bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mutator mutants of Escherichia coli carrying a defect in the DNA polymerase III τ subunit
Authors: Pham Phuong T. , Zhao Wei , Schaaper Roel M. 
Published: December 2005

SummaryTo investigate the possible role of accessory subunits of Escherichia coli DNA polymerase III holoenzyme (HE) in determining chromosomal replication fidelity, we have investigated the role of the dnaX gene. This gene encodes both the τ and γ subunits of HE, which play a central role in the organization and functioning of HE at the replication fork. We find that a classical, temperature‐sensitive dnaX allele, dnaX36, displays a pronounced mutator effect, characterized by an unusual specificity: preferential enhancement of transversions and −1 frameshifts. The latter occur predominantly at non‐run sequences. The dnaX36 defect does not affect the γ subunit, but produces a τ subunit carrying a missense substitution (E601K) in its C‐terminal domain (domain V) that is involved in interaction with the Pol III α subunit. A search for new mutators in the dnaX region of the chromosome yielded six additional dnaX mutators, all carrying a specific τ subunit defect. The new mutators displayed phenotypes similar to dnaX36: strong enhancement of transversions and frameshifts and only weak enhancement for transitions. The combined findings suggest that the τ subunit of HE plays an important role in determining the fidelity of the chromosomal replication, specifically in the avoidance of transversions and frameshift mutations.
A calcium‐dependent protein kinase regulates Plasmodium ookinete access to the midgut epithelial cell
Authors: Ishino Tomoko , Orito Yuki , Chinzei Yasuo , Yuda Masao 
Published: December 2005

Summary Plasmodium parasites are fertilized in the mosquito midgut and develop into motile zygotes, called ookinetes, which invade the midgut epithelium. Here we show that a calcium‐dependent protein kinase, CDPK3, of the rodent malarial parasite (Plasmodium berghei) is produced in the ookinete stage and has a critical role in parasite transmission to the mosquito vector. Targeted disruption of the CDPK3 gene decreased ookinete ability to infect the mosquito midgut by nearly two orders of magnitude. Electron microscopic analyses demonstrated that the disruptant ookinetes could not access midgut epithelial cells by traversing the layer covering the cell surface. An in vitro migration assay showed that these ookinetes lack the ability to migrate through an artificial gel, suggesting that this defect caused their failure to access the epithelium. In vitro migration assays also suggested that this motility is induced in the wild type by mobilization of intracellular stored calcium. These results indicate that a signalling pathway involving calcium and CDPK3 regulates ookinete penetration of the layer covering the midgut epithelium. Because humans do not possess CDPK family proteins, CDPK3 is a good target for blocking malarial transmission to the mosquito vector.
Studies on the fish catch efficiency of different types of fishing gear in Kaptai Reservoir, Bangladesh
Authors: Ahmed Khan Kamal U. , Hambrey John B. 
Published: December 2005

AbstractA comprehensive analysis of the efficiency of different fishing gear in capturing Cyprinidae (major carp) species in Kaptai Reservoir, Bangladesh, was conducted. The catch per unit effort (CPUE) data were collected during a 1‐year survey, covering a total of 493 independent fishing units spread across the four major fishing grounds of the reservoir. The study examines the CPUE and catch composition between months and study sites, and the effects of reservoir water level fluctuations, gear diversity and fish distribution patterns on the fish catches. The mean CPUE for all gear ranged between 2.91 and 30.86 kg unit−1 day−1. Analysis of variance showed significant differences among the fishing gear types. The CPUE differed significantly between months for lift nets, large‐meshed (LM) gill nets, cluster hooks and hand lines. None of the fishing gear exhibited significant differences between sites except for cluster hooks. The CPUE of small‐meshed (SM) seine nets was significantly higher than that of other gear. The reasons for such differences in the fish catches were identified as the choice of fishing places, the net sizes, the number of hooks, lures and baits, water turbidity, wind, waves and rainfall. The CPUE indices for lift nets showed significant variation between months for the Cyprinidae species. A significant variation in catch at the different sites was found for all nets, except SM seine nets. The contribution of the Cyprinidae species showed significant differences between sites only for hand lines. The coefficient of variation of CPUE for fishing nets did not vary much more than 55% (lift net), whereas the highest variation of 49% was recorded for hand lines among the hooks and line. Higher reservoir water levels were followed by reduced CPUEs for the Cyprinidae species and vice versa, whereas the highest water levels corresponded to the higher CPUE for the Clupeidae species.
Erratic judgements: re‐evaluating solutional erosion rates of limestones using erratic‐pedestal sites, including Norber, Yorkshire
Authors: Goldie H S 
Published: December 2005

The re‐interpretation of surface karst landforms in Northern England has led to a re‐examination of well‐known erratic‐pedestal sites that were the origin for karst denudation rates applied extensively, on the supposition that erratics protect underlying limestone from rainwater solution. Height of the pedestal has been used to calculate long‐term solutional‐lowering, as much as 50 cm in 15 ka (33.3 mm/ka) from UK sites. The sites include Norber and Scar Close, Yorkshire, UK. This paper shows that the sites have been misinterpreted, in particular at Norber where the erratics lie on a pre‐existing structurally stepped surface. Norber and several other sites also experience much mechanical weathering, in relatively weak, well‐fractured limestones, a process which must be distinguished from solution. Sites in strong, less‐fractured limestones demonstrate lower rates, which are sounder indications of land surface lowering. Some pedestals have been confirmed as partly resulting from solutional weathering in surrounding soil and vegetation. Re‐evaluation reduces solution rates to 3–13 cm in 15 ka. Applying such rates has profound implications for understanding limestone landscapes, challenging orthodox views.
Probing pocket depth at mobile/nonmobile teeth
Authors: Neiderud Anne‐Marie , Ericsson Ingvar , Lindhe Jan 
Published: December 2005

Abstract. The aim of the present investigation was to study the influence of an increased tooth mobility on the resistance offered by the periodontal tissues to probing. 6 beagle dogs were used. At the start of the experiment, the animals had clean teeth and normal gingival and periodontal conditions. In each dog, a device was installed in the lower left jaw quadrant to expose the third premolar (P3) to jiggling forces which would enhance the mobility of this “test” tooth. The contralateral tooth served as the non‐jiggled control. During the 3 months of experimentation, the teeth of the dogs were cleaned on a regular basis.Clinical examinations including tooth mobility measurements were performed on days 0 and 90. After the examination on Day 90, a probe was inserted in the buccal “pocket” of the mesial root of 3P and P3. The probe was retained with composite. Biopsies including the test or control tooth with adjacent buccal periodontal tissues were harvested, fixed and decalcified. Each biopsy was divided in one mesial and one distal portion (root). The distal portion was embedded in Epon, sectioned and stained in PAS and toluidine blue, while the mesial portion, following probe removal was embedded in paraffin, sectioned and stained in hematoxylin‐eosin. The sections were exposed to histometric and morphometric measurements. The findings demonstrated that tissue alterations which occur at mobile teeth may reduce the resistance offered by the periodontal tissues to clinical probing. Such alterations include (i) reduced height of the alveolar bone, (ii) reduced amount of collagen, and increased vascularity in the enlarged supracrestal connective tissue.
Clearance of sodium lauryl sulphate from the oral cavity
Authors: Fakhry‐Smith S. , Din C. , Nathoo S. A. , Gaffar A. 
Published: December 2005

AbstractSodium lauryl sulphate (SLS) is used in toothpaste and mouth rinses as an emulsifying and surface cleaning agent. SLS has been implicated in an increased incidence of oral irritation in subjects predisposed to recurrent aphthous stomatitis (RAU). Hence, the purpose of this study was to determine the levels of SLS found in the oral cavity following rinsing with an SLS containing mouth rinse and brushing with a SLS containing dentifrice. An analytical method to separate SLS from saliva and other complex systems was developed. The method used high performance liquid chromatography (HPLC) and detection performed using conductivity measurements. Standard curves with known concentrations showed a detection limit of less than 0.4 ug SLS/ml of fluid. 2 clinical studies were conducted to determine the amount of SLS retained in the mouth by a healthy population after rinsing or brushing with commercially available products. The results showed, after rinsing, that 96% of the available SLS from the rinse was recovered in the collected samples within 2 min. Similarly, after brushing. 86% of the SLS contained within the toothpaste was recovered from the collected samples within the first 10 min. These results showed that the amount of SLS retained in the oral cavity was minimal and the contact time between SLS and the oral cavity was very short. A 2nd study was conducted to measure the amount of SLS retained in the mouth by a population susceptible to RAU. After rinsing. 91% of the available SLS was recovered within the first 2 min. Following brushing. 89% of the SLS in the dentifrice was recovered within the first 10 min. These results were comparable to those determined by the study involving the healthy population.
A randomized controlled trial of a 2% minocycline gel as an adjunct to non‐surgical periodontal treatment, using a design with multiple matching criteria
Authors: Graça M. A. , Watts T. L. P. , Wilson R. F. , Palmer R. M. 
Published: December 2005

Graça MA, Watts TLP. Wilson RF, Palmer RM: A randomized controlled trial of a 2% minocycline gel as an adjunct to non‐surgical periodontal treatment, using a design with multiple matching criteria.Abstract Topical locally delivered minocycline is an adjunctive to non‐surgical periodontal treatment, but there are few reported trials. Previous trials have reported differences between changes in probing depth in treatment and control groups, but no differences in probing attachment level. In the present study, 30 subjects were paired according to gender, age, ethnic group, smoking habits, and probing depths. Both groups received intensive oral hygiene education and root planing with local anaesthesia. Active or placebo gel was placed subgingivally at planed sites in each subject according to a double‐blind protocol, immediately after instrumentation, and 2 and 4 weeks later. A periodontal examination was made with a constant force probe before instrumentation, and 6 and 12 weeks later. 2 subjects failed to complete the study, and their pairs were therefore not included in the analysis. Results were tested with analysis of covariance. Differences between groups in mean probing depth did not reach statistical significance at any visit (baseline: test (T)=5.93 mm, control (C)=5.74 mm; 6 weeks: T=3.53 mm, C = 3.63 mm; 12 weeks: T = 3.29 mm. C = 3.44 mm), but mean probing attachment levels were different (p<0.05) at both reassessments (baseline: T=6.86 mm, C=6.83 mm; 6 weeks: T=4.93 mm, C=5.30 mm; 12 weeks T=4.91 mm, C=5.27 mm). There was also a difference in the number of sites with bleeding on deep probing at 12 weeks (p<0.05). This trial showed that adjunctive minocycline gel provided a more advantageous outcome for nonsurgical periodontal treatment in terms of probing attachment level and bleeding on deep probing. This trial was a good example of experimental, as opposed to community, design, and used limited resources to show a clear result.
Embedded Sidewall Samplers and Sensors to Monitor the Subsurface
Authors: Murdoch Lawrence C. , Slack William W. , Harrar William , Siegrist Robert L. 
Published: December 2005

AbstractSubsurface properties such as moisture content, hydraulic head, or chemical composition may vary markedly over short vertical distances in soil and ground water systems, but conventional samplers and sensors placed in vertical boreholes are often unable to resolve these variations. To improve the resolution of subsurface monitoring, we have developed a method for accessing the side‐wall of a vertical or angled borehole at many discrete intervals along the entire length of the borehole. The method uses an access device that embeds sensors or sediment samplers laterally through the borehole sidewall into the undisturbed formation to distances slightly less than the diameter of the borehole. The access device can also obtain a core sample up to 15 cm long and 4 cm in diameter, and then insert a permeable sleeve for extracting fluid samples (water, gas, nonaqueous phase liquids). The system has been used under field conditions in the United States and Denmark to place electrodes capable of measuring water content (using time domain reflectometry [TDR] waveguides), Eh (using platinum electrodes), or electrical resistivity (using a four‐conductor electrode). At one site, as many as 22 water samplers and 19 resistivity electrodes were installed in a single borehole at vertical spacings as close as 7 cm. This approach was used to install horizontally oriented TDR waveguides at depths greater than 10 m, thereby extending the TDR technique to the study of deep vadose zones. Other applications include measurement of in situ Eh at a site where strong chemical oxidants were injected to remediate sediments contaminated by organic chemicals.
Utility of Simple Models for Capture Zone Delineation in Heterogeneous Unconfined Aquifers
Authors: Cole Bryce E. , Silliman Stephen E. 
Published: December 2005

AbstractMonte Carlo simulation is used to examine the utility of simple (homogeneous/isotropic) models for the delineation of wellhead protection areas (WHPAs) in heterogeneous, statistically anisotropic, unconfined aquifers. Capture zone geometry is investigated under two hydrologic conditions: regional gradient negligible compared to pumping and significant regional gradient compared to the local gradient due to pumping. Variability of capture zone geometry is quantified in terms of simple measurements (maximum transport distance and maximum width of the capture zone) and the probability of inclusion in the capture zone of a series of hypothetical contaminant source locations. These results indicate that substantial uncertainty exists in the delineation of a wellhead capture zone. This uncertainty is related, principally, to flow that occurs along preferential pathways associated with zones of high hydraulic conductivity. It is suggested that these uncertainties can be accommodated in one of three fashions depending on the value of land, the benefit of wellhead protection, and the availability of funds to perform more thorough field assessment. The first option is to modify the estimated capture zone by a factor of safety. In the absence of significant regional flow, a factor of safety of approximately three applied to the calculated fixed radius estimate of the capture zone appears to be sufficient for the conditions simulated in this project. In the case of a capture zone within a significant regional gradient, uncertainty in the location of the real capture zone will require safety factors on the width of the estimated capture zone on the order of 30, with a safety factor of approximately three in the longitudinal direction. The second option reduces these factors of safety by increasing the risk that the estimated capture zone will not cover the entire area of the real capture zone. Work available in the literature provides insight into the trade‐off between the size of the estimated capture zone and the risk endured. The third option is to reduce uncertainty in the vicinity of a wellhead through additional expenditure to allow the application of classic hydrologic techniques involving conditioning or inverse modeling.
Soil Vacuum Extraction of Perchloroethylene from the Borden Aquifer
Authors: Thomson Neil R. , Flynn David J. 
Published: December 2005

AbstractAn assessment of a conventional soil vacuum extraction (SVE) system to remove perchloroethylene (PCE), a dense nonaqueous phase liquid (DNAPL), was conducted in a dewatered 9 × 9 m block of the surficial sand aquifer located at the Canadian Forces Base (CFB), Borden, Ontario. Approximately two years prior to the installation and operation of the SVE system, 1250 kg of PCE were released under saturated conditions into this experimental cell, forming a heterogeneous DNAPL distribution. Using ground penetrating radar and neutron probe data in conjunction with detailed soil core data, it was determined that approximately 600 kg of PCE were available for removal by the SVE system after dewatering. Performance assessment of this SVE system was based on soil core data and monitoring of in situ gas concentration and pressure, soil temperature, and moisture content.After the first 25 days of operation, the SVE system had removed 230 kg of PCE, during which time the off‐gas concentration decreased by 70% from an initial concentration of close to 3500 ppmY After 432 days of operation, 63% (376 kg) of the estimated available mass was removed from the SVE target zone. In situ pressure measurements and sulphur hexafluoride tracer tests indicated that advective air movement occurred throughout the SVE target zone. Changes to the extraction well configuration and the use of short‐screened extraction drive points did not increase the mass removal performance.After 250 days of operation, eight soil cores were removed from the test cell, and bulk soil concentration and soil moisture content measurements were performed at 0.05 m increments along the length of each core. These data revealed zones where significant quantities of PCE remained, even though the cumulative mass removal profile for the SVE system was nonzero asymptotic. In general, these zones coincided with higher moisture content zones reflective of the heterogeneous nature of this porous medium.This investigation provides insight into some of the limitations of conventional SVE technology to clean up a sand aquifer contaminated with a DNAPL, given a reasonably good estimate of the before‐extraction mass conditions. In particular, the findings clearly show that the heterogeneous nature of the porous medium gives rise to a nonuniform moisture content, a heterogeneous pure phase distribution, and the development of preferential gas phase flow pathways. As a consequence, this will in general limit this technology to remove a considerable fraction of the DNAPL mass present. The results also shed light on the use of soil gas and bulk soil concentration data to provide a representative picture of the in situ mass distribution. And finally, an analysis of the system off‐gas data showed that continuous rather than pulsed operation of the extraction system increased mass removal.
On the Estimation of Stream Flow Depletion Parameters by Drawdown Analysis
Authors: Christensen Steen 
Published: December 2005

AbstractHunt (1999) derived a model for computation of stream flow depletion caused by pumping from a well near a stream that does not fully penetrate the aquifer. The model input includes the transmissivity (T) and the storativity (S) of the aquifer and the conductance of the stream bed (λ). We study the experimental and hydrogeological conditions for which drawdown analysis can be expected to produce T, S, and λ estimates that can be used in the model of Hunt (1999) to predict depletion with a specified accuracy. The study is conducted by using a combination of sensitivity analysis and uncertainty analysis. The analysis shows that it is always important to have an accurate estimate of λ in order to accurately predict depletion. Recommendations for the design of a pumping test near a stream are given to achieve this. The pumping well should be located close to the stream. Accurate drawdown measurements should be made both near the pumping well and near the stream, and the measurements should be used simultaneously to estimate T, S, and λ. The duration of the pumping test should be relatively long in order to obtain an accurate estimate of λ. A methodology is proposed in which a desired accuracy of either the estimates of T, S, and λ, or the stream flow predicted from these estimates, is used to estimate the duration of the pumping test. Some examples indicate that in many cases the duration of the test should be from an hour to one or two months. However, if S is large (∼10−1) and λ is small (10‐7 m/s) then the duration should be from several months to years. This would be expensive and not practical, so other methods should be used to estimate λ in this situation.
Simulation of Regional Ground Water Flow and Salt Water Intrusion in Hernando County, Florida
Authors: Guvanasen Varut , Wade Shirley C. , Barcelo Mark D. 
Published: December 2005

AbstractThe projected growth of Hernando County, located along the coast of west‐central Florida, has motivated the county and the Southwest Florida Water Management District to assess ground water resources in the area. As part of the Hernando County Water Resources Assessment Project, a computationally efficient modeling approach was developed to simulate regional ground water flow and salt water intrusion in two adjoining ground water basins in which Hernando County is located. In this modeling approach, the regional ground water flow simulation was divided into two stages: fresh water and sharp‐interface simulations. The first stage was performed using a calibrated fresh water model. Following the fresh water simulation, a calibrated sharp‐interface model was used to evaluate the potential extent of migration of the fresh water/salt water interface as a result of implementing ground water management scenarios. Predictive modeling results indicate that projected future ground water withdrawals will cause less than 0.6 m of additional drawdown within Hernando County. Results also suggest that by the year 2050 the fresh water/salt water interface will migrate landward less than 1.6 km from its 1994 position.
Type Curves for Pumping Test Analysis in Coastal Aquifers
Authors: Sakr Sameh Attiya 
Published: December 2005

AbstractConventional methods of analyzing pumping test data usually assume a single‐phase fluid condition. In coastal aquifer systems this condition is not valid when salt water underlies the production well screen. A set of type curves is developed for unsteady state flow toward a fresh water pumping well. The solution accounts for the nonlinear boundary conditions on the interface and for different interface geometry. The governing partial differential equations are solved using the finite‐element approximation for confined, homogeneous, and isotropic aquifer situations. The type curves were used to estimate the aquifer fresh water hydraulic conductivity and aquifer specific storage using pumping test data from a pumping well located on the coast of the Red Sea. The measured drawdowns are consistent with the predicted drawdown of the type curves.