To compare accuracy of genus and species level identification of presumptive enterococci isolates from the marine environment using conventional biochemical testing, four commercial identification ...systems and 16S rRNA sequence analysis. Ninety-seven environmental bacterial isolates identified as presumptive enterococci on mEI media were tested using conventional and Enterococcus genus screen biochemical tests, four commercial testing systems and 16S rRNA sequencing. Conventional and Enterococcus genus screen biochemical testing, 16S rRNA sequencing and two commercial test systems achieved an accuracy of >=94% for Enterococcus genus confirmation. Conventional biochemical testing and 16S rRNA sequencing achieved an accuracy of >=90% for species level identification. For confirmation of Enterococcus genus from mEI media, conventional or genus screen biochemical testing, 16S rRNA sequencing and the four commercial systems were correct 79-100% of the time. For speciation to an accuracy of 90% or better, either conventional biochemical testing or 16S rRNA sequencing is required. Accurate identification of presumptive environmental Enterococcus isolates to genus and species level is an integral part of laboratory quality assurance and further characterization of Enterococcus species from pollution incidents. This investigation determines the ability of six different methods to correctly identify environmental isolates.
Four bacterial source tracking (BST) methods, enterobacterial repetitive intergenic consensus sequence polymerase chain reaction (ERIC-PCR), automated ribotyping using HindIII, Kirby-Bauer antibiotic ...resistance analysis (KB-ARA) and pulsed-field gel electrophoresis (PFGE) were directly compared using the same collection of Escherichia coli isolates. The data sets from each BST method and from composite methods were compared for library accuracy and their ability to identify water isolates. Potential sources of faecal pollution were identified by watershed sanitary surveys. Domestic sewage and faecal samples from pets, cattle, avian livestock, other nonavian livestock, avian wildlife and nonavian wildlife sources were collected for isolation of E. coli. A total of 2275 E. coli isolates from 813 source samples were screened using ERIC-PCR to exclude clones and to maximize library diversity, resulting in 883 isolates from 745 samples selected for the library. The selected isolates were further analysed using automated ribotyping with HindIII, KB-ARA and PFGE. A total of 555 E. coli isolates obtained from 412 water samples were analysed by the four BST methods. A composite data set of the four BST methods gave the highest rates of correct classification (RCCs) with the fewest unidentified isolates than any single method alone. RCCs for the four-method composite data set and a seven-way split of source classes ranged from 22% for avian livestock to 83% for domestic sewage. Two-method composite data sets were also found to be better than individual methods, having RCCs similar to the four-method composite and identification of the same major sources of faecal pollution. The use of BST composite data sets may be more beneficial than the use of single methods. This is one of the first comprehensive comparisons using composite data from several BST methods. While the four-method approach provided the most desirable BST results, the use of two-method composite data sets may yield comparable BST results while providing for cost, labour and time savings.
The purpose of this work was to develop a robust technique for planning intensity-modulated radiation therapy (IMRT) for prostate cancer patients who are to be entered into a proposed ...hypofractionated dose escalation study. In this study the dose escalation will be restricted to the prostate alone, which may be regarded as a concurrent boost volume within the overall planning target volume (PTV). The dose to the prostate itself is to be delivered in 3 Gy fractions, and for this phase of the study the total prostate dose will be 57 Gy in 19 fractions, with 50 Gy prescribed to the rest of the PTV. If acute toxicity results are acceptable, the next phase will escalate doses to 60 Gy in 20 x 3 Gy fractions. There will be 30 patients in each arm. This work describes the class solution which was developed to create IMRT plans for this study, and which enabled the same set of inverse planning parameters to be used during optimization for every patient with minimal planner intervention. The resulting dose distributions were compared with those that would be achieved from a 3D conformal radiotherapy (3DCRT) technique that used a multileaf collimator (MLC) but no intensity modulation to treat the PTV, followed by a sequential boost to raise the prostate to 57 Gy. The two methods were tested on anatomical data sets for a series of 10 patients who would have been eligible for this study, and the techniques were compared in terms of doses to the target volumes and the organs at risk. The IMRT method resulted in much greater sparing of the rectum and bladder than the 3DCRT technique, whilst still delivering acceptable doses to the target volumes. In particular, the volume of rectum receiving the minimum PTV dose of 47.5 Gy was reduced from a mean value of 36.9% (range 23.4% to 61.0%) to 18.6% (10.3% to 29.0%). In conclusion, it was found possible to use a class solution approach to produce IMRT dose escalated plans. This IMRT technique has since been implemented clinically for patients enrolled in the hypofractionated dose escalation study.
In some influenza surveillance systems, timely transport to laboratories for reverse transcription-polymerase chain reaction (RT-PCR) testing is challenging.Guidelines suggest that samples can be ...stored at 4°Cfor up to 96 hours but the effect of longer storage times has not been systematically evaluated. We collected nasopharyngeal and oropharyngeal specimens from patients in Kenya and stored them in viral transport medium at 2 to 8°C before testing for influenza A and B using real-time RT-PCR. From April 2008 to November 2010, we collected 7,833 samples; 940 (12%) were positive for influenza. In multivariable analysis, specimens stored for six days were less likely to be influenza-positive compared to specimens stored between zero and one day (adjusted odds ratio (a OR): 0.49, 95%confidence interval (CI): 0.27–0.93). There was no statistically significant difference in influenza positivity of specimens stored for five days compared to zero to one day. There was no statistically significant relationship between days in refrigeration and cycle threshold(Ct) values for positive samples (p=0.31). We found that samples could remain in storage for at least five days without affecting the proportion-positive of samples,potentially increasing the feasibility of including influenza surveillance sites in remote areas.
Summary
We have examined the effect that acid deposition and other sources of acidity have had over the last 110–140 years on soil under woodland (Broadbalk and Geescroft Wildernesses) and grassland ...(Park Grass) comprising some of the Classical Experiments at Rothamsted Experimental Station. Changes in soil chemistry have been followed by analysing some of the unique archive of stored samples for pH, water‐soluble and exchangeable base cations, aluminium, iron and manganese, exchangeable acidity, cation exchange capacity (CEC) and soluble anions. Proton balances and historical data show the importance of acid deposition to acidification and concomitant changes in the chemistry of the soil. The pH of the surface soil of Geescroft Wilderness has fallen from 6.2 to 3.8 since 1883. The decrease in the pH of the unlimed, unfertilized plot on Park Grass was less over a similar period (from pH 5.2 to 4.2), illustrating the significant effect of the woodland canopy on the interception of acidifying pollutants. The effect of increasing acidity on the soil chemistry of Geescroft Wilderness is seen in its decreasing base saturation and CEC, with base cations moving down the soil profile. Clay minerals are being irreversibly weathered, and Mn and Al progressively mobilized, so that today Al occupies 70% of the exchange complex in the surface soil. Even with present reductions in sulphur deposition critical loads for sulphur, nitrogen and acidity are still exceeded. Such semi‐natural ecosystems are unsustainable under the current climate of pollution.
Intensity modulated radiation therapy can be achieved by driving the leaves of a multileaf collimator (MLC) across an x-ray therapy beam. Algorithms to generate the required leaf trajectories assume ...that the leaf positions are exactly known to the MLC controller. In practice, leaf positions depend upon calibration accuracy and stability and may vary within set tolerances. The purpose of this study was to determine the effects of potential leaf position inaccuracies on intensity modulated beams. Equations are derived which quantify the absolute error in delivered monitor units given a known error in leaf position. The equations have been verified by ionization chamber measurements in dynamically delivered flat fields, comparing deliveries in which known displacements have been applied to the defined leaf positions with deliveries without displacements applied. The equations are then applied to two clinical intensity modulations: an inverse planned prostate field and a breast compensating field. It is shown that leaf position accuracy is more critical for a highly modulated low-dose intensity profile than a moderately modulated high-dose intensity profile. Suggestions are given regarding the implications for quality control of dynamic MLC treatments.
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► IR spectra of nerve agents are dominated by peaks due to POC and PO vibrations. ► V agents have IR lines from PS stretching not found in G agents and simulants. ► IR spectroscopy ...can identify family (G or V) but not individual agents.
Since organophosphorus nerve agents are among the most toxic known chemical warfare agents, it is desirable to have a way to distinguish between one and another. Infrared spectroscopy is a common tool for identifying molecules. Given the difficulty in handling these chemicals, calculated IR spectra can be useful. Calculated IR spectra are presented for G agents, V agents, and simulants. Quantum chemistry calculations were performed using the Gaussian 03 package at the B3LYP/6-31+G(d,p) level of theory. The most prominent IR lines are due to vibrations of POC and PO groups within the molecules. It should be possible to distinguish between the G-series and V-series agents using IR spectroscopy, but unique identification of individual chemical agents is unlikely.
Nonenzymatic glycation of type IV collagen and matrix metalloproteinase susceptibility. The glomerular basement membrane (GBM) is damaged in diabetes through complex mechanisms that are not fully ...understood. Prominent among them is nonenzymatic protein glycation leading to the formation of so-called advanced glycation end products (AGEs). We examined the effects of in vitro glycation of intact collagen type IV in bovine lens capsule (LBM) and kidney glomerular (GBM) basement membranes on their susceptibility to matrix metalloproteinases, using stromelysin 1 (MMP-3) and gelatinase B (MMP-9). Sites of cleavage of unmodified LBM collagen were located in the triple helical region. In vitro glycation by glucose severely inhibited the release of soluble collagen cleavage peptides by MMP-3 and MMP-9. The distribution of AGEs within the three domains of collagen IV (7S, triple helical, and non-collagenous NC1) were compared for LBM glycation using AGE fluorescence, pentosidine quantitation, and immunoreactivity towards anti-AGE antibodies that recognize the AGE carboxymethyllysine (CML). Marked asymmetry was observed, with the flexible triple helical domain having the most pentosidine and fluorescent AGEs but the least CML. The in vivo relevance of these findings is supported by preliminary studies of AGE distribution in renal basement membrane (RBM) collagen IV domains from human kidneys of two insulin-dependent diabetics and one normal subject. Pentosidine and fluorescent AGE distributions of diabetic RBM were similar to LBM, but the CML AGE in diabetic kidney was less in the triple helical domain than in NCI. Our results support the hypothesis that nonenzymatic glycation of collagen IV contributes to the thickening of basement membranes, a hallmark of diabetic nephropathy.
Background: Previous studies of the relation between age and body fat reached differing conclusions concerning the question of whether body fat is lower in the elderly than in middle-aged persons. ...Objective: The objectives of this study were to characterize the relation between age and body fat in 4 ethnic groups and test the hypothesis that body fat is lower in the elderly than in middle-aged persons. Design: Body fat was measured in a sample of 1324 volunteers aged 20-94 y by using a 4-component model of body composition. Four ethnic groups were studied: Asians, blacks, Puerto Ricans, and whites. Regression models were developed for fat mass and fat percentage as functions of age. Results: In all but one of the groups, a highly significant curvilinear relation between age and body fat was found, indicating a peak amount of body fat in late middle age and lower amounts of body fat at younger and older ages (P < 0.001). The age at which maximum body fat was predicted in the various groups ranged from 53 to 61 y for fat mass and from 55 to 71 y for fat percentage. In Puerto Rican men there was no significant relation between age and fat mass, and the relation between age and fat percentage was linear and positively correlated. Conclusions: This study provided data on the relation between age and body fat in 4 ethnic groups and supported the hypothesis that body fat is lower in the elderly than in middle-aged persons.
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