bluuebunny/crossref_metadata_2025_split huggingface dataset:
Direct‐Push Electrical Conductivity Logging for High‐Resolution Hydrostratigraphic Characterization
Authors: Schulmeister M.K. , Butler J.J. , Healey J.M. , Zheng L. , Wysocki D.A. , McCall G.W. 
Published: February 2007

AbstractFine‐scale hydrostratigraphic features often play a critical role in controlling ground water flow and contaminant transport. Unfortunately, many conventional drilling‐ and geophysics‐based approaches are rarely capable of describing these features at the level of detail needed for contaminant predictions and remediation designs. Previous work has shown that direct‐push electrical conductivity (EC) logging can provide information about site hydrostratigraphy at a scale of relevance for contaminant transport investigations in many unconsolidated settings. In this study, we evaluate the resolution and quality of that information at a well‐studied research site that is underlain by highly stratified alluvial sediments. Geologic and hydrologic data, conventional geophysical logs, and particle‐size analyses are used to demonstrate the capability of direct‐push EC logging for the delineation of fine‐scale hydrostratigraphic features in saturated unconsolidated formations. When variations in pore‐fluid chemistry are small, the electrical conductivity of saturated media is primarily a function of clay content, and hydrostratigraphic features can be described at a level of detail (<2.5 cm in thickness) that has not previously been possible in the absence of continuous cores. Series of direct‐push EC logs can be used to map the lateral continuity of layers with non‐negligible clay content and to develop important new insights into flow and transport at a site. However, in sand and gravel intervals with negligible clay, EC logging provides little information about hydrostratigraphic features. As with all electrical logging methods, some site‐specific information about the relative importance of fluid and sediment contributions to electrical conductivity is needed. Ongoing research is directed at developing direct‐push methods that allow EC logging, water sampling, and hydraulic testing to be done concurrently.
Attenuation of a Mixed Chromium and Chlorinated Etjeme Ground Wate Plume in Estuarine Influenced Glaciated Sediments
Authors: Hellerich Lucas A. , Poneiera Matthew A. , Nikolaidis Nikolaos P. , Smets Barth F. , Dobbs Gregory M. 
Published: February 2007

AbstractThe natural attenuation behavior of a ground water contaminant plume containing chromium and chlorinated ethenes in glaciated sediments was assessed using traditional and nontraditional methods. The mixed waste is transported through and attenuated within an estuarine influenced ground water aquifer of spatially varying redox character and organic carbon content. Contaminant fate and speciation were assessed as a function of geochemical conditions. Total, speciation‐based, and sequential chemical extraction analyses were performed to determine contaminant partitioning and the redox capacity of the aquifer. Chromium speciation and partitioning were correlated with the reductive capacity and redox conditions of the aquifer sediments spatially distributed within the aquifer. Reductive dechlorination and partitioning of chlorinated ethenes were correlated with the organic carbon content and redox conditions of the aquifer sediments. The data showed that sharp redox gradients existed within the aquifer. Active reduction and retardation of both chromium and chlorinated ethenes was exhibited. The aqueous hexavalent chromium concentrations decreased to near nondetect levels in the vicinity of the receptor, whereas degradation products of higher‐order chlorinated ethenes increased as a fraction of the total chlorinated ethene concentrations along the length of the plume. The potential for competition for reducing power under specific cases within the aquifer was suggested by the data, highlighting the need to include contaminant interactions in natural attenuation assessments.
The Technical Case for Eliminating the Use of the TPH Analysis in Assessing and Regulating Dissolved Petroleum Hydrocarbons in Ground Water
Authors: Zemo Dawn A. , Foote Gary R. 
Published: February 2007

AbstractIn many states, the total petroleum hydrocarbons (TPH) analysis based on gas chromatography‐flame ionization detection (GC‐FID) is still being used to assess and regulate ground water quality at petroleum release sites. The soluble fraction of fresh crude oil or fresh products that could potentially be dissolved into the ground water is limited to relatively few petroleum hydrocarbon constituents (primarily the C6 to C14 aromatics). Research by numerous investigators has shown that the reported TPH concentrations of ground water samples frequently do not represent dissolved petroleum hydrocarbons but rather represent nondissolved petroleum or polar nonhydrocarbon compounds. Nondissolved petroleum is frequently entrained within a sample when sampling ground water within affected soil, and polar nonhydrocarbons are present in ground water as a result of petroleum biodegradation or other factors. These constituents are being measured because the TPH analysis does not include steps to remove nondissolved petroleum or a silica gel cleanup to remove polars.Many states have regulatory action levels for TPH in ground water that are in the 0.1 to 2 mg/L range. The technical basis for these action levels appears to be toxicity and/or organoleptic (taste and odor) properties of the dissolved petroleum hydrocarbons associated with fresh oil or fresh products. The presence of compounds measured as TPH that are not dissolved petroleum hydrocarbons has proven problematic for regulatory decision‐making because the comparison of concentration data to the regulatory criteria may not be correct. Because the TPH analysis does not reliably distinguish between dissolved petroleum hydrocarbons and other compounds, it should not be used to assess or regulate dissolved petroleum hydrocarbons, in ground water. We recommend that constituent‐specific analyses be used to assess and regulate ground water quality at petroleum hydrocarbon release sites. If TPH must be used due to regulatory requirements, samples should be cleaned up with silica gel to remove polars (and turbidity should be removed, if present) prior to analysis so that comparison to regulatory action levels that are based on properties of dissolved petroleum hydrocarbon constituents is technically appropriate.
Estimating Natural Attenuation Rate Constants Using a Fuzzy Framework
Authors: Uddameri Venkatesh 
Published: February 2007

AbstractFuzzy set theoretic approaches provide convenient tools to quantify subjective information and characterize the decision‐maker's preferences with minimal data. The estimation of natural attenuation and degradation rates, using the method of Buschek and Alcantar (1995), while pragmatic, is subject to significant imprecision due to mathematical simplifications and site complexities. In this paper, two fuzzy approaches, namely fuzzy arithmetic and fuzzy regression, are used to characterize the variability in the estimated degradation and attenuation rates. The variability in the input parameters can be characterized using membership functions that characterize the decision‐maker's perception of likely values. The choice of the membership function for critical inputs is seen to affect the variability in the estimated outputs. Similarly, the decision‐maker's belief related to the compatibility of the steady‐state model to represent the observed plume behavior at the site can also be quantified using a compatibility criterion. Sensitivity studies carried out using the fuzzy‐based estimation methodology are extremely useful to assess how differences in the decision‐makers’preferences will affect the estimated rate constants and associated variability. As such, the proposed methodology is of high value during negotiations related to monitored natural attenuation.
Carbon Isotope Fractionation of PCE and TCE During Dechlorination by Vitamin B12
Authors: Slater G.F. , Lollar B. Sherwood , Lesage S. , Brown S. 
Published: February 2007

AbstractReductive dechlorination of perchloroethylene (PCE) and trichloroethylene (TCE) by vitamin B12 is an analogue of the microbial reductive dechlorination reaction and is presently being applied as a remediation technique. Stable carbon isotopic analysis, an effective and powerful tool for the investigation and monitoring of contaminant remediation, was used to characterize the isotopic effects of reductive dechlorination of PCE and TCE by vitamin B12 in laboratory microcosms. In laboratory experiments, 10 mg/L vitamin B12 degraded >90% of the initial 20 mg/L PCE with TCE, the primary product of PCE degradation, accounting for between 64% and 72% of the PCE degraded. In experiments with TCE, 147 mg/L vitamin B12 degraded >90% of the initial 20 mg/L TCE with cis‐dichloroethene (cDCE), the primary product of degradation accounting for between 30% and 35% of the TCE degraded. Degradation of both PCE and TCE exhibited first‐order kinetics. Strong isotopic fractionation of the reactant PCE and of the reactant TCE was observed over the course of degradation. This fractionation could be described with a Rayleigh model using enrichment factors of −16.5%o and −15.8%o for PCE, and −17.2%o and −16.6%o for TCE. Fractionation was similar in all experiments, with a mean enrichment factor of −16.5%o ± 0.6%o. The occurrence of such large enrichment factors indicates that isotopic analysis can be used to monitor the dechlorination of PCE and TCE by vitamin B12 and remediation of ground water plumes. Evidence indicates that isotopic fractionation is taking place during complexation of the chlorinated ethenes to vitamin B12, as has been suggested for reductive dechlorination by zero valent iron. The differences between e values for this reaction and those observed for anaerobic biodegradation of the chlorinated ethenes suggest that there may be differences in the rate‐determining step for these two processes.
Natural Gradient Tracer Test to Evaluate Natural Attenuation of MTBE Under Anaerobic Conditions
Authors: Amerson Illa , Johnson Richard L. 
Published: February 2007

AbstractA natural gradient tracer test using perdeuterated MTBE was conducted in an anaerobic aquifer to determine the relative importance of dispersion and degradation in reducing MTBE concentrations in ground water. Preliminary ground water chemistry and hydraulic conductivity data were used to place the tracer within an existing dissolved MTBE plume at Port Hueneme, California. Following one year of transport, the tracer plume was characterized in detail.Longitudinal dispersion was identified as the dominant mechanism for lowering the perdeuterated MTBE concentrations. The method of moments was used to determine the longitudinal and lateral dispersion coefficients (0.85 m2/day and 0.08 m2/day, respectively). A mass‐balance analysis, carried out after one year of transport, accounted for 110% of the injected mass and indicated that no significant mass loss occurred. The plume structure created by zones of higher and lower hydraulic conductivity at the site was complex, consisting of several localized areas of high tracer concentration in a lower concentration plume. This is important because the aquifer has generally been characterized as exhibiting fairly minor heterogeneity. In addition, the tracer plume followed a curved flowpath that deviated from the more macroscopic direction of ground water flow inferred from local ground water elevation measurements and the behavior of the existing plume. Understanding the mass balance, plume structure, curvature of the tracer plume, and consequently natural attenuation behavior required the detailed sampling approach employed in this study. These data imply that a detailed understanding of site hydrogeology and an extensive sampling network may be critical for the correct interpretation of monitored natural attenuation of MTBE.
Field Studies on the Fate and Transport of Pharmaceutical Residues in Bank Filtration
Authors: Heberer Thomas , Mechlinski Andy , Fanck Britta , Knappe Andrea , Massmann Gudrun , Pekdeger Asaf , Fritz Birgit 
Published: February 2007

AbstractBank filtration and artificial ground water recharge are important, effective, and cheap techniques for surface water treatment and removal of microbes, as well as inorganic, and some organic, contaminants. Nevertheless, physical, chemical, and biological processes of the removal of impurities are not understood sufficiently. A research project titled Natural and Artificial Systems for Recharge and Infiltration attempts to provide more clarity in the processes affecting the removal of these contaminants. The project focuses on the fate and transport of selected emerging contaminants during bank filtration at two transects in Berlin, Germany. Several detections of pharmaceutically active compounds (PhACs) in ground water samples from bank filtration sites in Germany led to furthering research on the removal of these compounds during bank filtration. In this study, six PhACs including the analgesic drugs diclofenac and propyphenazone, the antiepileptic drugs carbamazepine and primidone, and the drug metabolites clofibric acid and 1‐acetyl‐1‐methyl‐2‐dimethyl‐oxamoyl‐2‐phenylhydrazide were found to leach from the contaminated streams and lakes into the ground water. These compounds were also detected at low concentrations in receiving public supply wells. Bank filtration either decreased the concentrations by dilution (e.g., for carbamazepine and primidone) and partial removal (e.g., for diclofenac), or totally removed PhACs (e.g., bezafibrate, indomethacine, antibiotics, and estrogens). Several PhACs, such as carbamazepine and especially primidone, were readily transported during bank filtration. They are thought to be good indicators for evaluating whether surface water is impacted by contamination from municipal sewage effluent or whether contamination associated with sewage effluent can be transported into ground water at ground water recharge sites.
Interferon-producing killer dendritic cells (IKDCs) arise via a unique differentiation pathway from primitive c-kitHiCD62L+ lymphoid progenitors
Authors: Welner Robert S. , Pelayo Rosana , Garrett Karla P. , Chen Xinrong , Perry S. Scott , Sun Xiao-Hong , Kee Barbara L. , Kincade Paul W. 
Published: February 2007

Abstract
Interferon-producing killer dendritic cells (IKDCs) have only recently been described and they share some properties with plasmacytoid dendritic cells (pDCs). We now show that they can arise from some of the same progenitors. However, IKDCs expressed little or no RAG-1, Spi-B, or TLR9, but responded to the TLR9 agonist CpG ODN by production of IFNγ. The RAG-1−pDC2 subset was more similar to IKDCs than RAG-1+ pDC1s with respect to IFNγ production. The Id-2 transcriptional inhibitor was essential for production of IKDCs and natural killer (NK) cells, but not pDCs. IKDCs developed from lymphoid progenitors in culture but, unlike pDCs, were not affected by Notch receptor ligation. While IKDCs could be made from estrogen-sensitive progenitors, they may have a slow turnover because their numbers did not rapidly decline in hormone-treated mice. Four categories of progenitors were compared for IKDC-producing ability in transplantation assays. Of these, Lin−Sca-1+c-KitHiThy1.1−L-selectin+ lymphoid progenitors (LSPs) were the best source. While NK cells resemble IKDCs in several respects, they develop from different progenitors. These observations suggest that IKDCs may arise from a unique differentiation pathway, and one that diverges early from those responsible for NK cells, pDCs, and T and B cells.
Expression of oncogenic K-ras from its endogenous promoter leads to a partial block of erythroid differentiation and hyperactivation of cytokine-dependent signaling pathways
Authors: Zhang Jing , Liu Yangang , Beard Caroline , Tuveson David A. , Jaenisch Rudolf , Jacks Tyler E. , Lodish Harvey F. 
Published: February 2007

Abstract
When overexpressed in primary erythroid progenitors, oncogenic Ras leads to the constitutive activation of its downstream signaling pathways, severe block of terminal erythroid differentiation, and cytokine-independent growth of primary erythroid progenitors. However, whether high-level expression of oncogenic Ras is required for these phenotypes is unknown. To address this issue, we expressed oncogenic K-ras (K-rasG12D) from its endogenous promoter using a tetracycline-inducible system. We show that endogenous K-rasG12D leads to a partial block of terminal erythroid differentiation in vivo. In contrast to results obtained when oncogenic Ras was overexpressed from retroviral vectors, endogenous levels of K-rasG12D fail to constitutively activate but rather hyperactivate cytokine-dependent signaling pathways, including Stat5, Akt, and p44/42 MAPK, in primary erythroid progenitors. This explains previous observations that hematopoietic progenitors expressing endogenous K-rasG12D display hypersensitivity to cytokine stimulation in various colony assays. Our results support efforts to modulate Ras signaling for treating hematopoietic malignancies.
Blast sampling for structural and functional analyses
Authors: Friedrich Anne , Ripp Raymond , Garnier Nicolas , Bettler Emmanuel , Deléage Gilbert , Poch Olivier , Moulinier Luc 
Published: February 2007

Abstract

Background
The post-genomic era is characterised by a torrent of biological information flooding the public databases. As a direct consequence, similarity searches starting with a single query sequence frequently lead to the identification of hundreds, or even thousands of potential homologues. The huge volume of data renders the subsequent structural, functional and evolutionary analyses very difficult. It is therefore essential to develop new strategies for efficient sampling of this large sequence space, in order to reduce the number of sequences to be processed. At the same time, it is important to retain the most pertinent sequences for structural and functional studies.

Results
An exhaustive analysis on a large scale test set (284 protein families) was performed to compare the efficiency of four different sampling methods aimed at selecting the most pertinent sequences. These four methods sample the proteins detected by BlastP searches and can be divided into two categories: two customisable methods where the user defines either the maximal number or the percentage of sequences to be selected; two automatic methods in which the number of sequences selected is determined by the program. We focused our analysis on the potential information content of the sampled sets of sequences using multiple alignment of complete sequences as the main validation tool. The study considered two criteria: the total number of sequences in BlastP and their associated E-values. The subsequent analyses investigated the influence of the sampling methods on the E-value distributions, the sequence coverage, the final multiple alignment quality and the active site characterisation at various residue conservation thresholds as a function of these criteria.

Conclusion
The comparative analysis of the four sampling methods allows us to propose a suitable sampling strategy that significantly reduces the number of homologous sequences required for alignment, while at the same time maintaining the relevant information concerning the active site residues.
iCartiGD: the Integrated Cartilage Gene Database
Authors: Yeung Ming-Yiu , Smith David K , Chan Matthew SY , Li Cheuk M , Wong Brian C , Cheung Kenneth MC , Luk Keith DK , Cheah Kathryn SE , Sham Pak , Chan Danny , Song You-Qiang 
Published: February 2007

Abstract

Background
Diseases of cartilage, such as arthritis and degenerative disc disease, affect the majority of the general population, particularly with ageing. Discovery and understanding of the genes and pathways involved in cartilage biology will greatly assist research on the development, degeneration and disorders of cartilage.

Description
We have established the Integrated Cartilage Gene Database (iCartiGD) of genes that are known, based on results from high throughput experiments, to be expressed in cartilage. Information about these genes is extracted automatically from public databases and presented as a single page report via a web-browser. A variety of flexible search options are provided and the chromosomal distribution of cartilage associated genes can be presented.

Conclusion
iCartiGD provides a comprehensive source of information on genes known to be expressed in cartilage. It will remain current due to its automatic update capability and provide researchers with an easily accessible resource for studies involving cartilage. Genetic studies of the development and disorders of cartilage will benefit from this database.
Interleukin-4 inhibition of interleukin-1-induced expression of matrix metalloproteinase-3 (MMP-3) is independent of lipoxygenase and PPARγ activation in human gingival fibroblasts
Authors: Stewart Denise , Javadi Masoud , Chambers Mariah , Gunsolly Chad , Gorski Grzegorz , Borghaei Ruth C 
Published: February 2007

AbstractBackgroundInterleukin 4 (IL-4) has been shown to suppress interleukin-1 (IL-1) induced expression of matrix metalloproteinase-3 (MMP-3) in human synovial and gingival fibroblasts, but the mechanism of suppression has not been determined. Activators of peroxisome proliferator-activated receptor-γ (PPARγ) have been shown to inhibit cytokine induced expression of MMPs in other cell types, and IL-4 has been shown to activate PPARγ by stimulating production of ligands through the lipoxygenase pathway. It has been suggested that PPARγ may inhibit expression of MMPs by competing with transcription factor AP-1 for binding to a putative composite binding element in the promoters. The objective of this study was to determine whether the suppressive effects of IL-4 on the IL-1 induced expression of MMP-3 involve activation of lipoxygenase and/or PPARγ.ResultsWestern blotting revealed the presence of PPARγ in nuclear extract of HGF. IL-1 induced binding of nuclear extract to the putative composite PPRE/AP-1 site was diminished in the presence of pioglitazone, but there was no evidence of any change in the composition of the retarded complexes, and no evidence of PPARγ binding to this site. Nordihydroguaiaretic acid (NDGA), a non-selective lipoxygenase inhibitor, and MK886, a specific inhibitor of 5-lipoxygenase, induced MMP-3 expression synergistically with IL-1. However IL-4 was still able to inhibit MMP-3 expression in the presence of NDGA or MK886 and IL-1. Activation of PPARγ with pioglitazone not only failed to inhibit IL-1 induced expression of MMP-3 mRNA, but rather super-induced MMP-3 in the presence of IL-1. PPARγ antagonist GW9662 failed to abolish the suppressive effects of IL-4. Another PPARγ activator, 15-deoxy-Delta12,14prostaglandin J2 (15dPGJ2), also super-induced MMP-3 mRNA, and this was due at least in part to increased transcription.ConclusionIL-4 suppression of IL-1-induced MMP-3 expression in HGF is independent of lipoxygenase activity and activation of PPARγ. Super-induction of MMP-3 by pioglitazone may have important implications for patients using pioglitazone to treat type II diabetes in the presence of chronic inflammation.