living arrangements, age and education are found to be associated with dietary diversity. Lone males, lone females, and households headed by people with no secondary school education, or aged over 75 years were most likely to experience lower levels of dietary diversity.Conclusions:  The finding that both poor education and low income in old age are associated with dietary diversity suggests the need for early life‐course interventions to improve nutritional outcomes. Nutrition education programs that also focus on those with poor education and low income, as well as lone person households and those aged over 75 years, may improve nutritional wellbeing, and thereby reduce public health costs.
Development of food groupings to guide dietary advice for people with diabetes
Authors: GILLEN Lynda J. , TAPSELL Linda C. 
Published: March 2006

AbstractObjective:  To describe the development and characteristics of a food categorisation system and its application to guide advice for diabetes treatment.Design and methods:  Foods commonly consumed by 16 adults with diabetes were grouped by macronutrient content and type of fat to form a set of reference food groups for dietary advice. Means for energy and macronutrients from individual food groups were then used to construct an overall intake pattern targeting 8000 kJ and relative amounts of carbohydrate, protein and fat (saturated fatty acids (SFA) < 10%E and (polyunsaturated fatty acids) PUFA ∼ 10%E). Variation in energy and macronutrients contributed by all foods partitioned into each food group was assessed by the coefficient of variation of data on the whole diet.Results:  To differentiate between sources of fat, 13 food groups emerged and 10 were deemed acceptable to nutritional guidelines for diabetes treatment. The food group pattern was judged adequate for the achievement of dietary recommendations with low‐potential variation in total energy (5%) and macronutrient proportions (protein 6%, fat 6%, carbohydrate 3%), but higher for fat types (SFA 22%, (monounsaturated fatty acids) MUFA 11%, PUFA 12%). Targeted proportions for fat types were achieved only when daily servings of PUFA‐rich, oils, nuts and oily fish or soy were included in an ideal intake pattern.Conclusions:  In theory, a dietary pattern constructed from food group sources of macronutrients and individual fat types results in low‐potential variation from recommended nutrient targets and, therefore, is appropriate to guide advice for the treatment of diabetes.
Cross Talk between a Fungal Blue-Light Perception System and the Cyclic AMP Signaling Pathway
Authors: Casas-Flores Sergio , Rios-Momberg Mauricio , Rosales-Saavedra Teresa , Martínez-Hernández Pedro , Olmedo-Monfil Vianey , Herrera-Estrella Alfredo 
Published: March 2006

ABSTRACT

Blue light regulates many physiological and developmental processes in fungi. In
Trichoderma atroviride
the complex formed by the BLR-1 and BLR-2 proteins appears to play an essential role as a sensor and transcriptional regulator in photoconidiation. Here we demonstrate that the BLR proteins are necessary for carbon deprivation induced conidiation, even in the absence of light, pointing to the existence of an unprecedented cross talk between light and carbon sensing. Further, in contrast to what has been found in all other fungal systems, clear BLR-independent blue-light responses, including the activation of protein kinase A (PKA) and the regulation of gene expression, were found. Expression of an antisense version of the
pkr-1
gene, encoding the regulatory subunit of PKA, resulted in a nonsporulating phenotype, whereas overexpression of the gene produced colonies that conidiate even in the dark. In addition, overexpression of
pkr-1
blocked the induction of early light response genes. Thus, our data demonstrate that PKA plays an important role in the regulation of light responses in
Trichoderma
. Together, these observations suggest that the BLR complex plays a general role in sensing environmental cues that trigger conidiation and that such a role can be separated from its function as a transcription factor.
The RIM101 Pathway Contributes to Yeast Cell Wall Assembly and Its Function Becomes Essential in the Absence of Mitogen-Activated Protein Kinase Slt2p
Authors: Castrejon F. , Gomez A. , Sanz M. , Duran A. , Roncero C. 
Published: March 2006

ABSTRACT

The
Saccharomyces cerevisiae ynl294cΔ
(
rim21Δ
) mutant was identified in our lab owing to its moderate resistance to calcofluor, although it also displayed all of the phenotypic traits associated with its function as the putative sensor (Rim21p) of the RIM101 pathway.
rim21Δ
also showed moderate hypersensitivity to sodium dodecyl sulfate, caffeine, and zymolyase, and the cell wall compensatory response in this mutant was very poor, as indicated by the almost complete absence of Slt2 phosphorylation and the modest increase in chitin synthesis after calcofluor treatment. However, the cell integrity pathway appeared functional after caffeine treatment or thermal stress.
rim21Δ
and
rim101Δ
mutant strains shared all of the cell-wall-associated phenotypes, which were reverted by the expression of Rim101-531p, the constitutively active form of this transcription factor. Therefore, the absence of a functional RIM101 pathway leads to cell wall defects.
rim21Δ
, as well as
rim101Δ
, was synthetic lethal with
slt2Δ
, a synthetic defect alleviated by osmotic stabilization of the media. The double mutants grown in osmotically stabilized media were extremely hypersensitive to zymolyase and showed thicker cell walls, with poorly defined mannoprotein layers. In contrast,
rim21Δ rlm1Δ
and
rim101Δ rlm1Δ
double mutants were fully viable. Taken together, these results show that the RIM101 pathway participates directly in cell wall assembly and that it acts in parallel with the protein kinase C pathway (PKC) in this process independently of the transcriptional effect of the compensatory response mediated by this route. In addition, these results provide new experimental evidence of the direct involvement of the PKC signal transduction pathway through the Sltp2 kinase in the construction of yeast cell walls.
Mapping of an Internal Protease Cleavage Site in the Ssy5p Component of the Amino Acid Sensor of
Saccharomyces cerevisiae
and Functional Characterization of the Resulting Pro- and Protease Domains by Gain-of-Function Genetics
Authors: Poulsen Peter , Lo Leggio Leila , Kielland-Brandt Morten C. 
Published: March 2006

ABSTRACT

Ssy5p is a 77-kDa protein believed to be a component of the SPS amino acid sensor complex in the plasma membrane of
Saccharomyces cerevisiae
. Ssy5p has been suggested to be a chymotrypsin-like serine protease that activates the transcription factor Stp1p upon exposure of the yeast to extracellular amino acid. Here we overexpressed and partially purified Ssy5p to improve our understanding of its structure and function. Antibodies against Ssy5p expressed in
Escherichia coli
were isolated and used to detect Ssy5p processing in
S. cerevisiae
cells. Partial purification and N-terminal sequencing of processed Ssy5p revealed in vivo cleavage of Ssy5p between amino acids 381 and 382. We also isolated constitutively signaling
SSY5
mutants and quantified target promoter activation and Stp1p processing. One mutant contained an amino acid substitution in the prodomain, whereas three others harbored amino acid substitutions in the protease domain. Dose-response analysis indicated that all four mutants exhibited increased basal levels of Stp1p processing. Interestingly, whereas the three constitutive mutants mapping to the protease domain of Ssy5p exhibited the decreased 50% effective concentration (EC
50
) characteristic of constitutive mutations previously found in Ssy1p, Ptr3p, and Ssy5p, the EC
50
of the mutation that maps to the prodomain of Ssy5p remained essentially unchanged. In a model of Ssy5p derived from its similarities with α-lytic protease from
Lysobacter enzymogenes
, the sites corresponding to the mutations in the protease domain are clustered in a region facing the prodomain, suggesting that this region interacts with the prodomain and participates in the conformational dynamics of sensing.
Structural Perspective on Mutations Affecting the Function of Multisubunit RNA Polymerases
Authors: Trinh Vincent , Langelier Marie-France , Archambault Jacques , Coulombe Benoit 
Published: March 2006

SUMMARY
High-resolution crystallographic structures of multisubunit RNA polymerases (RNAPs) have increased our understanding of transcriptional mechanisms. Based on a thorough review of the literature, we have compiled the mutations affecting the function of multisubunit RNA polymerases, many of which having been generated and studied prior to the publication of the first high-resolution structure, and highlighted the positions of the altered amino acids in the structures of both the prokaryotic and eukaryotic enzymes. The observations support many previous hypotheses on the transcriptional process, including the implication of the bridge helix and the trigger loop in the processivity of RNAP, the importance of contacts between the RNAP jaw-lobe module and the downstream DNA in the establishment of a transcription bubble and selection of the transcription start site, the destabilizing effects of ppGpp on the open promoter complex, and the link between RNAP processivity and termination. This study also revealed novel, remarkable features of the RNA polymerase catalytic mechanisms that will require additional investigation, including the putative roles of fork loop 2 in the establishment of a transcription bubble, the trigger loop in start site selection, and the uncharacterized funnel domain in RNAP processivity.
Chemoenzymatic and Template-Directed Synthesis of Bioactive Macrocyclic Peptides
Authors: Grünewald Jan , Marahiel Mohamed A. 
Published: March 2006

SUMMARY

Non-ribosomally synthesized peptides have compelling biological activities ranging from antimicrobial to immunosuppressive and from cytostatic to antitumor. The broad spectrum of applications in modern medicine is reflected in the great structural diversity of these natural products. They contain unique building blocks, such as
d
-amino acids, fatty acids, sugar moieties, and heterocyclic elements, as well as halogenated, methylated, and formylated residues. In the past decades, significant progress has been made toward the understanding of the biosynthesis of these secondary metabolites by nonribosomal peptide synthetases (NRPSs) and their associated tailoring enzymes. Guided by this knowledge, researchers genetically redesigned the NRPS template to synthesize new peptide products. Moreover, chemoenzymatic strategies were developed to rationally engineer nonribosomal peptides products in order to increase or alter their bioactivities. Specifically, chemical synthesis combined with peptide cyclization mediated by nonribosomal thioesterase domains enabled the synthesis of glycosylated cyclopeptides, inhibitors of integrin receptors, peptide/polyketide hybrids, lipopeptide antibiotics, and streptogramin B antibiotics. In addition to the synthetic potential of these cyclization catalysts, which is the main focus of this review, different enzymes for tailoring of peptide scaffolds as well as the manipulation of carrier proteins with reporter-labeled coenzyme A analogs are discussed.
Characterization of a Novel Virus Causing a Lethal Disease in Carp and Koi
Authors: Ilouze Maya , Dishon Arnon , Kotler Moshe 
Published: March 2006

SUMMARY

Since 1998 a lethal disease of carp and ornamental koi (Cyprinus carpio) has afflicted fisheries in North America, Europe, and Asia, causing severe economic losses to the fish farming industry. This review summarizes the isolation and identification of the disease-causing agent and describes the currently known molecular characteristics of this newly isolated virus, distinguishing it from other known large DNA viruses. In addition, we summarize the clinical and histopathological manifestations of the disease. Providing information on the immune response to this virus and evaluating the available means of diagnosis and protection should help to reduce the damage induced by this disease. This review does not discuss the economic aspects of the disease or the debate on whether the disease should be registered; both of these issues were recently reviewed in detail (O. L. M. Haenen, K. Way, S. M. Bergmann, and E. Ariel, Bull. Eur. Assoc. Fish Pathol.
24:
293-307, 2004; D. Pokorova, T. Vesely, V. Piackova, S. Reschova, and J. Hulova, Vet. Med. Czech.
50:
139-147, 2005).