Fujihara, M; Nishiyama, S; Hasegawa, S
1994-01-01
The effects of agars on the determination of the potency of polymyxin B sulfate by the agar plate diffusion method were investigated. The results showed that there were significant differences in the potency of polymyxin B sulfate between agars produced by different manufacturers. In order to investigate this phenomenon, two major components of polymyxin B sulfate, namely, the polymyxin B1 and B2 fractions, were isolated and purified by preparative high-pressure liquid chromatography, and the effects of agars on the potencies of these two components were individually examined. The results showed that there were significant differences in the relative potency of the B1 component versus that of the B2 component between the agar preparations produced by different manufacturers. On the basis of the relative potency of each of the components and the composition of the components, we developed a theoretical equation with which we could calculate the activity of polymyxin B sulfate on a certain agar. The values computed from the equation were consistent with those obtained from actual measurements. It was concluded that the effects of agars on the determination of polymyxin B sulfate activity will become evident only when the composition of the reference standard significantly differs from that of the samples. When the standard and samples have the same compositions, the sources of the agar preparation exert no effect on the determination of the potency by the agar plate diffusion method. PMID:7872766
Zhou, Ying; Zhang, Meijuan; Liu, Hui
2015-01-01
Objectives. To develop a new method for determining total antioxidants in serum and to evaluate the total antioxidant capacity of organisms. Design and Methods. Sodium hyposulfite (Na2S2O3) and serum were used to evaluate the linearity and precision of the potassium permanganate agar method. The area of serum diffusion in samples from 30 intensive care unit (ICU) patients compared with 44 healthy subjects was determined by the potassium permanganate agar method. Results. The linearity (R2 in the linear experiment of Na2S2O3 was 0.994; R2 in the linear experiment of serum was 0.987) and precision (coefficient of variation of area of high level serum diffusion within-run, between-run, and between-day and coefficient of variation of area of low serum diffusion within-run, between-run, and between-day were all less than 10%) were acceptable using the potassium permanganate agar method. Total antioxidants of serum between the ICU group and the healthy group were different (p = 0.002, two tailed). Conclusions. Total antioxidants in serum can be determined by the potassium permanganate agar method. The total antioxidant capacity of an organism can be evaluated by the amount of total antioxidants in serum.
Comparison of the antibacterial activity of chelating agents using the agar diffusion method
Technology Transfer Automated Retrieval System (TEKTRAN)
The agar diffusion assay was used to examine antibacterial activity of 2 metal chelators. Concentrations of 0 to 40 mM of ethylenediaminetetraacetic acid (EDTA) and ethylenediamine-N,N’-disuccinic acid (EDDS) were prepared in 1.0 M potassium hydroxide (KOH). The pH of the solutions was adjusted to 1...
Luddin, Norhayati; Ahmed, Hany Mohamed Aly
2013-01-01
Complete debridement and disinfection of the root canal system are fundamental requirements for successful endodontic treatment. Despite the morphological challenges of the internal root anatomy, root canal irrigants play an important role in the optimization of the root canal preparation, which is essentially a chemo-mechanical procedure. Enterococcus faecalis is one of the most resistant microorganisms that dominants the microbial ecosystem of persistent periradicular lesions in retreatment cases. For that reason, many in vitro and in vivo studies evaluated and compared the antibacterial activity of sodium hypochlorite and chlorhexidine at varying concentrations using different experimental models against this microorganism. However, many controversies with regard to the ideal irrigant and concentration do in fact exist. Hence, this review aims to discuss the antibacterial activity of these two main root canal irrigants against Enterococcus faecalis using the agar diffusion and direct contact methods and the possible modulating factors responsible for inconsistent findings among different studies. In addition, the disinfection potential of both chemical agents on gutta percha and Resilon cones are also discussed. The source of this review was conducted through an electronic literature search using PubMed database from December 1997 until December 2011, which analyze the related laboratory investigations of both irrigants, published in major endodontic journals. PMID:23349569
PEGGY C. KOHNER; ROBIN PATEL; JAMES R. UHL; KAY M. GARIN; MARLENE K. HOPKINS; LEE T. WEGENER; FRANKLIN R. COCKERILL
1997-01-01
An evaluation was undertaken to determine the optimal method for testing the susceptibilities of 100 clinical isolates and two reference strains of Enterococcus spp. to vancomycin in vitro. Six testing methods were studied by using the following media and incubation times: agar screen with the Synergy Quad Plate (Remel, Lenexa, Kans.), an in-house-prepared brain heart infusion (BHI) agar plate, and
Ambaye, A; Kohner, P C; Wollan, P C; Roberts, K L; Roberts, G D; Cockerill, F R
1997-01-01
An evaluation was undertaken to determine the optimal method for the in vitro susceptibility testing of 26 Nocardia asteroides complex isolates to the following antimicrobial agents: amikacin, ampicillin, amoxicillin-clavulanate, ceftriaxone, ciprofloxacin, erythromycin, imipenem, minocycline, and trimethoprim-sulfamethoxazole. Five testing methods were studied including the agar dilution, broth microdilution, and disk diffusion methods, the epsilometer test (E-test), and the BACTEC radiometric method. Results for each antimicrobial agent and each testing method were interpreted as indicating susceptibility, intermediate susceptibility, or resistance according to current guidelines of the National Committee for Clinical Laboratory Standards (NCCLS) for bacteria that grow aerobically and were then compared to a "gold standard" susceptibility test result. The gold standard result for each Nocardia isolate was established by a consensus of the results of the majority of testing methods used in the study. When the results were combined for all antimicrobial agents tested against all Nocardia isolates by all methods, the BACTEC radiometric method produced the highest level of agreement (97.9%) with the consensus results and had the fewest very major (n = 1), major (n = 2), and minor (n = 2) errors. In contrast, the results of the agar dilution method were in least agreement (93.2%) with the consensus results, and this method also produced the most very major (n = 8), major (n = 4), and, along with the disk diffusion method, minor (n = 6) errors. For all test methods, interpretive errors were most frequent when testing ampicillin or amoxicillin-clavulanate. Moreover, for all Nocardia nova isolates tested, ampicillin susceptibility results by any of the testing methods were not in agreement with the results of testing for beta-lactamase by the nitrocefin (Cefinase) disk method. We conclude that among the methods evaluated, the BACTEC radiometric method appeared to be the best for determining the in vitro susceptibilities of members of the N. asteroides complex to a panel of nine antimicrobial agents. However, none of the test methods, including the BACTEC method, accurately predicted the ampicillin resistance of the N. nova isolates tested, all of which produced beta-lactamase. Presuming that this beta-lactamase hydrolyzes ampicillin, this disparity may relate to the NCCLS breakpoints that were used, which may require modification for this antimicrobial agent when tested against N. nova isolates. PMID:9157140
ABIY AMBAYE; PEGGY C. KOHNER; PETER C. WOLLAN; KATHLEEN L. ROBERTS; GLENN D. ROBERTS; ANDFRANK R. COCKERILL
1997-01-01
An evaluation was undertaken to determine the optimal method for the in vitro susceptibility testing of 26 Nocardia asteroides complex isolates to the following antimicrobial agents: amikacin, ampicillin, amoxicillin- clavulanate, ceftriaxone, ciprofloxacin, erythromycin, imipenem, minocycline, and trimethoprim-sulfamethox- azole. Five testing methods were studied including the agar dilution, broth microdilution, and disk diffusion methods, the epsilometer test (E-test), and the BACTEC
Modeling development of inhibition zones in an agar diffusion bioassay
Chandrasekar, Vaishnavi; Knabel, Stephen J; Anantheswaran, Ramaswamy C
2015-01-01
A two-temperature agar diffusion bioassay is commonly used to quantify the concentration of nisin using Micrococcus luteus as the indicator microorganism. A finite element computational model based on Fick's second law of diffusion was used to predict the radius of the inhibition zone in this diffusion bioassay. The model developed was used to calculate nisin concentration profiles as a function of time and position within the agar. The minimum inhibitory concentration (MIC) of nisin against M. luteus was determined experimentally. The critical time (Tc) for growth of M. luteus within the agar diffusion bioassay was experimentally determined using incubation studies with nisin. The radius of the inhibition zone was predicted from the computational model as the location where the predicted nisin concentration at Tc was equal to MIC. The MIC was experimentally determined to be 0.156 ?g mL?1, and Tc was determined to be 7 h. Good agreement (R2 = 0.984) was obtained between model-predicted and experimentally determined inhibition zone radii.
Modeling development of inhibition zones in an agar diffusion bioassay.
Chandrasekar, Vaishnavi; Knabel, Stephen J; Anantheswaran, Ramaswamy C
2015-09-01
A two-temperature agar diffusion bioassay is commonly used to quantify the concentration of nisin using Micrococcus luteus as the indicator microorganism. A finite element computational model based on Fick's second law of diffusion was used to predict the radius of the inhibition zone in this diffusion bioassay. The model developed was used to calculate nisin concentration profiles as a function of time and position within the agar. The minimum inhibitory concentration (MIC) of nisin against M. luteus was determined experimentally. The critical time (T c) for growth of M. luteus within the agar diffusion bioassay was experimentally determined using incubation studies with nisin. The radius of the inhibition zone was predicted from the computational model as the location where the predicted nisin concentration at T c was equal to MIC. The MIC was experimentally determined to be 0.156 ?g mL(-1), and T c was determined to be 7 h. Good agreement (R (2) = 0.984) was obtained between model-predicted and experimentally determined inhibition zone radii. PMID:26405525
Disk diffusion, agar dilution and the E-test for susceptibility testing of Corynebacterium jeikeium.
Pennekamp, Andreas; Pünter, Verena; Zbinden, Reinhard
1996-02-01
OBJECTIVE: The susceptibilities to penicillin, tetracycline, erythromycin, gentamicin, vancomycin and teicoplanin of 58 strains of Corynebacterium jeikeium were assessed by disk diffusion and agar dilution reference methods. METHODS: Zone sizes and minimal inhibitory concentrations (MIC) by agar dilution were interpreted using the ranges in the NCCLS tables for organisms other than Haemophilus, Neisseria gonorrhoeae, and Streptococcus pneumoniae. RESULTS: By agar dilution, 14%, 88%, 17% and 26% of the 58 isolates were susceptible to penicillin, tetracycline, erythromycin, and gentamicin, respectively. Using the breakpoints for Listeria monocytogenes, all strains showed concordant results for penicillin by disk diffusion. Discrepancies in the interpretative categories by disk diffusion were found in four cases (two very major and two minor) for tetracycline, in nine (two very major, two major, and five minor) for erythromycin, and in 1 case (very major) for gentamicin. All 58 strains were susceptible to vancomycin and teicoplanin by agar dilution and disk diffusion. The overall agreement of interpretative disk diffusion for all six antibiotics was 95.9%. In addition, all strains were susceptible to both glycopeptides by E-test. However, for vancomycin the MIC results in 58.6% were two log2 dilutions and in 1.7% more than two log2 dilutions higher by E-test than by agar dilution, whereas for teicoplanin agreement within one log2 dilution was 100%. CONCLUSIONS: Further evaluation of methodologies of disk diffusion is required to obtain a better agreement for erythromycin and tetracycline. The criteria of the NCCLS for interpretation of disk diffusion are adequate for susceptibility testing of C. jeikeium to penicillin, gentamicin, vancomycin and teicoplanin. PMID:11866845
Hegstad, Kristin; Giske, Christian G; Haldorsen, Bjørg; Matuschek, Erika; Schønning, Kristian; Leegaard, Truls M; Kahlmeter, Gunnar; Sundsfjord, Arnfinn
2014-05-01
Different antimicrobial susceptibility testing methods to detect low-level vancomycin resistance in enterococci were evaluated in a Scandinavian multicenter study (n=28). A phenotypically and genotypically well-characterized diverse collection of Enterococcus faecalis (n=12) and Enterococcus faecium (n=18) strains with and without nonsusceptibility to vancomycin was examined blindly in Danish (n=5), Norwegian (n=13), and Swedish (n=10) laboratories using the EUCAST disk diffusion method (n=28) and the CLSI agar screen (n=18) or the Vitek 2 system (bioMérieux) (n=5). The EUCAST disk diffusion method (very major error [VME] rate, 7.0%; sensitivity, 0.93; major error [ME] rate, 2.4%; specificity, 0.98) and CLSI agar screen (VME rate, 6.6%; sensitivity, 0.93; ME rate, 5.6%; specificity, 0.94) performed significantly better (P=0.02) than the Vitek 2 system (VME rate, 13%; sensitivity, 0.87; ME rate, 0%; specificity, 1). The performance of the EUCAST disk diffusion method was challenged by differences in vancomycin inhibition zone sizes as well as the experience of the personnel in interpreting fuzzy zone edges as an indication of vancomycin resistance. Laboratories using Oxoid agar (P<0.0001) or Merck Mueller-Hinton (MH) agar (P=0.027) for the disk diffusion assay performed significantly better than did laboratories using BBL MH II medium. Laboratories using Difco brain heart infusion (BHI) agar for the CLSI agar screen performed significantly better (P=0.017) than did those using Oxoid BHI agar. In conclusion, both the EUCAST disk diffusion and CLSI agar screening methods performed acceptably (sensitivity, 0.93; specificity, 0.94 to 0.98) in the detection of VanB-type vancomycin-resistant enterococci with low-level resistance. Importantly, use of the CLSI agar screen requires careful monitoring of the vancomycin concentration in the plates. Moreover, disk diffusion methodology requires that personnel be trained in interpreting zone edges. PMID:24599985
Improved Susceptibility Disk Assay Method Employing an Agar Overlay Technique
Anderson, Blondell
1978-01-01
Susceptibility disks impregnated with 35 different antibiotics were assayed by the current Code of Federal Regulations method and by a new method employing an agar overlay. The new method, a simplified analytical procedure, exhibited improvement in zone definition and an increase in dose response. Assays performed by the new method were accurate and precise. The agar overlay technique appears to be superior to the current Code of Federal Regulations method. Images PMID:727765
Bailey, Tom A.
1983-01-01
The reliability, reproducibility, and usefulness of three screening methods -- the cellophane transfer, the agar plug transfer, and the agar dilution -- to screen aquatic fungicides were evaluated. Achlya flagellata and Saprolegnia hypogyna were exposed to 1, 10, and 100 mg/L of malachite green to test each method. The cellophane transfer and agar plug transfer techniques had similar reliability and reproducibility in rating fungicidal activity, and were both superior to the agar dilution technique. The agar plug transfer and agar dilution techniques adequately projected in vivo activity of malachite green, but the cellophane transfer technique overestimated its activity. Overall, the agar plug transfer technique most accurately rated the activity of malachite green and was the easiest test to perform. It therefore appears to be the method of choice for testing aquatic fungicides.
Methods for identifying lipoxygenase producing microorganisms on agar plates
2012-01-01
Plate assays for lipoxygenase producing microorganisms on agar plates have been developed. Both potassium iodide-starch and indamine dye formation methods were effective for detecting soybean lipoxygenase activity on agar plates. A positive result was also achieved using the ?-carotene bleaching method, but the sensitivity of this method was lower than the other two methods. The potassium iodide-starch and indamine dye formation methods were also applied for detecting lipoxygenase production by Trichoderma reesei and Pichia pastoris transformants expressing the lipoxygenase gene of the fungus Gaeumannomyces graminis. In both cases lipoxygenase production in the transformants could be identified. For detection of the G. graminis lipoxygenase produced by Aspergillus nidulans the potassium iodide-starch method was successful. When Escherichia coli was grown on agar and soybean lipoxygenase was applied on the culture lipoxygenase activity could clearly be detected by the indamine dye formation method. This suggests that the method has potential for screening of metagenomic libraries in E. coli for lipoxygenase activity. PMID:22449314
Hiraishi, Noriko; Sadek, Fernanda T.; King, Nigel M.; Ferrari, Marco; Pashley, David H.; Tay, Franklin R
2013-01-01
Purpose Cholesterol esterase is both a component of salivary hydrolases as well as an inflammatory cell-derived enzyme and has been shown to cause biodegradation of methacrylate-based resin composites. This study examined whether Resilon, a polycaprolactone-based thermoplastic root filling material is susceptible to biodegradation by cholesterol esterase using agar-well diffusion assay of serially-diluted aqueous Resilon emulsions that were dispersed in agar. Materials and methods Emulsions of Resilon and polycaprolactone were prepared and dispersed in agar on culture plates. Two different concentrations of a cholesterol esterase (0.3 and 1.2 U/mL) were prepared and fed to wells prepared in the agar plates using an agar-well diffusion assay for examination the degradation of polymeric materials. Results Degradation of the emulsified Resilon was manifested as the formation of clear zones of different sizes around the agar wells. No clear zones were observed in agar wells that contain sterile distilled water as the negative control. Clinical significance Although dispersion Resilon into an emulsion is not the way in which this material is employed as a root filling material, the potential for Resilon to be degraded by cholesterol esterase is of potential concern as one cannot limit the degradation of extruded Resilon from a root apex by monocyte-derived macrophages to just the anatomical root apex. As the present study employed a high concentration of cholesterol esterase, further studies should be directed to examining the degradation of Resilon using macrophage cell cultures. PMID:18578181
CATHERINE L. CLARK; MICHAEL R. JACOBS; PETER C. APPELBAUM
1998-01-01
The activities of levofloxacin and clarithromycin against 199 penicillin- and macrolide-susceptible and -resistant pneumococci were tested by agar and microdilution methods in air and by disk diffusion and E-test methods in air and CO2. For levofloxacin, >99.0% of strains were susceptible at <2.0 mg\\/ml with zone diameters of >17 mm, regardless of incubation in air or CO2. Although zone sizes
Diffusion of Methylene Blue in Phantoms of Agar Using a Photoacoustic Technique
NASA Astrophysics Data System (ADS)
Vilca-Quispe, L.; Alvarado-Gil, J. J.; Quintana, P.; Ordonez-Miranda, J.
2010-05-01
In this work, the kinetics of diffusion of methylene blue in agar aqueous solution is studied using a photoacoustic technique. Two agar phantoms solutions in water with a relation of mass/volume of 0.01% and 0.05% were analyzed. The study was performed using a modified Rosencwaig photoacoustic cell that is enclosed by transparent windows, on both sides. The sample is deposited directly on top of the upper window. A red light beam, at a fixed modulation frequency, is sent through the lower window illuminating the sample and inducing the photoacoustic effect inside the closed chamber of the cell. At the beginning of the experiment, a droplet of 100?L of agar solution is deposited; afterwards, the signal stabilizes, and 10?L of methylene blue aqueous solution (0.0125 g · mL-1) is added to the surface of the agar. During the first seconds of the experiment, the photoacoustic signal amplitude increases followed by a gradual and long decay. Results for modulation frequencies in the range from 10Hz to 80Hz for both agar concentrations are presented. A simple theoretical approach is presented to analyze the experimental data. It is demonstrated that the kinetics of the process can be parameterized as a function of the changes of an effective optical absorption coefficient. From these results, the characteristic time, in which the dye diffusion process stabilizes, is obtained. It is found that this time is larger for samples with a higher agar concentration. These differences provide important results for biomedical sciences in which agar gels are used as phantoms resembling some of the properties of living organs and tissues.
Aal-Saraj, Ali Burak; Ariffin, Zaihan; Masudi, Sam'an Malik
2012-08-01
The aim of this study was to evaluate the antimicrobial activity of a new experimental nano-hydroxyapatite epoxy resin-based sealer (Nanoseal) with several other commercially available sealers; AH26, Tubliseal, Sealapex and Roekoseal against Enterococcus faecalis, Pseudomonas aeruginosa, Streptococcus mutans, Streptococcus sobrinus and Escherichia coli for up to 7 days. Agar diffusion was used in this study. Fifty Muller-Hinton agar plates were prepared and divided into five experimental groups (n = 10), for each micro-organism. Another 10 agar plates were used as positive and negative controls. Endodontic sealers were tested against each micro-organism. Inhibition zones produced were recorded. The results of this study showed that all test materials exhibited inhibition zones towards the tested micro-organisms for 7 days except for Roekoseal, which showed no inhibition zones. Nanoseal and AH26 exhibited similar zones of inhibition. Significant difference was found between Nanoseal and the other tested sealers (P < 0.001). PMID:22827817
Traub, W H; Geipel, U; Leonhard, B
1998-01-01
Forty-two isolates of Enterococcus faecalis and 56 isolates of Enterococcus faecium, including 8 vancomycin-resistant strains, were examined for comparative susceptibility to 27 antimicrobial drugs with the agar dilution method, employing Mueller-Hinton (MHA), Iso-Sensitest (ISTA), and Wilkins-Chalgren (WCA) agar. The Bauer-Kirby agar disk diffusion method was used to comparatively test 24 of the agents in parallel. The enterococci yielded better growth on ISTA and WCA. However, WCA completely antagonized co-trimoxazole and, though less, fosfomycin. Importantly, WCA slightly reduced the activities of teicoplanin (minimal inhibitory concentrations, MICs, raised up to twofold) and vancomycin (MICs raised two- to fourfold) against enterococci and staphylococcal quality control strains. Therefore, WCA was judged unsuitable for susceptibility testing of enterococci. For E. faecalis no discrepancies between agar dilution MICs and inhibition zone diameters were encountered with augmentin, ampicillin, ampicillin-sulbactam, chloramphenicol, mupirocin, oxacillin, teicoplanin, and co-trimoxazole. Overall, MHA yielded fewer very major (category I) and major (category II) discrepancies than ISTA. However, numerous minor (category III), slight (category IV), minimal (category V), and/or negligible (category VI) discrepancies were encountered with ciprofloxacin, doxycycline, erythromycin, fosfomycin, fusidic acid, meropenem, ofloxacin and rifampin. With respect to E. faecium, only cefotaxime, mupirocin, oxacillin, and teicoplanin yielded nondiscrepant results. Several very major (I) and major (II) discrepancies were observed with augmentin, ampicillin, ampicillin-sulbactam, doxycycline, fusidic acid, imipenem, and penicillin G. Minor discrepancies (categories III-VI) were particularly numerous with augmentin, chloramphenicol, ciprofloxacin, doxycycline, and piperacillin. The largest numbers of negligible (VI) discrepancies were noted with fosfomycin, fusidic acid, and ofloxacin. It is recommended to test one cephalosporin (cefuroxime or the like) in parallel for educational purposes and to exclude fosfomycin, fusidic acid, and rifampin from test batteries because of the wide scatter of test results. The large number of minimal (V) discrepancies of ciprofloxacin against E. faecalis, the numerous minor (III) and slight (IV) discrepancies of chloramphenicol against E. faecium, and the not insignificant number of very major (I) and minor (III) discrepancies observed with meropenem against isolates of E. faecalis necessitated proposals for new disk intermediate susceptibility criteria. PMID:9681198
TODD A. DAVIES; LINDA M. KELLY; MICHAEL R. JACOBS; PETER C. APPELBAUM
2000-01-01
Agar dilution and microdilution (both in air) and E test and disk diffusion (both in air and CO2) were used to test the activity of telithromycin against 110 erythromycin-susceptible and 106 erythromycin-resistant pneumococci. The MICs at which 50 and 90% of strains are inhibited (MIC50s and MIC90s, respectively) for erythromycin-susceptible strains varied between 0.008 and 0.016 mg\\/ml and 0.016 and
Ogata, Silvio Kazuo; Gales, Ana Cristina; Kawakami, Elisabete
2014-01-01
Antimicrobial susceptibility testing for Helicobacter pylori is increasingly important due to resistance to the most used antimicrobials agents. Only agar dilution method is approved by CLSI, but it is difficult to perform routinely. We evaluated the reliability of E-test and disk diffusion comparing to agar dilution method on Helicobacter pylori antimicrobial susceptibility testing. Susceptibility testing was performed for amoxicillin, clarithromycin, furazolidone, metronidazole and tetracycline using E-test, disk-diffusion and agar dilution method in 77 consecutive Helicobacter pylori strains from dyspeptic children and adolescents. Resistance rates were: amoxicillin - 10.4%, 9% and 68.8%; clarithromycin - 19.5%, 20.8%, 36.3%; metronidazole - 40.2%33.7%, 38.9%, respectively by agar dilution, E-test and disk diffusion method. Furazolidone and tetracycline showed no resistance rates. Metronidazole presented strong correlation to E-test (r = 0.7992, p < 0.0001) and disk diffusion method (r=-0.6962, p < 0.0001). Clarithromycin presented moderate correlation to E-test (r = 0.6369, p < 0.0001) and disk diffusion method (r=?0.5656, p < 0.0001). Amoxicillin presented weak correlation to E-test (r = 0.3565, p = 0.0015) and disk diffusion (r=?0.3565, p = 0.0015). Tetracycline presented weak correlation with E-test (r = 0.2346, p = 0.04) and furazolidone to disk diffusion (r=?0.0288, p = 0.8038). E-test presented better agreement with gold standard. It is an easy and reliable method for Helicobacter pylori susceptibility testing. Disk diffusion method presented high disagreement and high rates of major errors. PMID:25763052
DeCross, A J; Marshall, B J; McCallum, R W; Hoffman, S R; Barrett, L J; Guerrant, R L
1993-01-01
Since the methods for metronidazole susceptibility testing of Helicobacter pylori have not been standardized or validated, we compared three methods that are used to test the metronidazole susceptibilities of 25 isolates of H. pylori. Specifically, we examined the methods of Steer's replicator agar dilution, tube broth microdilution, and modified Kirby-Bauer disk diffusion. The metronidazole disk zone sizes obtained by the disk diffusion method correlated well (r = 0.74) with the MICs obtained by the agar dilution method. Afterward, the disk diffusion method was used to characterize the metronidazole susceptibilities of 44 isolates of H. pylori. Dual therapy (bismuth and metronidazole) proved to be highly effective against metronidazole-susceptible strains (81.6% eradication rate) but fared poorly against resistant strains (16.7% eradication rate; P < 0.01). Using agar dilution testing, we validated the modified Kirby-Bauer disk diffusion method for metronidazole susceptibility testing of H. pylori and conclude that it is practical, accurate, and clinically applicable. PMID:8370723
Pasquetti, M; Chiavassa, E; Tizzani, P; Danesi, P; Peano, A
2015-10-01
Aim of this study was to verify whether Mueller-Hinton agar supplemented with 2 % glucose and methylene blue (MH-GM), which is used for disk diffusion susceptibility testing of Candida species by the Clinical and Laboratory Standards Institute, is suitable for testing Malassezia pachydermatis. A variant of the disk diffusion procedure utilizing a 9-mm tablet was used to test 31 isolates against clotrimazole and miconazole using MH-GM as test medium. The MH-GM agar optimally supported the growth of all M. pachydermatis isolates, provided that the yeast inoculum was prepared with a lipid source (Tween 40 and 80). Zone edges were frequently definite and clear, facilitating the measurement of zone size and minimizing subjectivity. The inhibition zones correlated with MIC values obtained in a broth dilution assay. The agar diffusion method with MH-GM as the test medium appears as a suitable procedure for testing the susceptibility of M. pachydermatis to CTZ and MCZ in clinical laboratories. This test format may allow processing a large number of isolates in epidemiological studies. This may in turn facilitate clarifying to what extent the problem "drug resistance" accounts for cases of treatment failure in dogs with Malassezia otitis and dermatitis. PMID:26138434
Mohamed, S; Flint, S; Palmer, J; Fletcher, G C; Pitt, J I
2013-09-01
A simple and rapid screening method was developed for the detection of citrinin in fungal cultures using Coconut Cream Agar (CCA) described previously for detecting aflatoxin and ochratoxin A. Fifteen isolates of Penicillium citrinum were inoculated onto CCA and incubated at 25 and 30°C for 10 days. All isolates produced a distinct yellow green fluorescence on CCA when the reverse side of the agar plates were viewed under long wavelength UV light. Detection was optimal at 25°C after four to 5 days of incubation. Isolates positive by the CCA method also tested positive for citrinin production by the TLC agar plug method after growth on CCA, Czapek yeast extract agar and yeast extract sucrose agar. Control cultures were negative by both methods, indicating that the CCA Petri dish method was suitable for screening cultures for citrinin production. PMID:23682683
Rhim, Jong-Whan; Wang, Long-Feng; Lee, Yonghoon; Hong, Seok-In
2014-03-15
Silver nanoparticles (AgNPs) were prepared by a laser ablation method and composite films with the AgNPs and agar were prepared by solvent casting method. UV-vis absorbance test and transmission electron microscopy (TEM) analysis results revealed that non-agglomerated spherical AgNPs were formed by the laser ablation method. The surface color of the resulting agar/AgNPs films exhibited the characteristic plasmonic effect of the AgNPs with the maximum absorption peaks of 400-407 nm. X-ray diffraction (XRD) test results also exhibited characteristic AgNPs crystals with diffraction peaks observed at 2? values of 38.39°, 44.49°, and 64.45°, which were corresponding to (111), (200), and (220) crystallographic planes of face-centered cubic (fcc) silver crystals, respectively. Thermogravimetric analysis (TGA) results showed that thermal stability of the agar/AgNPs composite films was increased by the inclusion of metallic silver. Water vapor barrier properties and surface hydrophobicity of the agar/AgNPs films increased slightly with the increase in AgNPs content but they were not statistically significant (p>0.05), while mechanical strength and stiffness of the composite films decreased slightly (p<0.05). The agar/AgNPs films exhibited distinctive antimicrobial activity against both Gram-positive (Listeria monocytogenes) and Gram-negative (Escherichia coli O157:H7) bacterial pathogens. PMID:24528754
Technology Transfer Automated Retrieval System (TEKTRAN)
The agar diffusion assay was used to examine antibacterial activity of alkaline salts of fatty acids (FA). Wells in agar media seeded with bacteria were filled with FA-potassium hydroxide (KOH) solutions, plates were incubated, and zones of inhibition were measured. The relationship between bacteric...
Variability of agar dilution-replicator method of yeast susceptibility testing.
Brass, C; Shainhouse, J Z; Stevens, D A
1979-06-01
The agar dilution method of in vitro susceptibility testing of fungi was analyzed with a Steers-type inoculum replicator, ten strains, and three drugs. The replicator reproducibly delivered the same inoculum to each series of plates. The minimal inhibitory concentrations of ketoconazole (an imidazole) and 5-fluorocytosine, but not that of the polyene nystatin, were dependent on the initial inoculum size. With the former two drugs, but not with the latter, minimal inhibitory concentrations were highly variable depending on the time of reading. Results with agar and broth dilution methods were divergent, and the differences in minimal inhibitory concentrations were variable in serial comparisons by the two methods. If the agar dilution minimal inhibitory concentrations were determined at first appearance of control growth, a commonly used end point, small variations in the time of reading (as could occur by variation in observer perception of when initial growth appears) induced large variations in the minimal inhibitory concentrations of 5-fluorocytosine and ketoconazole, particularly with rapidly growing strains. Results at 35 and 30 degrees C were similar. The differences in results with the three drugs suggest different mechanisms of action. The variability quantitated with the agar dilution method could result in variability in results between laboratories and even observers in the same laboratory. PMID:573098
Rapid fluorescence method for screening Salmonella spp. from enteric differential agars.
Aguirre, P M; Cacho, J B; Folgueira, L; López, M; García, J; Velasco, A C
1990-01-01
Four hundred thirty-two lactose-negative colonies isolated from human feces on stool differential agar media were flooded with one drop of MUCAP Test reagent (Biolife Italiana S.r.I., Milan, Italy) and observed under a Wood lamp for the development of a blue fluorescence over or around the colony. On the basis of manual and automated conventional tests for the screening of Salmonella spp., the MUCAP Test yielded the following results: 79 true-positives, 314 true-negatives, 35 false-positives, and 4 false-negatives (sensitivity, 95%; specificity, 90%; positive predictive value, 69%; negative predictive value, 99%). The specificity of the test performed on colonies isolated on MacConkey agar (95%) was higher than that performed on colonies isolated on SS agar (88%; P less than 0.03). The MUCAP Test is an easy, rapid, and sensitive method for the screening of colonies suspected of being Salmonella spp., reducing the number of biochemical tests needed. PMID:2405010
To maintain waters that are "fishable and swimmable", mandated by the Clean Water Act, the U.S. Environmental Protection Agency (EPA) is developing a list of approved methods for use in enumerating enterococci and E. coli in ambient waters. As part of this effort, we compared mEn...
Tsuboyama, Shoko; Kodama, Yutaka
2014-01-01
The liverwort Marchantia polymorpha L. is being developed as an emerging model plant, and several transformation techniques were recently reported. Examples are biolistic- and Agrobacterium-mediated transformation methods. Here, we report a simplified method for Agrobacterium-mediated transformation of sporelings, and it is termed Agar-utilized Transformation with Pouring Solutions (AgarTrap). The procedure of the AgarTrap was carried out by simply exchanging appropriate solutions in a Petri dish, and completed within a week, successfully yielding sufficient numbers of independent transformants for molecular analysis (e.g. characterization of gene/protein function) in a single experiment. The AgarTrap method will promote future molecular biological study in M. polymorpha. PMID:24259681
Technology Transfer Automated Retrieval System (TEKTRAN)
The agar diffusion assay was used to examine antibacterial activity of alkaline salts of caproic, caprylic, capric, lauric, and myristic acids. A 0.5M concentration of each fatty acid was dissolved in 1.0 M potassium hydroxide (KOH), and pH of the mixtures was adjusted to 10.5 with citric acid. Solu...
A new membrane filter (MF) medium, MI agar, recently validated for use in recovering chlorine-damaged total coloiforms (TC) and Escherichia coli from drinking water, was compared to the US Environmental Protection Agency (EPA)-approved MF method(mEndo agar and nutrient agar suppl...
Górny, Rafa? L; ?awniczek-Wa?czyk, Anna
2012-01-01
The effect of perpendicular and swirling aerozolization methods on the release of fungal fragments and spores from agar surface was studied. Three fungal species (Aspergillus versicolor, Cladosporium cladosporioides, Penicillium chrysogenum) were selected for the tests as they commonly occur indoors, create different hyphae structure when they grow on surfaces, and have different spore shapes, aerodynamic sizes, and formation mechanisms. As the tested surface, Petri dishes filled with malt extract agar, separately inoculated with fungal strains and cultivated to obtain an abundant and even growth were used. For the purpose of these experiments, a new aerosolization chamber was built in which HEPA-filtered air stream responsible for fungal propagule release was either perpendicularly directed towards the contaminated surface or set in swirling motion above it. The experiments were conducted at 2 air velocities, typical for outdoor environment (11.6 m/s) and ventilation ducts (29.1 m/s). Concentrations and size distributions of released fragments and spores were measured using an optical particle counter. The results showed that the propagule release depends on the direction (swirling motion was able to release up to 3.4 × 10(5) fragments and 3 × 10(5) spores from 1 cm( 2) of contaminated surface, i.e. significantly more than the perpendicularly directed air stream), velocity (the higher the swirling air velocity applied, the higher the number of released propagules) of the air stream above the contaminated surface, and varied due to the taxonomical species origin (the higher number of particulates was released by Aspergillus colonies). Hence, the efficient control of both microbial fragments and spores, not only in the air, but also in their source should be an integral part of the quality control procedure. PMID:22742802
Petra Luber; Edda Bartelt; Elke Genschow; Jutta Wagner; Helmut Hahn
2003-01-01
A standardized broth microdilution method was compared to the E test and an agar dilution method for the antimicrobial susceptibility testing of Campylobacter jejuni and C. coli isolates. A group of 47 human clinical isolates, 37 isolates from retail poultry, and 29 isolates from living turkeys (total, 113 isolates) was included in the study. These encompassed 92 C. jejuni and
Johnson, Ronald; Mills, John; Colón-Reveles, Judith
2009-01-01
A method modification study was conducted for the VIDAS Salmonella (SLM) assay (AOAC Performance Tested Method 020901) using the EasySLM method to validate a matrix extension for peanut butter. The VIDAS EasySLM method is a simple enrichment procedure compared to traditional Salmonella methods, requiring only pre-enrichment and a single selective enrichment media, Salmonella Xpress 2 (SX2) broth. SX2 replaces the two selective broths in traditional methods and eliminates the M broth transfer, incubation, and subsequent pooling of M broths prior to VIDAS assay. The validation study was conducted under the AOAC Research Institute Emergency Response Validation program. VIDAS SLM was compared to the U.S. Food and Drug Administration's Bacteriological Analytical Manual (FDA-BAM) method for detection of S. enterica ser. Typhimurium in peanut butter. All peanut butter samples were prepared, blind-coded, and shipped to the method developers' laboratory by Q Laboratories. In addition, Q Laboratories performed most probable number and reference method analyses on peanut butter samples. The VIDAS EasySLM ChromID Salmonella (SM2) Agar was previously validated in the Performance Tested Methods program for the detection of Salmonella in roast beef, raw ground pork, turkey, pork sausage, raw chicken breast, dry pet food, whole milk, ice cream, bagged spinach, shrimp (raw, peeled), raw cod, spent irrigation water, pecans, peanut butter, dry pasta, cake mix, ground black pepper, nonfat dry milk, liquid eggs, cantaloupe, and orange juice. In the matrix extension study for peanut butter, the VIDAS EasySLM method was shown to be equivalent to the appropriate reference culture procedure using both buffered peptone water pre-enrichment and the FDA-BAM lactose pre-enrichment in the two-step enrichment method with SX2 media. The current study extends the validation to include peanut butter. PMID:20166608
Beuchat, L R; Mann, David A; Gurtler, Joshua B
2007-11-01
A study was done to compare Nissui Compact Dry Yeast and Mold plates (CDYM), 3M Petrifilm Yeast and Mold count plates (PYM), dichloran-rose bengal chloramphenicol (DRBC) agar, and dichloran 18% glycerol (DG18) agar for enumerating yeasts and molds naturally occurring in 97 foods (grains, legumes, raw fruits and vegetables, nuts, dairy products, meats, and miscellaneous processed foods and dry mixes). Correlation coefficients for plates incubated for 5 days were DG18 versus DRBC (0.93), PYM versus DRBC (0.81), CDYM versus DG18 (0.81), PYM versus DG18 (0.80), CDYM versus DRBC (0.79), and CDYM versus PYM (0.75). The number of yeasts and molds recovered from a group of foods (n = 32) analyzed on a weight basis (CFU per gram) was not significantly different (alpha = 0.05) when samples were plated on DRBC, DG18, PYM, or CDYM. However, the order of recovery from foods (n = 65) in a group analyzed on a unit or piece basis, or a composite of both groups (n = 97), was DRBC > DG18 = CDYM > PYM. Compared with PYM, CDYM recovered equivalent, significantly higher (alpha = 0.05) or significantly lower (alpha = 0.05) numbers of yeasts and molds in 51.5, 27.8, and 20.6%, respectively, of the 97 foods tested; respective values were 68.8, 15.6, and 15.6% in the small group (n = 32) and 43.1, 33.8, and 23.1% in the large group (n = 65) of foods. The two groups contained different types of foods, the latter consisting largely (73.8%) of raw fruits (n = 16) and vegetables (n = 32). Differences in efficacy of the four methods in recovering yeasts and molds from foods in the two groups are attributed in part to differences in genera and predominant mycoflora. While DG18 agar, CDYM, and PYM appear to be acceptable for enumerating yeasts and molds in the foods analyzed in this study, overall, DRBC agar recovered higher numbers from the 97 test foods, thereby supporting its recommended use as a general purpose medium for mycological analysis. PMID:18044453
Vulindlu, M; Charlett, A; Surman, S; Lee, J V
2004-01-01
Pour and spread plates are the conventional methods of choice for the isolation and enumeration of heterotrophic microorganisms in treated water supplies. The tests are performed at 22 degrees C and 37 degrees C for 72 h and 48 h respectively. Counts at 22 degrees C are associated with pollution of water systems from external sources, while counts at 37 degrees C are used as an indication of treatment plant performance and the deterioration of the general quality of water. Conventional methods using Yeast Extract Agar for a pour plate and R2A agar for a spread plate were compared with the multidose IDEXX SimPlate method for the isolation and enumeration of heterotrophic bacteria in water. SimPlate gave a significantly higher count on average than the conventional methods. The R2A method showed the next highest count, being significantly higher than Yeast Extract Agar. In addition, unlike the pour and spread plate methods, SimPlate was easier to use, reduced labour, and the test results were far easier to read. PMID:15318522
Lavieri, Nicolas A; Sebranek, Joseph G; Cordray, Joseph C; Dickson, James S; Jung, Stephanie; Manu, David K; Mendonça, Aubrey F; Brehm-Stecher, Byron F; Stock, Joseph; Stalder, Kenneth J
2014-05-01
A sublethally injured bacterial cell has been defined as a cell that survives a stress such as heating, freezing, acid treatment, or other antimicrobial intervention but can repair the cellular damage exerted by the stressor and later regain its original ability to grow. Consequently, sublethally injured cells are not likely to be included in conventional enumeration procedures, which could result in unrealistically low counts unless efforts are made to encourage recovery of the injured cells before enumeration. The objective of this study was to evaluate the use of the thin agar layer (TAL) method for the recovery of pressure-injured and heat-injured Listeria monocytogenes in a tryptic soy broth with 0.6% yeast extract system. Pressure injury consisted of treatment of a culture of mixed L. monocytogenes strains with high hydrostatic pressure at 400 or 600 MPa for 1 s, 2 min, 4 min, or 6 min at a process temperature of 12±2 °C. Heat injury consisted of treatment of a culture of mixed L. monocytogenes strains at 60±1 °C for 3, 6, or 9 min. Growth media were tryptic soy agar (TSA) with 0.6% yeast extract, modified Oxford medium (MOX), and TAL, which consisted of a 7-ml layer of TSA overlaid onto solidified MOX. Counts of viable L. monocytogenes on TAL were higher than those on MOX in the heat-injury experiment but not in the pressure-injury experiment. Therefore, the effectiveness of the TAL method may be specific to the type of injury applied to the microorganism and should be investigated in a variety of cellular injury scenarios. PMID:24780340
2012-01-01
We recently established a method for isolating functional single cells from environmental samples using a micromanipulator (Functional single-cell (FSC) isolation), and applied it to the study of denitrifying bacteria in rice paddy soil (Ashida et al. 2010. Appl Microbiol Biotechnol 85:1211–1217). To further examine the advantages and possible disadvantages of the FSC method, we isolated denitrifying bacteria from the same rice paddy soil sample using both FSC and standard agar plate dilution (APD) methods and compared in this study. The proportion of denitrifying bacteria in the total isolates was more than 6-fold larger with FSC isolation (57.1%) compared with the APD method (9.2%). Denitrifying bacteria belonging to Alphaproteobacteria and Bacilli were commonly isolated using both methods, whereas those belonging to Betaproteobacteria, which had been found to be active in the denitrification-inductive paddy soil, were isolated only with the FSC method. On the other hand, Actinobacteria were only isolated using the APD method. The mean potential denitrification activity of the FSC isolates was higher than that of the APD isolates. Overall, FSC isolation was confirmed to be an excellent method for studying denitrifying bacteria compared with the standard agar plate dilution method. PMID:22985609
Valerie R Benning; Jeremy J Mathers
1999-01-01
A broth microdilution and a reference agar dilution method was used to determine minimal inhibitory concentrations (MICs) of five veterinary antimicrobials when tested against 96 animal-derived and six American Type Culture Collection (ATCC) strains of Clostridium perfringens. These antimicrobials [bacitracin methylenedisalicylate (bacitracin-MD), tylosin, virginiamycin, erthromycin and tetracycline] are approved for use in animal feed at different levels for growth enhancement,
Jennifer S. Lavender; Julie L. Kinzelman
2009-01-01
Molecular methods such as quantitative, real-time polymerase chain reaction (QPCR) are intended to shorten the period between sampling and publicly available results. Cross comparison studies in Racine, WI, USA evaluated QPCR against agar-based (US EPA Method 1600) and defined substrate (IDEXX Colilert-18®) methods for the detection and quantification of Escherichia coli and enterococci in a variety of aqueous environments (wastewater,
Modeling of the Bacillus subtilis Bacterial Biofilm Growing on an Agar Substrate
Wang, Xiaoling; Wang, Guoqing; Hao, Mudong
2015-01-01
Bacterial biofilms are organized communities composed of millions of microorganisms that accumulate on almost any kinds of surfaces. In this paper, a biofilm growth model on an agar substrate is developed based on mass conservation principles, Fick's first law, and Monod's kinetic reaction, by considering nutrient diffusion between biofilm and agar substrate. Our results show biofilm growth evolution characteristics such as biofilm thickness, active biomass, and nutrient concentration in the agar substrate. We quantitatively obtain biofilm growth dependence on different parameters. We provide an alternative mathematical method to describe other kinds of biofilm growth such as multiple bacterial species biofilm and also biofilm growth on various complex substrates. PMID:26355542
Nonlinear methods for solving the diffusion equation
Shober, Robert Anthony
1976-01-01
This thesis is concerned with methods for the transient solution of the neutron diffusion equations in one or two energy groups. Initially, nonlinear methods for solving the static diffusion equations using the finite ...
Sartory, David P; Gu, Haoyi; Chen, Chun-Ming
2008-07-01
This study compared the Quanti-Disc most probable number (MPN) test for heterotrophic bacteria from drinking water with the widely used yeast extract agar (YEA) pour plate method. The Quanti-Disc test module contains 50 reaction wells in which a medium has been pre-deposited. The medium contains a suite of three fluorogenic enzyme substrates selected for the detection of enzymes expressed widely by heterotrophic bacteria. The MPN of heterotrophic bacteria is calculated from the number of fluorescing reaction wells after incubation of a sample. Quanti-Disc and the YEA pour plate method were compared according to guidance on comparing methods given in United Kingdom national guidance and ISO 17994:2004. The two methods were also challenged with reference strains and isolates of heterotrophic bacteria from drinking water. This indicated that heterotrophic bacteria commonly encountered in drinking water are detected by both the YEA pour plate method and Quanti-Disc. Analysis of data from split water samples (723 for 37 degrees C tests and 872 for 22 degrees C tests) from nine geographically diverse laboratories in England and Wales demonstrated that the Quanti-Disc method is equivalent to the YEA pour plate method for the analysis of heterotrophic bacteria from drinking and similar waters at 37 degrees C, and superior to YEA for the analysis at 22 degrees C. The Quanti-Disc method is a simple and efficient alternative method for the enumeration of heterotrophic bacteria from drinking water. PMID:18534656
Aulenbach, Brent T.
2010-01-01
Bacteria holding-time experiments of up to 62 h were performed on five surface-water samples from four urban stream sites in the vicinity of Atlanta, GA, USA that had relatively high densities of coliform bacteria (Escherichia coli densities were all well above the US Environmental Protection Agency criterion of 126 colonies (100 ml)???1 for recreational waters). Holding-time experiments were done for fecal coliform using the membrane filtration modified fecal coliform (mFC) agar method and for total coliform and E. coli using the Colilert®-18 Quanti-Tray® method. The precisions of these analytical methods were quantified. Precisions determined for fecal coliform indicated that the upper bound of the ideal range of counts could reasonably be extended upward and would improve precision. For the Colilert®-18 method, analytical precisions were similar to the theoretical precisions for this method. Fecal and total coliform densities did not change significantly with holding times up to about 27 h. Limited information indicated that fecal coliform densities might be stable for holding times of up to 62 h, whereas total coliform densities might not be stable for holding times greater than about 27 h. E. coli densities were stable for holding times of up to 18 h—a shorter period than indicated from a previous studies. These results should be applicable to non-regulatory monitoring sampling designs for similar urban surface-water sample types.
Mathematical Methods for Diffusion MRI Processing
Lenglet, C.; Campbell, J.S.W.; Descoteaux, M.; Haro, G.; Savadjiev, P.; Wassermann, D.; Anwander, A.; Deriche, R.; Pike, G.B.; Sapiro, G.; Siddiqi, K.; Thompson, P.
2009-01-01
In this article, we review recent mathematical models and computational methods for the processing of diffusion Magnetic Resonance Images, including state-of-the-art reconstruction of diffusion models, cerebral white matter connectivity analysis, and segmentation techniques. We focus on Diffusion Tensor Images (DTI) and Q-Ball Images (QBI). PMID:19063977
Charles R. Sims; Victor L. Paetznick; Jose R. Rodriguez; Enuo Chen; Luis Ostrosky-Zeichner
2006-01-01
Agar-based antifungal susceptibility testing is an attractive alternative to the microdilution method. We examined the correlation between the microdilution, E-test, and disk diffusion methods for posaconazole against Candida spp. A total of 270 bloodstream isolates of Candida spp. with a broad range of posaconazole MICs were tested using the CLSI M27-A2 method for microdilution, as well as the M-44A method
Entis, P
1996-01-01
Twenty laboratories participated in a collaborative study to validate a 2-day hydrophobic grid membrane filter method using YM-11 agar for enumeration of yeast and mold in foods. Six naturally contaminated food products were included in the study: garlic powder, raw ground beef, walnuts, flour/meal, orange juice, and yogurt. The test method produced significantly higher results than the 5-day pour plate reference method for orange juice and significantly lower, though numerically similar, results for walnuts and yogurt. Differences between the test and reference methods were not significant for garlic powder, raw ground beef, or flour/meal. Repeatability and reproducibility were similar for both the test and reference methods in all cases. The hydrophobic grid membrane filter method for enumeration of yeast and mold in foods has been adopted by AOAC INTERNATIONAL. PMID:8823916
Radial diffusion method for determining tannin in plant extracts
Ann E. Hagerman
1987-01-01
Tannin in plant extracts can be determined by reacting the tannin with a protein and quantitating the precipitated complex. In the new assay described here, a tannin-containing solution is placed in a well in a protein-containing agar slab. As the tannin diffuses into the gel and complexes with protein, a visible ring of precipitation develops. The area of the ring
[Gel-producing properties of exopolysaccharide acrylamide in composition with agar-agar].
Vashchenko, L N; Litvinchuk, O A; Gvozdiak, R I; Votselko, S K
2004-01-01
A possibility to use a new polymer--exopolysaccharide acrylamide (EPAA)--for partial substitution of agar-agar in solid nutrient media in microbiology has been studied. It has been established than the EPAA in concentration 6.0-12.0 g/l with agar in concentration 10.0 g/l produce gel which is so strong as agar in concentration 15.0-20.0 g/l. Quality of gels produced depends an the method of EPAA mixing with agar. It has been shown that usage of EPAA in nutrient media does not affect growth, colony and cell morphology and biochemical properties of microorganisms. The use of EPAA to prepare nutrient media permits us to reduce expenditures for agar. PMID:15765869
Madonna J. Matar; Luis Ostrosky-Zeichner; Victor L. Paetznick; Jose R. Rodriguez; Enuo Chen; John H. Rex
2003-01-01
The activities of fluconazole and voriconazole against isolates of Candida spp. (n 400) were tested by the E-test, disk diffusion, and the National Committee for Clinical Laboratory Standards (NCCLS) M27-A2 broth microdilution-based reference methods. More than 96% of isolates found to be susceptible to fluconazole by the reference method were identified as susceptible by the agar-based methods. Lesser degrees of
ERIC Educational Resources Information Center
Foy, Barry G.
1977-01-01
Two demonstrations are described. Materials and instructions for demonstrating movement of molecules into cytoplasm using agar blocks, phenolphthalein, and sodium hydroxide are given. A simple method for demonstrating that the rate of diffusion of a gas is inversely proportional to its molecular weight is also presented. (AJ)
Sakai, Masao; Hosoda, Akifumi; Ogura, Kenjiro; Ikenaga, Makoto
2014-01-01
An agar-degrading bacterium was isolated from soil collected in a vegetable cropping field. The growth of this isolate was enhanced by supplying culture supernatants of bacteria belonging to the order Rhizobiales. Phylogenetic analysis based on 16S rRNA gene sequences indicated the novel bacterium, strain KA5-B(T), belonged to the genus Steroidobacter in Gammaproteobacteria, but differed from its closest relative, Steroidobacter denitrificans FS(T), at the species level with 96.5% similarity. Strain KA5-B(T) was strictly aerobic, Gram-negative, non-motile, non-spore forming, and had a straight to slightly curved rod shape. Cytochrome oxidase and catalase activities were positive. The strain grew on media containing culture supernatants in a temperature range of 15-37°C and between pH 4.5 and 9.0, with optimal growth occurring at 30°C and pH 6.0-8.0. No growth occurred at 10 or 42°C or at NaCl concentrations more than 3% (w/v). The main cellular fatty acids were iso-C15:0, C16:1?7c, and iso-C17:1?9c. The main quinone was ubiquinone-8 and DNA G+C content was 62.9 mol%. In contrast, strain FS(T) was motile, did not grow on the agar plate, and its dominant cellular fatty acids were C15:0 and C17:1?8c. Based on its phylogenetic and phenotypic properties, strain KA5-B(T) (JCM 18477(T) = KCTC 32107(T)) represents a novel species in genus Steroidobacter, for which the name Steroidobacter agariperforans sp. nov. is proposed. PMID:24621511
Guerrero, P; Etxabide, A; Leceta, I; Peñalba, M; de la Caba, K
2014-01-01
The chemical structure of the agar obtained from Gelidium sesquipedale (Rhodophyta) has been determined by (13)C nuclear magnetic resonance ((13)C NMR) and Fourier transform infrared spectroscopy (FTIR). Agar (AG) films with different amounts of soy protein isolate (SPI) were prepared using a thermo-moulding method, and transparent and hydrophobic films were obtained and characterized. FTIR analysis provided a detailed description of the binding groups present in the films, such as carboxylic, hydroxyl and sulfonate groups, while the surface composition was examined using X-ray photoelectron spectroscopy (XPS). The changes observed by FTIR and XPS spectra suggested interactions between functional groups of agar and SPI. This is a novel approach to the characterization of agar-based films and provides knowledge about the compatibility of agar and soy protein for further investigation of the functional properties of biodegradable films based on these biopolymers. PMID:24274535
Konopliannikov, A G; Lepekhina, L A; Kolesnikova, A I; Ermakov, V I
1986-01-01
Clonogenic cells forming colonies in agar cultures in diffusion chambers and those isolated from subcutaneously transplanted Lewis lung carcinoma do not differ in their sensitivity to 60Co gamma-rays with respect to tumor growth stages. The dose-survival curves for all studied cells are S-shaped with a small shoulder. A cumulative dose-survival curve for malignant clonogenic cells is characterized by the average value of mean lethal dose D0 = 2.24 Gy and extrapolation number n = 2.0. When exposed to gamma-neutron-radiation (252Cf) malignant clonogenic cells exhibit a nearly exponential dose-survival curve with D0 = 0.56 Gy (with respect to a neutron component). The RBE of gamma-neutron radiation (252Cf) is 2.5. PMID:3749472
Preparation of an agar-silver nanoparticles (A-AgNp) film for increasing the shelf-life of fruits.
Gudadhe, Janhavi A; Yadav, Alka; Gade, Aniket; Marcato, Priscyla D; Durán, Nelson; Rai, Mahendra
2014-12-01
Preparation of protective coating possessing antimicrobial properties is present day need as they increase the shelf life of fruits and vegetables. In the present study, preparation of agar-silver nanoparticle film for increasing the shelf life of fruits is reported. Silver nanoparticles (Ag-NPs) biosynthesised using an extract of Ocimum sanctum leaves, were mixed with agar-agar to prepare an agar-silver nanoparticles (A-AgNp) film. This film was surface-coated over the fruits, Citrus aurantifolium (Thornless lime) and Pyrus malus (Apple), and evaluated for the determination of antimicrobial activity of A-AgNp films using disc diffusion method, weight loss and shelf life of fruits. This study demonstrates that these A-AgNp films possess antimicrobial activity and also increase the shelf life of fruits. PMID:25429496
Grimes, J E; Page, L A
1978-01-01
Detection of chlamydial antibody in serums of wild birds was compared for the following methods: direct complement-fixation (DCF), modified DCF (MDCF), and agar-gel precipitin (AGP). The birds species used were great-tailed grackles (Cassidix mexicanus), common grackles (Quiscalus quiscula), brown-headed cowbirds (Molothrus ater), bronzed cowbirds (Tangavius aeneus), and mourning doves (Zenaida macroura). The birds were either inoculated with an isolate of Chlamydia psittaci obtained originally from turkeys or kept as uninoculated cagemates. DCF detected antibody in most inoculated common grackles, mourning doves, and brown-headed cowbirds. It was unreliable, however, for great-tailed grackles and bronzed cowbirds inoculated intramuscularly. MDCF method detected antibody in all inoculated birds except 1 mourning dove, and gave higher titers than did DCF. AGP detected antibody in all inoculated brown-headed cowbirds and all mourning doves, 1 inoculated and 1 exposed great-tailed grackle, and none of the other 2 species. Chlamydiae were apparently transmitted to the uninoculated great-tailed and common grackles and mourning doves, for antibody was detected by all 3 methods in these species kept as uninoculated cagemates. PMID:100098
Niederstebruch, N; Sixt, D
2013-02-01
In the industrial world, the agar diffusion test is a standard procedure for the susceptibility testing of bacteria isolates. Beta-hemolytic Streptococcus spp. are tested with Müller-Hinton agar supplemented with 5 % blood, a so-called blood agar. The results are interpreted using standardized tables, which only exist for this type of nutrient matrix. Because of a number difficulties, both with respect to technical issues and to manual skills, blood agar is not a feasible option in many developing countries. Beta-hemolytic Streptococcus spp. also grow on Standard Nutrient Agar 1 (StNA1). This suggests using that type of nutrient medium for running agar diffusion tests. However, there are no standardized tables that can be used for interpreting the diameters of the zones of inhibition on StNA1 1. Using the existing standardized tables for blood agar to interpret cultures on StNA1 1 would be of great benefit under such circumstances where blood agar is not available. With this in mind, we conducted comparative tests to evaluate the growth characteristics of beta-hemolytic Streptococcus spp. on StNA1 1 compared to Müller-Hinton agar supplemented with 5 % sheep blood. In this study, we were able to show that beta-hemolytic Streptococcus spp. develop similar zones of inhibition on blood agar and on StNA1 1. Therefore, it is suggested that, for the interpretation of antibiograms of beta-hemolytic Streptococcus spp. performed on StNA1 1, the standard tables for blood agar can be used. PMID:22926453
Technology Transfer Automated Retrieval System (TEKTRAN)
Two sampling techniques, agar extraction (AE) and centrifuge sugar flotation extraction (CSFE) were compared to determine their relative efficacy to recover immature stages of Culicoides spp from salt marsh substrates. Three types of samples (seeded with known numbers of larvae, homogenized field s...
Development of a selective agar plate for the detection of Campylobacter spp. in fresh produce.
Yoo, Jin-Hee; Choi, Na-Young; Bae, Young-Min; Lee, Jung-Su; Lee, Sun-Young
2014-10-17
This study was conducted to develop a selective medium for the detection of Campylobacter spp. in fresh produce. Campylobacter spp. (n=4), non-Campylobacter (showing positive results on Campylobacter selective agar) strains (n=49) isolated from fresh produce, indicator bacteria (n=13), and spoilage bacteria isolated from fresh produce (n=15) were plated on four Campylobacter selective media. Bolton agar and modified charcoal cefoperazone deoxycholate agar (mCCDA) exhibited higher sensitivity for Campylobacter spp. than did Preston agar and Hunt agar, although certain non-Campylobacter strains isolated from fresh produce by using a selective agar isolation method, were still able to grow on Bolton agar and mCCDA. To inhibit the growth of non-Campylobacter strains, Bolton agar and mCCDA were supplemented with 5 antibiotics (rifampicin, polymyxin B, sodium metabisulfite, sodium pyruvate, ferrous sulfate) and the growth of Campylobacter spp. (n=7) and non-Campylobacter strains (n=44) was evaluated. Although Bolton agar supplemented with rifampicin (BR agar) exhibited a higher selectivity for Campylobacter spp. than did mCCDA supplemented with antibiotics, certain non-Campylobacter strains were still able to grow on BR agar (18.8%). When BR agar with various concentrations of sulfamethoxazole-trimethoprim were tested with Campylobacter spp. (n=8) and non-Campylobacter (n=7), sulfamethoxazole-trimethoprim was inhibitory against 3 of 7 non-Campylobacter strains. Finally, we validated the use of BR agar containing 50mg/L sulfamethoxazole (BRS agar) or 0.5mg/L ciprofloxacin (BRCS agar) and other selective agars for the detection of Campylobacter spp. in chicken and fresh produce. All chicken samples were positive for Campylobacter spp. when tested on mCCDA, BR agar, and BRS agar. In fresh produce samples, BRS agar exhibited the highest selectivity for Campylobacter spp., demonstrating its suitability for the detection of Campylobacter spp. in fresh produce. PMID:25126968
THE INFLUENCE OF COLLOIDS UPON THE DIFFUSION OF HAEMOLYSINS.
Flexner, S; Noguchi, H
1906-08-01
Acids, alkalies, salts, glucosides, and certain toxins diffuse more quickly into 0.9 per cent. salt solution than into agar-agar and gelatin suspensions. The inhibitory effect of the colloids grows with increase in concentration, which increase affects both the velocity and extent of the diffusion. In the case of gelatin the degree of diffusion is approximately in inverse proportion to the square root of the concentration. Agar-agar in strengths up to 2 per cent. inhibits far less than gelatin in 10 per cent. suspensions; and the difference in degree of inhibition exercised by 0.5 per cent. and 2 per cent. agar-agar is a small one. Haemolytic substances diffuse from gelatin into agar-agar more slowly than from saline into agar-agar. But the velocity of diffusion from agar-agar into gelatin is greater than from saline into gelatin. The effects of differences in concentration of the haemolytic agent vary according to the agent and the manner of its solution. When the haemolyser is dissolved in salt solution the diffusion of 1/100 N. and 1/1000 N. solutions (saponin) is almost identical; while with solanin the stronger solutions diffuse faster. When the haemolyser is dissolved in the colloid diffusion into fluid media is nearly proportional to the concentrations of the haemolytic agent. The velocity of diffusion into and from colloids is in general proportional to the square root of the time. Acids, alkalies, salts, and glucosides act in a manner which is in agreement with this rule. Cobra lysin and tetanolysin do not act in conformity with the rule. Cobra lysin appears to diffuse into colloids more slowly, proportionally, than cobra neurotoxin, and tetanospasmin more slowly than tetanolysin. The biological method described in this paper for studying diffusion in colloids is applicable to haemolytic and some other toxic substances, and, with accuracy possibly only to such substances possessing relatively simple compositions. Since all diffusion in the living body takes place within colloidal media of different concentrations, it would seem desirable to perfect methods through which the interaction of toxic chemicals and the fluids and cells of the body may in a manner be imitated in vitro. Through this means our knowledge of toxicology may well be extended. PMID:19867059
Maheux, Andrée F.; Bérubé, Ève; Boudreau, Dominique K.; Villéger, Romain; Cantin, Philippe; Boissinot, Maurice; Bissonnette, Luc
2013-01-01
We first determined the analytical specificity and ubiquity (i.e., the ability to detect all or most strains) of a Clostridium perfringens-specific real-time PCR (rtPCR) assay based on the cpa gene (cpa rtPCR) by using a bacterial strain panel composed of C. perfringens and non-C. perfringens Clostridium strains. All non-C. perfringens Clostridium strains tested negative, whereas all C. perfringens strains tested positive with the cpa rtPCR, for an analytical specificity and ubiquity of 100%. The cpa rtPCR assay was then used to confirm the identity of 116 putative C. perfringens isolates recovered after filtration of water samples and culture on mCP agar. Colonies presenting discordant results between the phenotype on mCP agar and cpa rtPCR were identified by sequencing the 16S rRNA and cpa genes. Four mCP?/rtPCR+ colonies were identified as C. perfringens, whereas 3 mCP+/rtPCR? colonies were identified as non-C. perfringens. The cpa rtPCR was negative with all 51 non-C. perfringens strains and positive with 64 of 65 C. perfringens strains. Finally, we compared mCP agar and a CRENAME (concentration and recovery of microbial particles, extraction of nucleic acids, and molecular enrichment) procedure plus cpa rtPCR (CRENAME + cpa rtPCR) for their abilities to detect C. perfringens spores in drinking water. CRENAME + cpa rtPCR detected as few as one C. perfringens CFU per 100 ml of drinking water sample in less than 5 h, whereas mCP agar took at least 25 h to deliver results. CRENAME + cpa rtPCR also allows the simultaneous and sensitive detection of Escherichia coli and C. perfringens from the same potable water sample. In itself, it could be used to assess the public health risk posed by drinking water potentially contaminated with pathogens more resistant to disinfection. PMID:24077714
Thermal characterization of magnetically aligned carbonyl iron/agar composites.
Diaz-Bleis, D; Vales-Pinzón, C; Freile-Pelegrín, Y; Alvarado-Gil, J J
2014-01-01
Composites of magnetic particles into polymeric matrices have received increasing research interest due to their capacity to respond to external magnetic or electromagnetic fields. In this study, agar from Gelidium robustum has been chosen as natural biocompatible polymer to build the matrix of the magnetic carbonyl iron particles (CIP) for their uses in biomedical fields. Heat transfer behavior of the CIP-agar composites containing different concentrations (5, 10, 15, 20, 25 and 30% w/w) of magnetically aligned and non-aligned CIP in the agar matrix was studied using photothermal radiometry (PTR) in the back-propagation emission configuration. The morphology of the CIP-agar composites with aligned and non-aligned CIP under magnetic field was also evaluated by scanning electron microscopy (SEM). The results revealed a dominant effect of CIP concentration over the alignment patterns induced by the magnetic field, which agrees with the behavior of the thermal diffusivity and thermal conductivity. Agar served as a perfect matrix to be used with CIP, and CIP-agar composites magnetically aligned at 20% CIP concentration can be considered as promising 'smart' material for hyperthermia treatments in the biomedical field. PMID:24274482
Multiclass Data Segmentation using Diffuse Interface Methods on Graphs
Bertozzi, Andrea L.
a general approach to multiclass segmentation of high-dimensional data on graphs, motivated by the diffuse1 Multiclass Data Segmentation using Diffuse Interface Methods on Graphs Cristina Garcia-based algorithms for multiclass segmentation of high-dimensional data on graphs. The algorithms use a diffuse
Syneresis and delayed detachment in agar plates
Thibaut Divoux; Bosi Mao; Patrick Snabre
2015-02-20
Biogels made of crosslinked polymers such as proteins or polysaccharides behave as porous soft solids and store large amount of solvent. These gels undergo spontaneous aging, called syneresis that consists in the shrinkage of the gel matrix and the progressive expulsion of the solvent. As a result, a biogel originally casted in a container often lose contact with the container sidewalls, and the detachment time is a priori difficult to anticipate since it may occur over variable time spans (from hours to days). Here we report on the syneresis phenomena in agar plates that consist in Petri dishes filled with a gel mainly composed of agar. Direct observations and speckle pattern correlation analysis allow us to rationalize the delayed detachment of the gel from the sidewall of the Petri dish. The detachment time $t^*$ is surprisingly not controlled by the mass loss as one would intuitively expect. Instead, $t^*$ is strongly correlated to the gel minimum thickness $e_{min}$ measured along the sidewall of the plate, and increases as a robust function of $e_{min}$ independently of the prior mass-loss history. Time-resolved correlation spectroscopy atypically applied to such weakly diffusive media gives access to the local thinning rate of the gel. This technique also allows us to detect the gel micro-displacements that are triggered by the water evaporation prior to the detachment, and even to anticipate the latter from a few hours. Our work provides observables to predict the detachment time of agar gels in dishes, and highlights the relevance of speckle pattern correlation analysis for the quantitative investigation of the syneresis dynamics in biopolymer gels.
New methods in Diffusion Weighted and Diffusion Tensor Imaging
Bammer, Roland; Holdsworth, Samantha J.; Veldhuis, Wouter B.; Skare, Stefan T.
2009-01-01
Synopsis Considerable strides have been made by countless individual researchers in diffusion-weighted imaging (DWI) to push DWI from an experimental tool – limited to a few institutions with specialized instrumentation – to a powerful tool used routinely for diagnostic imaging. Despite its current success, the field of DWI constantly evolves and progress has been made on several fronts, awaiting adoption by vendors and clinical users to bring in the next generation of DWI. These developments are primarily comprised of improved robustness against patient and physiologic motion, increased spatial resolution, new biophysical and tissue models, and new clinical applications for DWI. This article aims to provide a succinct overview of some of these new developments and a description of some of the major challenges associated with DWI. Trying to understand some of these challenges is helpful not only to the technically savvy MRI user, but also to radiologists who are interested in the potential strengths and weaknesses of these techniques, what is in the “diffusion pipeline”, and in how to interpret artifacts on DWI scans. PMID:19406353
Spectral methods for identifying scalar diffusions
Lars Peter Hansen; José Alexandre Scheinkman; Nizar Touzi
1998-01-01
This paper shows how to identify nonparametrically scalar stationary diffusions from discrete-time data. The local evolution of the diffusion is characterized by a drift and diffusion coefficient along with the specification of boundary behavior. We recover this local evolution from two objects that can be inferred directly from discrete-time data: the stationary density and a conveniently chosen eigenvalue–eigenfunction pair of
New method to measure liquid diffusivity by analyzing an instantaneous diffusion image.
Sun, Licun; Meng, Weidong; Pu, Xiaoyun
2015-09-01
A novel optical method was applied to measure the binary liquid diffusion coefficient (D) quickly. Equipped with an asymmetric liquid-core cylindrical lens (ALCL), the spatially resolving ability of the ALCL in measuring refractive index of liquid was utilized to obtain the gradient distribution of the liquid concentration along diffusive direction. Based on Fick's second law, the D value was then calculated by analyzing diffusion images. It was worth mentioning that only one instantaneous diffusive image was required to measure D value by the method, reducing the measurement time greatly from several hours in traditional methods to a few seconds. The diffusion coefficients of ethylene glycol diffusing in pure water, at temperatures from 288.15 to 308.15 K, were measured by analyzing instantaneous diffusion images, the results were consistent well with the values measured by using holographic interferometry and Taylor dispersion methods. The method is characterized by faster measurement, direct observation of diffusive process, and easy operation, which provides a new method in measuring diffusion coefficient of liquids rapidly. PMID:26368418
Persson, M; Flock, J-I; van der Linden, J
2003-08-01
Postoperative wound infections are often a result of peri-operative contamination by Staphylococcus aureus. With a new insufflation device, a gas diffuser, it has become possible to establish a local micro-environment of almost 100% carbon dioxide in an open surgical wound. The device enables ventilation of the wound with an antiseptic agent, which in gaseous form can be delivered as a low uniform dose to all parts of the wound. The use of carbon dioxide (CO2) as a carrier gas eliminates possible inflammability of an antiseptic agent and helps to concentrate it to the site of interest by gravity. Using the above delivery system we have demonstrated the antibacterial effect of gaseous ethanol on S. aureus inoculated on sterile filter disks and blood agar plates, respectively. Ethanol is a very potent antiseptic agent with known properties, which makes it suitable for testing the maximal decontamination level. On filter disks, CO2 carrying vapour from a 95% ethanol solution decreased the number of colony-forming units after 5 min of exposure (P=0.04), and killed all bacteria within 10-15 min (P<0.001). In the presence of organic material, i.e. on exposed blood agar plates, the colony size decreased with exposure time, and no colonies were detected after 60 min of exposure (P<0.001). Antiseptic gas derived from 70% ethanol solution was less effective than that from 95% ethanol (P<0.001). CO2 humidified with water did not have a significant effect on number or size of the colonies. Our findings suggest that intraoperative wound antisepsis with a gas mixture of CO2 and an antiseptic agent delivered with a gas diffuser, may be a simple method to reduce the risk of postoperative wound infection. PMID:12919760
A vertical diffusion method for the microbiological assay of isoniazid
Lloyd, Janet; Mitchison, D. A.
1964-01-01
A method is described for the assay of isoniazid in serum and other fluids by diffusion along slopes of Löwenstein-Jensen medium inoculated with tubercle bacilli. The method is convenient, rapid and robust, but is less accurate than diffusion systems for the assay of some other substances. PMID:14227431
Range Image Segmentation by an Effective Jump-Diffusion Method
Zhu, Song Chun
maps of terrain and city scenes with accuracy up to 1 centimeter. As these range images provide muchRange Image Segmentation by an Effective Jump-Diffusion Method Feng Han, Zhuowen Tu, and Song-Chun Zhu Abstract--This paper presents an effective jump-diffusion method for segmenting a range image
Diffuse-Interface Methods in Fluid Mechanics
NASA Technical Reports Server (NTRS)
Anderson, D. M.; McFadden, G. B.; Wheeler, A. A.
1997-01-01
The authors review the development of diffuse-interface models of hydrodynamics and their application to a wide variety of interfacial phenomena. The authors discuss the issues involved in formulating diffuse-interface models for single-component and binary fluids. Recent applications and computations using these models are discussed in each case. Further, the authors address issues including sharp-interface analyses that relate these models to the classical free-boundary problem, related computational approaches to describe interfacial phenomena, and related approaches describing fully-miscible fluids.
Yeh, Ellen; Pinsky, Benjamin A.; Banaei, Niaz; Baron, Ellen Jo
2009-01-01
Background Blood agar is used for the identification and antibiotic susceptibility testing of many bacterial pathogens. In the developing world, microbiologists use human blood agar because of the high cost and inhospitable conditions for raising wool sheep or horses to supply blood. Many pathogens either fail to grow entirely or exhibit morphologies and hemolytic patterns on human blood agar that confound colony recognition. Furthermore, human blood can be hazardous to handle due to HIV and hepatitis [1], [2]. This study investigated whether blood from hair sheep, a hardy, low-maintenance variety of sheep adapted for hot climates, was suitable for routine clinical microbiology studies. Methods and Findings Hair sheep blood obtained by jugular venipuncture was anticoagulated by either manual defibrination or collection in human blood bank bags containing citrate-phosphate-dextrose. Trypticase soy 5% blood agar was made from both forms of hair sheep blood and commercial defibrinated wool sheep blood. Growth characteristics, colony morphologies, and hemolytic patterns of selected human pathogens, including several streptococcal species, were evaluated. Specialized identification tests, including CAMP test, reverse CAMP test, and satellite colony formation with Haemophilus influenzae and Abiotrophia defectiva were also performed. Mueller-Hinton blood agar plates prepared from the three blood types were compared in antibiotic susceptibility tests by disk diffusion and E-test. Conclusions The results of all studies showed that blood agar prepared from citrated hair sheep blood is suitable for microbiological tests used in routine identification and susceptibility profiling of human pathogens. The validation of citrated hair sheep blood eliminates the labor-intensive and equipment-requiring process of manual defibrination. Use of hair sheep blood, in lieu of human blood currently used by many developing world laboratories and as an alternative to cost-prohibitive commercial sheep blood, offers the opportunity to dramatically improve the safety and accuracy of laboratory diagnosis of pathogenic bacteria in resource-poor countries. PMID:19578541
A Bayesian method with reparameterization for diffusion tensor imaging
NASA Astrophysics Data System (ADS)
Zhou, Diwei; Dryden, Ian L.; Koloydenko, Alexey; Li, Bai
2008-03-01
A multi-tensor model with identifiable parameters is developed for diffusion weighted MR images. A new parameterization method guarantees the symmetric positive-definiteness of the diffusion tensor. We set up a Bayesian method for parameter estimation. To investigate properties of the method, Monte Carlo simulated data from three distinct DTI direction schemes have been analyzed. The multi-tensor model with automatic model selection has also been applied to a healthy human brain dataset. Standard tensor-derived maps are obtained when the single-tensor model is fitted to a region of interest with a single dominant fiber direction. High anisotropy diffusion flows and main diffusion directions can be shown clearly in the FA map and diffusion ellipsoid map. For another region containing crossing fiber bundles, we estimate and display the ellipsoid map under the single tensor and double-tensor regimes of the multi-tensor model, suitably thresholding the Bayes factor for model selection.
NASA Astrophysics Data System (ADS)
Sant, Marco; Papadopoulos, George K.; Theodorou, Doros N.
2010-04-01
The concentration dependence of self-diffusivity is investigated by means of a novel method, extending our previously developed second-order Markov process model to periodic media. Introducing the concept of minimum-crossing surface, we obtain a unique decomposition of the self-diffusion coefficient into two parameters with specific physical meanings. Two case studies showing a maximum in self-diffusivity as a function of concentration are investigated, along with two cases where such a maximum cannot be present. Subsequently, the method is applied to the large cavity pore network of the ITQ-1 (Mobil tWenty tWo, MWW) zeolite for methane (displaying a maximum in self-diffusivity) and carbon dioxide (no maximum), explaining the diffusivity trend on the basis of the evolution of the model parameters as a function of concentration.
A microfluidic method to measure small molecule diffusion in hydrogels.
Evans, Stephanie M; Litzenberger, Andrew L; Ellenberger, Anne E; Maneval, James E; Jablonski, Erin L; Vogel, Brandon M
2014-02-01
Drug release from a fluid-contacting biomaterial is simulated using a microfluidic device with a channel defined by solute-loaded hydrogel; as water is pumped through the channel, solute transfers from the hydrogel into the water. Optical analysis of in-situ hydrogels, characterization of the microfluidic device effluent, and NMR methods were used to find diffusion coefficients of several dyes (model drugs) in poly(ethylene glycol) diacrylate (PEG-DA) hydrogels. Diffusion coefficients for methylene blue and sulforhodamine 101 in PEG-DA calculated using the three methods are in good agreement; both dyes are mobile in the hydrogel and elute from the hydrogel at the aqueous channel interface. However, the dye acid blue 22 deviates from typical diffusion behavior and does not release as expected from the hydrogel. Importantly, only the microfluidic method is capable of detecting this behavior. Characterizing solute diffusion with a combination of NMR, optical and effluent methods offer greater insight into molecular diffusion in hydrogels than employing each technique individually. The NMR method made precise measurements for solute diffusion in all cases. The microfluidic optical method was effective for visualizing diffusion of the optically active solutes. The optical and effluent methods show potential to be used to screen solutes to determine if they elute from a hydrogel in contact with flowing fluid. Our data suggest that when designing a drug delivery device, analyzing the diffusion from the molecular level to the device level is important to establish a complete picture of drug elution, and microfluidic methods to study such diffusion can play a key role. PMID:24411384
An improved method for treating Monte Carlo-diffusion interfaces
Densmore, J. D. (Jeffery D.)
2004-01-01
Discrete Diffusion Monte Carlo (DDMC) has been suggested as a technique for increasing the efficiency of Monte Carlo simulations in diffusive media. In this technique, Monte Carlo particles travel discrete steps between spatial cells according to a discretized diffusion equation. An important part of the DDMC method is the treatment of the interface between a transport region, where standard Monte Carlo is used, and a diffusive region, where DDMC is employed. Previously developed DDMC methods use the Marshak boundary condition at transport diffusion-interfaces, and thus produce incorrect results if the Monte Carlo-calculated angular flux incident on the interface surface is anisotropic. In this summary we present a new interface method based on the asymptotic diffusion-limit boundary condition, which is able to produce accurate solutions if the incident angular flux is anisotropic. We show that this new interface technique has a simple Monte Carlo interpretation, and can be used in conjunction with the existing DDMC method. With a set of numerical simulations, we demonstrate that this asymptotic interface method is much more accurate than the previously developed Marshak interface method.
Methods of exploring energy diffusion in lattices with finite temperature
Ping Hwang; Hong Zhao
2011-06-15
We discuss two methods for exploring energy diffusion in lattices with finite temperature in this paper. The first one is the energy-kick (EK) method. To apply this method, one adds an external energy kick to a particle in the lattice, and tracks its evolution by evolving the kicked system. The second one is the fluctuation-correlation (FC) method. The formula for calculating the probability density function (PDF) using the canonical ensemble is slightly revised and extended to the microcanonical ensemble. We show that the FC method has advantages over the EK method theoretically and technically. Theoretically, the PDF obtained by the FC method reveals the diffusion processes of the inner energy while the PDF obtained by the EK method represents that of the kick energy. The diffusion processes of the inner energy and the external energy added to the system, i.e., the kick energy, may be different quantitatively and even qualitatively depending on models. To show these facts, we study not only the equilibrium systems but also the stationary nonequilibrium systems. Examples showing that the inner energy and the kick energy may have different diffusion behavior are reported in both cases. The technical advantage enables us to study the long-time diffusion processes and thus avoids the finite-time effect.
A Fractional Lie Group Method For Anomalous Diffusion Equations
Guo-cheng Wu
2010-09-21
Lie group method provides an efficient tool to solve a differential equation. This paper suggests a fractional partner for fractional partial differential equations using a fractional characteristic method. A space-time fractional diffusion equation is used as an example to illustrate the effectiveness of the Lie group method.
Watson, E. Bruce
Oxygen self-diffusion ``fast-paths'' in titanite single crystals and a general method for deconvolving self-diffusion profiles with ``tails'' X.Y. Zhang a,b,*, E.B. Watson a , D.J. Cherniak that might affect lattice diffusion, there may be extended line- or planar defects along which fast diffusion
The method for detecting diffusion ring diameter in Hemagglutinin measuring
NASA Astrophysics Data System (ADS)
Jing, Wenbo; Liu, Xue; Duan, Jin; Wang, Xiao-man
2014-11-01
The diffuser ring diameter measurement is the most critical in hemagglutinin Measuring. The traditional methods, such as a vernier caliper or high-definition scanned images are subjective and low for the measurement data reliability. Propose high-resolution diffusion ring image for drop-resolution processing, adaptive Canny operator and local detection method to extract complete and clear diffusion ring boundaries, and finally make use of polynomial interpolation algorithm to make diffusion ring outer boundary pixel coordinates achieve sub-pixel accuracy and the least-squares fitting circle algorithm to calculate the precise center of the circle and the diameter of the diffuser ring. Experimental results show that the method detection time is only 63.61ms, which is a faster speed; diffuser ring diameter estimation error can achieve 0.55 pixel, high stability in experimental data. This method is adapted to the various types of influenza vaccine hemagglutinin content measurements, and has important value in the influenza vaccine quality detection.
A Fast Semi-implicit Method for Anisotropic Diffusion
Sharma, Prateek
2010-01-01
Simple finite differencing of the diffusion equation, when diffusion is only along a given direction, does not ensure that the numerically calculated heat fluxes are in the correct direction. This can lead to negative temperatures for the anisotropic thermal diffusion equation. In a previous paper we proposed a monotonicity-preserving explicit method which uses limiters (analogous to those used in the solution of hyperbolic equations) to interpolate the temperature gradients at cell faces. However, being explicit, this method was limited by a restrictive Courant-Friedrichs-Lewy (CFL) stability timestep. Here we propose a conservative, directionally-split, semi-implicit method which is unconditionally stable irrespective of the timestep. Although not strictly monotonicity preserving, our method gives only small amplitude temperature oscillations at large temperature gradients, and the oscillations are damped in time. With numerical experiments we show that our semi-implicit method can achieve large speed-ups c...
Agar polysaccharides from Gracilaria species (Rhodophyta, Gracilariaceae).
Marinho-Soriano, E
2001-07-26
Yield, physical and chemical properties of agar from three agarophytes species (Gracilaria gracilis, G. dura and G. bursa-pastoris) were determined. The agar yield from the three species varied significantly (P<0.01). The highest yields of agar (34.8%) and the lowest (30%) were obtained from G. bursa-pastoris and G. gracilis, respectively. Highest gel strength (630+/-15 g cm(-2)) was obtained from agar extracted from G. gracilis and lowest from G. bursa-pastoris (26+/-3.6 g cm(-2)). The values of 3,6-anhydrogalactose were similar for G. gracilis and G. dura and there were no significant differences among the species. The sulfate contents varied significantly (P<0.01) and the higher value was obtained from G. bursa-pastoris. Among the three species, G. gracilis showed superior agar quality than the other two species, hence it can be considered a good potential source for industrial use. PMID:11472802
Simple method for determining water diffusion coefficient in conducting polymers
Pentti Passiniemi
1995-01-01
Water increases electrical conductivity of polyaniline. A simple method of the conductivity measurement for determining the diffusion coefficient D of water in conducting polymer matrices is presented in this work. The geometry of the conducting polymer samples can vary in wide range and the initial water content can be totally arbitrary. With the method based on the general theory D(H2O)
Recovery of Sublethally Injured Bacteria Using Selective Agar Overlays.
ERIC Educational Resources Information Center
McKillip, John L.
2001-01-01
This experiment subjects bacteria in a food sample and an environmental sample to conditions of sublethal stress in order to assess the effectiveness of the agar overlay method to recover sublethally injured cells compared to direct plating onto the appropriate selective medium. (SAH)
Practical method for diffusion welding of steel plate in air.
NASA Technical Reports Server (NTRS)
Moore, T. J.; Holko, K. H.
1972-01-01
Description of a simple and easily applied method of diffusion welding steel plate in air which does not require a vacuum furnace or hot press. The novel feature of the proposed welding method is that diffusion welds are made in air with deadweight loading. In addition, the use of an autogenous (self-generated) surface-cleaning principle (termed 'auto-vac cleaning') to reduce the effects of surface oxides that normally hinder diffusion welding is examined. A series of nine butt joints were diffusion welded in thick sections of AISI 1020 steel plate. Diffusion welds were attempted at three welding temperatures (1200, 1090, and 980 C) using a deadweight pressure of 34,500 N/sq m (5 psi) and a two-hour hold time at temperature. Auto-vac cleaning operations prior to welding were also studied for the same three temperatures. Results indicate that sound welds were produced at the two higher temperatures when the joints were previously fusion seal welded completely around the periphery. Also, auto-vac cleaning at 1200 C for 2-1/2 hours prior to diffusion welding was highly beneficial, particularly when subsequent welding was accomplished at 1090 C.
Bilinear diffusion quantum Monte Carlo methods
NASA Astrophysics Data System (ADS)
Arias de Saavedra, F.; Kalos, M. H.
2003-02-01
The standard method of quantum Monte Carlo for the solution of the Schrödinger equation in configuration space can be described quite generally as devising a random walk that generates—at least asymptotically—populations of random walkers whose probability density is proportional to the wave function of the system being studied. While, in principle, the energy eigenvalue of the Hamiltonian can be calculated with high accuracy, estimators of operators that do not commute the Hamiltonian cannot. Bilinear quantum Monte Carlo (BQMC) is an alternative in which the square of the wave function is sampled in a somewhat indirect way. More specifically, one uses a pair of walkers at positions x and y and introduces stochastic dynamics to sample ?i(x)t(x,y)?j(y), where ?i(x) and ?j(y) are eigenfunctions of (possibly different) Hamiltonians, and t(x,y) is a kernel that correlates positions x and y. Using different Hamiltonians permits the accurate computation of small energy differences. We review the conceptual basis of BQMC, discuss qualitatively and analytically the problem of the fluctuations in the branching, and present partial solutions to that problem. Finally we exhibit numerical results for some model systems including harmonic oscillators and the hydrogen and helium atoms. Further research will be necessary to make this a practical and generally applicable scheme.
The whole-block method and water diffusion in olivine
NASA Astrophysics Data System (ADS)
Ferriss, E.; Plank, T. A.; Walker, D.
2013-12-01
Accurate knowledge of the diffusion rates and mechanisms of water (hydrogen) in geologic materials is critical for geologic applications such as understanding the deep earth water cycle and determining ascent rates of pre-eruptive magmas. However, diffusion rates and mechanisms are often poorly known. Obtaining robust diffusion profile data for water with transmission FTIR traditionally requires cutting the sample after an experiment to isolate the central slice. Here we develop a method for interpreting diffusion profile data in three dimensions without cutting the sample. This 'whole-block' method is nondestructive, which simplifies the analytical procedure and allows multiple experiments on the same sample (e.g., a time series or reversal). Whole-block data represent concentration values that are integrated through the entire sample in the direction parallel to the infrared beam ray path during the measurement, and they are determined by taking the average value of a non-path-integrated 3 dimensional model (e.g., based on error functions or infinite sums in a rectangular parallelepiped) down the ray path for a given position. The whole-block method was tested by comparing whole-block profiles with profiles cut from the center of an oriented diopside sample after a dehydration experiment [1]. Water profiles were measured in the cut slice by both SIMS and FTIR. The results of the two methods are in good agreement both with each other and with diffusion profiles calculated based on the results of the whole-block method. Interpreting whole block measurements without taking into account the integration effects through the crystal can lead to errors in calculated diffusivities and inferred mechanisms. We have used numerical simulations to demonstrate as much as a half an order of magnitude error (typically indicating diffusivities that are too fast) if whole-block data are interpreted using non-path integrated diffusion models. The largest errors are in short and/or fast directions, in which diffusion profiles are well developed. Whole block data also inevitably involve central values that are contaminated by edge concentrations integrated in the signal. This integration effect results in a plateau in the whole-block data that may complicate the interpretation of the whole-block data. For example, previous experimental work on water diffusion in olivine has identified a central plateau using whole block measurements, and this plateau is interpreted to result from a transitional state between two diffusion mechanisms [2]. However, a whole-block model also produces a reasonable fit to this data using the observed initial concentration of zero and a single-step diffusion mechanism. Thus, whole block effects need to be taken into account for the accurate determination of diffusivities and mechanisms. [1] Ferriss et al 2012 AGU; [2] Demouchy&Mackwell 2006 Phys Chem Mineral 33(5).
The Flux-integral Method for Multidimensional Convection and Diffusion
NASA Technical Reports Server (NTRS)
Leonard, B. P.; Macvean, M. K.; Lock, A. P.
1994-01-01
The flux-integral method is a procedure for constructing an explicit, single-step, forward-in-time, conservative, control volume update of the unsteady, multidimensional convection-diffusion equation. The convective plus diffusive flux at each face of a control-volume cell is estimated by integrating the transported variable and its face-normal derivative over the volume swept out by the convecting velocity field. This yields a unique description of the fluxes, whereas other conservative methods rely on nonunique, arbitrary pseudoflux-difference splitting procedures. The accuracy of the resulting scheme depends on the form of the subcell interpolation assumed, given cell-average data. Cellwise constant behavior results in a (very artificially diffusive) first-order convection scheme. Second-order convection-diffusion schemes correspond to cellwise linear (or bilinear) subcell interpolation. Cellwise quadratic subcell interpolants generate a highly accurate convection-diffusion scheme with excellent phase accuracy. Under constant-coefficient conditions, this is a uniformly third-order polynomial interpolation algorithm (UTOPIA).
Some Experiments With Agar-Grown Seedlings
ERIC Educational Resources Information Center
Freeland, P. W.
1973-01-01
Two percent agar gel is reported as a better medium for germination and growth studies. Students can be encouraged to undertake many simple experiments and make precise observations by using this medium. (PS)
Newton-Krylov methods applied to nonequilibrium radiation diffusion
D. A. Knoll; W. J. Rider; G. L. Olsen
1998-01-01
The authors present results of applying a matrix-free Newton-Krylov method to a nonequilibrium radiation diffusion problem. Here, there is no use of operator splitting, and Newton`s method is used to convert the nonlinearities within a time step. Since the nonlinear residual is formed, it is used to monitor convergence. It is demonstrated that a simple Picard-based linearization produces a sufficient
Method of making gas diffusion layers for electrochemical cells
Frisk, Joseph William (Oakdale, MN); Boand, Wayne Meredith (Lino Lakes, MN); Larson, James Michael (Saint Paul, MN)
2002-01-01
A method is provided for making a gas diffusion layer for an electrochemical cell comprising the steps of: a) combining carbon particles and one or more surfactants in a typically aqueous vehicle to make a preliminary composition, typically by high shear mixing; b) adding one or more highly fluorinated polymers to said preliminary composition by low shear mixing to make a coating composition; and c) applying the coating composition to an electrically conductive porous substrate, typically by a low shear coating method.
Thermal diffusivity of nonflat plates using the flash method
Salazar, Agustin; Fuente, Raquel; Apinaniz, Estibaliz; Mendioroz, Arantza [Departamento de Fisica Aplicada I, Escuela Tecnica Superior de Ingenieria, Universidad del Pais Vasco, Alameda Urquijo s/n, 48013 Bilbao (Spain)
2011-01-15
The flash method is the standard technique to measure the thermal diffusivity of solid samples. It consists of heating the front surface of an opaque sample by a brief light pulse and detecting the temperature evolution at its rear surface. The thermal diffusivity is obtained by measuring the time corresponding to the half maximum of the temperature rise, which only depends on the sample thickness and thermal diffusivity through a simple formula. Up to now, the flash method has been restricted to flat samples. In this work, we extend the flash method to measure the thermal diffusivity of nonflat samples. In particular, we focus on plates with cylindrical and spherical shapes. The theoretical model indicates that the same expression for flat samples can also be applied to cylindrical and spherical plates, except for extremely curved samples. Accordingly, a curvature limit for the application of the expression for flat samples is established. Flash measurements on lead foils of cylindrical shape confirm the validity of the model.
Modeling the flow in diffuse interface methods of solidification
NASA Astrophysics Data System (ADS)
Subhedar, A.; Steinbach, I.; Varnik, F.
2015-08-01
Fluid dynamical equations in the presence of a diffuse solid-liquid interface are investigated via a volume averaging approach. The resulting equations exhibit the same structure as the standard Navier-Stokes equation for a Newtonian fluid with a constant viscosity, the effect of the solid phase fraction appearing in the drag force only. This considerably simplifies the use of the lattice Boltzmann method as a fluid dynamics solver in solidification simulations. Galilean invariance is also satisfied within this approach. Further, we investigate deviations between the diffuse and sharp interface flow profiles via both quasiexact numerical integration and lattice Boltzmann simulations. It emerges from these studies that the freedom in choosing the solid-liquid coupling parameter h provides a flexible way of optimizing the diffuse interface-flow simulations. Once h is adapted for a given spatial resolution, the simulated flow profiles reach an accuracy comparable to quasiexact numerical simulations.
Protein crystallization in low gravity by step gradient diffusion method
NASA Astrophysics Data System (ADS)
Sygusch, Jurgen; Coulombe, René; Cassanto, John M.; Sportiello, Michael G.; Todd, Paul
1996-05-01
Two-step crystallization experiments were conducted in low gravity employing a liquid-liquid diffusion method in an effort to eliminate problems associated with protein crystal growth under the supersaturating conditions required for nucleation. Experiments were performed in diffusion cells formed by the sliding of blocks on orbit. Step gradient diffusion experiments consisted of first exposing protein solutions in diffusion half-wells for brief periods to initiating buffer solutions of high precipitant concentrations to induce nucleation followed by exposure of the same protein solutions to solutions of lower precipitant concentration to promote growth of induced nuclei into crystals. To avoid convective disturbances that occur when solutions of discrepant densities are interfaced at normal gravity, crystallization of hen egg-white lysozyme and rabbit skeletal muscle aldolase by step gradient diffusion was investigated in low gravity on four NASA space shuttle flights. In general, the largest crystals of both proteins formed at the highest initiating precipitant concentration used, which is consistent with nuclei formation upon brief exposure to high precipitant concentration, and that these nuclei are competent for sustained growth at lower precipitant concentration. The two-step approach dissociates nucleation events from crystal growth allowing parameters affecting nucleation kinetics such as time, precipitant concentration and temperature of nucleation to be varied separately from conditions used for post-nucleation growth.
Lin, Guoxing
2015-10-01
Pulsed field gradient (PFG) diffusion measurement has a lot of applications in NMR and MRI. Its analysis relies on the ability to obtain the signal attenuation expressions, which can be obtained by averaging over the accumulating phase shift distribution (APSD). However, current theoretical models are not robust or require approximations to get the APSD. Here, a new formalism, an effective phase shift diffusion (EPSD) equation method is presented to calculate the APSD directly. This is based on the idea that the gradient pulse effect on the change of the APSD can be viewed as a diffusion process in the virtual phase space (VPS). The EPSD has a diffusion coefficient, K(?)(t)D rad(?)/s(?), where ? is time derivative order and ? is a space derivative order, respectively. The EPSD equations of VPS are built based on the diffusion equations of real space by replacing the diffusion coefficients and the coordinate system (from real space coordinate to virtual phase coordinate). Two different models, the fractal derivative model and the fractional derivative model from the literature were used to build the EPSD fractional diffusion equations. The APSD obtained from solving these EPSD equations were used to calculate the PFG signal attenuation. From the fractal derivative model the attenuation is exp(-?(?)g(?)?(?) [Formula: see text] t(?)), a stretched exponential function (SEF) attenuation, while from the fractional derivative model the attenuation is E?,1(-?(?)g(?)?(?) [Formula: see text] t(?)), a Mittag-Leffler function (MLF) attenuation. The MLF attenuation can be reduced to SEF attenuation when ?=1, and can be approximated as a SEF attenuation when the attenuation is small. Additionally, the effect of finite gradient pulse widths (FGPW) is calculated. From the fractal derivative model, the signal attenuation including FGPW effect is [Formula: see text] . The results obtained in this study are in good agreement with the results in literature. Several expressions that describe signal attenuation have not been reported and that can be of great importance for the PFG experiments. This EPSD equation method provides a new, simple path to calculate signal attenuation of PFG NMR experiments. PMID:26384777
Esipov, S E
1998-01-01
Several varieties of relative biological activity estimation are comparatively analyzed and illustrated by an example of tylosin. For visual demonstration the estimates with the equation of a straight line are represented graphically. It is concluded that the design equations in the State Pharmacopeia XI (USSR) should be respectively replaced. The advantages of the variety for the biological activity estimation with the one-point intercept form of the equation of a straight line are illustrated by particular examples. PMID:9606490
A diffusion accelerated solution method for the nonlinear characteristic scheme
Wareing, T.A.; Walters, W.F.; Morel, J.E.
1995-02-01
Recently the nonlinear characteristic scheme for spatially discretizing the discrete-ordinate equations was introduced. This scheme is accurate for both optically thin and optically thick spatial meshes and produces strictly positive angular and scalar fluxes. The nonlinear characteristic discrete-ordinate equations can be solved using the source iteration method; however, it is well known that the this method converges prohibitively slowly for optically thick problems with scattering ratios at or near unity. In this paper we describe a diffusion accelerated solution method for solving the nonlinear characteristic equations in slab geometry.
Preparation and characterization of agar/clay nanocomposite films: the effect of clay type.
Rhim, Jong-Whan; Lee, Soo-Bin; Hong, Seok-In
2011-04-01
Agar-based nanocomposite films with different types of nanoclays, such as Cloisite Na+, Cloisite 30B, and Cloisite 20A, were prepared using a solvent casting method, and their tensile, water vapor barrier, and antimicrobial properties were tested. Tensile strength (TS), elongation at break (E), and water vapor permeability (WVP) of control agar film were 29.7±1.7 MPa, 45.3±9.6%, and (2.22±0.19)×10(-9) g·m/m2·s·Pa, respectively. All the film properties tested, including transmittance, tensile properties, WVP, and X-ray diffraction patterns, indicated that Cloisite Na+ was the most compatible with agar matrix. TS of the nanocomposite films prepared with 5% Cloisite Na+ increased by 18%, while WVP of the nanocomposite films decreased by 24% through nanoclay compounding. Among the agar/clay nanocomposite films tested, only agar/Cloisite 30B nanocomposite film showed a bacteriostatic function against?Listeria monocytogenes. PMID:21535851
Physical-mechanical properties of agar/?-carrageenan blend film and derived clay nanocomposite film.
Rhim, Jong-Whan
2012-12-01
Binary blend films with different mixing ratio of agar and ?-carrageenan were prepared using a solution casting method with and without nanoclay and the effect of their composition on the mechanical, water vapor barrier, and water resistance properties was tested. The tensile strength (TS) of the ?-carrageenan film was greater than that of agar film. The water vapor permeability (WVP) of the agar film was lower than that of ?-carrageenan film, the swelling ratio (SR) and water solubility (WS) of ?-carrageenan film were higher than those of agar film. Each property of the binary blend films varied proportionately depending on the mixing ratio of each component. The XRD result indicated that the nanocomposite with agar/?-carrageenan/clay (Cloisite(®) Na(+)) was intercalated. Consequently, the mechanical strength, water vapor barrier properties, and water contact angle (CA) were significantly (P < 0.05) improved through nanocomposite formation. PMID:23170836
Fixed-node diffusion Monte Carlo method for lithium systems
NASA Astrophysics Data System (ADS)
Rasch, K. M.; Mitas, L.
2015-07-01
We study lithium systems over a range of a number of atoms, specifically atomic anion, dimer, metallic cluster, and body-centered-cubic crystal, using the fixed-node diffusion Monte Carlo method. The focus is on analysis of the fixed-node errors of each system, and for that purpose we test several orbital sets in order to provide the most accurate nodal hypersurfaces. The calculations include both core and valence electrons in order to avoid any possible impact by pseudopotentials. To quantify the fixed-node errors, we compare our results to other highly accurate calculations, and wherever available, to experimental observations. The results for these Li systems show that the fixed-node diffusion Monte Carlo method achieves accurate total energies, recovers 96 -99 % of the correlation energy, and estimates binding energies with errors bounded by 0.1 eV /at .
Support Operators Method for the Diffusion Equation in Multiple Materials
Winters, Andrew R.; Shashkov, Mikhail J.
2012-08-14
A second-order finite difference scheme for the solution of the diffusion equation on non-uniform meshes is implemented. The method allows the heat conductivity to be discontinuous. The algorithm is formulated on a one dimensional mesh and is derived using the support operators method. A key component of the derivation is that the discrete analog of the flux operator is constructed to be the negative adjoint of the discrete divergence, in an inner product that is a discrete analog of the continuum inner product. The resultant discrete operators in the fully discretized diffusion equation are symmetric and positive definite. The algorithm is generalized to operate on meshes with cells which have mixed material properties. A mechanism to recover intermediate temperature values in mixed cells using a limited linear reconstruction is introduced. The implementation of the algorithm is verified and the linear reconstruction mechanism is compared to previous results for obtaining new material temperatures.
Wuthiekanun, Vanaporn; Amornchai, Premjit; Langla, Sayan; White, Nicholas J; Day, Nicholas P J; Limmathurotsakul, Direk; Peacock, Sharon J
2015-08-01
Leptospira Vanaporn Wuthiekanun (LVW) agar was used to develop a disk diffusion assay for Leptospira spp. Ten pathogenic Leptospira isolates were tested, all of which were susceptible to 17 antimicrobial agents (amoxicillin/clavulanic acid, amoxicillin, azithromycin, cefoxitin, ceftazidime, ceftriaxone, chloramphenicol, ciprofloxacin, clindamycin, doripenem, doxycycline, gentamicin, linezolid, nitrofurantoin, penicillin, piperacillin/tazobactam, and tetracycline). All 10 isolates had no zone of growth inhibition for four antimicrobials (fosfomycin, nalidixic acid, rifampicin, and trimethoprim/sulfamethoxazole). Of the ten Leptospira, seven had a growth inhibition zone of ? 21 mm for aztreonam, the zone diameter susceptibility break point for Enterobacteriaceae. This assay could find utility as a simple screening method during the epidemiological surveillance of antimicrobial resistance in Leptospira spp. PMID:26055750
Wuthiekanun, Vanaporn; Amornchai, Premjit; Langla, Sayan; White, Nicholas J.; Day, Nicholas P. J.; Limmathurotsakul, Direk; Peacock, Sharon J.
2015-01-01
Leptospira Vanaporn Wuthiekanun (LVW) agar was used to develop a disk diffusion assay for Leptospira spp. Ten pathogenic Leptospira isolates were tested, all of which were susceptible to 17 antimicrobial agents (amoxicillin/clavulanic acid, amoxicillin, azithromycin, cefoxitin, ceftazidime, ceftriaxone, chloramphenicol, ciprofloxacin, clindamycin, doripenem, doxycycline, gentamicin, linezolid, nitrofurantoin, penicillin, piperacillin/tazobactam, and tetracycline). All 10 isolates had no zone of growth inhibition for four antimicrobials (fosfomycin, nalidixic acid, rifampicin, and trimethoprim/sulfamethoxazole). Of the ten Leptospira, seven had a growth inhibition zone of ? 21 mm for aztreonam, the zone diameter susceptibility break point for Enterobacteriaceae. This assay could find utility as a simple screening method during the epidemiological surveillance of antimicrobial resistance in Leptospira spp. PMID:26055750
Diffusely reflecting paints including polytetrafluoroethylene and method of manufacture
NASA Technical Reports Server (NTRS)
Schutt, J. B.; Shai, M. C. (inventors)
1985-01-01
The invention pertains to a high diffuse, reflective paint comprising an alcohol soluble binder, polytetrafluoroethylene (TFE) and an alcohol for coating a substrate and forming an optical reference with a superior Lambertian characteristic. A method for making the paint by first mixing the biner and alcohol, and thereafter by mixing in outgassed TFE is described. A wetting agent may be employed to aid the mixing process.
Minutes to Millennia: Diffusion Methods in Subduction-Related Volcanism
NASA Astrophysics Data System (ADS)
Morgan, D. J.; Allan, A.; Wilson, C. J. N.; Charlier, B. L.; Davidson, J.
2014-12-01
Diffusion methods have several advantages as relative geochronometers in volcano-related magmatic processes: diffusion stops on eruption, locking in short timescale information; methods are relatively easy to implement; and suitable material is generally abundant. Such methods also pose significant, accompanying challenges: the need for accurate melt palaeothermometry, uncertainties in diffusion parameters, and sometimes even a cryptic connection between mineral zonation and timescale. As all timescales are relative to an event, timing is not absolute, and care must be taken in interpretation. Yet for all the difficulties, diffusion tools are seeing more widespread usage. This has come about because of the potential of diffusion methods to interrogate certain pre-eruptive processes operating over timescales of relevance to human timescales and responses, having direct bearing on hazard mitigation procedures. In studying subduction zone systems we have a wide range of minerals to choose from but will, in subduction-related, andesitic-to-rhyolitic systems, usually be operating away from the relatively well-constrained system of olivine, and instead be dealing with mineral phases that offer different challenges, such as plagioclase, quartz, sanidine, amphibole, orthopyroxene, Fe-Ti oxides and mica. Timescales here span a wide range across different mineral-element combinations, from minutes for Li in plagioclase and quartz to days by Fe-Ti oxides, years by orthopyroxene Fe-Mg and decades to millennia with plagioclase, sanidine and quartz. This contribution will focus on the interpretation of diffusion signals in minerals found in subduction-related volcanic systems. To understand what any modelled timescale means, the process which formed the relevant zonation pattern is absolutely key, yet often elusive. Variations in P, T, X conditions really drive the crystallisation process yet certain zonation patterns are non-unique. This ambiguity necessitates painstaking petrological and geochemical detective work to understand where the zoning came from to begin with, and which parameter or parameters were truly driving the zonation. The rewards are insights into short-lived processes occurring in the build up to, or process of, eruption, which are not accessible via other mechanisms.
Fokker-Planck-Kolmogorov Method or Diffusion Equation Method
Jaap Wijker
In the previous parts, random vibration of linear dynamic systems are discussed. In general, spacecraft structures are considered\\u000a to behave linearly and the modal characteristics play an important role in the design and verification process. In this part,\\u000a random vibrations of nonlinear dynamic systems where modal properties do not exist will be briefly discussed. Many solution\\u000a methods exist to solve
Lange, Mario; Müller, Carolin; Peiter, Edgar
2014-05-15
Fungal mycelium grown in liquid culture is easy to harvest for RNA extraction and gene expression analyses, but liquid cultures often develop rather heterogeneously. In contrast, growth of fungal mycelium on agar plates is highly reproducible. However, this biological material cannot be harvested easily for downstream analyses. This article describes a PVDF (polyvinylidene difluoride) membrane-assisted agar plate culture method that enables the harvest of mycelium grown on agar plates. This culture method leads to a strongly reduced variation in gene expression between biological replicates and requires less growth space as compared with liquid cultures. PMID:24607793
Effective Thermal Diffusivity Study of Powder Biocomposites via Photoacoustic Method
NASA Astrophysics Data System (ADS)
Mariucci, V. V. G.; da Cruz, J. A.; Bonadio, T. G. M.; Picolloto, A. M.; Weinand, W. R.; Lima, W. M.; Medina, A. N.; Bento, A. C.
2015-10-01
The effective thermal diffusivity for biocomposites of hydroxyapatite (HAp), and niobium pentoxide (Nb2O5) on powder form was studied via photoacoustic method adapted for porous materials. The concentration of each element was accompanied with the results of X-ray diffractometer (XRD) and scanning electron microscopy (SEM). A theoretical model for the thermal coupling of a three layered sample, designed to contain the powder material is proposed. The method for mixtures obeyed the formula [(1 - x) H A p + ( x) N b 2O5] for 0.0 ? x ? 1.0. Experimental results for effective thermal diffusivity ranged between (6.4 ± 0.3) × 10-6 m2 s-1 and (9.8 ± 0.4) × 10-6 m2 s-1 for x ? 0.7. Values of the effective thermal diffusivity have decreased sharply to (0.7 ± 0.03) ×10-6 m2 s-1 for x > 0.7. SEM micrographs showed a coating of HAp over the particles of Nb2O5 for some mixtures.
Effective Thermal Diffusivity Study of Powder Biocomposites via Photoacoustic Method
NASA Astrophysics Data System (ADS)
Mariucci, V. V. G.; da Cruz, J. A.; Bonadio, T. G. M.; Picolloto, A. M.; Weinand, W. R.; Lima, W. M.; Medina, A. N.; Bento, A. C.
2015-07-01
The effective thermal diffusivity for biocomposites of hydroxyapatite (HAp), and niobium pentoxide (Nb2O5) on powder form was studied via photoacoustic method adapted for porous materials. The concentration of each element was accompanied with the results of X-ray diffractometer (XRD) and scanning electron microscopy (SEM). A theoretical model for the thermal coupling of a three layered sample, designed to contain the powder material is proposed. The method for mixtures obeyed the formula [(1 - x)H A p + (x)N b 2O5] for 0.0 ? x ? 1.0. Experimental results for effective thermal diffusivity ranged between (6.4 ± 0.3) × 10-6 m2 s-1 and (9.8 ± 0.4) × 10-6 m2 s-1 for x ? 0.7. Values of the effective thermal diffusivity have decreased sharply to (0.7 ± 0.03) ×10-6 m2 s-1 for x > 0.7. SEM micrographs showed a coating of HAp over the particles of Nb2O5 for some mixtures.
Three-dimensional characterization of bacterial microcolonies on solid agar-based culture media.
Drazek, Laurent; Tournoud, Maud; Derepas, Frédéric; Guicherd, Maryse; Mahé, Pierre; Pinston, Frédéric; Veyrieras, Jean-Baptiste; Chatellier, Sonia
2015-02-01
For the last century, in vitro diagnostic process in microbiology has mainly relied on the growth of bacteria on the surface of a solid agar medium. Nevertheless, few studies focused in the past on the dynamics of microcolonies growth on agar surface before 8 to 10h of incubation. In this article, chromatic confocal microscopy has been applied to characterize the early development of a bacterial colony. This technology relies on a differential focusing depth of the white light. It allows one to fully measure the tridimensional shape of microcolonies more quickly than classical confocal microscopy but with the same spatial resolution. Placing the device in an incubator, the method was able to individually track colonies growing on an agar plate, and to follow the evolution of their surface or volume. Using an appropriate statistical modeling framework, for a given microorganism, the doubling time has been estimated for each individual colony, as well as its variability between colonies, both within and between agar plates. A proof of concept led on four bacterial strains of four distinct species demonstrated the feasibility and the interest of the approach. It showed in particular that doubling times derived from early tri-dimensional measurements on microcolonies differed from classical measurements in micro-dilutions based on optical diffusion. Such a precise characterization of the tri-dimensional shape of microcolonies in their late-lag to early-exponential phase could be beneficial in terms of in vitro diagnostics. Indeed, real-time monitoring of the biomass available in a colony could allow to run well established microbial identification workflows like, for instance, MALDI-TOF mass-spectrometry, as soon as a sufficient quantity of material is available, thereby reducing the time needed to provide a diagnostic. Moreover, as done for pre-identification of macro-colonies, morphological indicators such as three-dimensional growth profiles derived from microcolonies could be used to perform a first pre-identification step, but in a shorten time. PMID:25533218
A simple agar plate assay for screening siderophore producer yeasts.
Calvente, V; de Orellano, M E; Sansone, G; Benuzzi, D; Sanz de Tosetti, M I
2001-12-01
Yeasts produce hydroxamate-type siderophores (iron-binding compounds) in response to Fe-stress conditions. Because these siderophores are important to the biocontrol of postharvest diseases of apple and pears, a method for screening siderophore producer yeast was developed. The screening method was carried out in special Petri dishes with eight or nine wells (25-mm diameter). These wells were filled with siderophore production medium and seeded with yeasts isolated from epiphytic apple microflora. After yeasts grew (24-48 h), holes (2-mm diameter) were made in the agar of each well. Holes were filled with an acid solution of ferric perchlorate. After 10-15 min, reddish halos appeared in the bottom of the plate and their intensities were compared with standards. Standards were prepared in the same special dish with rhodotorulic acid solutions (concentrations between 0.05 and 1 g/l) plus 2% agar. When agar solidified into wells, holes were made and filled with ferric perchlorate solution. Color intensities of reddish halos were proportional to siderophore concentration and the detection limit was 0.1 g/l. It was possible to correlate the production of siderophore in solid medium with the results obtained in liquid medium. The methodology was also a useful tool for making a preliminary assessment of the influence of different factors on the siderophore production. PMID:11714517
Newton-Krylov methods applied to nonequilibrium radiation diffusion
Knoll, D.A.; Rider, W.J.; Olsen, G.L.
1998-03-10
The authors present results of applying a matrix-free Newton-Krylov method to a nonequilibrium radiation diffusion problem. Here, there is no use of operator splitting, and Newton`s method is used to convert the nonlinearities within a time step. Since the nonlinear residual is formed, it is used to monitor convergence. It is demonstrated that a simple Picard-based linearization produces a sufficient preconditioning matrix for the Krylov method, thus elevating the need to form or store a Jacobian matrix for Newton`s method. They discuss the possibility that the Newton-Krylov approach may allow larger time steps, without loss of accuracy, as compared to an operator split approach where nonlinearities are not converged within a time step.
A diffusive information preservation method for small Knudsen number flows
Fei, Fei; Fan, Jing
2013-06-15
The direct simulation Monte Carlo (DSMC) method is a powerful particle-based method for modeling gas flows. It works well for relatively large Knudsen (Kn) numbers, typically larger than 0.01, but quickly becomes computationally intensive as Kn decreases due to its time step and cell size limitations. An alternative approach was proposed to relax or remove these limitations, based on replacing pairwise collisions with a stochastic model corresponding to the Fokker–Planck equation [J. Comput. Phys., 229, 1077 (2010); J. Fluid Mech., 680, 574 (2011)]. Similar to the DSMC method, the downside of that approach suffers from computationally statistical noise. To solve the problem, a diffusion-based information preservation (D-IP) method has been developed. The main idea is to track the motion of a simulated molecule from the diffusive standpoint, and obtain the flow velocity and temperature through sampling and averaging the IP quantities. To validate the idea and the corresponding model, several benchmark problems with Kn ? 10{sup ?3}–10{sup ?4} have been investigated. It is shown that the IP calculations are not only accurate, but also efficient because they make possible using a time step and cell size over an order of magnitude larger than the mean collision time and mean free path, respectively.
A diffusive information preservation method for small Knudsen number flows
NASA Astrophysics Data System (ADS)
Fei, Fei; Fan, Jing
2013-06-01
The direct simulation Monte Carlo (DSMC) method is a powerful particle-based method for modeling gas flows. It works well for relatively large Knudsen (Kn) numbers, typically larger than 0.01, but quickly becomes computationally intensive as Kn decreases due to its time step and cell size limitations. An alternative approach was proposed to relax or remove these limitations, based on replacing pairwise collisions with a stochastic model corresponding to the Fokker-Planck equation [J. Comput. Phys., 229, 1077 (2010); J. Fluid Mech., 680, 574 (2011)]. Similar to the DSMC method, the downside of that approach suffers from computationally statistical noise. To solve the problem, a diffusion-based information preservation (D-IP) method has been developed. The main idea is to track the motion of a simulated molecule from the diffusive standpoint, and obtain the flow velocity and temperature through sampling and averaging the IP quantities. To validate the idea and the corresponding model, several benchmark problems with Kn ˜ 10-3-10-4 have been investigated. It is shown that the IP calculations are not only accurate, but also efficient because they make possible using a time step and cell size over an order of magnitude larger than the mean collision time and mean free path, respectively.
Charles Y. Hachem; Jill E. Clarridge; Rita Reddy; Robert Flamm; Dolores G. Evans; S. Ken Tanaka; David Y. Graham
1996-01-01
The optimal method for the determination of the minimum inhibitory concentration (MIC) of antimicrobials against Helicobacter pylori has not been established. The epsilometer agar diffusion gradient test (E-Test; AB Biodisk, Solna, Sweden) was compared with broth microdilution, the reference method, and disk diffusion for the antimicrobial susceptibility testing of 122 clinical isolates of H. pylori to ampicillin, clarithromycin, and metronidazole.
Le Page, S; van Belkum, A; Fulchiron, C; Huguet, R; Raoult, D; Rolain, J-M
2015-09-01
The disk diffusion (DD) method remains the most popular manual technique for antibiotic susceptibility testing (AST) in clinical microbiology laboratories. This is because of its simplicity, reproducibility, and limited cost compared to (automated) microdilution systems, which are usually less sensitive at detecting certain important mechanisms of resistance. Here, we evaluate the PREVI® Isola automated seeder system using a new protocol for spreading bacterial suspensions (eight deposits of calibrated inocula of bacteria, followed by two rounds of rotation) in comparison with manual DD reference testing on a large series of clinical and reference strains. The average time required for seeding one agar plate for DD with this new protocol was 51 s per plate, i.e., 70 agar plates/h. Reproducibility and repeatability was assessed on three reference and three randomly chosen clinical strains, as usually requested by the European Committee on Antimicrobial Susceptibility Testing (EUCAST), and was excellent compared to the manual method. The standard deviations of zones of growth inhibition showed no statistical discrimination. The correlation between the two methods, assessed using 294 clinical isolates and a panel of six antibiotics (n?=?3,528 zones of growth inhibition measured), was excellent, with a correlation coefficient of 0.977. The new PREVI® Isola protocol adapted for DD had a sensitivity of 99 % and a specificity of 100 % compared to the manual technique for interpreting DD as recommended by the EUCAST. PMID:26092031
Luminescent DNA- and agar-based membranes.
Leones, R; Fernandes, M; Ferreira, R A S; Cesarino, I; Lima, J F; Carlos, L D; Bermudez, V de Zea; Magon, C J; Donoso, J P; Silva, M M; Pawlicka, A
2014-09-01
Luminescent materials containing europium ions are investigated for different optical applications. They can be obtained using bio-macromolecules, which are promising alternatives to synthetic polymers based on the decreasing oil resources. This paper describes studies of the DNA- and Agar-europium triflate luminescent membranes and its potential technological applications are expanded to electroluminescent devices. Polarized optical microscopy demonstrated that the samples are birefringent with submicrometer anisotropy. The X-ray diffraction analysis revealed predominantly amorphous nature of the samples and the atomic force microscopy images showed a roughness of the membranes of 409.0 and 136.1 nm for the samples of DNA10Eu and Agar1.11Eu, respectively. The electron paramagnetic resonance spectra of the DNA(n)Eu membranes with the principal lines at g ? 2.0 and g ? 4.8 confirmed uniform distribution of rare earth ions in a disordered matrix. Moreover, these strong and narrow resonance lines for the samples of DNA(n)Eu when compared to the Agar(n)Eu suggested a presence of paramagnetic radicals arising from the DNA matrix. The emission spectra suggested that the Eu3+ ions occupy a single local environment in both matrices and the excitation spectra monitored around the Eu emission lines pointed out that the Eu3+ ions in the Agar host were mainly excited via the broad band component rather than by direct intra-4f(6) excitation, whereas the opposite case occurred for the DNA-based sample. PMID:25924317
Migration of chemotactic bacteria in soft agar: role of gel concentration
O. A. Croze; G. P. Ferguson; M. E. Cates; W. C. K. Poon
2011-08-06
We study the migration of chemotactic wild-type Escherichia coli populations in semisolid (soft) agar in the concentration range C = 0.15-0.5% (w/v). For C < 0.35%, expanding bacterial colonies display characteristic chemotactic rings. At C = 0.35%, however, bacteria migrate as broad circular bands rather than sharp rings. These are growth/diffusion waves arising because of suppression of chemotaxis by the agar and have not been previously reported experimentally to our knowledge. For C = 0.4-0.5%, expanding colonies do not span the depth of the agar and develop pronounced front instabilities. The migration front speed is weakly dependent on agar concentration at C < 0.25%, but decreases sharply above this value. We discuss these observations in terms of an extended Keller-Segel model for which we derived novel transport parameter expressions accounting for perturbations of the chemotactic response by collisions with the agar. The model makes it possible to fit the observed front speed decay in the range C = 0.15-0.35%, and its solutions qualitatively reproduce the observed transition from chemotactic to growth/diffusion bands. We discuss the implications of our results for the study of bacteria in porous media and for the design of improved bacteriological chemotaxis assays.
Migration of Chemotactic Bacteria in Soft Agar: Role of Gel Concentration
Croze, Ottavio A.; Ferguson, Gail P.; Cates, Michael E.; Poon, Wilson C.K.
2011-01-01
We study the migration of chemotactic wild-type Escherichia coli populations in semisolid (soft) agar in the concentration range C = 0.15–0.5% (w/v). For C?0.35%, expanding bacterial colonies display characteristic chemotactic rings. At C = 0.35%, however, bacteria migrate as broad circular bands rather than sharp rings. These are growth/diffusion waves arising because of suppression of chemotaxis by the agar and have not been previously reported experimentally to our knowledge. For C = 0.4–0.5%, expanding colonies do not span the depth of the agar and develop pronounced front instabilities. The migration front speed is weakly dependent on agar concentration at C < 0.25%, but decreases sharply above this value. We discuss these observations in terms of an extended Keller-Segel model for which we derived novel transport parameter expressions accounting for perturbations of the chemotactic response by collisions with the agar. The model makes it possible to fit the observed front speed decay in the range C = 0.15–0.35%, and its solutions qualitatively reproduce the observed transition from chemotactic to growth/diffusion bands. We discuss the implications of our results for the study of bacteria in porous media and for the design of improved bacteriological chemotaxis assays. PMID:21806920
Migration of chemotactic bacteria in soft agar: role of gel concentration.
Croze, Ottavio A; Ferguson, Gail P; Cates, Michael E; Poon, Wilson C K
2011-08-01
We study the migration of chemotactic wild-type Escherichia coli populations in semisolid (soft) agar in the concentration range C = 0.15-0.5% (w/v). For C?0.35%, expanding bacterial colonies display characteristic chemotactic rings. At C = 0.35%, however, bacteria migrate as broad circular bands rather than sharp rings. These are growth/diffusion waves arising because of suppression of chemotaxis by the agar and have not been previously reported experimentally to our knowledge. For C = 0.4-0.5%, expanding colonies do not span the depth of the agar and develop pronounced front instabilities. The migration front speed is weakly dependent on agar concentration at C < 0.25%, but decreases sharply above this value. We discuss these observations in terms of an extended Keller-Segel model for which we derived novel transport parameter expressions accounting for perturbations of the chemotactic response by collisions with the agar. The model makes it possible to fit the observed front speed decay in the range C = 0.15-0.35%, and its solutions qualitatively reproduce the observed transition from chemotactic to growth/diffusion bands. We discuss the implications of our results for the study of bacteria in porous media and for the design of improved bacteriological chemotaxis assays. PMID:21806920
TIME-DOMAIN METHODS FOR DIFFUSIVE TRANSPORT IN SOFT MATTER
Fricks, John; Yao, Lingxing; Elston, Timothy C.; Gregory Forest, And M.
2015-01-01
Passive microrheology [12] utilizes measurements of noisy, entropic fluctuations (i.e., diffusive properties) of micron-scale spheres in soft matter to infer bulk frequency-dependent loss and storage moduli. Here, we are concerned exclusively with diffusion of Brownian particles in viscoelastic media, for which the Mason-Weitz theoretical-experimental protocol is ideal, and the more challenging inference of bulk viscoelastic moduli is decoupled. The diffusive theory begins with a generalized Langevin equation (GLE) with a memory drag law specified by a kernel [7, 16, 22, 23]. We start with a discrete formulation of the GLE as an autoregressive stochastic process governing microbead paths measured by particle tracking. For the inverse problem (recovery of the memory kernel from experimental data) we apply time series analysis (maximum likelihood estimators via the Kalman filter) directly to bead position data, an alternative to formulas based on mean-squared displacement statistics in frequency space. For direct modeling, we present statistically exact GLE algorithms for individual particle paths as well as statistical correlations for displacement and velocity. Our time-domain methods rest upon a generalization of well-known results for a single-mode exponential kernel [1, 7, 22, 23] to an arbitrary M-mode exponential series, for which the GLE is transformed to a vector Ornstein-Uhlenbeck process.
Pavelic, Z P; Vaughan, M M; Slocum, H K; Rustum, Y M
1981-11-01
Two simple techniques are described for preparing sections from soft agar colony cultures of tumor cells. Tumor cells grown in soft agar can be frozen, sectioned, and stained and/or fixed in formalin, embedded in paraffin, sectioned, mounted on glass slides, and stained. The methods are simple and reproducible. These cells can be stained with various stains and the staining quality is excellent. The paraffin blocks and microscope slides can be stored for permanent record. The use of these techniques should provide better understanding of the histomorphologic characteristics of neoplastic cells which grow in soft agar and should expand and refine prognosis and diagnosis of malignant tumors. PMID:6176051
Girardello, Raquel; Bispo, Paulo J M; Yamanaka, Tiago M; Gales, Ana C
2012-07-01
Polymyxins have been the only alternative therapeutic option for the treatment of serious infections caused by multidrug-resistant Acinetobacter baumannii or Pseudomonas aeruginosa isolates. For this reason, it is of crucial importance that susceptibility tests provide accurate results when testing these drug-pathogen combinations. In this study, the effect of cation concentration variability found on different commercial brands of Mueller-Hinton agar (MHA) for testing polymyxin B susceptibility was evaluated. The polymyxin B susceptibilities determined using Etest and disk diffusion were compared to those determined by the CLSI reference broth microdilution method. In general, the polymyxin B MIC values were higher when determined by Etest than when determined by broth microdilution against both A. baumannii and P. aeruginosa isolates. A high very major error rate (10%) was observed, as well as a trend toward lower MICs, compared to those determined by broth microdilution when the Merck MHA was tested by Etest. Poor essential agreement rates (10 to 70%) were observed for P. aeruginosa when all MHA brands were tested by Etest. Although an excellent categorical agreement rate (100%) was seen between the disk diffusion and broth microdilution methods for P. aeruginosa, larger zones of inhibition were shown obtained using the Merck MHA. The high cation concentration variability found for the MHA brands tested correlated to the low accuracy, and discrepancies in the polymyxin B MICs were determined by Etest method, particularly for P. aeruginosa isolates. PMID:22553247
Water vapor adsorption isotherms of agar-based nanocomposite films.
Rhim, Jong-Whan
2011-10-01
Adsorption isotherms of agar and agar/clay nanocomposite films prepared with different types of nanoclays, that is, a natural montmorillonite (Cloisite Na(+) ) and 2 organically modified montmorillonites (Cloisite 30B and Cloisite 20A), were determined at 3 different temperatures (10, 25, and 40 °C). The water vapor adsorption behavior of the nanocomposite films was found to be greatly influenced with the type of clay. The Guggenheim-Anderson-de Boer (GAB) isotherm model parameters were estimated by using both polynomial regression and nonlinear regression methods and it was found that the GAB model fitted adequately for describing experimental adsorption isotherm data for the film samples. The monolayer moisture content (m(o) ) of the film samples was also greatly affected by the type of nanoclay used, that is, m(o) of nanocomposite films was significantly lower than that of the neat agar film. Nanocomposite films prepared with hydrophobic nanoclays (Cloisite 30B and Cloisite 20A) exhibited lower m(o) values than those prepared with hydrophilic nanoclay (Cloisite Na(+) ). PMID:22417601
Agar medium for differential enumeration of lactic streptococci.
Reddy, M S; Vedamuthu, E R; Washam, C J; Reinbold, G W
1972-12-01
An agar medium containing arginine and calcium citrate as specific substrates, diffusible (K(2)HPO(4)) and undiffusible (CaCO(3)) buffer systems, and bromocresol purple as the pH indicator was developed to differentiate among lactic streptococci in pure and mixed cultures. Milk was added as the sole source of carbohydrate (lactose) and to provide growth-stimulating factors. Production of acid from lactose caused developing bacterial colonies to seem yellow. Subsequent arginine utilization by Streptococcus lactis and S. diacetilactis liberated ammonia, resulting in a localized pH shift back toward neutrality and a return of the original purple indicator hue. The effects of production of acid from lactose and ammonia were fixed around individual colonies by the buffering capacity of CaCO(3). After 36 hr at 32 C in a candle oats jar, colonies of S. cremoris were yellow, whereas colonies of S. lactis and S. diacetilactis were white. S. diacetilactis, on further incubation, utilized suspended calcium citrate, and, after 6 days, the citrate-degrading colonies exhibited clear zoning against a turbid background, making them easily distinguishable from the colonies of the other two species. The medium proved suitable for quantitative differential enumeration when compared with another widely used general agar medium for lactic streptococci. PMID:16349952
Introduction to the variational and diffusion Monte Carlo methods
Toulouse, Julien; Umrigar, C J
2015-01-01
We provide a pedagogical introduction to the two main variants of real-space quantum Monte Carlo methods for electronic-structure calculations: variational Monte Carlo (VMC) and diffusion Monte Carlo (DMC). Assuming no prior knowledge on the subject, we review in depth the Metropolis-Hastings algorithm used in VMC for sampling the square of an approximate wave function, discussing details important for applications to electronic systems. We also review in detail the more sophisticated DMC algorithm within the fixed-node approximation, introduced to avoid the infamous Fermionic sign problem, which allows one to sample a more accurate approximation to the ground-state wave function. Throughout this review, we discuss the statistical methods used for evaluating expectation values and statistical uncertainties. In particular, we show how to estimate nonlinear functions of expectation values and their statistical uncertainties.
Extrapolation techniques applied to matrix methods in neutron diffusion problems
NASA Technical Reports Server (NTRS)
Mccready, Robert R
1956-01-01
A general matrix method is developed for the solution of characteristic-value problems of the type arising in many physical applications. The scheme employed is essentially that of Gauss and Seidel with appropriate modifications needed to make it applicable to characteristic-value problems. An iterative procedure produces a sequence of estimates to the answer; and extrapolation techniques, based upon previous behavior of iterants, are utilized in speeding convergence. Theoretically sound limits are placed on the magnitude of the extrapolation that may be tolerated. This matrix method is applied to the problem of finding criticality and neutron fluxes in a nuclear reactor with control rods. The two-dimensional finite-difference approximation to the two-group neutron fluxes in a nuclear reactor with control rods. The two-dimensional finite-difference approximation to the two-group neutron-diffusion equations is treated. Results for this example are indicated.
NASA Astrophysics Data System (ADS)
Akimoto, Takuma; Seki, Kazuhiko
2015-08-01
Diffusion of molecules in cells plays an important role in providing a biological reaction on the surface by finding a target on the membrane surface. The water retardation (slow diffusion) near the target assists the searching molecules to recognize the target. Here, we consider effects of the surface diffusivity on the effective diffusivity, where diffusion on the surface is slower than that in bulk. We show that the ensemble-averaged mean-square displacements increase linearly with time when the desorption rate from the surface is finite, which is valid even when the diffusion on the surface is anomalous (subdiffusion). Moreover, this slow diffusion on the surface affects the fluctuations of the time-averaged mean-square displacements (TAMSDs). We find that fluctuations of the TAMSDs remain large when the measurement time is smaller than a characteristic time, and decays according to an increase of the measurement time for a relatively large measurement time. Therefore, we find a transition from nonergodic (distributional) to ergodic diffusivity in a target search process. Moreover, this fluctuation analysis provides a method to estimate an unknown surface diffusivity.
Low density, microcellular, dopable, agar/gelatin foams for pulsed power experiments
McNamara, W.F. [Orion International Technologies, Inc., Albuquerque, NM (United States); Aubert, J.H. [Sandia National Lab., Albuquerque, NM (United States)
1997-04-01
Low-density, microcellular foams prepared from the natural polymers agar and gelatin have been developed for pulsed-power physics experiments. Numerous experiments were supported with foams having densities at or below 10 mg/cm{sup 3}. For some of the experiments, the agar/gelatin foam was uniformly doped with metallic elements using soluble salts. Depending on the method of preparation, cell sizes were typically below 10 microns and for one process were below 1.0 micron.
Stokkou, Sofia; Geginat, Gernot; Schlüter, Dirk; Tammer, Ina
2015-03-01
Sepsis represents a life-threatening infection requiring the immediate start of antibacterial treatment to reduce morbidity. Thus, laboratories use direct antimicrobial susceptibility testing (AST) to rapidly generate preliminary results from positive blood cultures. As the direct AST has not yet been published to be evaluated with EUCAST breakpoints, the purpose of the study was to investigate the reliability of the direct agar diffusion test to correctly produce AST results from positive monobacterial blood cultures compared with the VITEK2-based definitive AST, when current EUCAST breakpoints were used. A total of 428 isolates from unselected monobacterial routine blood cultures and 110 challenge strains were included. Direct agar diffusion-based and standard VITEK2-based AST of 2803 bacterium-drug combinations yielded a total clinical category agreement of 95.47% with 1.28% very major errors and 3.42% combined major and minor errors. On the species level, very major errors were observed in the species-drug combinations Enterococcus spp.-high-level gentamicin (10.87%) and Staphylococcus spp.-rifampicin (5%), only. No very major errors occurred with Enterobacteriaceae and Pseudomonas aeruginosa. In most species-drug combinations, the direct agar diffusion test using EUCAST breakpoints precisely predicted the result of the definitive antibiotic susceptibility test and, thus, it can be used to optimize empiric antibiotic therapy until definitive results are available. PMID:25883798
Stokkou, Sofia; Geginat, Gernot; Schlüter, Dirk
2015-01-01
Sepsis represents a life-threatening infection requiring the immediate start of antibacterial treatment to reduce morbidity. Thus, laboratories use direct antimicrobial susceptibility testing (AST) to rapidly generate preliminary results from positive blood cultures. As the direct AST has not yet been published to be evaluated with EUCAST breakpoints, the purpose of the study was to investigate the reliability of the direct agar diffusion test to correctly produce AST results from positive monobacterial blood cultures compared with the VITEK2-based definitive AST, when current EUCAST breakpoints were used. A total of 428 isolates from unselected monobacterial routine blood cultures and 110 challenge strains were included. Direct agar diffusion-based and standard VITEK2-based AST of 2803 bacterium–drug combinations yielded a total clinical category agreement of 95.47% with 1.28% very major errors and 3.42% combined major and minor errors. On the species level, very major errors were observed in the species–drug combinations Enterococcus spp.–high-level gentamicin (10.87%) and Staphylococcus spp.–rifampicin (5%), only. No very major errors occurred with Enterobacteriaceae and Pseudomonas aeruginosa. In most species–drug combinations, the direct agar diffusion test using EUCAST breakpoints precisely predicted the result of the definitive antibiotic susceptibility test and, thus, it can be used to optimize empiric antibiotic therapy until definitive results are available. PMID:25883798
NSDL National Science Digital Library
2011-12-09
In this lab, learners evaluate the relative effectiveness of various chemical substances (i.e. garlic powder, bathroom cleaner, mouthwash, etc.) as antimicrobial agents. Learners use the agar diffusion method to determine "zones of inhibition." This lesson guide includes background information, questions for learners, and additional activity ideas.
Migration of chemotactic bacteria in soft agar: role of gel concentration
Croze, O A; Cates, M E; Poon, W C K
2011-01-01
We study the migration of chemotactic wild type Escherichia coli populations in semi-solid (`soft') agar in the concentration range C = 0.15-0.5% (w/v). For C < 0.35%, expanding bacterial colonies display characteristic chemotactic `rings'. At C = 0.35%, however, we observe broadband migration rather than rings. These are growth/diffusion waves arising because of suppression of chemotaxis by the agar and have not been previously reported experimentally. For C=0.4-0.5% expanding colonies do not span the depth of the agar and develop pronounced front instabilities. The rate of increase of the colony radius (front speed) v_F, is weakly dependent of agar concentration below C = 0.25%, but decreases sharply above this value. We discuss these observations in terms of an extended Keller-Segel model for which we derived novel expressions for transport parameters accounting for perturbations of the chemotactic response by collisions with the agar. The observed front speed decay could be well fitted with the model i...
A Critical Study of Agglomerated Multigrid Methods for Diffusion
NASA Technical Reports Server (NTRS)
Nishikawa, Hiroaki; Diskin, Boris; Thomas, James L.
2011-01-01
Agglomerated multigrid techniques used in unstructured-grid methods are studied critically for a model problem representative of laminar diffusion in the incompressible limit. The studied target-grid discretizations and discretizations used on agglomerated grids are typical of current node-centered formulations. Agglomerated multigrid convergence rates are presented using a range of two- and three-dimensional randomly perturbed unstructured grids for simple geometries with isotropic and stretched grids. Two agglomeration techniques are used within an overall topology-preserving agglomeration framework. The results show that multigrid with an inconsistent coarse-grid scheme using only the edge terms (also referred to in the literature as a thin-layer formulation) provides considerable speedup over single-grid methods but its convergence deteriorates on finer grids. Multigrid with a Galerkin coarse-grid discretization using piecewise-constant prolongation and a heuristic correction factor is slower and also grid-dependent. In contrast, grid-independent convergence rates are demonstrated for multigrid with consistent coarse-grid discretizations. Convergence rates of multigrid cycles are verified with quantitative analysis methods in which parts of the two-grid cycle are replaced by their idealized counterparts.
A Critical Study of Agglomerated Multigrid Methods for Diffusion
NASA Technical Reports Server (NTRS)
Thomas, James L.; Nishikawa, Hiroaki; Diskin, Boris
2009-01-01
Agglomerated multigrid techniques used in unstructured-grid methods are studied critically for a model problem representative of laminar diffusion in the incompressible limit. The studied target-grid discretizations and discretizations used on agglomerated grids are typical of current node-centered formulations. Agglomerated multigrid convergence rates are presented using a range of two- and three-dimensional randomly perturbed unstructured grids for simple geometries with isotropic and highly stretched grids. Two agglomeration techniques are used within an overall topology-preserving agglomeration framework. The results show that multigrid with an inconsistent coarse-grid scheme using only the edge terms (also referred to in the literature as a thin-layer formulation) provides considerable speedup over single-grid methods but its convergence deteriorates on finer grids. Multigrid with a Galerkin coarse-grid discretization using piecewise-constant prolongation and a heuristic correction factor is slower and also grid-dependent. In contrast, grid-independent convergence rates are demonstrated for multigrid with consistent coarse-grid discretizations. Actual cycle results are verified using quantitative analysis methods in which parts of the cycle are replaced by their idealized counterparts.
A Simple Method of Determining Diffusion Coefficient by Digital Laser Speckle Correlation
Giuseppe Schirripa Spagnolo; Dario Ambrosini; Antonio Ponticiello; Domenica Paoletti
1996-01-01
A laser speckle technique is proposed for the study of diffusion in transparent liquid mixtures. The diffusion constants may be deduced by a simple manipulation of the speckle patterns recorded during the diffusion process. The proposed method, checked with the LiBr-water system, gives reasonable agreement with existing data.
Simple generic method for predicting the effect of strain on surface diffusion D. J. Shu,1
Simons, Jack
Simple generic method for predicting the effect of strain on surface diffusion D. J. Shu,1 Feng Liu with the intrinsic surface stress induced by an adatom along its diffusion pathways. We demonstrate a simple ge, by first-principles calculations, that the effect of external strain on surface diffusion is inherently
Kali, Arunava; Stephen, Selvaraj; Umadevi, Sivaraman
2014-01-01
Although conventional antibiotic susceptibility tests are most commonly performed for methicillin-resistant Staphylococcus aureus (MRSA), the results of these phenotypic tests are dependent on the standardization of the culture conditions. The aim of the study was to evaluate the conventional phenotypic screening tests in comparison to the mecA gene polymerase chain reaction (PCR). One hundred and two clinical isolates of MRSA identified by the oxacillin disk diffusion were subjected to PCR for the mecA gene and by the cefoxitin disk diffusion test and culture on oxacillin screen agar, mannitol salt agar, and methicillin-resistant Staphylococcus aureus Agar (MeReSA) selective medium, for MRSA. Although all 102 isolates were resistant in oxacillin and cefoxitin disk diffusion, 92 (90.1%) isolates were positive for the mecA gene. The sensitivities of the mannitol salt agar, MeReSA agar, and oxacillin screen agar were 89.13, 97.82, and 98.91%, respectively. The oxacillin screen agar may be recommended for confirming methicillin resistance in the disk diffusion test in resource-poor settings, where molecular methods are not available. PMID:25179712
Nawaz, Muhammad Asif; Karim, Asad; Aman, Afsheen; Marchetti, Roberta; Qader, Shah Ali Ul; Molinaro, Antonio
2015-04-01
Maltose degrading enzyme was immobilized within agar-agar support via entrapment method due to its industrial utilization. The maximum immobilization efficiency (82.77%) was achieved using 4.0% agar-agar keeping the diameter of bead up to 3.0 mm. The matrix entrapment showed maximum catalytic activity at pH 7.0 and temperature 65 °C. Substrate saturation kinetics showed that the K m of immobilized enzyme increased from 1.717 to 2.117 mM ml(-1) where as Vmax decreased from 8,411 to 7,450 U ml(-1 )min(-1) as compared to free enzyme. The immobilization significantly increased the stability of maltase against various temperatures and immobilized maltase retain 100% of its original activity after 2 h at 50 °C, whereas the free maltase only showed 60% residual activity under same condition. The reusability of entrapped maltase showed activity up to 12 cycles and retained 50% of activity even after 5th cycle. Storage stability of agar entrapped maltase retain 73% of its initial activity even after 2 months when stored at 30 °C while free enzyme showed only 37% activity at same storage conditions. PMID:25326060
NASA Astrophysics Data System (ADS)
Yang, Linlin; Sun, Hai; Fu, Xudong; Wang, Suli; Jiang, Luhua; Sun, Gongquan
2014-07-01
A novel method for measuring effective diffusion coefficient of porous materials is developed. The oxygen concentration gradient is established by an air-breathing proton exchange membrane fuel cell (PEMFC). The porous sample is set in a sample holder located in the cathode plate of the PEMFC. At a given oxygen flux, the effective diffusion coefficients are related to the difference of oxygen concentration across the samples, which can be correlated with the differences of the output voltage of the PEMFC with and without inserting the sample in the cathode plate. Compared to the conventional electrical conductivity method, this method is more reliable for measuring non-wetting samples.
Method for manufacturing nuclear radiation detector with deep diffused junction
Hall
1977-01-01
Germanium radiation detectors are manufactured by diffusing lithium into high purity p-type germanium. The diffusion is most readily accomplished from a lithium-lead-bismuth alloy at approximately 430Â°C and is monitored by a quartz half cell containing a standard composition of this alloy. Detectors having n-type cores may be constructed by converting high purity p-type germanium to n-type by a lithium diffusion
AEROSOL SIZE MEASUREMENT BY ELECTRICAL MOBILITY AND DIFFUSION ANALYSIS - A COMPARISON OF METHODS
The principle of the electrical aerosol analyzer method is reviewed and the diffusion battery method is described in detail. An appendix explains the basis of the calculations used. The diffusion battery method is complicated by counting losses of very small particles, inherent t...
An integration factor method for stochastic and stiff reaction-diffusion systems
NASA Astrophysics Data System (ADS)
Ta, Catherine; Wang, Dongyong; Nie, Qing
2015-08-01
Stochastic effects are often present in the biochemical systems involving reactions and diffusions. When the reactions are stiff, existing numerical methods for stochastic reaction diffusion equations require either very small time steps for any explicit schemes or solving large nonlinear systems at each time step for the implicit schemes. Here we present a class of semi-implicit integration factor methods that treat the diffusion term exactly and reaction implicitly for a system of stochastic reaction-diffusion equations. Our linear stability analysis shows the advantage of such methods for both small and large amplitudes of noise. Direct use of the method to solving several linear and nonlinear stochastic reaction-diffusion equations demonstrates good accuracy, efficiency, and stability properties. This new class of methods, which are easy to implement, will have broader applications in solving stochastic reaction-diffusion equations arising from models in biology and physical sciences.
Lessing, Paul A.
2004-09-07
An electrochemically active hydrogen diffusion barrier which comprises an anode layer, a cathode layer, and an intermediate electrolyte layer, which is conductive to protons and substantially impermeable to hydrogen. A catalytic metal present in or adjacent to the anode layer catalyzes an electrochemical reaction that converts any hydrogen that diffuses through the electrolyte layer to protons and electrons. The protons and electrons are transported to the cathode layer and reacted to form hydrogen. The hydrogen diffusion barrier is applied to a polymeric substrate used in a storage tank to store hydrogen under high pressure. A storage tank equipped with the electrochemically active hydrogen diffusion barrier, a method of fabricating the storage tank, and a method of preventing hydrogen from diffusing out of a storage tank are also disclosed.
Lessing, Paul A. (Idaho Falls, ID)
2008-07-22
An electrochemically active hydrogen diffusion barrier which comprises an anode layer, a cathode layer, and an intermediate electrolyte layer, which is conductive to protons and substantially impermeable to hydrogen. A catalytic metal present in or adjacent to the anode layer catalyzes an electrochemical reaction that converts any hydrogen that diffuses through the electrolyte layer to protons and electrons. The protons and electrons are transported to the cathode layer and reacted to form hydrogen. The hydrogen diffusion barrier is applied to a polymeric substrate used in a storage tank to store hydrogen under high pressure. A storage tank equipped with the electrochemically active hydrogen diffusion barrier, a method of fabricating the storage tank, and a method of preventing hydrogen from diffusing out of a storage tank are also disclosed.
Drinking water regulations under the Final Coliform Rule require that total coliform-positive drinking water samples be examined for the presence of Escherichia coli or fecal coliforms. The current U.S. Environmental Protection Agency-approved membrane filter (MF) method for E. c...
Biological treatment of textile dyes by agar-agar immobilized consortium in a packed bed reactor.
Patel, Yogesh; Gupte, Akshaya
2015-03-01
The decolorization of Acid Maroon V was investigated using bacterial consortium EDPA containing Enterobacter dissolvens AGYP1 and Pseudomonas aeruginosa AGYP2 immobilized in different entrapment matrices. The consortium displayed 96% removal of dye (100 mg/l) within 6 h when immobilized in agar-agar. Under optimum concentrations of agar-agar (3.0% w/v) and cell biomass (0.9 g% w/v), the consortium displayed decolorization for 18 successive batches of Acid Maroon V and also decolorized 14 other different textile dyes. A packed bed reactor under batch mode showed 89% decolorization of dye after 56 repetitive cycles. Under continuous flow mode, maximum color removal was achieved with bed length of 36 cm, hydraulic retention time of 2.66 h, and dye concentration of 100 mg/l. Additionally, the reactor decolorized relatively higher concentrations (100-2000 mg/l) of dye. The synthetic dye wastewater containing five textile dyes was decolorized 92% with 62% COD reduction using an immobilized consortium. PMID:25842535
Control of the pattern of perithecium development in Sordaria fimicola on agar medium.
Pollock, R T
1975-06-01
In a Sordaria fimicola (Rob.) Ces. and de Not. colony grown on agar medium in a petri plate, perithecia developed in a narrow band around the plate edge after the colony margin reached the edge. Physical wounding of the colony carried out shortly before or during the time perithecia were developing around the plate edge stimulated perithecium development in the wound area. Diffusion barriers were created by cutting small trenches in the agar parallel to the plate edge. The trenches were made at several different positions between the plate center and edge using cultures of several different ages, and the resultant distribution of perithecia along the trench edges suggested that the colony center and periphery produce diffusible inhibitors of perithecium development. These inhibitors may be responsible, in part, for the observed pattern of perithecium development in the colony. PMID:1158169
Improving agar electrospinnability with choline-based deep eutectic solvents.
Sousa, Ana M M; Souza, Hiléia K S; Uknalis, Joseph; Liu, Shih-Chuan; Gonçalves, Maria P; Liu, LinShu
2015-09-01
Very recently our group has produced novel agar-based fibers by an electrospinning technique using water as solvent and polyvinyl alcohol (PVA) as co-blending polymer. Here, we tested the deep eutectic solvent (DES), (2-hydroxyethyl)trimethylammonium chloride/urea prepared at 1:2 molar ratio, as an alternative solvent medium for agar electrospinning. The electrospun materials were collected with an ethanol bath adapted to a previous electrospinning set-up. One weight percent agar-in-DES showed improved viscoelasticity and hence, spinnability, when compared to 1wt% agar-in-water and pure agar nanofibers were successfully electrospun if working above the temperature of sol-gel transition (?80°C). By changing the solvent medium we decreased the PVA concentration (5wt% starting solution) and successfully produced composite fibers with high agar contents (50/50 agar/PVA). Best composite fibers were formed with the 50/50 and 30/70 agar/PVA solutions. These fibers were mechanically resistant, showed tailorable surface roughness and diverse size distributions, with most of the diameters falling in the sub-micron range. Both nano and micro forms of agar fibers (used separately or combined) may have potential for the design of new and highly functional agar-based materials. PMID:26116384
Numerical Simulation of DAM Break by Adaptive Stencil Diffuse Interface Method
NASA Astrophysics Data System (ADS)
Ding, L.; Shu, C.; Zhao, N.
This paper presents the application of an adaptive stencil diffuse interface method to the simulation of dam break problem. The adaptive stencil diffuse interface method is the combination of the diffuse interface method and a stencil adaptive algorithm, where the diffuse interface method is used as the solver, and the adaptive stencil refinement scheme is applied to improve the resolution around the interface so that the fine-scale interface behavior can be captured. In this paper, we use this method to simulate the dam break problem, study the dam height and leading edge position, and compare our results with the experiment data available in the literature. It is shown that the results using the adaptive stencil diffuse interface method agree very well with the experimental results.
Fast Explicit Operator Splitting Method for Convection-Diffusion Equations
Kurganov, Alexander
to the one- and two-dimensional systems of convection-diffusion equations which model the polymer flooding) processes in fluid mechanics, astrophysics, me- teorology, multiphase flow in oil reservoirs, polymer flow
January 16, 2008 18:35 WSPC/INSTRUCTION FILE article MCMC METHODS FOR DIFFUSION BRIDGES
Stuart, Andrew
January 16, 2008 18:35 WSPC/INSTRUCTION FILE article MCMC METHODS FOR DIFFUSION BRIDGES ALEXANDROS.voss@warwick.ac.uk We present and study a Langevin MCMC approach for sampling nonlinear diffusion bridges. The method with respect to the target bridge, derived by applying the Langevin idea on the bridge pathspace
Andualem, Berhanu; Gessesse, Amare
2013-01-01
Objective To investigate and optimize microbial media that substitute peptone agar using brebra seed defatted flour. Methods 'Defatted process, inoculums preparation, evaluation of bacterial growth, preparation of cooked and hydrolyzed media and growth turbidity of tested bacteria were determined. Results Two percent defatted flour was found to be suitable concentration for the growth of pathogenic bacteria: Escherichia coli (ATCC 25922) (E. coli), Pseudomonas aeruginosa (ATCC 27853), Salmonella (NCTC 8385) and Shigella flexneri (ATCC 12022) (S. flexneri), while 3% defatted flour was suitable for Staphylococcus aureus (ATCC 25923) (S. aureus). E. coli (93±1) and S. flexneri (524±1) colony count were significantly (P?0.05) greater in defatted flour without supplement than in supplemented medium. E. coli [(3.72×109±2) CFU/mL], S. aureus [(7.4×109±2) CFU/mL], S. flexneri [(4.03×109±2) CFU/mL] and Salmonella [(2.37×109±1) CFU/mL] in non-hydrolyzed sample were statistically (P?0.05) greater than hydrolyzed one and commercial peptone agar. Colony count of Salmonella [(4.55×109±3) CFU/mL], S. flexneri [(5.40×109±3) CFU/mL] and Lyesria moncytogenes (ATCC 19116) [(5.4×109±3) CFU/mL] on raw defatted flour agar was significantly (P?0.05) greater than cooked defatted flour and commercial peptone agar. Biomass of E. coli, S. aureus, Salmonella and Enterococcus faecalis in non-hydrolyzed defatted flour is highly increased over hydrolyzed defatted flour and commercial peptone broth. Conclusions The defatted flour agar was found to be better microbial media or comparable with peptone agar. The substances in it can serve as sources of carbon, nitrogen, vitamins and minerals that are essential to support the growth of microorganisms without any supplements. Currently, all supplements of peptone agar are very expensive in the market. PMID:24075344
Effect of Storage of Mueller-Hinton Agar Plates on Zone Sizes for Antimicrobial Testing
Dewees, Linda B.; Poupard, James A.; Morton, Harry E.
1970-01-01
The length of time Mueller-Hinton agar plates can be stored at 4 C without affecting the size of zones of inhibition in susceptibility testing by the Bauer-Kirby method was studied. It was found that these plates can be stored for 3 weeks at 4 C without an appreciable affect on zone sizes. Storage of plates in sealed plastic bags did not alter the results significantly. The findings indicate that commercially prepared Mueller-Hinton agar plates, which may be several days old when received at the laboratory, are suitable for use in routine susceptibility tests by the Bauer-Kirby method. PMID:4991956
Tsuboyama-Tanaka, Shoko; Kodama, Yutaka
2015-03-01
The dioecious liverwort, Marchantia polymorpha L., is an emerging model plant. Various molecular biological techniques have been optimized for M. polymorpha for the past several years, and recently we reported a simplified Agrobacterium-mediated transformation method using sporelings (immature thalli from spores) of M. polymorpha. This method, termed AgarTrap (Agar-utilized Transformation with Pouring Solutions), completed by exchanging appropriate solutions on a single Petri dish to produce a sufficient number of independent transgenic sporelings. However, because spores are produced by crosses between males and females, the genetic backgrounds of resulting transgenic sporelings are not uniform. To easily produce transgenic liverworts with a uniform genetic background using AgarTrap, we developed an AgarTrap-mediated transformation method using intact gemmae/gemmalings produced by asexual reproduction. Using AgarTrap with male and female gemmae/gemmalings produced a sufficient number of independent transgenic gemmalings with uniform genetic backgrounds. The optimized transformation efficiencies were approximately 30 and 50 % in males and females, respectively. As with AgarTrap using sporelings, AgarTrap using intact gemmae/gemmalings will be useful in promoting studies of the molecular biology of M. polymorpha. PMID:25663453
Evaluation of the Chromogenic Agar chromID C. difficile
Burghoffer, Béatrice; Lalande, Valérie; Barbut, Frederic
2013-01-01
Three selective media (chromID C. difficile agar, taurocholate cycloserine cefoxitin agar [TCCA; homemade], and CLO medium) were compared from 406 stool samples of patients suspected of having Clostridium difficile infection. The sensitivities of chromID C. difficile agar at 24 h and 48 h, CLO medium, and TCCA were 74.1%, 87%, 85.2%, and 70.4%, respectively. PMID:23269743
Evaluation of the chromogenic agar chromID C. difficile.
Eckert, Catherine; Burghoffer, Béatrice; Lalande, Valérie; Barbut, Frederic
2013-03-01
Three selective media (chromID C. difficile agar, taurocholate cycloserine cefoxitin agar [TCCA; homemade], and CLO medium) were compared from 406 stool samples of patients suspected of having Clostridium difficile infection. The sensitivities of chromID C. difficile agar at 24 h and 48 h, CLO medium, and TCCA were 74.1%, 87%, 85.2%, and 70.4%, respectively. PMID:23269743
A Multiresolution Method for Parameter Estimation of Diffusion Processes.
Kou, S C; Olding, Benjamin P; Lysy, Martin; Liu, Jun S
2012-12-01
Diffusion process models are widely used in science, engineering and finance. Most diffusion processes are described by stochastic differential equations in continuous time. In practice, however, data is typically only observed at discrete time points. Except for a few very special cases, no analytic form exists for the likelihood of such discretely observed data. For this reason, parametric inference is often achieved by using discrete-time approximations, with accuracy controlled through the introduction of missing data. We present a new multiresolution Bayesian framework to address the inference difficulty. The methodology relies on the use of multiple approximations and extrapolation, and is significantly faster and more accurate than known strategies based on Gibbs sampling. We apply the multiresolution approach to three data-driven inference problems - one in biophysics and two in finance - one of which features a multivariate diffusion model with an entirely unobserved component. PMID:25328259
A Multiresolution Method for Parameter Estimation of Diffusion Processes
Kou, S. C.; Olding, Benjamin P.; Lysy, Martin; Liu, Jun S.
2014-01-01
Diffusion process models are widely used in science, engineering and finance. Most diffusion processes are described by stochastic differential equations in continuous time. In practice, however, data is typically only observed at discrete time points. Except for a few very special cases, no analytic form exists for the likelihood of such discretely observed data. For this reason, parametric inference is often achieved by using discrete-time approximations, with accuracy controlled through the introduction of missing data. We present a new multiresolution Bayesian framework to address the inference difficulty. The methodology relies on the use of multiple approximations and extrapolation, and is significantly faster and more accurate than known strategies based on Gibbs sampling. We apply the multiresolution approach to three data-driven inference problems – one in biophysics and two in finance – one of which features a multivariate diffusion model with an entirely unobserved component. PMID:25328259
Kanmani, Paulraj; Rhim, Jong-Whan
2014-02-15
The use of synthetic petroleum based packaging films caused serious environmental problems due to their difficulty in recycling and poor biodegradability. Therefore, present study was aimed to develop natural biopolymer-based antimicrobial packaging films as an alternative for the synthetic packaging films. As a natural antimicrobial agent, grapefruit seed extract (GSE) has been incorporated into agar to prepare antimicrobial packaging film. The films with different concentrations of GSE were prepared by a solvent casting method and the resulting composite films were examined physically and mechanically. In addition, the films were characterized by FE-SEM, XRD, FT-IR and TGA. The incorporation of GSE caused increase in color, UV barrier, moisture content, water solubility and water vapor permeability, while decrease in surface hydrophobicity, tensile strength and elastic modulus of the films. As the concentration of GSE increased from 0.6 to 13.3 ?g/mL, the physical and mechanical properties of the films were affected significantly. The addition of GSE changed film microstructure of the film, but did not influence the crystallinity of agar and thermal stability of the agar-based films. The agar/GSE films exhibited distinctive antimicrobial activity against three test food pathogens, such as Listeria monocytogenes, Bacillus cereus and Escherichia coli. These results suggest that agar/GSE films have potential to be used in an active food packaging systems for maintaining food safety and extending the shelf-life of the packaged food. PMID:24507339
Ge, Beilei; Bodeis, Sonya; Walker, Robert D; White, David G; Zhao, Shaohua; McDermott, Patrick F; Meng, Jianghong
2002-10-01
The performance of the Etest and agar dilution for in vitro antimicrobial susceptibility of Campylobacter spp. was evaluated using a quality control strain Campylobactor jejuni ATCC 33560, and 81 C. jejuni and 54 Campylobacter coli isolates recovered from retail raw meats. Seven antimicrobial agents: chloramphenicol, ciprofloxacin, doxycycline, erythromycin, gentamicin, nalidixic acid and tetracycline, were tested using the two methods, whereas azithromycin was tested using the Etest only. The correlation between the Etest and agar dilution MICs varied greatly depending on the antimicrobial agents tested. The overall agreement of MICs (+/-1 log(2) dilution) between the two methods was 61.9%, ranging from 21.4% for nalidixic acid to 92.6% for gentamicin. MICs obtained using the Etest were generally lower than those by agar dilution regardless of the species of organism tested. MIC(50) and/or MIC(90) values were at least one dilution lower for the Etest than for agar dilution when testing chloramphenicol, ciprofloxacin, doxycycline, erythromycin and nalidixic acid. Based on the agar dilution MICs, the resistant rate of the 135 Campylobacter isolates was highest for tetracycline (82.2%), followed by doxycycline (78.5%), nalidixic acid (21.5%), ciprofloxacin (20.7%) and erythromycin (17.0%). None of the isolates demonstrated resistance to chloramphenicol or gentamicin. The study indicated that the Etest results were not in complete agreement with the agar dilution test. Although the Etest has been proven to be a satisfactory testing method, its use for Campylobacter susceptibility testing requires further standardization. The study also showed that C. jejuni and C. coli isolates resistant to antimicrobials used for treating campylobacteriosis were common in retail raw meats. PMID:12356792
Atomic diffusion theory challenging the Cahn-Hilliard method
NASA Astrophysics Data System (ADS)
Nastar, M.
2014-10-01
Our development of the self-consistent mean-field (SCMF) kinetic theory for nonuniform alloys leads to the statement that kinetic correlations induced by the vacancy diffusion mechanism have a dramatic effect on nanoscale diffusion phenomena, leading to nonlinear features of the interdiffusion coefficients. Lattice rate equations of alloys including nonuniform gradients of chemical potential are derived within the Bragg-Williams statistical approximation and the third shell kinetic approximation of the SCMF theory. General driving forces including deviations of the free energy from a local equilibrium thermodynamic formulation are introduced. These deviations are related to the variation of vacancy motion due to the spatial variation of the alloy composition. During the characteristic time of atomic diffusion, multiple exchanges of the vacancy with the same atoms may happen, inducing atomic kinetic correlations that depend as well on the spatial variation of the alloy composition. As long as the diffusion driving forces are uniform, the rate equations are shown to obey in this form the Onsager formalism of thermodynamics of irreversible processes (TIP) and the TIP-based Cahn-Hilliard diffusion equation. If now the chemical potential gradients are not uniform, the continuous limit of the present SCMF kinetic equations does not coincide with the Cahn-Hilliard (CH) equation. In particular, the composition gradient and higher derivative terms depending on kinetic parameters add to the CH thermodynamic-based composition gradient term. Indeed, a diffusion equation written as a mobility multiplied by a thermodynamic formulation of the driving forces is shown to be inadequate. In the reciprocal space, the thermodynamic driving force has to be multiplied by a nonlinear function of the wave vector accounting for the variation of kinetic correlations with composition inhomogeneities. Analytical expressions of the effective interdiffusion coefficient are given for two limit behaviors of the vacancy, the latter treated as either a conservative species (fixed concentration) or a nonconservative species (time-dependent equilibrium concentration). Relying on the same vacancy diffusion model, we perform kinetic Monte Carlo simulations starting from a sinusoidal composition modulation in binary model alloys, with no interaction or nearest-neighbor interactions leading to clustering or ordering tendencies, along the [100] crystallographic direction of a body centered cubic (bcc) lattice. The resulting temporal variation of the modulation amplitude is compared to the corresponding SCMF equations. Qualitative and satisfying quantitative agreements systematically strengthen our theoretical conclusions. The model alloys are shown to be representative enough of some real alloys, so that one may expect these new heterogeneous correlation effects to be non-negligible in these alloys.
An adaptive meshfree diffusion wavelet method for partial differential equations on the sphere
NASA Astrophysics Data System (ADS)
Goyal, Kavita; Mehra, Mani
2014-09-01
An adaptive meshfree diffusion wavelet method for solving partial differential equations (PDEs) on the sphere is developed. Approximation formulae for Laplacian-Beltrami (?2) and gradient (??) operators are derived using radial basis functions (RBFs), and the convergence of these approximations to ?2 and ?? is verified for two test functions. The matrix approximating the Laplace-Beltrami operator is used for the construction of the diffusion wavelet. The diffusion wavelet is used for the adaptation of node arrangement as well as for the fast computation of dyadic powers of the matrices involved in the numerical solution of the PDE. The efficiency of the method is that the same operator is used for the construction of the diffusion wavelet and for the approximation of the differential operators. As a part of the wavelet method the behaviour of the compression error with respect to different parameters involved in the construction of the diffusion wavelet is tested. The CPU time taken by the proposed method is compared with the CPU time taken by the RBF based collocation method and it is observed that the proposed method performs better. The method is tested on three test problems namely spherical diffusion equation (linear), problem of computing a moving steep front (nonlinear) and problem of Turing patterns (system of nonlinear reaction-diffusion equations).
NASA Astrophysics Data System (ADS)
Hoffmann, Thomas; Dorrestein, Pieter C.
2015-08-01
Matrix deposition on agar-based microbial colonies for MALDI imaging mass spectrometry is often complicated by the complex media on which microbes are grown. This Application Note demonstrates how consecutive short spray pulses of a matrix solution can form an evenly closed matrix layer on dried agar. Compared with sieving dry matrix onto wet agar, this method supports analyte cocrystallization, which results in significantly more signals, higher signal-to-noise ratios, and improved ionization efficiency. The even matrix layer improves spot-to-spot precision of measured m/z values when using TOF mass spectrometers. With this technique, we established reproducible imaging mass spectrometry of myxobacterial cultures on nutrient-rich cultivation media, which was not possible with the sieving technique.
A fully implicit method for 3D quasi-steady state magnetic advection-diffusion.
Siefert, Christopher; Robinson, Allen Conrad
2009-09-01
We describe the implementation of a prototype fully implicit method for solving three-dimensional quasi-steady state magnetic advection-diffusion problems. This method allows us to solve the magnetic advection diffusion equations in an Eulerian frame with a fixed, user-prescribed velocity field. We have verified the correctness of method and implementation on two standard verification problems, the Solberg-White magnetic shear problem and the Perry-Jones-White rotating cylinder problem.
Sevtap Arikan; Victor Paetznick; John H. Rex
2002-01-01
We compared the disk diffusion and broth microdilution methods for susceptibility testing of caspofungin against Aspergillus (n 78) and Fusarium (n 22) isolates. Microdilution testing followed the NCCLS M-38P guidelines but was performed in antibiotic medium 3 supplemented to 2% glucose (AM3). Disk diffusion assays were performed on AM3 agar plates with a 2-g caspofungin disk. By both methods, caspofungin
Nehorai, Arye
obtained using the finite element method and find good consistency. We solve the inverse problem using correctly. Keywords: Diffuse optical tomography, diffusion approximation, Feynman-Kac formula, interacting and tissue's optical properties (e.g., the absorption coefficient µa and the scattering coefficient µs
Ji-Ming Hu; Jin-Tao Zhang; Jian-Qing Zhang; Chu-Nan Cao
2004-01-01
The diffusion coefficients of water and Cl- ion in epoxy coatings on aluminum alloys LY12 were investigated by electrochemical impedance spectroscopy (EIS). The key task in the present work remained in the model fitting of EIS data, from which coating capacitance was derived and was used to calculate water diffusion coefficient by the commonly used “capacitance method”. Moreover, by the
A multigrid Newton-Krylov method for flux-limited radiation diffusion
Rider, W.J.; Knoll, D.A.; Olson, G.L.
1998-09-01
The authors focus on the integration of radiation diffusion including flux-limited diffusion coefficients. The nonlinear integration is accomplished with a Newton-Krylov method preconditioned with a multigrid Picard linearization of the governing equations. They investigate the efficiency of the linear and nonlinear iterative techniques.
Evaluation of Methods to Correct for IR Loss in Eppley PSP Diffuse Measurements
Oregon, University of
Evaluation of Methods to Correct for IR Loss in Eppley PSP Diffuse Measurements Frank Vignola. Specifically, diffuse measurements of an Eppley PSP pyranometer are compared to those made with a Schenk Star data to estimate IR loss for Eppley PSP pyranometers. KEYWORDS: Pyranometer, pyrgeometer, irradiance
Determination of diffusion lengths in silicon by an X-ray method
NASA Technical Reports Server (NTRS)
Lamneck, J. H., Jr.
1970-01-01
By calibrating X-ray machine with cells of known diffusion lengths, measurements on test cells can be madeate rate of one every two minutes with standard deviation of less than two percent. test cells are compared with calibration cells whose diffusion lengths have been measured by an electron beam method.
A Review of Diffusion Tensor Magnetic Resonance Imaging Computational Methods and Software Tools
Hasan, Khader M.; Walimuni, Indika S.; Abid, Humaira; Hahn, Klaus R.
2010-01-01
In this work we provide an up-to-date short review of computational magnetic resonance imaging (MRI) and software tools that are widely used to process and analyze diffusion-weighted MRI data. A review of different methods used to acquire, model and analyze diffusion-weighted imaging data (DWI) is first provided with focus on diffusion tensor imaging (DTI). The major preprocessing, processing and post-processing procedures applied to DTI data are discussed. A list of freely available software packages to analyze diffusion MRI data is also provided. PMID:21087766
Multistage Classification for Bacterial Colonies Recognition on Solid Agar Images
Signoroni, Alberto
, bacterial cultures are incubated for reproducing optimum conditions for human pathogens bacteria growth. Vi the growth of certain bacterial species. Solid agar choice is taken according to diagnostic needs. By lookingMultistage Classification for Bacterial Colonies Recognition on Solid Agar Images Alessandro
Diffusion NMR methods applied to xenon gas for materials study.
Mair, R W; Rosen, M S; Wang, R; Cory, D G; Walsworth, R L
2002-12-01
We report initial NMR studies of (i) xenon gas diffusion in model heterogeneous porous media and (ii) continuous flow laser-polarized xenon gas. Both areas utilize the pulsed gradient spin-echo (PGSE) techniques in the gas phase, with the aim of obtaining more sophisticated information than just translational self-diffusion coefficients--a brief overview of this area is provided in the Introduction. The heterogeneous or multiple-length scale model porous media consisted of random packs of mixed glass beads of two different sizes. We focus on observing the approach of the time-dependent gas diffusion coefficient, D(t) (an indicator of mean squared displacement), to the long-time asymptote, with the aim of understanding the long-length scale structural information that may be derived from a heterogeneous porous system. We find that D(t) of imbibed xenon gas at short diffusion times is similar for the mixed bead pack and a pack of the smaller sized beads alone, hence reflecting the pore surface area to volume ratio of the smaller bead sample. The approach of D(t) to the long-time limit follows that of a pack of the larger sized beads alone, although the limiting D(t) for the mixed bead pack is lower, reflecting the lower porosity of the sample compared to that of a pack of mono-sized glass beads. The Pade approximation is used to interpolate D(t) data between the short- and long-time limits. Initial studies of continuous flow laser-polarized xenon gas demonstrate velocity-sensitive imaging of much higher flows than can generally be obtained with liquids (20-200 mm s-1). Gas velocity imaging is, however, found to be limited to a resolution of about 1 mm s-1 owing to the high diffusivity of gases compared with liquids. We also present the first gas-phase NMR scattering, or diffusive-diffraction, data, namely flow-enhanced structural features in the echo attenuation data from laser-polarized xenon flowing through a 2 mm glass bead pack. PMID:12807139
Experimental Verification to Obtain Intrinsic Thermal Diffusivity by Laser-Flash Method
NASA Astrophysics Data System (ADS)
Akoshima, M.; Hay, B.; Neda, M.; Grelard, M.
2013-05-01
There is a need to obtain highly reliable values of thermophysical properties. The thermal conductivity of solids is often calculated from the thermal diffusivity, specific heat, and density, respectively, measured by the laser-flash method, differential scanning calorimetry, and Archimedes' method. The laser-flash method is one of the most well-known methods for measuring the thermal diffusivity of solids above room temperature. This method is very convenient to measure the thermal diffusivity without contact in a short time. On the other hand, it is considered as an absolute reference measurement method, in particular, because only measurements of basic quantities such as time, temperature, length, and electrical quantities are required, and because the uncertainty of measurement can be analytically evaluated. However, it could be difficult in some cases to obtain reliable thermal-diffusivity values. The measurement results can indeed depend on experimental conditions; in particular, the pulse heating energy. A procedure to obtain the intrinsic thermal-diffusivity value was proposed by National Metrology Institute of Japan (NMIJ). Here, "intrinsic" means unique for the material, independent of measurement conditions. In this method, apparent thermal-diffusivity values are first measured by changing the pulse heating energy at the same test temperature. Then, the intrinsic thermal diffusivity is determined by extrapolating these apparent thermal diffusivities to a zero energy pulse. In order to verify and examine the applicability of the procedure for intrinsic thermal-diffusivity measurements, we have measured the thermal diffusivity of some materials (metals, ceramics) using the laser-flash method with this extrapolation procedure. NMIJ and Laboratoire National de Metrologie et d'essais (LNE) have laser-flash thermal-diffusivity measurement systems that are traceable to SI units. The thermal diffusivity measured by NMIJ and LNE on four materials shows good agreement, although they used different measurement systems and different analysis methods of the temperature-rise curve. Experimental verification on the procedure was carried out using the measured results. Some problems and considered solutions for laser-flash thermal-diffusivity measurements are discussed.
Liu, Hsi; Taylor, Thomas H; Pettus, Kevin; Trees, David
2014-05-01
We studied whether the Etest can be used as an alternative to agar dilution to determine antimicrobial susceptibilities of ceftriaxone, cefixime, and cefpodoxime in Neisseria gonorrhoeae surveillance. One hundred fifteen clinical and laboratory isolates of N. gonorrhoeae were tested following the Clinical Laboratory Improvement Amendments (CLIA)-approved CLSI standard agar dilution method and, separately, by the Etest according to the manufacturer's recommendations. The MICs were determined and compared. Ten laboratory-generated mutants were used to simulate substantially nonsusceptible specimens. The Etest and agar dilution methods were well correlated. Statistical tests produced regression R2 values of 88%, 82%, and 85% and Pearson correlation coefficients of 92%, 91%, and 92% for ceftriaxone, cefixime, and cefpodoxime, respectively. When paired comparisons were made, the two tests were 88.7%, 80%, and 87% within 1 log2 dilution from each other for ceftriaxone, cefixime, and cefpodoxime, respectively. The within-2-log2 agreements were 99.1%, 98.3%, and 94.8% for ceftriaxone, cefixime, and cefpodoxime, respectively. Notwithstanding the good correlations and the within-2-log2 general agreement, the Etest results produced slightly lower MICs than the agar dilution results. In conclusion, we found that the Etest can be effectively used as an alternative to agar dilution testing to determine the susceptibility of N. gonorrhoeae to ceftriaxone, cefixime, and cefpodoxime, although we recommend further research into extremely resistant isolates. For isolates within the typical range of clinical MICs, reexamination of the Etest interpretation of susceptible and nonsusceptible categories would likely allow for successful transition from agar dilution to the Etest. PMID:24554750
Lou, Shishu; Zhu, Huishi; Hu, Shaoxu; Zhao, Chunhua; Han, Peide
2015-01-01
Characterization of the diffusion length of solar cells in space has been widely studied using various methods, but few studies have focused on a fast, simple way to obtain the quantified diffusion length distribution on a silicon wafer. In this work, we present two different facile methods of doing this by fitting photoluminescence images taken in two different wavelength ranges or from different sides. These methods, which are based on measuring the ratio of two photoluminescence images, yield absolute values of the diffusion length and are less sensitive to the inhomogeneity of the incident laser beam. A theoretical simulation and experimental demonstration of this method are presented. The diffusion length distributions on a polycrystalline silicon wafer obtained by the two methods show good agreement. PMID:26364565
Lou, Shishu; Zhu, Huishi; Hu, Shaoxu; Zhao, Chunhua; Han, Peide
2015-01-01
Characterization of the diffusion length of solar cells in space has been widely studied using various methods, but few studies have focused on a fast, simple way to obtain the quantified diffusion length distribution on a silicon wafer. In this work, we present two different facile methods of doing this by fitting photoluminescence images taken in two different wavelength ranges or from different sides. These methods, which are based on measuring the ratio of two photoluminescence images, yield absolute values of the diffusion length and are less sensitive to the inhomogeneity of the incident laser beam. A theoretical simulation and experimental demonstration of this method are presented. The diffusion length distributions on a polycrystalline silicon wafer obtained by the two methods show good agreement. PMID:26364565
A Novel Chromogenic Ester Agar Medium for Detection of Salmonellae
Cooke, Venitia M.; Miles, R. J.; Price, R. G.; Richardson, A. C.
1999-01-01
A novel agar medium, chromogenic Salmonella esterase (CSE) agar, for the differentiation of salmonellae is described. The agar contains peptones and nutrient extracts together with the following (grams per liter unless otherwise specified): 4-[2-(4-octanoyloxy-3,5-dimethoxyphenyl)-vinyl]-quinolinium-1-(propan-3-yl carboxylic acid) bromide (SLPA-octanoate; bromide form), 0.3223; lactose, 14.65; trisodium citrate dihydrate, 0.5; Tween 20, 3.0; ethyl 4-dimethylaminobenzoate, 0.035% (wt/vol), novobiocin, 70 mg liter?1. The key component of the medium is SLPA-octanoate, a newly synthesized ester formed from a C8 fatty acid and a phenolic chromophore. In CSE agar, the ester is hydrolyzed by Salmonella spp. to yield a brightly colored phenol which remains tightly bound within colonies. After 24 h of incubation at 37 or 42°C, colonies of typical Salmonella spp. were burgundy colored on a transparent yellow background, whereas non-Salmonella spp. were white, cream, yellow or transparent. CSE agar was evaluated by using a panel of strains including a high proportion of Salmonella and non-Salmonella strains giving atypical reactions on other differential agars. The sensitivity (93.1%) of CSE agar for non-typhi salmonellae compared favorably with those of Rambach (82.8%), xylose-lysine-deoxycholate (XLD; 91.4%), Hektoen-enteric (89.7%), and SM ID (91.4%) agars. The specificity (93.9%) was also comparable to those of other Salmonella media (SM ID agar, 95.9%; Rambach agar, 91.8%; XLD agar, 91.8%; Hektoen-enteric agar, 87.8%). Strains of Citrobacter freundii and Proteus spp. giving false-positive reactions with other media gave a negative color reaction on CSE agar. CSE agar enabled the detection of >30 Salmonella serotypes, including agona, anatum, enteritidis, hadar, heidelberg, infantis, montevideo, thompson, typhimurium, and virchow, which accounted for 91.8% of the salmonella isolates recorded by the Public Health Laboratory Service (Colindale, London, England) for 1997. PMID:9925620
Dingkang Zhang; Farzad Rahnema; Abderrafi M. Ougouag
2013-09-01
A local incident flux response expansion transport method is developed to generate transport solutions for coupling to diffusion theory codes regardless of their solution method (e.g., fine mesh, nodal, response based, finite element, etc.) for reactor core calculations in both two-dimensional (2-D) and three-dimensional (3-D) cylindrical geometries. In this approach, a Monte Carlo method is first used to precompute the local transport solution (i.e., response function library) for each unique transport coarse node, in which diffusion theory is not valid due to strong transport effects. The response function library is then used to iteratively determine the albedo coefficients on the diffusion-transport interfaces, which are then used as the coupling parameters within the diffusion code. This interface coupling technique allows a seamless integration of the transport and diffusion methods. The new method retains the detailed heterogeneity of the transport nodes and naturally constructs any local solution within them by a simple superposition of local responses to all incoming fluxes from the contiguous coarse nodes. A new technique is also developed for coupling to fine-mesh diffusion methods/codes. The local transport method/module is tested in 2-D and 3-D pebble-bed reactor benchmark problems consisting of an inner reflector, an annular fuel region, and a controlled outer reflector. It is found that the results predicted by the transport module agree very well with the reference fluxes calculated directly by MCNP in both benchmark problems.
NASA Technical Reports Server (NTRS)
Miller, Teresa Y.; He, Xiao-Min; Carter, Daniel C.
1992-01-01
Crystals of human serum albumin have been successfully grown in a variety of gels using crystallization conditions otherwise equivalent to those utilized in the popular hanging-drop vapor-equilibrium method. Preliminary comparisons of gel grown crystals with crystals grown by the vapor diffusion method via both ground-based and microgravity methods indicate that crystals superior in size and quality may be grown by limiting solutal convection. Preliminary X-ray diffraction statistics are presented.
M. Niewerth; V. Splanemann; H. C. Korting; J. Ring; D. Abeck
1998-01-01
Fifty dermatophyte strains, recently obtained from clinical material, belonging to 4 different species were examined for their susceptibility to 5 systemic or topical antimycotic agents using both an agar macrodilution and a broth microdilution test. Antimycotics compared were griseofulvin, itraconazole, sertaconazole, terbinafine and ciclopiroxolamine. A comparison of the minimum inhibitory concentrations (MIC) clearly showed differences between the two test methods
An electrochemical approach to monitor pH change in agar media during plant tissue culture
Min Wang; Yang Ha
2007-01-01
In this work, metal oxide microelectrodes were developed to monitor pH change in agar media during plant tissue culture. An antimony wire was produced by a new approach “capillary melt method”. The surface of the obtained antimony wire was oxidized in a potassium nitrate melt to fabricate an antimony oxide film for pH sensing. Characterization results show that the oxide
Hamilton, Richard P; Heal, Mathew R
2004-01-01
This study was carried out in response to suggestions that the measurement of NO2 by Palmes-type passive diffusion tubes (PDT) is affected by the method of preparation of the triethanolamine (TEA) absorbent coating on the ...
A Robust and Efficient Method for Steady State Patterns in Reaction-Diffusion Systems
Chen, Long
from cell polarization [9, 16] to animal coats [19, 21]. To study the reaction-diffusion equations and more robust in convergence than typical nonlinear solvers (e.g., Newton's method) in finding the inhomo
A method for optimizing the cosine response of solar UV diffusers
NASA Astrophysics Data System (ADS)
Pulli, Tomi; Kärhä, Petri; Ikonen, Erkki
2013-07-01
Instruments measuring global solar ultraviolet (UV) irradiance at the surface of the Earth need to collect radiation from the entire hemisphere. Entrance optics with angular response as close as possible to the ideal cosine response are necessary to perform these measurements accurately. Typically, the cosine response is obtained using a transmitting diffuser. We have developed an efficient method based on a Monte Carlo algorithm to simulate radiation transport in the solar UV diffuser assembly. The algorithm takes into account propagation, absorption, and scattering of the radiation inside the diffuser material. The effects of the inner sidewalls of the diffuser housing, the shadow ring, and the protective weather dome are also accounted for. The software implementation of the algorithm is highly optimized: a simulation of 109 photons takes approximately 10 to 15 min to complete on a typical high-end PC. The results of the simulations agree well with the measured angular responses, indicating that the algorithm can be used to guide the diffuser design process. Cost savings can be obtained when simulations are carried out before diffuser fabrication as compared to a purely trial-and-error-based diffuser optimization. The algorithm was used to optimize two types of detectors, one with a planar diffuser and the other with a spherically shaped diffuser. The integrated cosine errors—which indicate the relative measurement error caused by the nonideal angular response under isotropic sky radiance—of these two detectors were calculated to be f2=1.4% and 0.66%, respectively.
Rafal Augustyniak; Fabien Ferrage; Raphaël Paquin; Olivier Lequin; Geoffrey Bodenhausen
We present new NMR methods to measure slow translational diffusion coefficients of biomolecules. Like the heteronuclear stimulated\\u000a echo experiment (XSTE), these new methods rely on the storage of information about spatial localization during the diffusion\\u000a delay as longitudinal polarization of nuclei with long T1 such as nitrogen-15. The new BEST-XSTE sequence combines features of Band-selective Excitation Short-Transient (BEST) and\\u000a XSTE
Accurate determination of specific heat at high temperatures using the flash diffusivity method
NASA Technical Reports Server (NTRS)
Vandersande, J. W.; Zoltan, A.; Wood, C.
1989-01-01
The flash diffusivity method of Parker et al. (1961) was used to measure accurately the specific heat of test samples simultaneously with thermal diffusivity, thus obtaining the thermal conductivity of these materials directly. The accuracy of data obtained on two types of materials (n-type silicon-germanium alloys and niobium), was + or - 3 percent. It is shown that the method is applicable up to at least 1300 K.
Physics-Based Preconditioning and the Newton–Krylov Method for Non-equilibrium Radiation Diffusion
V. A. Mousseau; D. A. Knoll; W. J. Rider
2000-01-01
An algorithm is presented for the solution of the time dependent reaction-diffusion systems which arise in non-equilibrium radiation diffusion applications. This system of nonlinear equations is solved by coupling three numerical methods, Jacobian-free Newton–Krylov, operator splitting, and multigrid linear solvers. An inexact Newton's method is used to solve the system of nonlinear equations. Since building the Jacobian matrix for problems
Physics-Based Preconditioning and the Newton-Krylov Method for Non-equilibrium Radiation Diffusion
V. A. Mousseau; D. A. Knoll; W. J. Rider
2000-01-01
An algorithm is presented for the solution of the time dependent reaction-diffusion systems which arise in non-equilibrium radiation diffusion applications. This system of nonlinear equations is solved by coupling three numerical methods, Jacobian-free Newton-Krylov, operator splitting, and multigrid linear solvers. An inexact Newton's method is used to solve the system of nonlinear equations. Since building the Jacobian matrix for problems
A diffusion accelerated Sn transport method for radiation transport on a general quadrilateral mesh
Alcouffe, R.E.
1989-01-01
We present the development of a diffusion accelerated Sn transport method for the solution of temperature coupled radiation flow problems on a spatial mesh of arbitrary quadrilaterals in R-Z geometry. The diffusion acceleration equation is derived from the diamond-like transport spatial discretization. The effectiveness of the DSA method is shown on an example calculation and also computation times are indicated. 3 refs., 3 figs.
An efficient wavelet analysis method to film-pore diffusion model arising in mathematical chemistry.
Hariharan, G
2014-04-01
In this paper, we have established an efficient Legendre wavelet based approximation method to solve film-pore diffusion model arising in engineering. Film-pore diffusion model is widely used to determine study the kinetics of adsorption systems. The use of Legendre wavelet based approximation method is found to be accurate, simple, fast, flexible, convenient, and computationally attractive. It is shown that film-pore diffusion model satisfactorily describe kinetics of methylene blue adsorption onto the three low-cost adsorbents, Guava, teak and gulmohar plant leaf powders, used in this study. PMID:24562792
Cosmic-ray diffusion modeling: Solutions using variational methods
NASA Astrophysics Data System (ADS)
Tautz, R. C.; Lerche, I.
2013-05-01
The diffusion of energetic particles in turbulent magnetic fields is usually described via the two-point, two-time velocity correlation function. A variational principle is used to determine the characteristic function that results from the Fourier-transformed correlation function. Both for a linear approximation and for the wave vector set to zero, explicit solutions are derived that depend on the Fokker-Planck coefficient of pitch-angle scattering. It is shown that, for an isotropic form of the Fokker-Planck coefficient, the characteristic function is divergent, which can be remedied only by using a Fokker-Planck coefficient that is finite at all pitch angles.
Martínez-Mier, E. Angeles; Soto-Rojas, Armando E.; Buckley, Christine M.; Margineda, Jorge; Zero, Domenick T.
2010-01-01
Objective The aim of this study was to assess methods currently used for analyzing fluoridated salt in order to identify the most useful method for this type of analysis. Basic research design Seventy-five fluoridated salt samples were obtained. Samples were analyzed for fluoride content, with and without pretreatment, using direct and diffusion methods. Element analysis was also conducted in selected samples. Fluoride was added to ultra pure NaCl and non-fluoridated commercial salt samples and Ca and Mg were added to fluoride samples in order to assess fluoride recoveries using modifications to the methods. Results Larger amounts of fluoride were found and recovered using diffusion than direct methods (96%–100% for diffusion vs. 67%–90% for direct). Statistically significant differences were obtained between direct and diffusion methods using different ion strength adjusters. Pretreatment methods reduced the amount of recovered fluoride. Determination of fluoride content was influenced both by the presence of NaCl and other ions in the salt. Conclusion Direct and diffusion techniques for analysis of fluoridated salt are suitable methods for fluoride analysis. The choice of method should depend on the purpose of the analysis. PMID:20088217
The Study of Thermal Diffusivity Measurement of Composite Materials by Unsteady Probe Method
NASA Astrophysics Data System (ADS)
Saiki, Yukihiro; Yamada, Etsuro; Ikeda, Hiroshi
The object of this study is to research the possibility of in-line measurement of the thermal diffusivity on composite materials, such as suspension and emulsion, by previously developed apparatus for the dynamic viscosity. The calibration curve between the thermal diffusivity and any physical quantity that can be measured by this apparatus is proposed by the numerical analysis. The experimental results were obtained by using the dispersed materials composed agargel cooking oil (as matrix) and Ti02 particle. Nondimensional effective thermal diffusivity that is the ratio of the effective thermal diffusivity of dispersed materials to the one of the matrix are compared with previous results obtained by periodic heating method. These data of nondimensional values show good agreement with each other. From these results, this measurement apparatus may be applicable for the thermal diffusivity measurement of dispersed materals.
S. Karimi; K. B. Nakshatrala
2015-04-10
The lattice Boltzmann method (LBM) has established itself as a valid numerical method in computational fluid dynamics. Recently, multiple-relaxation-time LBM has been proposed to simulate anisotropic advection-diffusion processes. The governing differential equations of advective-diffusive systems are known to satisfy maximum principles, comparison principles, the non-negative constraint, and the decay property. In this paper, it will be shown that current single- and multiple-relaxation-time lattice Boltzmann methods fail to preserve these mathematical properties for transient diffusion-type equations. It will also be shown that the discretization of Dirichlet boundary conditions will affect the performance of lattice Boltzmann methods in meeting these mathematical principles. A new way of discretizing the Dirichlet boundary conditions is also proposed. Several benchmark problems have been solved to illustrate the performance of lattice Boltzmann methods and the effect of discretization of boundary conditions with respect to the aforementioned mathematical properties for transient diffusion and advection-diffusion equations.
A Multigrid Newton-Krylov Method for Multimaterial Equilibrium Radiation Diffusion1
William J. Rider; Dana A. Knoll; Gordon L. Olsony
1999-01-01
We focus on a fully implicit, nonlinearly converged, solution of multimaterial equilibrium radiation diffusion problems. The nonlinear method of solution is a Newton-Krylov (generalized minimum residual, GMRES) method preconditioned by a multigrid method. The multigrid iteration matrix results from a Picard-type linearization of the governing equations. The governing equation is highly nonlinear with the principal forms of nonlinearity found in
T. J. Moroney; I. W. Turner
2006-01-01
The finite volume method is the favoured numerical technique for solving (possibly coupled, nonlinear, anisotropic) diffusion equations. The method transforms the original problem into a system of nonlinear, algebraic equations through the process of discretisation. The accuracy of this discretisation determines to a large extent the accuracy of the final solution.A new method of discretisation is presented, designed to achieve
GALERKIN METHODS IN AGE AND SPACE FOR A POPULATION MODEL WITH NONLINEAR DIFFUSION
Ayati, Bruce P.
GALERKIN METHODS IN AGE AND SPACE FOR A POPULATION MODEL WITH NONLINEAR DIFFUSION BRUCE P. AYATI. 3, pp. 1064Â1076 Abstract. We present Galerkin methods in both the age and space variables of methods, where the approximation space in age is the space of piecewise constant functions. In this paper
Diffusion Rate Tomography for Time Domain Electromagnetic Induction Methods
NASA Astrophysics Data System (ADS)
Kazlauskas, E. M.; Weiss, C. J.
2010-12-01
Although it is now routine to invert near-surface electromagnetic induction data in terms of ground conductivity, geoelectromagnetic inversion remains an open research problem because of its intrinsic non-uniqueness and the need to balance computational efficiency with recovering models bearing some resemblance to real geologic structure. The most popular approach for fitting electromagnetic data is analogous to seismic full-waveform inversion. Whether the data are in the time- or frequency-domain, a model is sought which recovers either the amplitude and phase, or the transient response of some measured waveform. However, imperfect knowledge of the source waveform has the potential to erroneously introduce unwarranted geologic structure in the final recovered earth model. Hence, we explore here an alternative approach that mitigates these effects in highly attenuated electromagnetic data. Rather than inverting for the full waveform response, Diffusion Rate Tomography (DiRT) is based on inverting for the arrival time of some key, diagnostic feature in the measured data. This procedure eliminates any error introduced by incomplete knowledge of the source amplitude due to miscalibration, instrument drift, or battery drainage. Time-domain electromagnetic sounding experiments conducted with a horizontal loop transmitter and offset receiver coil provide a useful test of the concept. As induced eddy currents from the transmitter diffuse beneath the receiver, a polarity change occurs in the vertical component of the observed magnetic field. This polarity change (or zero crossing) is our invertible diagnostic, and given a range of offsets between the transmitter and receiver antennae, the zero-crossing moveout curve constitutes the data we invert. Examples of DiRT for a range of geologic settings will be presented and compared against results from smooth, full-waveform inversion. Interestingly, although DiRT works on fewer data than the full-waveform inversion, there is strong similarity in the recovered models, suggesting future work in examining redundancy in electromagnetic data or optimal regularization schemes.
RAFFAELE PICCOLOMINI; GIOVANNI DI BONAVENTURA; GIOVANNI CATAMO; FLAVIA CARBONE; MATTEO NERI
1997-01-01
The Epsilometer test (E test; AB Biodisk, Solna, Sweden), a new quantitative technique for the determination of antimicrobial susceptibility, was compared to reference methods (agar dilution and broth microdilution) for the antimicrobial susceptibility testing of Helicobacter pylori. Seventy-one H. pylori strains isolated from patients with duodenal ulcers were tested against 20 antimicrobial agents. The E test and the agar dilution
Diffusion-synthetic acceleration methods for the discrete-ordinates equations
Larsen, E.W.
1983-01-01
The diffusion-synthetic acceleration (DSA) method is an iterative procedure for obtaining numerical solutions of discrete-ordinates problems. The DSA method is operationally more complicated than the standard source-iteration (SI) method, but if encoded properly it converges much more rapidly, especially for problems with diffusion-like regions. In this article we describe the basic ideas beind the DSA method and give a (roughly chronological) review of its long development. We conclude with a discussion which covers additional topics, including some remaining open problems and the status of current efforts aimed at solving these problems.
V. M. M. Lobo; D. B. Murtinho; M. H. Gil; F. P. Garcia; A. J. M. Valente
1996-01-01
An open-ended capillary cell has been developed to measure thermodynamic diffusion coefficients of electrolytes, in aqueous solution, in swelled polymeric membranes. Also a new method to determine the integral diffusion coefficient of water in membranes is presented. In this work we present a description of the methods as well as the experimental results of the diffusion coefficients of potassium chloride
Henderson, Thomas C.
Multisensor Methods to Estimate Thermal Diffusivity Thomas C. Henderson1, Gwen Knight1 and Edward. In many application scenarios, the thermal diffusivity is unknown and must be estimated in order of minimization methods (the Golden Mean and Lagarias' simplex) to determine the thermal diffusivity coefficient
21 CFR 866.4600 - Ouchterlony agar plate.
Code of Federal Regulations, 2010 CFR
2010-04-01
...MICROBIOLOGY DEVICES Immunology Laboratory Equipment and Reagents § 866.4600 Ouchterlony agar plate. (a...through gel which originally contained neither of these reagents. As the reagents come in contact with each other, they...
21 CFR 866.4600 - Ouchterlony agar plate.
Code of Federal Regulations, 2012 CFR
2012-04-01
...and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Immunology Laboratory Equipment and Reagents § 866.4600 Ouchterlony agar...
21 CFR 866.4600 - Ouchterlony agar plate.
Code of Federal Regulations, 2014 CFR
2014-04-01
...and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Immunology Laboratory Equipment and Reagents § 866.4600 Ouchterlony agar...
21 CFR 866.4600 - Ouchterlony agar plate.
Code of Federal Regulations, 2011 CFR
2011-04-01
...and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Immunology Laboratory Equipment and Reagents § 866.4600 Ouchterlony agar...
Method of applying a cerium diffusion coating to a metallic alloy
Jablonski, Paul D. (Salem, OR); Alman, David E. (Benton, OR)
2009-06-30
A method of applying a cerium diffusion coating to a preferred nickel base alloy substrate has been discovered. A cerium oxide paste containing a halide activator is applied to the polished substrate and then dried. The workpiece is heated in a non-oxidizing atmosphere to diffuse cerium into the substrate. After cooling, any remaining cerium oxide is removed. The resulting cerium diffusion coating on the nickel base substrate demonstrates improved resistance to oxidation. Cerium coated alloys are particularly useful as components in a solid oxide fuel cell (SOFC).
Densmore, Jeffery D., E-mail: jdd@lanl.gov [Computational Physics and Methods Group, Los Alamos National Laboratory, P.O. Box 1663, MS D409, Los Alamos, NM 87545 (United States); Thompson, Kelly G., E-mail: kgt@lanl.gov [Computational Physics and Methods Group, Los Alamos National Laboratory, P.O. Box 1663, MS D409, Los Alamos, NM 87545 (United States); Urbatsch, Todd J., E-mail: tmonster@lanl.gov [Computational Physics and Methods Group, Los Alamos National Laboratory, P.O. Box 1663, MS D409, Los Alamos, NM 87545 (United States)
2012-08-15
Discrete Diffusion Monte Carlo (DDMC) is a technique for increasing the efficiency of Implicit Monte Carlo radiative-transfer simulations in optically thick media. In DDMC, particles take discrete steps between spatial cells according to a discretized diffusion equation. Each discrete step replaces many smaller Monte Carlo steps, thus improving the efficiency of the simulation. In this paper, we present an extension of DDMC for frequency-dependent radiative transfer. We base our new DDMC method on a frequency-integrated diffusion equation for frequencies below a specified threshold, as optical thickness is typically a decreasing function of frequency. Above this threshold we employ standard Monte Carlo, which results in a hybrid transport-diffusion scheme. With a set of frequency-dependent test problems, we confirm the accuracy and increased efficiency of our new DDMC method.
First-Order Hyperbolic System Method for Time-Dependent Advection-Diffusion Problems
NASA Technical Reports Server (NTRS)
Mazaheri, Alireza; Nishikawa, Hiroaki
2014-01-01
A time-dependent extension of the first-order hyperbolic system method for advection-diffusion problems is introduced. Diffusive/viscous terms are written and discretized as a hyperbolic system, which recovers the original equation in the steady state. The resulting scheme offers advantages over traditional schemes: a dramatic simplification in the discretization, high-order accuracy in the solution gradients, and orders-of-magnitude convergence acceleration. The hyperbolic advection-diffusion system is discretized by the second-order upwind residual-distribution scheme in a unified manner, and the system of implicit-residual-equations is solved by Newton's method over every physical time step. The numerical results are presented for linear and nonlinear advection-diffusion problems, demonstrating solutions and gradients produced to the same order of accuracy, with rapid convergence over each physical time step, typically less than five Newton iterations.
A new method of optimal design for a two-dimensional diffuser by using dynamic programming
NASA Technical Reports Server (NTRS)
Gu, Chuangang; Zhang, Moujin; Chen, XI; Miao, Yongmiao
1991-01-01
A new method for predicting the optimal velocity distribution on the wall of a two dimensional diffuser is presented. The method uses dynamic programming to solve the optimal control problem with inequality constraints of state variables. The physical model of optimization is designed to prevent the separation of the boundary layer while approaching the maximum pressure ratio in a diffuser of a specified length. The computational results are in fair agreement with the experimental ones. Optimal velocity distribution on a diffuser wall is said to occur when the flow decelerates quickly at first and then smoothly, while the flow is near separation, but always protected from it. The optimal velocity distribution can be used to design the contour of the diffuser.
Thermal Diffusivity Measurements of CMSX-4 Alloy by the Laser-Flash Method
R. Abdul Abas; M. Hayashi; S. Seetharaman
2007-01-01
In the present work, thermal diffusivity measurements have been carried out on industrial samples of CMSX-4 nickel-base superalloy\\u000a using the laser-flash method with emphasis on studying the effect of temperature and microstructure on the thermal diffusivity.\\u000a The measurements were performed in the temperature range from 298 to 1623 K covering both solid as well as liquid ranges.\\u000a Below 1253 K,
Jianfeng Zhu; Yong-tao Zhang; Stuart A. Newman; Mark S. Alber
2009-01-01
Nonlinear reaction-diffusion systems which are often employed in mathematical modeling in developmental biology are usually\\u000a highly stiff in both diffusion and reaction terms. Moreover, they are typically considered on multidimensional complex geometrical\\u000a domains because of complex shapes of embryos. We overcome these computational challenges by combining discontinuous Galerkin\\u000a (DG) finite element methods with Strang type symmetrical operator splitting technique, on
Method of fluxless brazing and diffusion bonding of aluminum containing components
NASA Technical Reports Server (NTRS)
Featherston, A. B.; Okelly, K. P. (inventors)
1976-01-01
A method of diffusion bonding and fluxless brazing of aluminum containing components is reported. The aluminum surfaces are freed of any aluminum oxide coating and are coated with a polymeric sealer which can be thermally removed leaving essentially no residue. The polymeric sealer is being removed in a substantially oxygen free environment, and the aluminum components are then being brazed or diffusion bonded without the use of a flux to remove oxide coating.
Viscoelastic characterization of low-velocity impact of a solid ball on an agar gel
NASA Astrophysics Data System (ADS)
Ara, K.; Katsuragi, H.
2013-02-01
A viscoelastic characterization method using low-velocity impact is experimentally studied. A steel ball is dropped from a certain height and impacts on an agar gel target with 1-4 m/s velocity. The motion of the impactor ball is captured by a high-speed camera. Instantaneous penetration depth, velocity, and acceleration of the impactor are computed from the high-speed video data. The obtained kinematic data are analyzed in terms of the equation of motion of the impactor. Specifically, we compute the impact viscosity and impact elasticity, assuming a simple impact drag force model. The impact drag force model consists of a linear viscous term, a linear elastic term, and a constant term. From the estimated impact viscosity, we confirm that the Reynolds number is relatively low (less than 10). This low Reynolds number is consistent with the simple linear viscous assumption. From the estimated impact elasticity, we can calculate the speed of sound and the strength of target agar gel. In order to examine the velocity dependence of the elasticity, we also perform very slow (less than 0.1 mm/s) penetration tests using the same agar gel samples. The comparison between impact elasticity and slow penetration elasticity reveals the weak velocity strengthening of agar gel.
Advanced computational methods for nodal diffusion, Monte Carlo, and S[sub N] problems
Martin, W.R.
1993-01-01
This document describes progress on five efforts for improving effectiveness of computational methods for particle diffusion and transport problems in nuclear engineering: (1) Multigrid methods for obtaining rapidly converging solutions of nodal diffusion problems. A alternative line relaxation scheme is being implemented into a nodal diffusion code. Simplified P2 has been implemented into this code. (2) Local Exponential Transform method for variance reduction in Monte Carlo neutron transport calculations. This work yielded predictions for both 1-D and 2-D x-y geometry better than conventional Monte Carlo with splitting and Russian Roulette. (3) Asymptotic Diffusion Synthetic Acceleration methods for obtaining accurate, rapidly converging solutions of multidimensional SN problems. New transport differencing schemes have been obtained that allow solution by the conjugate gradient method, and the convergence of this approach is rapid. (4) Quasidiffusion (QD) methods for obtaining accurate, rapidly converging solutions of multidimensional SN Problems on irregular spatial grids. A symmetrized QD method has been developed in a form that results in a system of two self-adjoint equations that are readily discretized and efficiently solved. (5) Response history method for speeding up the Monte Carlo calculation of electron transport problems. This method was implemented into the MCNP Monte Carlo code. In addition, we have developed and implemented a parallel time-dependent Monte Carlo code on two massively parallel processors.
Accelerated molecular dynamics and equation-free methods for simulating diffusion in solids.
Deng, Jie; Zimmerman, Jonathan A.; Thompson, Aidan Patrick; Brown, William Michael (Oak Ridge National Laboratories, Oak Ridge, TN); Plimpton, Steven James; Zhou, Xiao Wang; Wagner, Gregory John; Erickson, Lindsay Crowl
2011-09-01
Many of the most important and hardest-to-solve problems related to the synthesis, performance, and aging of materials involve diffusion through the material or along surfaces and interfaces. These diffusion processes are driven by motions at the atomic scale, but traditional atomistic simulation methods such as molecular dynamics are limited to very short timescales on the order of the atomic vibration period (less than a picosecond), while macroscale diffusion takes place over timescales many orders of magnitude larger. We have completed an LDRD project with the goal of developing and implementing new simulation tools to overcome this timescale problem. In particular, we have focused on two main classes of methods: accelerated molecular dynamics methods that seek to extend the timescale attainable in atomistic simulations, and so-called 'equation-free' methods that combine a fine scale atomistic description of a system with a slower, coarse scale description in order to project the system forward over long times.
Aguilera-Arreola, M G; Portillo-Muñoz, M I; Rodríguez-Martínez, C; Castro-Escarpulli, G
2012-08-01
Selective screening media for the detection and identification of Aeromonas strains are needed to guide primary isolation procedures in the clinical laboratory. This study compared the selective CromoCen® AGN chromogenic agar medium for the detection and identification of Aeromonas strains that were isolated from various samples against the conventional selective agar media that are commonly used for the isolation of this organism in food, environmental and clinical samples. The Miles and Misra and ecometric methods were used to evaluate the microbiological performance of CromoCen® AGN chromogenic agar medium, which was shown to be satisfactory. A total of 14 reference Aeromonas strains, 44 wild strains and 106 clinical stool specimens were examined using both non-chromogenic selective agars that are commonly used for Aeromonas isolation and CromoCen® AGN agar. The latter exhibited 94.73% sensitivity and 100% specificity for the various samples. On CromoCen® AGN agar medium, Aeromonas formed colonies with light green, greenish and salmon pigments with or without a surrounding wide transparent zone (halo) of 2-3mm in diameter around the entire border. This medium is recommended for the isolation and potential identification of the Aeromonas genus. PMID:22561188
A First-Passage Kinetic Monte Carlo method for reaction–drift–diffusion processes
Mauro, Ava J.; Sigurdsson, Jon Karl; Shrake, Justin; Atzberger, Paul J.; Isaacson, Samuel A.
2014-02-15
Stochastic reaction–diffusion models are now a popular tool for studying physical systems in which both the explicit diffusion of molecules and noise in the chemical reaction process play important roles. The Smoluchowski diffusion-limited reaction model (SDLR) is one of several that have been used to study biological systems. Exact realizations of the underlying stochastic processes described by the SDLR model can be generated by the recently proposed First-Passage Kinetic Monte Carlo (FPKMC) method. This exactness relies on sampling analytical solutions to one and two-body diffusion equations in simplified protective domains. In this work we extend the FPKMC to allow for drift arising from fixed, background potentials. As the corresponding Fokker–Planck equations that describe the motion of each molecule can no longer be solved analytically, we develop a hybrid method that discretizes the protective domains. The discretization is chosen so that the drift–diffusion of each molecule within its protective domain is approximated by a continuous-time random walk on a lattice. New lattices are defined dynamically as the protective domains are updated, hence we will refer to our method as Dynamic Lattice FPKMC or DL-FPKMC. We focus primarily on the one-dimensional case in this manuscript, and demonstrate the numerical convergence and accuracy of our method in this case for both smooth and discontinuous potentials. We also present applications of our method, which illustrate the impact of drift on reaction kinetics.
A First-Passage Kinetic Monte Carlo method for reaction-drift-diffusion processes
NASA Astrophysics Data System (ADS)
Mauro, Ava J.; Sigurdsson, Jon Karl; Shrake, Justin; Atzberger, Paul J.; Isaacson, Samuel A.
2014-02-01
Stochastic reaction-diffusion models are now a popular tool for studying physical systems in which both the explicit diffusion of molecules and noise in the chemical reaction process play important roles. The Smoluchowski diffusion-limited reaction model (SDLR) is one of several that have been used to study biological systems. Exact realizations of the underlying stochastic processes described by the SDLR model can be generated by the recently proposed First-Passage Kinetic Monte Carlo (FPKMC) method. This exactness relies on sampling analytical solutions to one and two-body diffusion equations in simplified protective domains. In this work we extend the FPKMC to allow for drift arising from fixed, background potentials. As the corresponding Fokker-Planck equations that describe the motion of each molecule can no longer be solved analytically, we develop a hybrid method that discretizes the protective domains. The discretization is chosen so that the drift-diffusion of each molecule within its protective domain is approximated by a continuous-time random walk on a lattice. New lattices are defined dynamically as the protective domains are updated, hence we will refer to our method as Dynamic Lattice FPKMC or DL-FPKMC. We focus primarily on the one-dimensional case in this manuscript, and demonstrate the numerical convergence and accuracy of our method in this case for both smooth and discontinuous potentials. We also present applications of our method, which illustrate the impact of drift on reaction kinetics.
Asgari, Setareh; Jahanshahi, Mohsen; Rahimpour, Ahmad
2014-09-26
In the present work a novel kind of dense nanoporous composite matrix for expanded bed application has been successfully first prepared with Nickel powder as a densifier and was covered with Agar-Agar layer as a skeleton, through the method of water-in-oil emulsification. Agar-Agar is a porous and inexpensive polymer. In order to fabricate cost-effective adsorbent with favorable qualities Agar-Agar polymer was used. Thereafter, the customized composite particle was modified by pseudo-affinity dye-ligand, Reactive Blue 4 (RB4), aimed at preparing a pseudo-affinity adsorbent (RB4-Agar-Ni) for bioprodut adsorption from aqueous solution. Bovine Serum Albumin (BSA) was selected as a model protein to investigate the adsorption behavior in batchwise and expanded bed chromatography, and the obtained results were evaluated with that of Streamline™ (Amersham-Pharmacia Biotech, Sweden). Spherical appearance and porous structure of composite particles were observed by the optical microscope (OM) and scanning electronic microscope (SEM). The results suggested that the matrices followed the logarithmic normal size distribution with the range of 65-300 ?m and average diameter of 126.81-151.47 ?m, proper wet density of 1.64-2.78 g/ml, water content of 62.74-34%, porosity of 98-90% and pore size of about 38-130 nm. For better comprehension of the impact of solid phase properties on the performance of the expanded bed, the expansion and hydrodynamic properties of a composite matrix with a series of densities was evaluated and estimated by the retention time distribution method (RTD) in an expanded bed and was compared with that of other matrices. According to obtained results the expansion factors under the same fluid velocity decreased by increasing the matrix density. Moreover, the axial dispersion coefficient (Dax) is the most appropriate parameter for evaluating the stability of expanded bed, on various operating conditions, such as different flow velocity, bed expansion degree, viscosity of the liquid phase and the density of adsorbent. It was observed that the application of matrix with high density was proper for high operation, fluid velocity, since the addition of densifier improves the rigidity of the matrix. Three momentous factors, pH, ionic strength and initial concentration of BSA were analyzed. The best results showed that the adsorption equilibrium isotherms seems to follow a typical Langmuir isotherm and also the maximum adsorption capacity (qm) of BSA on RB4-Agar-Ni (64.01 mg/ml adsorbent) was higher than that on RB4-Streamline commercial adsorbent (about 54 mg.ml adsorbent). Additionally kinetic adsorption processes were characterized by the pseudo-first-order and pseudo-second-order kinetics equations. The experimental data followed the pseudo-first-order kinetic equation. Also the breakthrough curves were investigated. It was found that dynamic binding capacity (DBC) decreased with increasing the flow rate and the values of DBC decreased from 21.08 to 11.15 mg/ml adsorbent when the density of composite beads increased from 1.64 to 2.78 g/ml. All results indicate that the prepared composite is promising for efficient bioproduct adsorption with good hydrodynamic characteristics, high stability and it is suitable for expanded bed usage as a cost-effective adsorbent. PMID:25152492
MRI Phantoms – Are There Alternatives to Agar?
Hellerbach, Alexandra; Schuster, Verena; Jansen, Andreas; Sommer, Jens
2013-01-01
The suitability of different gelling agents as MRI phantoms was evaluated in terms of homogeneity, gel stability and reproducibility. Time and effort for preparation were also taken into account. The relaxation times of various gel compositions were estimated. Carbomer-980 and Carbopol-974P were determined to be promising novel phantom materials. These gelling agents are readily available, inexpensive and easy to handle given that thermal treatment is not required. Furthermore, the viscoelasticity of their polymer network is pH-dependent. With such characteristics, it was even possible to embed sensitive objects and retrieve them after testing. This was demonstrated with a fiber phantom for Diffusion Weighted MRI applications. Since Carbomer-980 and Carbopol-974P are non-hazardous, they are also suitable for multimodal setups (e.g., MRI as well as ultrasonic imaging). PMID:23940563
The Local Discontinuous Galerkin Method for Time-Dependent Convection-Diffusion Systems
NASA Technical Reports Server (NTRS)
Cockburn, Bernardo; Shu, Chi-Wang
1997-01-01
In this paper, we study the Local Discontinuous Galerkin methods for nonlinear, time-dependent convection-diffusion systems. These methods are an extension of the Runge-Kutta Discontinuous Galerkin methods for purely hyperbolic systems to convection-diffusion systems and share with those methods their high parallelizability, their high-order formal accuracy, and their easy handling of complicated geometries, for convection dominated problems. It is proven that for scalar equations, the Local Discontinuous Galerkin methods are L(sup 2)-stable in the nonlinear case. Moreover, in the linear case, it is shown that if polynomials of degree k are used, the methods are k-th order accurate for general triangulations; although this order of convergence is suboptimal, it is sharp for the LDG methods. Preliminary numerical examples displaying the performance of the method are shown.
I. O. Golosnoy; J. K. Sykulski
Application of a finite difference front fixing method to various problems with moving boundaries and non- linear material properties is discussed. Advantages and implementation problems of the method are highlighted. Particular attention is given to conservation properties of the algorithm and accurate solutions close to the moving boundaries. The algorithm is tested using a well-known solution of the plane diffusion
A LEVEL SET METHOD FOR ANISOTROPIC GEOMETRIC DIFFUSION IN 3D IMAGE PROCESSING
Rumpf, Martin
interest in various appli- cations. Especially in medical imaging different image generation hardwareA LEVEL SET METHOD FOR ANISOTROPIC GEOMETRIC DIFFUSION IN 3D IMAGE PROCESSING TOBIAS PREUSSER AND MARTIN RUMPF Abstract. A new morphological multiscale method in 3D image processing is presented which
M. Kwater; K. Ruebenbauer; U. D. Wdowik
1993-01-01
The fullest information about the diffusivity in solids at microscopic scale (atomic) can be provided by methods sensitive to both energy and momentum transfer. Due to the fact that jumps are usually of short distance and the motion is rather slow one requires a high energy resolution at relatively significant and well-defined momentum transfers. Hence, only two methods have been
Walker diffusion method for calculation of transport properties of finite composite systems.
Van Siclen, Clinton DeW
2002-02-01
A heterogeneous medium may be represented by a scalar field of local transport coefficients (e.g., conductivity) or by a "resistor network" derived from that scalar field. In either case the effective (macroscopic) and local (microscopic) transport properties may be calculated by the walker diffusion method. Some sample calculations for disordered systems are presented to demonstrate the method. PMID:11863624
J. M. Hyman; M. Shashkov
2001-01-01
We have constructed mimetic finite difference methods for both the TE and TM modes for 2-D Maxwell's curl equations and equations of magnetic diffusion with discontinuous coefficients on nonorthogonal, nonsmooth grids. The discrete operators were derived using the discrete vector and tensor analysis to satisfy discrete analogs of the main theorems of vector analysis. Because the finite difference methods satisfy
The Galerkin/least-squares method for advective-diffusive equations
NASA Technical Reports Server (NTRS)
Hughes, T. J. R.; Franca, L. P.; Hulbert, G. M.; Johan, Z.; Shakib, F.
1988-01-01
Galerkin/least-squares finite-element methods are presented for advective-diffusive equations. Galerkin/least-squares represents a conceptual simplification of streamline-upwind Petrov-Galerkin methods, and is in fact applicable to a wide variety of other problem types. A convergence analysis and error estimates are presented. Some numerical results for compressible Navier-Stokes flows are presented.
Walker Diffusion Method for Calculation of Transport Properties of Finite Composite Systems
Van Siclen, Clinton D
2002-01-01
A heterogeneous medium may be represented by a scalar field of local transport coefficients (e.g., conductivity) or by a “resistor network” derived from that scalar field. In either case the effective (macroscopic) and local (microscopic) transport properties may be calculated by the walker diffusion method. Some sample calculations for disordered systems are presented to demonstrate the method.
Nonlinear Multigrid Methods for Second Order Differential Operators with Nonlinear Diffusion
Jimack, Peter
for a general second order nonlinear operator. The comparison is based upon a detailed analysis of their costsNonlinear Multigrid Methods for Second Order Differential Operators with Nonlinear Diffusion, Nottingham, NG7 2RD Abstract Nonlinear multigrid methods such as the Full Approximation Scheme (FAS
Margherita Beruto; Paolo Curir; Pierre Debergh
1999-01-01
Summary The type of gelling agent can influence to a large extent clonal propagation of Ranunculus asiaticus L. through axillary bud stimulation. In preliminary experiments we identified three agar brands (Oxoid=OX, Merck=MK, and\\u000a Roth=RT) which affect the availability of water and minerals to tissues in different ways. In the present study we investigate\\u000a the influence of these agars on the in
An efficient nonlinear solution method for non-equilibrium radiation diffusion
D. A. Knoll; W. J. Rider; G. L. Olsen
1999-01-01
A new nonlinear solution method is developed and applied to a non-equilibrium radiation diffusion problem. With this new method, Newton-like super-linear convergence is achieved in the nonlinear iteration, without the complexity of forming or inverting the Jacobian from a standard Newton method. The method is a unique combination of an outer Newton-based iteration and an inner conjugate gradient-like (Krylov) iteration.
An efficient nonlinear solution method for non-equilibrium radiation diffusion
D. A. Knoll; W. J. Rider; G. L. Olson
1999-01-01
A new nonlinear solution method is developed and applied to a non-equilibrium radiation diffusion problem. With this new method, Newton-like super-linear convergence is achieved in the nonlinear iteration, without the complexity of forming or inverting the Jacobian from a standard Newton method. The method is a unique combination of an outer Newton-based iteration and and inner conjugate gradient-like (Krylov) iteration.
The Diffusion of Evaluation Methods among Public Relations Practitioners.
ERIC Educational Resources Information Center
Dozier, David M.
A study explored the relationships between public relations practitioners' organizational roles and the type of evaluation methods they used on the job. Based on factor analysis of role data obtained from an earlier study, four organizational roles were defined and ranked: communication manager, media relations specialist, communication liaison,…
Practical method of diffusion-welding steel plate in air
NASA Technical Reports Server (NTRS)
Holko, K. H.; Moore, T. J.
1971-01-01
Method is ideal for critical service requirements where parent metal properties are equaled in notch toughness, stress rupture and other characteristics. Welding technique variations may be used on a variety of materials, such as carbon steels, alloy steels, stainless steels, ceramics, and reactive and refractory materials.
REE diffusivities in melilite - A preliminary study using the SIMS depth profile method
NASA Astrophysics Data System (ADS)
Ito, M.; Yurimoto, H.; Morioka, M.; Hagasawa, H.
1997-03-01
Diffusivities of the rare earth elements (REE), La, Pr, Tb and Tm, have been measured for synthetic single crystal of melilite (kermanite, Ca2MgSi2O7) using depth profile method by secondary ion mass spectrometry (SIMS), for the purpose of confirming the possible diffusive fractionation of REE in the Allende CAIs, etc. In our previous works, we have measured the diffusivities of divalent cations and REE (Gd, Tm, and Sc) in kermanite using radioactive tracers. However, tracer experiment is limited by availability of radioactive isotopes with half-lives and half-ray energies which are adequate for diffusion measurement. By using SIMS, any REE can be measured in principle, unless an oxide ion interferes measurement of metal ion with the same mass number. In addition, SIMS has higher spatial resolution (of a few nm rather than m) in tracer experiments or EPMA.
Negative Magnetic Eddy Diffusivities from the Test-field Method and Multiscale Stability Theory
NASA Astrophysics Data System (ADS)
Andrievsky, Alexander; Brandenburg, Axel; Noullez, Alain; Zheligovsky, Vladislav
2015-10-01
The generation of a large-scale magnetic field in the kinematic regime in the absence of an ?-effect is investigated by following two different approaches: the test-field method and the multiscale stability theory relying on the homogenization technique. Our computations of the magnetic eddy diffusivity tensor of the parity-invariant flow IV of G. O. Roberts and the modified Taylor–Green flow confirm the findings of previous studies and also explain some of their apparent contradictions. The two flows have large symmetry groups; this is used to considerably simplify the eddy diffusivity tensor. Finally, a new analytic result is presented: upon expressing the eddy diffusivity tensor in terms of solutions to auxiliary problems for the adjoint operator, we derive relations between the magnetic eddy diffusivity tensors that arise for mutually reverse small-scale flows {\\boldsymbol{v}}(x) and -{\\boldsymbol{v}}(x).
NASA Astrophysics Data System (ADS)
Ansari, Mohammad Ali; Alikhani, Saeid; Mohajerani, Ezeddin; Massudi, Reza
2012-03-01
In this study, the diffusion of photons in turbid media, like biological tissue has been studied. Due to scattering and absorption of photons in such media, the study of photon propagation in biological tissue is complicated. The several numerical methods have been presented to simulate the behavior of diffused photons. Recently, Boundary Integral Method (BIM) has been offered to simulate photon migration inside biological tissues. This method has advantage, e.g. lower computational time in compared with other numerical methods. In this study, the accuracy and precision of BIM compares with another numerical method like Monte Carlo technique and finite difference method, and also the calculated results obtained by BIM and Monte Carlo method evaluate with measured results. Furthermore, the effects of scattering and absorption coefficient of tissue on the measured signal are studied.
Washington State University: Defects and Diffusion studied by Hyperfine Methods
NSDL National Science Digital Library
The Hyperfine Interactions Laboratory at Washington State University addresses its research of "how solids are affected by mechanical, thermal, chemical, or irradiation treatment" with atom-scale resolution. Students and researchers can discover their nuclear hyperfine interactions methods. To learn about the Laboratory's research, users can find detailed descriptions, pictures, publications, meeting abstracts, and more. The website features undergraduate, graduate, postdocs, and visiting scientist research opportunities. Users can also find out about the International Conference on Hyperfine Interactions held in August 2004.
Information Theoretic Methods for Diffusion-Weighted MRI Analysis
Angelos Barmpoutis; Baba C. Vemuri
2008-01-01
Concepts from Information Theory have been used quite widely in Image Processing, Computer Vision and Medical Image Analysis\\u000a for several decades now. Most widely used concepts are that of KL-divergence, minimum description length (MDL), etc. These\\u000a concepts have been popularly employed for image registration, segmentation, classification etc. In this chapter we review\\u000a several methods, mostly developed by our group at
Matias Rauma; Gunnar Johanson
2009-01-01
Recent work in our laboratory shows that it is possible to measure the minute weight changes of skin during exposure to chemical vapor using the thermogravimetric analysis (TGA) method. Further, the TGA weight curves can be analyzed with a two-compartment diffusion model, yielding two sets of diffusion and skin:air partition coefficients. In this study, the dermal diffusion of six chemical
NASA Technical Reports Server (NTRS)
Penner, Reginald M.; Vandyke, Leon S.; Martin, Charles R.
1987-01-01
The current pulse E sub oc relaxation method and its application to the determination of diffusion coefficients in electrochemically synthesized polypyrrole thin films is described. Diffusion coefficients for such films in Et4NBF4 and MeCN are determined for a series of submicron film thicknesses. Measurement of the double-layer capacitance, C sub dl, and the resistance, R sub u, of polypyrrole thin films as a function of potential obtained with the galvanostatic pulse method is reported. Measurements of the electrolyte concentration in reduced polypyrrole films are also presented to aid in the interpretation of the data.
Numerical methods and stochastic simulation algorithms for reaction-drift-diffusion systems
NASA Astrophysics Data System (ADS)
Mauro, Ava J.
In recent years, there has been increased awareness that stochasticity in chemical reactions and diffusion of molecules can have significant effects on the outcomes of intracellular processes, particularly given the low copy numbers of many proteins and mRNAs present in a cell. For such molecular species, the number and locations of molecules can provide a more accurate and detailed description than local concentration. In addition to diffusion, drift in the movements of molecules can play a key role in the dynamics of intracellular processes, and can often be modeled as arising from potential fields. Examples of sources of drift include active transport, variations in chemical potential, material heterogeneities in the cytoplasm, and local interactions with subcellular structures. This dissertation presents a new numerical method for simulating the stochastically varying numbers and locations of molecular species undergoing chemical reactions and drift-diffusion. The method combines elements of the First-Passage Kinetic Monte Carlo (FPKMC) method for reaction--diffusion systems and the Wang--Peskin--Elston lattice discretization of the Fokker--Planck equation that describes drift-diffusion processes in which the drift arises from potential fields. In the FPKMC method, each molecule is enclosed within a "protective domain", either by itself or with a small number of other molecules. To sample when a molecule leaves its protective domain or a reaction occurs, the original FPKMC method relies on analytic solutions of one- and two-body diffusion equations within the protective domains, and therefore cannot be used in situations with non-constant drift. To allow for such drift in our new method (hereafter Dynamic Lattice FPKMC or DL-FPKMC), each molecule undergoes a continuous-time random walk on a lattice within its protective domain, and the lattices change adaptively over time. One of the most commonly used spatial models for stochastic reaction-diffusion systems is the Smoluchowski diffusion-limited reaction (SDLR) model. The DL-FPKMC method generates convergent realizations of an extension of the SDLR model that includes drift from potentials. We present detailed numerical results demonstrating the convergence and accuracy of our method for various types of potentials (smooth, discontinuous, and constant). We also present several illustrative applications of DL-FPKMC, including examples motivated by cell biology.
Voineskos, Aristotle N; O'Donnell, Lauren J; Lobaugh, Nancy J; Markant, Doug; Ameis, Stephanie H; Niethammer, Marc; Mulsant, Benoit H; Pollock, Bruce G; Kennedy, James L; Westin, Carl Fredrik; Shenton, Martha E
2009-04-01
MR diffusion tensor imaging (DTI) can measure and visualize organization of white matter fibre tracts in vivo. DTI is a relatively new imaging technique, and new tools developed for quantifying fibre tracts require evaluation. The purpose of this study was to compare the reliability of a novel clustering approach with a multiple region of interest (MROI) approach in both healthy and disease (schizophrenia) populations. DTI images were acquired in 20 participants (n=10 patients with schizophrenia: 56+/-15 years; n=10 controls: 51+/-20 years) (1.5 T GE system) with diffusion gradients applied in 23 non-collinear directions, repeated three times. Whole brain seeding and creation of fibre tracts were then performed. Interrater reliability of the clustering approach, and the MROI approach, were each evaluated and the methods compared. There was high spatial (voxel-based) agreement within and between the clustering and MROI methods. Fractional anisotropy, trace, and radial and axial diffusivity values showed high intraclass correlation (p<0.001 for all tracts) for each approach. Differences in scalar indices of diffusion between the clustering and MROI approach were minimal. The excellent interrater reliability of the clustering method and high agreement with the MROI method, quantitatively and spatially, indicates that the clustering method can be used with confidence. The clustering method avoids biases of ROI drawing and placement, and, not limited by a priori predictions, may be a more robust and efficient way to identify and measure white matter tracts of interest. PMID:19159690
An adaptive pseudo-spectral method for reaction diffusion problems
NASA Technical Reports Server (NTRS)
Bayliss, A.; Gottlieb, D.; Matkowsky, B. J.; Minkoff, M.
1987-01-01
The spectral interpolation error was considered for both the Chebyshev pseudo-spectral and Galerkin approximations. A family of functionals I sub r (u), with the property that the maximum norm of the error is bounded by I sub r (u)/J sub r, where r is an integer and J is the degree of the polynomial approximation, was developed. These functionals are used in the adaptive procedure whereby the problem is dynamically transformed to minimize I sub r (u). The number of collocation points is then chosen to maintain a prescribed error bound. The method is illustrated by various examples from combustion problems in one and two dimensions.
Hideki Murakami; Masao Kobayashi; Hirofumi Takeuchi; Yoshiaki Kawashima
1999-01-01
Purpose: The objectives of this study were to establish a new preparation method for poly(DL-lactide-co-glycolide) (PLGA) nanoparticles by modifying the spontaneous emulsification solvent diffusion (SESD) method and to elucidate the mechanism of nanoparticle formation on the basis of the phase separation principle of PLGA and poly(vinyl alcohol) (PVA) in the preparation system. Methods: PLGA nanoparticles were prepared by the modified-SESD
Method of fabricating reflection-mode EUV diffusers
Anderson, Erik; Naulleau, Patrick P.
2005-03-01
Techniques for fabricating well-controlled, random relief, engineered surfaces that serve as substrates for EUV optical devices are accomplished with grayscale exposure. The method of fabricating a multilevel EUV optical element includes: (a) providing a substrate; (b) depositing a layer of curable material on a surface of the substrate; (c) creating a relief profile in a layer of cured material from the layer of curable material wherein the relief profile comprises multiple levels of cured material that has a defined contour; and (d) depositing a multilayer reflection film over the relief profile wherein the film has an outer contour that substantially matches that of the relief profile. The curable material can comprise photoresist or a low dielectric constant material.
Agar-block microcosms for controlled plant tissue decomposition by aerobic fungi.
Schilling, Jonathan S; Jacobson, K Brook
2011-01-01
The two principal methods for studying fungal biodegradation of lignocellulosic plant tissues were developed for wood preservative testing (soil-block; agar-block). It is well-accepted that soil-block microcosms yield higher decay rates, fewer moisture issues, lower variability among studies, and higher thresholds of preservative toxicity. Soil-block testing is thus the more utilized technique and has been standardized by American Society for Testing and Materials (ASTM) (method D 1413-07). The soil-block design has drawbacks, however, using locally-variable soil sources and in limiting the control of nutrients external (exogenous) to the decaying tissues. These drawbacks have emerged as a problem in applying this method to other, increasingly popular research aims. These modern aims include degrading lignocellulosics for bioenergy research, testing bioremediation of co-metabolized toxics, evaluating oxidative mechanisms, and tracking translocated elements along hyphal networks. Soil-blocks do not lend enough control in these applications. A refined agar-block approach is necessary. Here, we use the brown rot wood-degrading fungus Serpula lacrymans to degrade wood in agar-block microcosms, using deep Petri dishes with low-calcium agar. We test the role of exogenous gypsum on decay in a time-series, to demonstrate the utility and expected variability. Blocks from a single board rip (longitudinal cut) are conditioned, weighed, autoclaved, and introduced aseptically atop plastic mesh. Fungal inoculations are at each block face, with exogenous gypsum added at interfaces. Harvests are aseptic until the final destructive harvest. These microcosms are designed to avoid block contact with agar or Petri dish walls. Condensation is minimized during plate pours and during incubation. Finally, inoculum/gypsum/wood spacing is minimized but without allowing contact. These less technical aspects of agar-block design are also the most common causes of failure and the key source of variability among studies. Video publication is therefore useful in this case, and we demonstrate low-variability, high-quality results. PMID:21339715
A Domain Decomposition Method for Time Fractional Reaction-Diffusion Equation
Bao, Weimin; Tang, Guojian; Jiang, Yuewen; Liu, Jie
2014-01-01
The computational complexity of one-dimensional time fractional reaction-diffusion equation is O(N2M) compared with O(NM) for classical integer reaction-diffusion equation. Parallel computing is used to overcome this challenge. Domain decomposition method (DDM) embodies large potential for parallelization of the numerical solution for fractional equations and serves as a basis for distributed, parallel computations. A domain decomposition algorithm for time fractional reaction-diffusion equation with implicit finite difference method is proposed. The domain decomposition algorithm keeps the same parallelism but needs much fewer iterations, compared with Jacobi iteration in each time step. Numerical experiments are used to verify the efficiency of the obtained algorithm. PMID:24778594
Numerical simulation of diffusion MRI signals using an adaptive time-stepping method
NASA Astrophysics Data System (ADS)
Li, Jing-Rebecca; Calhoun, Donna; Poupon, Cyril; Le Bihan, Denis
2014-01-01
The effect on the MRI signal of water diffusion in biological tissues in the presence of applied magnetic field gradient pulses can be modelled by a multiple compartment Bloch-Torrey partial differential equation. We present a method for the numerical solution of this equation by coupling a standard Cartesian spatial discretization with an adaptive time discretization. The time discretization is done using the explicit Runge-Kutta-Chebyshev method, which is more efficient than the forward Euler time discretization for diffusive-type problems. We use this approach to simulate the diffusion MRI signal from the extra-cylindrical compartment in a tissue model of the brain gray matter consisting of cylindrical and spherical cells and illustrate the effect of cell membrane permeability.
H. Vandenhove; K. Antunes; J. Wannijn; L. Duquène; M. Van Hees
2007-01-01
The measurement of diffusive gradients in thin films (DGT) has been proposed as a surrogate for metal uptake by plants. A small-scale experiment was performed to test the predictive capacity of the DGT method with respect to uranium availability and uptake by ryegrass. Correlation analyses were performed to compare the results obtained with the DGT device with more conventional bioavailability
Growth of Cell Colonies in Soft Agar from Biopsies of Different Human Solid Tumors1
Zlatko P. Pavelic; Harry K. Slocum; Youcef M. Rustum; Patrick J. Creaven; Norma J. Nowak; Constantine Karakousis; Hiroshi Takita; Arnold Mittelman
Colony growth in soft agar of cells disaggregated from 87 solid tumor specimens was evaluated. Tumors were disaggre gated by an enzymatic method consisting of microtome slicing of tissues and incubation at 37Â° for 2 hr in Roswell Park Memorial Institute Tissue Culture Medium 1640 containing 10% fetal bovine serum, 0.8% collagenase II, and 0.002% DNase I. Tumor cells were
A deterministic Lagrangian particle separation-based method for advective-diffusion problems
NASA Astrophysics Data System (ADS)
Wong, Ken T. M.; Lee, Joseph H. W.; Choi, K. W.
2008-12-01
A simple and robust Lagrangian particle scheme is proposed to solve the advective-diffusion transport problem. The scheme is based on relative diffusion concepts and simulates diffusion by regulating particle separation. This new approach generates a deterministic result and requires far less number of particles than the random walk method. For the advection process, particles are simply moved according to their velocity. The general scheme is mass conservative and is free from numerical diffusion. It can be applied to a wide variety of advective-diffusion problems, but is particularly suited for ecological and water quality modelling when definition of particle attributes (e.g., cell status for modelling algal blooms or red tides) is a necessity. The basic derivation, numerical stability and practical implementation of the NEighborhood Separation Technique (NEST) are presented. The accuracy of the method is demonstrated through a series of test cases which embrace realistic features of coastal environmental transport problems. Two field application examples on the tidal flushing of a fish farm and the dynamics of vertically migrating marine algae are also presented.
Jana M. Swenson; George E. Killgore; Fred C. Tenover
2004-01-01
Although both broth microdilution (BMD) and disk diffusion (DD) are listed by NCCLS as acceptable meth- ods for testing Acinetobacter spp. for antimicrobial susceptibility, few studies have compared the results gen- erated by the two methods. We tested 196 isolates of Acinetobacter spp. from nine U.S. hospitals and from the Centers for Disease Control culture collection by using BMD and
DEVELOPMENT OF LOW-DIFFUSION FLUX-SPLITTING METHODS FOR DENSE GAS-SOLID FLOWS
The development of a class of low-diffusion upwinding methods for computing dense gas-solid flows is presented in this work. An artificial compressibility/low-Mach preconditioning strategy is developed for a hyperbolic two-phase flow equation system consisting of separate solids ...
The Mutual Diffusion Coefficient of Ethanol-Water Mixtures: Determination by a Rapid, New Method
K. C. Pratt; W. A. Wakeham
1974-01-01
Mutual diffusion coefficients for liquid mixtures of ethanol and water have been measured over the entire range of composition and for temperatures from 25 to 65 degrees C at a pressure of 1 bar (105 Pa). At the lowest temperature, the results establish the validity of a new experimental method based upon Taylor's analysis of solute dispersion in laminar flow.
CLOSED-LOOP CONTROL OF VORTEX SHEDDING IN A SEPARATED DIFFUSER USING AN INVERSE METHOD
Colonius, Tim
; and others), algorithms were designed so that the motion at the peak vortex-shedding frequency was stabilized) to describe the wake motion and suppressed vortex shedding in computa- tions by placing sensors in the wakeCLOSED-LOOP CONTROL OF VORTEX SHEDDING IN A SEPARATED DIFFUSER USING AN INVERSE METHOD Takao Suzuki
New contactless method for thermal diffusivity measurements using modulated photothermal radiometry
NASA Astrophysics Data System (ADS)
Pham Tu Quoc, S.; Cheymol, G.; Semerok, A.
2014-05-01
Modulated photothermal radiometry is a non-destructive and contactless technique for the characterization of materials. It has two major advantages: a good signal-to-noise ratio through a synchronous detection and a low dependence on the heating power and the optical properties of the sample surface. This paper presents a new method for characterizing the thermal diffusivity of a material when the phase shift between a modulated laser power signal and the thermal signal of a plate sample is known at different frequencies. The method is based on a three-dimensional analytical model which is used to determine the temperature amplitude and the phase in the laser heating of the plate. A new simple formula was developed through multi-parametric analysis to determine the thermal diffusivity of the plate with knowledge of the frequency at the minimum phase shift, the laser beam radius r0 and the sample thickness L. This method was developed to control the variation of the thermal diffusivity of nuclear components and it was first applied to determine the thermal diffusivity of different metals: 304 L stainless steel, nickel, titanium, tungsten, molybdenum, zinc, and iron. The experimental results were obtained with 5%-10% accuracy and corresponded well with the reference values. The present paper also demonstrates the limit of application of this method for plate with thickness r0/100 ? L ? r0/2. The technique is deemed interesting for the characterization of barely accessible components that require a contactless measurement.
New contactless method for thermal diffusivity measurements using modulated photothermal radiometry.
Pham Tu Quoc, S; Cheymol, G; Semerok, A
2014-05-01
Modulated photothermal radiometry is a non-destructive and contactless technique for the characterization of materials. It has two major advantages: a good signal-to-noise ratio through a synchronous detection and a low dependence on the heating power and the optical properties of the sample surface. This paper presents a new method for characterizing the thermal diffusivity of a material when the phase shift between a modulated laser power signal and the thermal signal of a plate sample is known at different frequencies. The method is based on a three-dimensional analytical model which is used to determine the temperature amplitude and the phase in the laser heating of the plate. A new simple formula was developed through multi-parametric analysis to determine the thermal diffusivity of the plate with knowledge of the frequency at the minimum phase shift, the laser beam radius r0 and the sample thickness L. This method was developed to control the variation of the thermal diffusivity of nuclear components and it was first applied to determine the thermal diffusivity of different metals: 304 L stainless steel, nickel, titanium, tungsten, molybdenum, zinc, and iron. The experimental results were obtained with 5%-10% accuracy and corresponded well with the reference values. The present paper also demonstrates the limit of application of this method for plate with thickness r0/100 ? L ? r0/2. The technique is deemed interesting for the characterization of barely accessible components that require a contactless measurement. PMID:24880399
Direct and diffuse insolation using approximation methods applied to horizontal surface insolation
G. W. Sadler
1975-01-01
A method of representing the solar insolation at the earth's surface under clear sky conditions as a function of the apparent solar irradiation at air mass zero (A), the atmospheric extinction coefficient (B), and the ratio of diffuse to normal incidence radiation (C). Theoretical, experimental and meteorological records of horizontal surface insolation under clear skies are used to study the
Liquid-phase thermal diffusion isotope separation apparatus and method having tapered column
Rutherford, W.M.
1985-12-04
A thermal diffusion counterflow method and apparatus for separating isotopes in solution in which the solution is confined in a long, narrow, vertical slit which tapers from bottom to top. The variation in the width of the slit permits maintenance of a stable concentration distribution with relatively long columns, thus permitting isotopic separation superior to that obtained in the prior art.
ERROR ANALYSIS OF DIFFUSION APPROXIMATION METHODS FOR MULTISCALE SYSTEMS IN REACTION KINETICS
Erban, Radek
ERROR ANALYSIS OF DIFFUSION APPROXIMATION METHODS FOR MULTISCALE SYSTEMS IN REACTION KINETICS SIMON in a container of volume V is described, at time t, by its N-dimensional state vector X(t) [X1(t), X2(t] of the algorithm in Table 1.1 requires to specify propensity functions which are, for mass-action reaction kinetics
Barriers to the diffusion and uptake of BRDF research and methods
C. L. Walthall; M. J. Barnsley
2000-01-01
Despite a long and successful history, involving both measurements and models, the diffusion of research and the uptake of methods involving multi?angle data and Bidirectional Reflectance Distribution Function (BRDF) models have been surprisingly limited. This paper examines the probable cultural, educational, technical and practical reasons for this and advances a number of possible solutions. More specifically, it examines issues relating
Cheng Guan Koay; Lin-Ching Chang; John D. Carew; Carlo Pierpaoli; Peter J. Basser
2006-01-01
A unifying theoretical and algorithmic framework for diffusion tensor estimation is presented. Theoretical connections among the least squares (LS) methods, (linear least squares (LLS), weighted linear least squares (WLLS), nonlinear least squares (NLS) and their constrained counterparts), are established through their respective objective functions, and higher order derivatives of these objective functions, i.e., Hessian matrices. These theoretical connections provide new
INVERSION: a robust method for co-registration of T1 and diffusion weighted MRI images
Leahy, Richard M.
INVERSION: a robust method for co-registration of T1 and diffusion weighted MRI images Chitresh · Multi-contrast images registration is useful to fuse information from different modalities. · Normalized in a T1w brain image is approximately the inverse of the contrast in a T2w image. · Intensity order
Comparison of Eulerian and Lagrangian Monte Carlo PDF methods for turbulent diffusion flames
H. Möbus; P. Gerlinger; D. Brüggemann
2001-01-01
Methods based on Monte Carlo solutions of the transport equation for the joint probability density function (pdf) of scalars are considered to be among the most promising approaches for modeling turbulent reactive flows. For the treatment of convection and diffusion two approaches are well established, either from Eulerian or Lagrangian point of view. Simply speaking, the former is computationally less
Liquid-phase thermal diffusion isotope separation apparatus and method having tapered column
Rutherford, William M. (Dayton, OH)
1988-05-24
A thermal diffusion counterflow method and apparatus for separating isotopes in solution in which the solution is confined in a long, narrow, vertical slit which tapers from bottom to top. The variation in the width of the slit permits maintenance of a stable concentration distribution with relatively long columns, thus permitting isotopic separation superior to that obtainable in the prior art.
Zhang, Fengying; Ngoc, Nguyen Thi Quynh; Tay, Bao Hui; Mendyk, Aleksander; Shao, Yu-Hsuan; Lau, Raymond
2015-01-01
Novel roughness-controlled mannitol/LB Agar microparticles were synthesized by polymorphic transformation and self-assembly method using hexane as the polymorphic transformation reagent and spray-dried mannitol/LB Agar microparticles as the starting material. As-prepared microparticles were characterized by Fourier transform infrared spectra (FTIR), X-ray diffraction spectra (XRD), differential scanning calorimetry (DSC), scanning electron microscopy (SEM), thermal gravimetric analysis (TGA), and Andersen Cascade Impactor (ACI). The XRD and DSC results indicate that after immersing spray-dried mannitol/LB Agar microparticles in hexane, ?-mannitol was completely transformed to ?-mannitol in 1 h, and all the ?-mannitol was transformed to ? form after 14 days. SEM shows that during the transformation the nanobelts on the spray-dried mannitol/LB Agar microparticles become more dispersed and the contour of the individual nanobelts becomes more noticeable. Afterward, the nanobelts self-assemble to nanorods and result in rod-covered mannitol/LB Agar microparticles. FTIR indicates new hydrogen bonds were formed among mannitol, LB Agar, and hexane. SEM images coupled with image analysis software reveal that different surface morphology of the microparticles have different drug adhesion mechanisms. Comparison of ACI results and image analysis of SEM images shows that an increase in the particle surface roughness can increase the fine particle fractions (FPFs) using the rod-covered mannitol microparticles as drug carriers. Transformed microparticles show higher FPFs than commercially available lactose carriers. An FPF of 28.6 ± 2.4% was achieved by microparticles transformed from spray-dried microparticles using 2% mannitol(w/v)/LB Agar as feed solution. It is comparable to the highest FPF reported in the literature using lactose and spray-dried mannitol as carriers. PMID:25423614
A new in-situ method to determine the apparent gas diffusion coefficient of soils
NASA Astrophysics Data System (ADS)
Laemmel, Thomas; Paulus, Sinikka; Schack-Kirchner, Helmer; Maier, Martin
2015-04-01
Soil aeration is an important factor for the biological activity in the soil and soil respiration. Generally, gas exchange between soil and atmosphere is assumed to be governed by diffusion and Fick's Law is used to describe the fluxes in the soil. The "apparent soil gas diffusion coefficient" represents the proportional factor between the flux and the gas concentration gradient in the soil and reflects the ability of the soil to "transport passively" gases through the soil. One common way to determine this coefficient is to take core samples in the field and determine it in the lab. Unfortunately this method is destructive and needs laborious field work and can only reflect a small fraction of the whole soil. As a consequence insecurity about the resulting effective diffusivity on the profile scale must remain. We developed a new in-situ method using new gas sampling device, tracer gas and inverse soil gas modelling. The gas sampling device contains several sampling depths and can be easily installed into vertical holes of an auger, which allows for fast installation of the system. At the lower end of the device inert tracer gas is injected continuously. The tracer gas diffuses into the surrounding soil. The resulting distribution of the tracer gas concentrations is used to deduce the diffusivity profile of the soil. For Finite Element Modeling of the gas sampling device/soil system the program COMSOL is used. We will present the results of a field campaign comparing the new in-situ method with lab measurements on soil cores. The new sampling pole has several interesting advantages: it can be used in-situ and over a long time; so it allows following modifications of diffusion coefficients in interaction with rain but also vegetation cycle and wind.
Rani, G Usha; Mishra, Sumit; Pathak, Gopal; Jha, Usha; Sen, Gautam
2013-10-01
Synthesis of graft copolymers under the influence of microwave radiation alone is a rapid, efficient, clean, cheap, convenient, energy-saving and green method. Grafting of poly(2-hydroxyethylmethacrylate) on agar backbone was carried out under the influence of microwave radiation. The synthesis is optimized in terms of percentage grafting and intrinsic viscosity, by varying the microwave irradiation time and monomer (2-hydroxyethylmethacrylate) concentration. The synthesized graft copolymers have been characterized by intrinsic viscosity measurement, FTIR spectroscopy, UV-spectroscopy, elemental analysis (C, H, N, & S), thermal studies and scanning electron microscopy (SEM). Flocculation efficacy of the synthesized graft copolymers was studied in 0.25% kaolin and 1% coal fine suspension, through 'jar test' procedure. Further, flocculation efficacy of the best grade, coagulant (alum) and agar were studied for possible application in remediation of metals from river water. PMID:23850679
A new method for determining binary diffusion coefficients in dilute condensable vapors
C. C. M. Luijten; K. J. Bosschaart; M. E. H. Van Dongen
1997-01-01
A new method for determining binary diffusion coefficients in dilute condensable vapors is outlined. The method is based on condensational droplet growth. It can be used in a large range of pressures and temperatures, even below the freezing point of the condensing vapor. Results are obtained for the mixtures water-nitrogen and water-helium in the pressure range 11–44 bar. The product
Quantitative comparison of reconstruction methods for intra-voxel fiber recovery from diffusion MRI.
Daducci, Alessandro; Canales-Rodríguez, Erick Jorge; Descoteaux, Maxime; Garyfallidis, Eleftherios; Gur, Yaniv; Lin, Ying-Chia; Mani, Merry; Merlet, Sylvain; Paquette, Michael; Ramirez-Manzanares, Alonso; Reisert, Marco; Reis Rodrigues, Paulo; Sepehrband, Farshid; Caruyer, Emmanuel; Choupan, Jeiran; Deriche, Rachid; Jacob, Mathews; Menegaz, Gloria; Pr?kovska, Vesna; Rivera, Mariano; Wiaux, Yves; Thiran, Jean-Philippe
2014-02-01
Validation is arguably the bottleneck in the diffusion magnetic resonance imaging (MRI) community. This paper evaluates and compares 20 algorithms for recovering the local intra-voxel fiber structure from diffusion MRI data and is based on the results of the "HARDI reconstruction challenge" organized in the context of the "ISBI 2012" conference. Evaluated methods encompass a mixture of classical techniques well known in the literature such as diffusion tensor, Q-Ball and diffusion spectrum imaging, algorithms inspired by the recent theory of compressed sensing and also brand new approaches proposed for the first time at this contest. To quantitatively compare the methods under controlled conditions, two datasets with known ground-truth were synthetically generated and two main criteria were used to evaluate the quality of the reconstructions in every voxel: correct assessment of the number of fiber populations and angular accuracy in their orientation. This comparative study investigates the behavior of every algorithm with varying experimental conditions and highlights strengths and weaknesses of each approach. This information can be useful not only for enhancing current algorithms and develop the next generation of reconstruction methods, but also to assist physicians in the choice of the most adequate technique for their studies. PMID:24132007
NASA Technical Reports Server (NTRS)
Chau, Jessica Furrer; Or, Dani; Sukop, Michael C.; Steinberg, S. L. (Principal Investigator)
2005-01-01
Liquid distributions in unsaturated porous media under different gravitational accelerations and corresponding macroscopic gaseous diffusion coefficients were investigated to enhance understanding of plant growth conditions in microgravity. We used a single-component, multiphase lattice Boltzmann code to simulate liquid configurations in two-dimensional porous media at varying water contents for different gravity conditions and measured gas diffusion through the media using a multicomponent lattice Boltzmann code. The relative diffusion coefficients (D rel) for simulations with and without gravity as functions of air-filled porosity were in good agreement with measured data and established models. We found significant differences in liquid configuration in porous media, leading to reductions in D rel of up to 25% under zero gravity. The study highlights potential applications of the lattice Boltzmann method for rapid and cost-effective evaluation of alternative plant growth media designs under variable gravity.
Chau, Jessica Furrer; Or, Dani; Sukop, Michael C
2005-08-01
Liquid distributions in unsaturated porous media under different gravitational accelerations and corresponding macroscopic gaseous diffusion coefficients were investigated to enhance understanding of plant growth conditions in microgravity. We used a single-component, multiphase lattice Boltzmann code to simulate liquid configurations in two-dimensional porous media at varying water contents for different gravity conditions and measured gas diffusion through the media using a multicomponent lattice Boltzmann code. The relative diffusion coefficients (D rel) for simulations with and without gravity as functions of air-filled porosity were in good agreement with measured data and established models. We found significant differences in liquid configuration in porous media, leading to reductions in D rel of up to 25% under zero gravity. The study highlights potential applications of the lattice Boltzmann method for rapid and cost-effective evaluation of alternative plant growth media designs under variable gravity. PMID:16173154
NASA Astrophysics Data System (ADS)
Effenberger, F.
2014-09-01
Numerical solution methods for Stochastic Differential Equations (SDEs) have become an important tool to study charged particle transport, due to their simplicity and conformance with modern computer architecture. Their field of application ranges from the detailed calculation of solar energetic particle events to the cosmic ray transport in the outer heliosphere and in the Galaxy. At the heart of the applicability of SDEs to kinetic equations is the fundamental equivalence between the Fokker-Planck diffusion equation of parabolic type and an SDE involving a Wiener process to represent the stochastic Brownian motion of (pseudo-)particles. This equivalence has recently been extended to anomalous diffusion involving a Fokker-Planck equation of fractional order and generalized Lévy distributions. Numerical tests and applications of this approach to anomalous diffusion and future prospects of the SDE approach in the space physics context are outlined.
Farzad Rahnema; Dingkang Zhang; Abderrafi Ougouag; Frederick Gleicher
2011-04-04
The main objective of this research is to develop an integrated diffusion/transport (IDT) method to substantially improve the accuracy of nodal diffusion methods for the design and analysis of Very High Temperature Reactors (VHTR). Because of the presence of control rods in the reflector regions in the Pebble Bed Reactor (PBR-VHTR), traditional nodal diffusion methods do not accurately model these regions, within which diffusion theory breaks down in the vicinity of high neutron absorption and steep flux gradients. The IDT method uses a local transport solver based on a new incident flux response expansion method in the controlled nodes. Diffusion theory is used in the rest of the core. This approach improves the accuracy of the core solution by generating transport solutions of controlled nodes while maintaining computational efficiency by using diffusion solutions in nodes where such a treatment is sufficient. The transport method is initially developed and coupled to the reformulated 3-D nodal diffusion model in the CYNOD code for PBR core design and fuel cycle analysis. This method is also extended to the prismatic VHTR. The new method accurately captures transport effects in highly heterogeneous regions with steep flux gradients. The calculations of these nodes with transport theory avoid errors associated with spatial homogenization commonly used in diffusion methods in reactor core simulators
A finite volume method for trace element diffusion and partitioning during crystal growth
NASA Astrophysics Data System (ADS)
Hesse, Marc A.
2012-09-01
A finite volume method on a uniform grid is presented to compute the polythermal diffusion and partitioning of a trace element during the growth of a porphyroblast crystal in a uniform matrix and in linear, cylindrical and spherical geometry. The motion of the crystal-matrix interface and the thermal evolution are prescribed functions of time. The motion of the interface is discretized and it advances from one cell boundary to next as the prescribed interface position passes the cell center. The appropriate conditions for the flux across the crystal-matrix interface are derived from discrete mass conservation. Numerical results are benchmarked against steady and transient analytic solutions for isothermal diffusion with partitioning and growth. Two applications illustrate the ability of the model to reproduce observed rare-earth element patterns in garnets (Skora et al., 2006) and water concentration profiles around spherulites in obsidian (Watkins et al., 2009). Simulations with diffusion inside the growing crystal show complex concentration evolutions for trace elements with high diffusion coefficients, such as argon or hydrogen, but demonstrate that rare-earth element concentrations in typical metamorphic garnets are not affected by intracrystalline diffusion.
Anjum, M F; Lemma, F; Cork, D J; Meunier, D; Murphy, N; North, S E; Woodford, N; Haines, J; Randall, L P
2013-12-01
The aim of this work was to develop a molecular method using loop-mediated isothermal amplification (LAMP) for detection of extended spectrum ?-lactamase (ESBL)-producing Enterobacteriaceae from meat, and to compare it with different isolation agars and microarrays. LAMP assays were developed for CTX-M groups 1, 2, and 9 and OXA-10-like genes. Chicken, lamb, beef, pork, and turkey samples were spiked with 10, 100, and 1,000 cfu/gram using 8 strains of ESBL-producing Enterobacteriaceae (CTX-M sequence types 1, 2, 3, 14, 15, OXA-11, SHV-2, TEM-52) +/- a mix of competitor organisms. Samples were enriched overnight in buffered peptone water (BPW) +/- antibacterials before plating to CHROMagar CTX, OXOID ESBL Brilliance agar, and MacConkey agar with 1 mg/L cefotaxime. Selected BPW broths were also tested using LAMP assays, microarrays and using cefpodoxime discs on agar. For isolation/detection of ESBL producers from beef, pork, lamb, and turkey spiked with 10 or 100 cfu/gram ESBL (natural flora only), all agars and the LAMP assays showed 100% sensitivity and specificity for ESBL spike strains. For chicken samples, both LAMP and chromogenic agars showed improved sensitivity and specificity for isolation of ESBLs compared with MacConkey agar, particularly with competitor bacteria added. In comparison, the cefpodoxime disc method and microarray showed reduced sensitivity. PMID:24329955
A quantitative radioluminographic imaging method for evaluating lateral diffusion rates in skin.
Rush, Allison K; Miller, Matthew A; Smith, Edward D; Kasting, Gerald B
2015-10-28
A method is presented for measuring the lateral diffusion coefficients of exogenously applied compounds on excised skin. The method involves sequential high resolution imaging of the spatial distribution of ?-radiation associated with [(14)C]-labeled compounds to monitor the development of the concentration profile on the skin surface. It is exemplified by measurements made on three radiolabeled test compounds - caffeine, testosterone, and zinc pyrithione (ZnPT) - administered as solutions. Lateral diffusivity is expected to be an important determinant of the topical bioavailability of ZnPT, which is characteristically administered as a fine suspension and must reach microorganisms in molecular form to exert biocidal activity. Application of the test compounds at levels below and above their estimated saturation doses in the upper stratum corneum allows one to distinguish between diffusion-limited and dissolution rate-limited kinetics. The effective lateral diffusivities of the two chemically stable reference compounds, caffeine and testosterone, were (1-4)×10(-9)cm(2)/s and (3-9)×10(-9)cm(2)/s, respectively. Lateral transport of [(14)C] associated with ZnPT was formulation-dependent, with effective diffusivities of (1-2)×10(-9)cm(2)/s in water and (3-9)×10(-9)cm(2)/s in a 1% body wash solution. These differences are thought to be related to molecular speciation and/or the presence of a residual surfactant phase on the skin surface. All values were greater than those estimated for the transverse diffusivities of these compounds in stratum corneum by factors ranging from 250 to over 2000. Facile lateral transport on skin, combined with a low transdermal permeation rate, may thus be seen to be a key factor in the safe and effective use of ZnPT as a topical antimicrobial agent. PMID:26241749
GPU-accelerated 3D neutron diffusion code based on finite difference method
Xu, Q.; Yu, G.; Wang, K. [Dept. of Engineering Physics, Tsinghua Univ. (China)
2012-07-01
Finite difference method, as a traditional numerical solution to neutron diffusion equation, although considered simpler and more precise than the coarse mesh nodal methods, has a bottle neck to be widely applied caused by the huge memory and unendurable computation time it requires. In recent years, the concept of General-Purpose computation on GPUs has provided us with a powerful computational engine for scientific research. In this study, a GPU-Accelerated multi-group 3D neutron diffusion code based on finite difference method was developed. First, a clean-sheet neutron diffusion code (3DFD-CPU) was written in C++ on the CPU architecture, and later ported to GPUs under NVIDIA's CUDA platform (3DFD-GPU). The IAEA 3D PWR benchmark problem was calculated in the numerical test, where three different codes, including the original CPU-based sequential code, the HYPRE (High Performance Pre-conditioners)-based diffusion code and CITATION, were used as counterpoints to test the efficiency and accuracy of the GPU-based program. The results demonstrate both high efficiency and adequate accuracy of the GPU implementation for neutron diffusion equation. A speedup factor of about 46 times was obtained, using NVIDIA's Geforce GTX470 GPU card against a 2.50 GHz Intel Quad Q9300 CPU processor. Compared with the HYPRE-based code performing in parallel on an 8-core tower server, the speedup of about 2 still could be observed. More encouragingly, without any mathematical acceleration technology, the GPU implementation ran about 5 times faster than CITATION which was speeded up by using the SOR method and Chebyshev extrapolation technique. (authors)
Quantitative evaluation of registration methods for atlas-based diffuse optical tomography
NASA Astrophysics Data System (ADS)
Wu, Xue; Eggebrecht, Adam T.; Culver, Joseph P.; Zhan, Yuxuan; Basevi, Hector; Dehghani, Hamid
2013-06-01
In Diffuse Optical Tomography (DOT), an atlas-based model can be used as an alternative to a subject-specific anatomical model for recovery of brain activity. The main step of the generation of atlas-based subject model is the registration of atlas model to the subject head. The accuracy of the DOT then relies on the accuracy of registration method. In this work, 11 registration methods are quantitatively evaluated. The registration method with EEG 10/20 systems with 19 landmarks and non-iterative point to point algorithm provides approximately 1.4 mm surface error and is considered as the most efficient registration method.
A Monte Carlo synthetic-acceleration method for solving the thermal radiation diffusion equation
Evans, Thomas M.; Mosher, Scott W.; Slattery, Stuart R.; Hamilton, Steven P.
2014-02-01
We present a novel synthetic-acceleration-based Monte Carlo method for solving the equilibrium thermal radiation diffusion equation in three spatial dimensions. The algorithm performance is compared against traditional solution techniques using a Marshak benchmark problem and a more complex multiple material problem. Our results show that our Monte Carlo method is an effective solver for sparse matrix systems. For solutions converged to the same tolerance, it performs competitively with deterministic methods including preconditioned conjugate gradient and GMRES. We also discuss various aspects of preconditioning the method and its general applicability to broader classes of problems.
Hyperspectral Imaging for Detecting Pathogens Grown on Agar Plates
Technology Transfer Automated Retrieval System (TEKTRAN)
This paper is concerned with the development of a hyperspectral imaging technique for detecting and identifying one of the most common foodborne pathogens, Campylobacter. Direct plating using agars is an effective tool for laboratory tests and analyses of microorganisms. The morphology (size, growth...
Improving agar electrospinnability with choline-based deep eutectic solvents
Technology Transfer Automated Retrieval System (TEKTRAN)
One percent agar (% wt) was dissolved in the deep eutectic solvent (DES), (2-hydroxyethyl) trimethylammonium chloride/urea at a 1:2 molar ratio, and successfully electrospun into nanofibers. An existing electrospinning set-up, operated at 50 deg C, was adapted for use with an ethanol bath to collect...
Internal structure and thermo-viscoelastic properties of agar ionogels.
Sharma, Anshu; Rawat, Kamla; Solanki, Pratima R; Aswal, V K; Kohlbrecher, J; Bohidar, H B
2015-12-10
Ionic liquids (IL) can alter the physical properties of agar hydrogels. Rheology studies show that gels with wide range of storage moduli (gel strength) G0 values ranging from 1 to 20KPa could be made in imidazolium based IL solutions where the IL concentration may not exceed 5% (w/v). Gelation and gel melting temperatures (tgel and Tm) could be altered by as much as?10°C. Small angle neutron scattering studies revealed the presence of fibre bundles of agar double helices having typical length of 120nm that increased to ?180nm under favorable conditions. These structures gain flexibility from the cladding of the agar bundles by IL molecules which in turn caused partial charge neutralization of its surface. Raman spectroscopy revealed differential hydration of these bundles. It was found that IL molecules with longer alkyl chain (more hydrophobic) altered the gel homogeneity, and changed its thermal and mechanical properties significantly. Therefore, customization of agar hydrogels in green solvent medium (IL solutions) widens the scope of its application potential that may include sensing. PMID:26428165
Transferring a Bacterial Culture to an Agar Slant
NSDL National Science Digital Library
This video from CUNY Kingsborough Community College describes how to transfer a bacterial culture to an agar slant. The brief demonstration is described step by step and would be easy to replicate in a laboratory setting. Running time for the video is 0:34.
Promyou, Surassawadee; Ketsa, Saichol; van Doorn, Wouter G
2014-11-15
The early visible effects of pollination in orchids are likely due to pollinia-borne chemicals. In Dendrobium we tested whether such compounds were water soluble and would diffuse in solid-aqueous phase, and determined both 1-aminocyclopropane-1-carboxylic acid (ACC) concentrations and auxin activity. Following pollination, the flower peduncle showed epinastic movement, followed by yellowing of the flower lip, flower senescence and ovary growth. Placing pollinia on agar blocks for 3, 6, 9 or 12h, prior to transferring them to the stigma, increased the time to these early postpollination effects or prevented them. Placing agar blocks that had been used for contact with the pollinia on the stigma also induced the early postpollination effects. The concentrations of ACC, the direct precursor of ethylene, in pollinia was lower the longer the pollinia had been in contact with the agar blocks, whilst the ACC content in the agar blocks increased with the period of contact. The auxin activity of the agar blocks also increased with the time of contact with pollinia. It is concluded that chemicals in the pollinia are responsible for the early visible postpollination effects, and that these (a) rapidly diffuse in aqueous media, and (b) comprise at least ACC and compounds with auxin activity. The idea is discussed that ACC plus auxin is adequate for the production of the early postpollination effects. PMID:25240156
Tchitchekova, Deyana S; Morthomas, Julien; Ribeiro, Fabienne; Ducher, Roland; Perez, Michel
2014-07-21
A novel method for accurate and efficient evaluation of the change in energy barriers for carbon diffusion in ferrite under heterogeneous stress is introduced. This method, called Linear Combination of Stress States, is based on the knowledge of the effects of simple stresses (uniaxial or shear) on these diffusion barriers. Then, it is assumed that the change in energy barriers under a complex stress can be expressed as a linear combination of these already known simple stress effects. The modifications of energy barriers by either uniaxial traction/compression and shear stress are determined by means of atomistic simulations with the Climbing Image-Nudge Elastic Band method and are stored as a set of functions. The results of this method are compared to the predictions of anisotropic elasticity theory. It is shown that, linear anisotropic elasticity fails to predict the correct energy barrier variation with stress (especially with shear stress) whereas the proposed method provides correct energy barrier variation for stresses up to ?3 GPa. This study provides a basis for the development of multiscale models of diffusion under non-uniform stress. PMID:25053312
NASA Astrophysics Data System (ADS)
Li, Xianping; Huang, Weizhang
2010-10-01
Heterogeneous anisotropic diffusion problems arise in the various areas of science and engineering including plasma physics, petroleum engineering, and image processing. Standard numerical methods can produce spurious oscillations when they are used to solve those problems. A common approach to avoid this difficulty is to design a proper numerical scheme and/or a proper mesh so that the numerical solution validates the discrete counterpart (DMP) of the maximum principle satisfied by the continuous solution. A well known mesh condition for the DMP satisfaction by the linear finite element solution of isotropic diffusion problems is the non-obtuse angle condition that requires the dihedral angles of mesh elements to be non-obtuse. In this paper, a generalization of the condition, the so-called anisotropic non-obtuse angle condition, is developed for the finite element solution of heterogeneous anisotropic diffusion problems. The new condition is essentially the same as the existing one except that the dihedral angles are now measured in a metric depending on the diffusion matrix of the underlying problem. Several variants of the new condition are obtained. Based on one of them, two metric tensors for use in anisotropic mesh generation are developed to account for DMP satisfaction and the combination of DMP satisfaction and mesh adaptivity. Numerical examples are given to demonstrate the features of the linear finite element method for anisotropic meshes generated with the metric tensors.
Peter Piliouras; Glen C. Ulett; Christopher Ashhurst-Smith; Robert G. Hirst; Robert E. Norton
2002-01-01
Melioidosis is caused by the Gram-negative soil saprophyte, Burkholderia pseudomallei and is endemic in tropical and subtropical regions of southeast Asia and northern Australia. Cotrimoxazole has been traditionally used for the therapy of melioidosis despite results indicating resistance often produced in the disc diffusion test against B. pseudomallei. This inconsistency was addressed by comparing this method with the agar dilution,
Bibi, Zainab; Shahid, Faiza; Ul Qader, Shah Ali; Aman, Afsheen
2015-04-01
Microbial xylanases, specially endo-?-1,4-xylanase catalyzes the hydrolysis of xylan, is considered one of the most significant hydrolases. It has numerous applications but most extensively is utilized in paper and pulp industry as a bio-bleaching agent. Immobilization technique is comprehensively studied with the expectation of modifying and improving enzyme stability and characteristics for commercial purposes. Currently, matrix entrapment technique is applied to immobilize endo-?-1,4-xylanase within agar-agar gel beads produced by Geobacillus stearothermophilus KIBGE-IB29. Maximal enzyme immobilization yield was achieved at 2.5% of agar-agar concentration. Optimized conditions demonstrated an increase in the optimal reaction time from 05 min to 30 min and incubation temperature from 50 °C to 60 °C with reference to free enzyme whereas; no effect was observed for optimum pH. Entrapment technique uniquely changed the kinetic parameters of immobilized endo-?-1,4-xylanase (Km: 0.5074 mg min(-1) to 0.5230 mg min(-1) and Vmax: 4773 U min(-1) to 968 U min(-1)) as compared to free enzyme. However, immobilized enzyme displayed broad thermal stability and retained 79.0% of its initial activity at 80 °C up to 30 min whereas; free enzyme completely lost its activity at this temperature. With respect to economic feasibility, the immobilized enzyme showed impressive recycling efficiency up to six reaction cycles. PMID:25603143
On assessment of numerical methods for diffusion-combustion flow with fast chemistry
NASA Astrophysics Data System (ADS)
Funami, Yuki; Shimada, Toru
2012-11-01
Boundary-layer combustion, a major characteristic of a hybrid rocket engine, is a complex phenomenon of fluid dynamics and combustion. Its rate-limiting process is diffusion, whereas combustion reactions are generally very fast. One of numerical approaches for this is to solve simultaneously the Navier-Stokes equations with the transport equation for the mixture fraction. Chemical composition of the combustion gas can be determined by solving local chemical equilibrium for a given flow and mixture fraction fields. The governing equations for a diffusion-combustion flow with fast chemistry are characterized by the convective term, the diffusion term, and the chemical equilibrium calculation. As seen from the numerical methods for these, the convective-flux Jacobian and the numerical flux schemes, upwind higher precision approximation and limiter design, and chemical equilibrium calculation method. This study is focused especially on upwind higher precision approximation method. In this paper, by solving test problems such as quasi-one-dimensional hybrid rocket flow, assessment is made on a variety of numerical methods with respect to precision and convergence.
Augustyniak, Rafal; Ferrage, Fabien; Paquin, Raphaël; Lequin, Olivier; Bodenhausen, Geoffrey
2011-07-01
We present new NMR methods to measure slow translational diffusion coefficients of biomolecules. Like the heteronuclear stimulated echo experiment (XSTE), these new methods rely on the storage of information about spatial localization during the diffusion delay as longitudinal polarization of nuclei with long T(1) such as nitrogen-15. The new BEST-XSTE sequence combines features of Band-selective Excitation Short-Transient (BEST) and XSTE methods. By avoiding the saturation of all protons except those of amide groups, one can increase the sensitivity by 45% in small proteins. The new experiment which combines band-Selective Optimized Flip-Angle Short-Transient with XSTE (SOFAST-XSTE) offers an alternative when very short recovery delays are desired. A modification of the HSQC-edited version of the XSTE experiment offers enhanced sensitivity and access to higher resolution in the indirect dimension. These new methods have been applied to detect changes in diffusion coefficients due to dimerization or proteolysis of Engrailed 2, a partially disordered protein. PMID:21603954
A variational meshfree method for solving time-discrete diffusion equations
NASA Astrophysics Data System (ADS)
Krottje, Johannes K.
2006-08-01
A meshfree method is developed for solving time-discrete diffusion equations that arise in models in brain research. Important criteria for a suitable method are flexibility with respect to domain geometry and the ability to work with very small moving sources requiring easy refinement possibilities. One part of the work concerns a meshfree discretization of the modified Helmholtz equation based on the related minimization problem and a local least-squares function approximation. In a second part, a node choosing algorithm is presented that moves around randomly distributed nodes for optimizing the node distribution and varying the node density as needed. The method is illustrated by two numerical tests.
NASA Astrophysics Data System (ADS)
Kang, Q.; Chen, L.
2014-12-01
Although short-term production of unconventional gas depends on the area of contact created by hydraulic fracturing and connections with pre-existing natural fracture networks, sustainable recovery is limited by transfer of gas from nanoporous matrix into the fractures, because the permeability of hydraulic fractures is orders of magnitude higher than that of the shale matrix. Therefore, a fundamental understanding of hydrocarbon mobility in shale matrix is urgently needed for improving recovery efficiencies. Shale transport properties (diffusivity, permeability, and electronic conductivity), which are critical for understanding the fundamental transport mechanisms, are still poorly understood. There have been some studies using experimental techniques such as scanning electron microscopy (SEM) to visualize the nanoscale structures of shale. Due to the ultra-low porosity and permeability, it is difficult to experimentally investigate the fundamental transport processes inside the shale or accurately measure the transport properties. Advanced pore-scale numerical methods, e.g., the lattice Boltzman method (LBM) may provide an alternative approach. In the present study, three-dimensional nanoscale porous structures of shale are reconstructed based on SEM images of shale samples. Characterization analysis of the nanoscale reconstructed shale is performed, including determination of porosity, pore size distribution, specific surface area, and pore connectivity. The LBM flow model and diffusion model are adopted to simulate fluid flow and Knudsen diffusion in the reconstructed shale, respectively. Tortuosity, intrinsic permeability, and effective Knudsen diffusivity are numerically predicted. The tortuosity is much higher than what is commonly employed in Bruggeman equation. Correction of the intrinsic permeability by taking into consideration the contribution of Knudsen diffusion, which leads to the apparent permeability, is performed. The correction factor under different Knudsen number and pressure conditions are estimated and compared with existing corrections reported in the literature.
Non-invasive measurements of tissue hemodynamics with hybrid diffuse optical methods
NASA Astrophysics Data System (ADS)
Durduran, Turgut
Diffuse optical techniques were used to measure hemodynamics of tissues non-invasively. Spectroscopy and tomography of the brain, muscle and implanted tumors were carried out in animal models and humans. Two qualitatively different methods, diffuse optical tomography and diffuse correlation tomography, were hybridized permitting simultaneous measurement of total hemoglobin concentration, blood oxygen saturation and blood flow. This combination of information was processed further to derive estimates of oxygen metabolism (e.g. CMRO 2) in tissue. The diffuse correlation measurements of blood flow were demonstrated in human tissues, for the first time, demonstrating continous, non-invasive imaging of oxygen metabolism in large tissue volumes several centimeters below the tissue surface. The bulk of these investigations focussed on cerebral hemodynamics. Extensive validation of this methodology was carried out in in vivo rat brain models. Three dimensional images of deep tissue hemodynamics in middle cerebral artery occlusion and cortical spreading depression (CSD) were obtained. CSD hemodynamics were found to depend strongly on partial pressure of carbon dioxide. The technique was then adapted for measurement of human brain. All optical spectroscopic measurements of CMRO2 during functional activation were obtained through intact human skull non-invasively. Finally, a high spatio-temporal resolution measurement of cerebral blood flow due to somatosensory cortex activation following electrical forepaw stimulation in rats was carried out with laser speckle flowmetry. New analysis methods were introduced for laser speckle flowmetry. In other organs, deep tissue hemodynamics were measured on human calf muscle during exercise and cuff-ischemia and were shown to have some clinical utility for peripheral vascular disease. In mice tumor models, the measured hemodynamics were shown to be predictive of photodynamic therapy efficacy, again suggesting promise of clinical utility. In total, the research has pioneered the development of diffuse optical measurements of blood flow, oxygenation and oxygen metabolism in a large range of research and clinical applications.
Corrections to linear methods for diffuse optical tomography using approximation error modelling
Tarvainen, Tanja; Kolehmainen, Ville; Kaipio, Jari P.; Arridge, Simon R.
2010-01-01
Linear reconstruction methods in diffuse optical tomography have been found to produce reasonable good images in cases in which the variation in optical properties within the medium is relatively small and a reference measurement with known background optical properties is available. In this paper we examine the correction of errors when using a first order Born approximation with an infinite space Green’s function model as the basis for linear reconstruction in diffuse optical tomography, when real data is generated on a finite domain with possibly unknown background optical properties. We consider the relationship between conventional reference measurement correction and approximation error modelling in reconstruction. It is shown that, using the approximation error modelling, linear reconstruction method can be used to produce good quality images also in situations in which the background optical properties are not known and a reference is not available. PMID:21258459
Preparation of a stable silica membrane by a counter diffusion chemical vapor deposition method
Mikihiro Nomura; Kenta Ono; Suraj Gopalakrishnan; Takashi Sugawara; Shin-Ichi Nakao
2005-01-01
A stable silica membrane having excellent H2\\/N2 permeance ratio (over 1000) was prepared by the counter diffusion chemical vapor deposition method using tetramethyl orthosilicate (TMOS) and O2 as reactants at 873K. TMOS and O2 were provided in the opposing geometry of the substrates, and silica layer was deposited in the substrate pores. Apparent activation energies through the silica membranes increased
New contactless method for thermal diffusivity measurements using modulated photothermal radiometry
Pham Tu Quoc, S., E-mail: sang.phamtuquoc@cea.fr; Cheymol, G.; Semerok, A. [French Alternative Energies and Atomic Energy Commission, Division of Nuclear Energy, DEN/DANS/DPC/SEARS/LISL, 91191 Gif/Yvette (France)] [French Alternative Energies and Atomic Energy Commission, Division of Nuclear Energy, DEN/DANS/DPC/SEARS/LISL, 91191 Gif/Yvette (France)
2014-05-15
Modulated photothermal radiometry is a non-destructive and contactless technique for the characterization of materials. It has two major advantages: a good signal-to-noise ratio through a synchronous detection and a low dependence on the heating power and the optical properties of the sample surface. This paper presents a new method for characterizing the thermal diffusivity of a material when the phase shift between a modulated laser power signal and the thermal signal of a plate sample is known at different frequencies. The method is based on a three-dimensional analytical model which is used to determine the temperature amplitude and the phase in the laser heating of the plate. A new simple formula was developed through multi-parametric analysis to determine the thermal diffusivity of the plate with knowledge of the frequency at the minimum phase shift, the laser beam radius r{sub 0} and the sample thickness L. This method was developed to control the variation of the thermal diffusivity of nuclear components and it was first applied to determine the thermal diffusivity of different metals: 304 L stainless steel, nickel, titanium, tungsten, molybdenum, zinc, and iron. The experimental results were obtained with 5%–10% accuracy and corresponded well with the reference values. The present paper also demonstrates the limit of application of this method for plate with thickness r{sub 0}/100 ? L ? r{sub 0}/2. The technique is deemed interesting for the characterization of barely accessible components that require a contactless measurement.
Bowen, Constance Mary; Stanton, Marietta; Manno, Martin
2012-01-01
Routine screening of mechanically ventilated patients for delirium is essential for prompt recognition and management; however, this represents a change in practice. Rogers' Diffusion of Innovations Theory can be useful as a strategy to facilitate adoption of a practice change. This case study describes the effectiveness of identifying barriers to a change in practice and developing strategies, specific to Rogers' innovation decision process, for implementing the Confusion Assessment Method for the intensive care unit. PMID:22367153
NASA Astrophysics Data System (ADS)
Suga, Shinsuke
2014-11-01
We propose accurate explicit numerical schemes based on the lattice Boltzmann (LB) method for multi-dimensional diffusion equations. In LB schemes, the velocity models D2Q9 and D2Q13 are used for two-dimensional equations and D3Q19 and D3Q25 for three-dimensional equations. We introduce free parameters that characterize the weight of the equilibrium distribution functions to reduce numerical errors. Consistency analysis through the fourth-order Chapman-Ensgok expansion of the distribution functions gives an approximate diffusion equation with error terms up to fourth-order. The relaxation parameter and weight parameters are determined so that second-order error terms are eliminated in the approximate equation. Stability analysis shows that we can find a relaxation parameter so that each of the presented schemes is stable for given diffusion coefficients and discretizing parameters. Numerical experiments for the isotropic and anisotropic benchmark problems show that the presented schemes derived from the velocity models D2Q13 and D3Q25 are useful for numerical simulations of practical problems governed by two- and three-dimensional diffusion equations, respectively. In particular, schemes in which the value of the relaxation parameter is set to be 1 demonstrate a fourth-order accuracy under the stability condition.
NASA Astrophysics Data System (ADS)
Dhara, Ashis K.; Mukhopadhyay, Sudipta
2012-03-01
The computer aided diagnostic (CAD) system has been developed to assist radiologist for early detection and analysis of lung nodules. For pulmonary nodule detection, image preprocessing is required to remove the anatomical structure of lung parenchyma and to enhance the visibility of pulmonary nodules. In this paper a hybrid preprocessing technique using geometry based diffusion and selective enhancement filtering have been proposed. This technique provides a unified preprocessing framework for solid nodule as well as ground glass opacity (GGO) nodules. Geometry based diffusion is applied to smooth the images by preserving the boundary. In order to improve the sensitivity of pulmonary nodule detection, selective enhancement filter is used to highlight blob like structure. But selective enhancement filter sometimes enhances the structures like blood vessel and airways other than nodule and results in large number of false positive. In first step, geometry based diffusion (GBD) is applied for reduction of false positive and in second step, selective enhancement filtering is used for further reduction of false negative. Geometry based diffusion and selective enhancement filtering has been used as preprocessing step separately but their combined effect was not investigated earlier. This hybrid preprocessing approach is suitable for accurate calculation of voxel based features. The proposed method has been validated on one public database named Lung Image Database Consortium (LIDC) containing 50 nodules (30 solid and 20 GGO nodule) from 30 subjects and one private database containing 40 nodules (25 solid and 15 GGO nodule) from 30 subjects.
Evaluation of Methods to Correct for IR Loss in Eppley PSP Diffuse Measurements
Vignola, F.; Long, Charles N.; Reda, I.
2007-09-13
The IR loss in diffuse measurements made by thermopile pyranometers is examined. Diffuse measurements are used for the study of IR losses to minimize the effects of beam irradiance and therefore much of the cosine response error influences. Specifically, diffuse measurements of an Eppley PSP pyranometer are compared to those made with a Schenk Star pyranometer. Eppley B&W and Star type pyranometers suffer minimal IR loss because the reference and receiving junctions of the thermopile are at the same thermal level. The difference between diffuse values can be attributed to calibration and cosine response errors as well as IR loss. Therefore it is necessary to separate out the various sources of error and examination of the differences over various times of the year can help, at least for systematic errors. Several methods of correcting for IR loss will be examined. First subtracting out the average nighttime offset during the day will be tested. Next an extrapolation between early morning and late evening offsets will be tested. This should help eliminate the IR offset in both the morning and evening, but underestimate the IR losses during the rest of the day. Correlations of the remaining IR losses with temperature, relative humidity, and irradiance will be evaluated. In addition, the IR losses will be studied both for clear days and for totally overcast periods. Pyrgeometer measurements will also be compared to the estimated IR losses. The above measurements and comparisons will help quantify the magnitude and variation of the IR losses.
Physics-based preconditioning and the Newton-Krylov method for non-equilibrium radiation diffusion
Mousseau, V.A.; Knoll, D.A.; Rider, W.J.
2000-05-20
An algorithm is presented for the solution of the time dependent reaction-diffusion systems which arise in non-equilibrium radiation diffusion applications. This system of nonlinear equations is solved by coupling three numerical methods, Jacobian-free Newton-Krylov, operator splitting, and multigrid linear solvers. An inexact Newton's method is used to solve the system of nonlinear equations. Since building the Jacobian matrix for problems of interest can be challenging, the authors employ a Jacobian-free implementation of Newton's method, where the action of the Jacobian matrix on a vector is approximated by a first order Taylor series expansion. Preconditioned generalized minimal residual (PGMRES) is the Krylov method used to solve the linear systems that come from the iterations of Newton's method. The preconditioner in this solution method is constructed using a physics-based divide and conquer approach, often referred to as operator splitting. This solution procedure inverts the scalar elliptic systems that make up the preconditioner using simple multigrid methods. The preconditioner also addresses the strong coupling between equations with local 2 x 2 block solves. The intra-cell coupling is applied after the inter-cell coupling has already been addressed by the elliptic solves. Results are presented using this solution procedure that demonstrate its efficiency while incurring minimal memory requirements.
Boardman, Allison; Jayawardena, Asitha; Oprescu, Florin; Cook, Thomas; Morcuende, Jose A
2011-01-01
The Ponseti method for correcting clubfoot is a safe, effective, and minimally invasive treatment that has recently been implemented in Latin America. This study evaluates the initial impact and unique barriers to the diffusion of the Ponseti method throughout this region. Structured interviews were conducted with 30 physicians practicing the Ponseti method in three socioeconomically diverse countries: Chile, Peru and Guatemala. Since learning the Ponseti method, these physicians have treated approximately 1,740 clubfoot patients, with an estimated 1,705 (98%) patients treated using the Ponseti method, and 35 (2%) patients treated using surgical techniques. The barriers were classified into the following themes: physician education, health care system of the country, culture and beliefs of patients, physical distance and transport, financial barriers for patients, and parental compliance with the method. The results yielded several common barriers throughout Latin America including lack of physician education, physical distance to the treatment centers, and financial barriers for patients. Information from this study can be used to inform, and to implement and evaluate specific strategies to improve the diffusion of the Ponseti method for treating clubfoot throughout Latin America. PMID:22096416
Computing quasi-linear diffusion coefficients using the delta-f particle-in-cell method
Austin, T. M.; Smithe, D. N.; Ranjbar, V.
2009-11-26
Linear wave codes AORSA and TORIC couple to the bounce-averaged nonlinear Fokker-Planck code CQL3D through quasi-linear diffusion coefficients. Both linear wave codes rely on the quasi-local approximation that includes only first-order parallel and perpendicular gradient variations of cyclotron frequency and ignores field line curvature along with temperature and density gradient effects. The delta-f particle-in-cell (DFPIC) method has been successfully used for simulating ion-cyclotron fast wave behavior. This method also permits particle behavior such as multiple pass resonance, banana orbits, and superadiabaticity. We present new work on generating quasi-linear diffusion coefficients using the DFPIC method that will permit the electromagnetic particle-in-cell (EMPIC) code, VORPAL, to couple to CQL3D and to compare to AORSA and TORIC. A new multiple weight delta-f approach will be presented that converts velocity derivatives to action derivatives and yields a full tensor quasi-linear diffusion coefficient.
Contribution to an effective design method for stationary reaction-diffusion patterns.
Szalai, István; Horváth, Judit; De Kepper, Patrick
2015-06-01
The British mathematician Alan Turing predicted, in his seminal 1952 publication, that stationary reaction-diffusion patterns could spontaneously develop in reacting chemical or biochemical solutions. The first two clear experimental demonstrations of such a phenomenon were not made before the early 1990s when the design of new chemical oscillatory reactions and appropriate open spatial chemical reactors had been invented. Yet, the number of pattern producing reactions had not grown until 2009 when we developed an operational design method, which takes into account the feeding conditions and other specificities of real open spatial reactors. Since then, on the basis of this method, five additional reactions were shown to produce stationary reaction-diffusion patterns. To gain a clearer view on where our methodical approach on the patterning capacity of a reaction stands, numerical studies in conditions that mimic true open spatial reactors were made. In these numerical experiments, we explored the patterning capacity of Rabai's model for pH driven Landolt type reactions as a function of experimentally attainable parameters that control the main time and length scales. Because of the straightforward reversible binding of protons to carboxylate carrying polymer chains, this class of reaction is at the base of the chemistry leading to most of the stationary reaction-diffusion patterns presently observed. We compare our model predictions with experimental observations and comment on agreements and differences. PMID:26117122
Contribution to an effective design method for stationary reaction-diffusion patterns
NASA Astrophysics Data System (ADS)
Szalai, István; Horváth, Judit; De Kepper, Patrick
2015-06-01
The British mathematician Alan Turing predicted, in his seminal 1952 publication, that stationary reaction-diffusion patterns could spontaneously develop in reacting chemical or biochemical solutions. The first two clear experimental demonstrations of such a phenomenon were not made before the early 1990s when the design of new chemical oscillatory reactions and appropriate open spatial chemical reactors had been invented. Yet, the number of pattern producing reactions had not grown until 2009 when we developed an operational design method, which takes into account the feeding conditions and other specificities of real open spatial reactors. Since then, on the basis of this method, five additional reactions were shown to produce stationary reaction-diffusion patterns. To gain a clearer view on where our methodical approach on the patterning capacity of a reaction stands, numerical studies in conditions that mimic true open spatial reactors were made. In these numerical experiments, we explored the patterning capacity of Rabai's model for pH driven Landolt type reactions as a function of experimentally attainable parameters that control the main time and length scales. Because of the straightforward reversible binding of protons to carboxylate carrying polymer chains, this class of reaction is at the base of the chemistry leading to most of the stationary reaction-diffusion patterns presently observed. We compare our model predictions with experimental observations and comment on agreements and differences.
Neutron matter at zero temperature with an auxiliary field diffusion Monte Carlo method
NASA Astrophysics Data System (ADS)
Sarsa, A.; Fantoni, S.; Schmidt, K. E.; Pederiva, F.
2003-08-01
The recently developed auxiliary field diffusion Monte Carlo method is applied to compute the equation of state and the compressibility of neutron matter. By combining diffusion Monte Carlo method for the spatial degrees of freedom and auxiliary field Monte Carlo method to separate the spin-isospin operators, quantum Monte Carlo can be used to simulate the ground state of many-nucleon systems (A?100). We use a path constraint to control the fermion sign problem. We have made simulations for realistic interactions, which include tensor and spin-orbit two-body potentials as well as three-nucleon forces. The Argonne v'8 and v'6 two-nucleon potentials plus the Urbana or Illinois three-nucleon potentials have been used in our calculations. We compare with fermion hypernetted chain results. We report on the results of a periodic box fermi hypernetted chain calculation, which is also used to estimate the finite size corrections to our quantum Monte Carlo simulations. Our auxiliary field diffusion Monte Carlo (AFDMC) results for v6 models of pure neutron matter are in reasonably good agreement with equivalent correlated basis function (CBF) calculations, providing energies per particle which are slightly lower than the CBF ones. However, the inclusion of the spin-orbit force leads to quite different results particularly at relatively high densities. The resulting equation of state from AFDMC calculations is harder than the one from previous Fermi hypernetted chain studies commonly used to determine the neutron star structure.
Method and apparatus for determining minority carrier diffusion length in semiconductors
Goldstein, Bernard (Princeton, NJ); Dresner, Joseph (Princeton, NJ); Szostak, Daniel J. (Mercerville, NJ)
1983-07-12
Method and apparatus are provided for determining the diffusion length of minority carriers in semiconductor material, particularly amorphous silicon which has a significantly small minority carrier diffusion length using the constant-magnitude surface-photovoltage (SPV) method. An unmodulated illumination provides the light excitation on the surface of the material to generate the SPV. A manually controlled or automatic servo system maintains a constant predetermined value of the SPV. A vibrating Kelvin method-type probe electrode couples the SPV to a measurement system. The operating optical wavelength of an adjustable monochromator to compensate for the wavelength dependent sensitivity of a photodetector is selected to measure the illumination intensity (photon flux) on the silicon. Measurements of the relative photon flux for a plurality of wavelengths are plotted against the reciprocal of the optical absorption coefficient of the material. A linear plot of the data points is extrapolated to zero intensity. The negative intercept value on the reciprocal optical coefficient axis of the extrapolated linear plot is the diffusion length of the minority carriers.
A deterministic particle method for one-dimensional reaction-diffusion equations
NASA Technical Reports Server (NTRS)
Mascagni, Michael
1995-01-01
We derive a deterministic particle method for the solution of nonlinear reaction-diffusion equations in one spatial dimension. This deterministic method is an analog of a Monte Carlo method for the solution of these problems that has been previously investigated by the author. The deterministic method leads to the consideration of a system of ordinary differential equations for the positions of suitably defined particles. We then consider the time explicit and implicit methods for this system of ordinary differential equations and we study a Picard and Newton iteration for the solution of the implicit system. Next we solve numerically this system and study the discretization error both analytically and numerically. Numerical computation shows that this deterministic method is automatically adaptive to large gradients in the solution.
A model assay to demonstrate how intrinsic factors affect diffusion of bacteriocins.
Blom, H; Katla, T; Hagen, B F; Axelsson, L
1997-09-16
A rapid and simple method to elucidate how intrinsic factors in a given food product affect bacteriocin diffusion and efficacy is described. The basic idea of this assay is to help predict which bacteriocin or other inhibitory substance to select for a given product, where increased security towards specific microorganisms is wanted. In an agar plate model system the effect of five factors (number of indicator cells, pH and concentration of NaCl, agar and soy oil) on the diffusion of the bacteriocins sakacin A, sakacin P, pediocin PA-1, piscicolin 61 and nisin was studied. An experimental design permitting simultaneous evaluation of the effect of all factors was used. The results indicated that each bacteriocin has a characteristic intrinsic factor effect profile. However, pH and load of indicator cells affect all the bacteriocins. PMID:9506275
Yücesoy, M; Esen, N; Yulu?, N
2001-08-01
This study was performed to investigate the use of chromogenic tube and methyl blue-Sabouraud agar for the presumptive identification of Candida albicans. 124 clinical isolates, including 111 C.albicans and 13 Candida spp strains, which had been identified by morphology on cornmeal tween 80 agar and Vitek automated identification system, were included. Three different identification procedures, a) germ tube test, b) chromogenic tube test by using CHROMagar Candida and c) methyl blue-Sabouraud agar test, were performed to the strains. 88 of 111 (79.3%) C.albicans strains were detected to be positive by germ tube test. 87 (78.4%), 97 (87.4%) and 102 (91.9%) of these isolates were identified as C.albicans by chromogenic tube test after 2, 8 and 24 hours of incubation, respectively. 88 (79.3%), 92 (82.9%) and 88 (79.3%) of the isolates were correctly identified as C.albicans by methyl blue-Sabouraud agar test after 2, 8 and 24 hours of incubation, respectively. The sensitivity and specificity values were found to be 79.3 and 69.2 for the germ tube test. These values ranged between 78.4-91.9% and 69.2-76.9% for chromogenic tube test and 79.3-82.9% and 76.9-84.6% for methyl blue-Sabouraud agar depending on the incubation period. It can be concluded that the use of chromogenic tube and methyl blue-Sabouraud agar are rapid, simple and objective methods for the identification of C.albicans strains. PMID:11733655
NASA Astrophysics Data System (ADS)
Zhang, Xiaofeng
2012-03-01
Image formation in fluorescence diffuse optical tomography is critically dependent on construction of the Jacobian matrix. For clinical and preclinical applications, because of the highly heterogeneous characteristics of the medium, Monte Carlo methods are frequently adopted to construct the Jacobian. Conventional adjoint Monte Carlo method typically compute the Jacobian by multiplying the photon density fields radiated from the source at the excitation wavelength and from the detector at the emission wavelength. Nonetheless, this approach assumes that the source and the detector in Green's function are reciprocal, which is invalid in general. This assumption is particularly questionable in small animal imaging, where the mean free path length of photons is typically only one order of magnitude smaller than the representative dimension of the medium. We propose a new method that does not rely on the reciprocity of the source and the detector by tracing photon propagation entirely from the source to the detector. This method relies on the perturbation Monte Carlo theory to account for the differences in optical properties of the medium at the excitation and the emission wavelengths. Compared to the adjoint methods, the proposed method is more valid in reflecting the physical process of photon transport in diffusive media and is more efficient in constructing the Jacobian matrix for densely sampled configurations.
Atzberger, Paul J. [University of California, Department of Mathematics, Santa Barbara, CA 93106 (United States)], E-mail: atzberg@math.ucsb.edu
2010-05-01
Stochastic partial differential equations are introduced for the continuum concentration fields of reaction-diffusion systems. The stochastic partial differential equations account for fluctuations arising from the finite number of molecules which diffusively migrate and react. Spatially adaptive stochastic numerical methods are developed for approximation of the stochastic partial differential equations. The methods allow for adaptive meshes with multiple levels of resolution, Neumann and Dirichlet boundary conditions, and domains having geometries with curved boundaries. A key issue addressed by the methods is the formulation of consistent discretizations for the stochastic driving fields at coarse-refined interfaces of the mesh and at boundaries. Methods are also introduced for the efficient generation of the required stochastic driving fields on such meshes. As a demonstration of the methods, investigations are made of the role of fluctuations in a biological model for microorganism direction sensing based on concentration gradients. Also investigated, a mechanism for spatial pattern formation induced by fluctuations. The discretization approaches introduced for SPDEs have the potential to be widely applicable in the development of numerical methods for the study of spatially extended stochastic systems.
Mupirocin-mucin agar for selective enumeration of Bifidobacterium bifidum.
Pechar, Radko; Rada, Vojtech; Parafati, Lucia; Musilova, Sarka; Bunesova, Vera; Vlkova, Eva; Killer, Jiri; Mrazek, Jakub; Kmet, Vladimir; Svejstil, Roman
2014-11-17
Bifidobacterium bifidum is a bacterial species exclusively found in the human intestinal tract. This species is becoming increasingly popular as a probiotic organism added to lyophilized products. In this study, porcine mucin was used as the sole carbon source for the selective enumeration of B. bifidum in probiotic food additives. Thirty-six bifidobacterial strains were cultivated in broth with mucin. Only 13 strains of B. bifidum utilized the mucin to produce acids. B. bifidum was selectively enumerated in eight probiotic food supplements using agar (MM agar) containing mupirocin (100 mg/L) and mucin (20 g/L) as the sole carbon source. MM agar was fully selective if the B. bifidum species was presented together with Bifidobacterium animalis subsp. lactis, Bifidobacterium breve, and Bifidobacterium longum subsp. longum species and with lactic acid bacteria (lactobacilli, streptococci). Isolated strains of B. bifidum were identified using biochemical, PCR, MALDI-TOF procedures and 16S rRNA gene sequencing. The novel selective medium was also suitable for the isolation of B. bifidum strains from human fecal samples. PMID:25217723
Numerical methods of solving a system of multi-dimensional nonlinear equations of the diffusion type
NASA Technical Reports Server (NTRS)
Agapov, A. V.; Kolosov, B. I.
1979-01-01
The principles of conservation and stability of difference schemes achieved using the iteration control method were examined. For the schemes obtained of the predictor-corrector type, the conversion was proved for the control sequences of approximate solutions to the precise solutions in the Sobolev metrics. Algorithms were developed for reducing the differential problem to integral relationships, whose solution methods are known, were designed. The algorithms for the problem solution are classified depending on the non-linearity of the diffusion coefficients, and practical recommendations for their effective use are given.
An implicit method for radiative transfer with the diffusion approximation in SPH
Serge Viau; Pierre Bastien; Seung-Hoon Cha
2006-02-06
An implicit method for radiative transfer in SPH is described. The diffusion approximation is used, and the hydrodynamic calculations are performed by a fully three--dimensional SPH code. Instead of the energy equation of state for an ideal gas, various energy states and the dissociation of hydrogen molecules are considered in the energy calculation for a more realistic temperature and pressure determination. In order to test the implicit code, we have performed non--isothermal collapse simulations of a centrally condensed cloud, and have compared our results with those of finite difference calculations performed by MB93. The results produced by the two completely different numerical methods agree well with each other.
Eric Mittelstaedt; Anne Davaille; Peter E. van Keken; Nuno Gracias; Javier Escartin
2010-01-01
Diffuse flow velocimetry (DFV) is introduced as a new, noninvasive, optical technique for measuring the velocity of diffuse hydrothermal flow. The technique uses images of a motionless, random medium (e.g., rocks) obtained through the lens of a moving refraction index anomaly (e.g., a hot upwelling). The method works in two stages. First, the changes in apparent background deformation are calculated
Chen, Li; Zhang, Lei; Kang, Qinjun; Viswanathan, Hari S.; Yao, Jun; Tao, Wenquan
2015-01-01
Porous structures of shales are reconstructed using the markov chain monte carlo (MCMC) method based on scanning electron microscopy (SEM) images of shale samples from Sichuan Basin, China. Characterization analysis of the reconstructed shales is performed, including porosity, pore size distribution, specific surface area and pore connectivity. The lattice Boltzmann method (LBM) is adopted to simulate fluid flow and Knudsen diffusion within the reconstructed shales. Simulation results reveal that the tortuosity of the shales is much higher than that commonly employed in the Bruggeman equation, and such high tortuosity leads to extremely low intrinsic permeability. Correction of the intrinsic permeability is performed based on the dusty gas model (DGM) by considering the contribution of Knudsen diffusion to the total flow flux, resulting in apparent permeability. The correction factor over a range of Knudsen number and pressure is estimated and compared with empirical correlations in the literature. For the wide pressure range investigated, the correction factor is always greater than 1, indicating Knudsen diffusion always plays a role on shale gas transport mechanisms in the reconstructed shales. Specifically, we found that most of the values of correction factor fall in the slip and transition regime, with no Darcy flow regime observed. PMID:25627247
Chen, Li; Zhang, Lei; Kang, Qinjun; Viswanathan, Hari S; Yao, Jun; Tao, Wenquan
2015-01-01
Porous structures of shales are reconstructed using the markov chain monte carlo (MCMC) method based on scanning electron microscopy (SEM) images of shale samples from Sichuan Basin, China. Characterization analysis of the reconstructed shales is performed, including porosity, pore size distribution, specific surface area and pore connectivity. The lattice Boltzmann method (LBM) is adopted to simulate fluid flow and Knudsen diffusion within the reconstructed shales. Simulation results reveal that the tortuosity of the shales is much higher than that commonly employed in the Bruggeman equation, and such high tortuosity leads to extremely low intrinsic permeability. Correction of the intrinsic permeability is performed based on the dusty gas model (DGM) by considering the contribution of Knudsen diffusion to the total flow flux, resulting in apparent permeability. The correction factor over a range of Knudsen number and pressure is estimated and compared with empirical correlations in the literature. For the wide pressure range investigated, the correction factor is always greater than 1, indicating Knudsen diffusion always plays a role on shale gas transport mechanisms in the reconstructed shales. Specifically, we found that most of the values of correction factor fall in the slip and transition regime, with no Darcy flow regime observed. PMID:25627247
NASA Astrophysics Data System (ADS)
Chen, Li; Zhang, Lei; Kang, Qinjun; Viswanathan, Hari S.; Yao, Jun; Tao, Wenquan
2015-01-01
Porous structures of shales are reconstructed using the markov chain monte carlo (MCMC) method based on scanning electron microscopy (SEM) images of shale samples from Sichuan Basin, China. Characterization analysis of the reconstructed shales is performed, including porosity, pore size distribution, specific surface area and pore connectivity. The lattice Boltzmann method (LBM) is adopted to simulate fluid flow and Knudsen diffusion within the reconstructed shales. Simulation results reveal that the tortuosity of the shales is much higher than that commonly employed in the Bruggeman equation, and such high tortuosity leads to extremely low intrinsic permeability. Correction of the intrinsic permeability is performed based on the dusty gas model (DGM) by considering the contribution of Knudsen diffusion to the total flow flux, resulting in apparent permeability. The correction factor over a range of Knudsen number and pressure is estimated and compared with empirical correlations in the literature. For the wide pressure range investigated, the correction factor is always greater than 1, indicating Knudsen diffusion always plays a role on shale gas transport mechanisms in the reconstructed shales. Specifically, we found that most of the values of correction factor fall in the slip and transition regime, with no Darcy flow regime observed.
GPU-Accelerated Finite Element Method for Modelling Light Transport in Diffuse Optical Tomography.
Schweiger, Martin
2011-01-01
We introduce a GPU-accelerated finite element forward solver for the computation of light transport in scattering media. The forward model is the computationally most expensive component of iterative methods for image reconstruction in diffuse optical tomography, and performance optimisation of the forward solver is therefore crucial for improving the efficiency of the solution of the inverse problem. The GPU forward solver uses a CUDA implementation that evaluates on the graphics hardware the sparse linear system arising in the finite element formulation of the diffusion equation. We present solutions for both time-domain and frequency-domain problems. A comparison with a CPU-based implementation shows significant performance gains of the graphics accelerated solution, with improvements of approximately a factor of 10 for double-precision computations, and factors beyond 20 for single-precision computations. The gains are also shown to be dependent on the mesh complexity, where the largest gains are achieved for high mesh resolutions. PMID:22013431
Dating of iron gall ink using the dissolution-diffusion method.
Li, Biao; Xie, Peng
2015-03-01
In many criminal and civil cases, some questioned documents are written with iron gall ink. Determining the date when an iron gall ink entry was written can be important to assess the authenticity of a document. A dissolution-diffusion method was successfully employed to draw aging curves of iron gall ink entries stored in controlled conditions over 40 months. Calibration curves were created to indicate the relationship between the average dissolution-diffusion rate of ink components and the age of ink entries stored under natural aging conditions. As preliminary findings of this study, the mixed solution of dimethyl formamide (DMF) and anhydrous ethanol was suitable to dissolve the dye of iron gall ink strokes made at different time. It was also determined that brands of iron gall inks, types of paper, and thickness of iron gall ink strokes had varying impacts on estimating the dates of iron gall ink strokes. PMID:25677356
Engle, Mark A.; Olea, Ricardo A.; O'Keefe, Jennifer M. K.; Hower, James C.; Geboy, Nicholas J.
2013-01-01
Coal fires occur in nature spontaneously, contribute to increases in greenhouse gases, and emit atmospheric toxicants. Increasing interest in quantifying coal fire emissions has resulted in the adaptation and development of specialized approaches and adoption of numerical modeling techniques. Overview of these methods for direct estimation of diffuse gas emissions from coal fires is presented in this paper. Here we take advantage of stochastic Gaussian simulation to interpolate CO2 fluxes measured using a dynamic closed chamber at the Ruth Mullins coal fire in Perry County, Kentucky. This approach allows for preparing a map of diffuse gas emissions, one of the two primary ways that gases emanate from coal fires, and establishing the reliability of the study both locally and for the entire fire. Future research directions include continuous and automated sampling to improve quantification of gaseous coal fire emissions.
A tracer-based inversion method for diagnosing eddy-induced diffusivity and advection
NASA Astrophysics Data System (ADS)
Bachman, S. D.; Fox-Kemper, B.; Bryan, F. O.
2015-02-01
A diagnosis method is presented which inverts a set of tracer flux statistics into an eddy-induced transport intended to apply for all tracers. The underlying assumption is that a linear flux-gradient relationship describes eddy-induced tracer transport, but a full tensor coefficient is assumed rather than a scalar coefficient which allows for down-gradient and skew transports. Thus, Lagrangian advection and anisotropic diffusion not necessarily aligned with the tracer gradient can be diagnosed. In this method, multiple passive tracers are initialized in an eddy-resolving flow simulation. Their spatially-averaged gradients form a matrix, where the gradient of each tracer is assumed to satisfy an identical flux-gradient relationship. The resulting linear system, which is overdetermined when using more than three tracers, is then solved to obtain an eddy transport tensor R which describes the eddy advection (antisymmetric part of R) and potentially anisotropic diffusion (symmetric part of R) in terms of coarse-grained variables. The mathematical basis for this inversion method is presented here, along with practical guidelines for its implementation. We present recommendations for initialization of the passive tracers, maintaining the required misalignment of the tracer gradients, correcting for nonconservative effects, and quantifying the error in the diagnosed transport tensor. A method is proposed to find unique, tracer-independent, distinct rotational and divergent Lagrangian transport operators, but the results indicate that these operators are not meaningfully relatable to tracer-independent eddy advection or diffusion. With the optimal method of diagnosis, the diagnosed transport tensor is capable of predicting the fluxes of other tracers that are withheld from the diagnosis, including even active tracers such as buoyancy, such that relative errors of 14% or less are found.
Oosterveld, B J; Thijssen, J M; Hartman, P C; Romijn, R L; Rosenbusch, G J
1991-08-01
A study was performed to find and test quantitative methods of analysing echographic signals for the differentiation of diffuse liver diseases. An on-line data acquisition system was used to acquire radiofrequency (RF) echo signals from volunteers and patients. Several methods to estimate the frequency-dependent attenuation coefficient were evaluated, in which a correction for the frequency and depth-dependent diffraction and focusing effects caused by the sound beam was applied. Using the estimated value of the attenuation coefficient the RF signals themselves were corrected to remove the depth dependencies caused by the sound beam and by the frequency-dependent attenuation. After this preprocessing the envelope of the corrected RF signals was calculated and B-mode images were reconstructed. The texture was analysed in the axial direction by first- and second-order statistical methods. The accuracy and precision of the attenuation methods were assessed by using computer simulated RF signals and RF data obtained from a tissue-mimicking phantom. The phantom measurements were also used to test the performance of the methods to correct for the depth dependencies. The echograms of 163 persons, both volunteers and patients suffering from a diffuse liver disease (cirrhosis, hepatitis, haemochromatosis), were recorded. The mutual correlations between the estimated parameters were used to preselect parameters contributing independent information, and which can subsequently be used in a discriminant analysis to differentiate between the various diseased conditions. PMID:1924541
NASA Astrophysics Data System (ADS)
Price, H. C.; Murray, B. J.; Mattsson, J.; O'Sullivan, D.; Wilson, T. W.; Baustian, K. J.; Benning, L. G.
2014-04-01
Recent research suggests that under certain temperature and relative humidity conditions atmospheric aerosol may be present in the form of a glassy solid. In order to understand the impacts that this may have on aerosol-cloud interactions and atmospheric chemistry, knowledge of water diffusion within such aerosol particles is required. Here, a method is described in which Raman spectroscopy is used to observe D2O diffusion in high-viscosity aqueous solutions, enabling a quantitative assessment of water diffusion coefficients, Dwater, as a function of relative humidity. Results for sucrose solutions compare well with literature data at 23.5 ± 0.3 °C, and demonstrate that water diffusion is slow (Dwater ~5 × 10-17 m2 s-1), but not arrested, just below the glass transition at a water activity of 0.2. Room temperature water diffusion coefficients are also presented for aqueous levoglucosan and an aqueous mixture of raffinose, dicarboxylic acids and ammonium sulphate: at low humidity, diffusion is retarded but still occurs on millisecond to second timescales in atmospherically relevant-sized particles. The effect of gel formation on diffusion in magnesium sulfate solutions is shown to be markedly different from the gradual decrease in diffusion coefficients of highly viscous liquids. We show that using the Stokes-Einstein equation to determine diffusion timescales from viscosity leads to values which are more than 5 orders of magnitude too big, which emphasises the need to make measurements of diffusion coefficients. In addition, comparison of bounce fraction data for levoglucosan with measured diffusion data reveals that even when particles bounce the diffusion timescales for water are a fraction of a second for a 100 nm particle. This suggests a high bounce fraction does not necessarily indicate retarded water diffusion.
Self-feeding MUSE: a robust method for high resolution diffusion imaging using interleaved EPI.
Zhang, Zhe; Huang, Feng; Ma, Xiaodong; Xie, Sheng; Guo, Hua
2015-01-15
Single-shot echo planar imaging (EPI) with parallel imaging techniques has been well established as the most popular method for clinical diffusion imaging, due to its fast acquisition and motion insensitivity. However, this approach is limited by the relatively low spatial resolution and image distortion. Interleaved EPI is able to break the limitations but the phase variations among different shots must be considered for artifact suppression. The introduction of multiplexed sensitivity-encoding (MUSE) can address the phase issue using sensitivity encoding (SENSE) for self-navigation of each interleave. However, MUSE has suboptimal results when the number of shots is high. To achieve higher spatial resolution and lower geometric distortion, we introduce two new schemes into the MUSE framework: 1) a self-feeding mechanism is adopted by using prior information regularized SENSE in order to obtain reliable phase estimation; and 2) retrospective motion detection and data rejection strategies are performed to exclude unusable data corrupted by severe pulsatile motions. The proposed method is named self-feeding MUSE (SF-MUSE). Experiments on healthy volunteers demonstrate that this new SF-MUSE approach provides more accurate motion-induced phase estimation and fewer artifacts caused by data corruption when compared with the original MUSE method. SF-MUSE is a robust method for high resolution diffusion imaging and suitable for practical applications with reasonable scan time. PMID:25451470
Localized axial Green's function method for the convection-diffusion equations in arbitrary domains
NASA Astrophysics Data System (ADS)
Lee, Wanho; Kim, Do Wan
2014-10-01
A localized axial Green's function method (LAGM) is proposed for the convection-diffusion equation. The axial Green's function method (AGM) enables us to calculate the numerical solution of a multi-dimensional problem using only one-dimensional Green's functions for the axially split differential operators. This AGM has been developed not only for the elliptic boundary value problems but also for the steady Stokes flows, however, this paper is concerned with the localization of the AGM. This localization of the method is needed for practical purpose when computing the axial Green's function, specifically for the convection-diffusion equation on a line segment that we call the local axial line. Although our focus is mainly on the convection-dominated cases in arbitrary domains, this method can solve other cases in a unified way. Numerical results show that, despite irregular types of discretization on an arbitrary domain, we can calculate the numerical solutions using the LAGM without loss of accuracy even in cases of large convection. In particular, it is also shown that randomly distributed axial lines are available in our LAGM and complicated domains are not a burden.
Liu, Changchun; Sadik, Mohamed M; Mauk, Michael G; Edelstein, Paul H; Bushman, Frederic D; Gross, Robert; Bau, Haim H
2014-01-01
Real-time amplification and quantification of specific nucleic acid sequences plays a major role in medical and biotechnological applications. In the case of infectious diseases, such as HIV, quantification of the pathogen-load in patient specimens is critical to assess disease progression and effectiveness of drug therapy. Typically, nucleic acid quantification requires expensive instruments, such as real-time PCR machines, which are not appropriate for on-site use and for low-resource settings. This paper describes a simple, low-cost, reaction-diffusion based method for end-point quantification of target nucleic acids undergoing enzymatic amplification. The number of target molecules is inferred from the position of the reaction-diffusion front, analogous to reading temperature in a mercury thermometer. The method was tested for HIV viral load monitoring and performed on par with conventional benchtop methods. The proposed method is suitable for nucleic acid quantification at point of care, compatible with multiplexing and high-throughput processing, and can function instrument-free. PMID:25477046
Albanese, Claudio
A Numerical Method for Pricing Electricity Derivatives for Jump-Diffusion Processes Based.tompaidis@mccombs.utexas.edu Corresponding author. Tel. 512-4715252, Fax 512-4710587. #12;A Numerical Method for Pricing Electricity method for pricing derivatives on electricity prices. The method is based on approximating the generator
Syst. Biol. 49(2):278305, 2000 Phylogenetic Relationships of Agaric Fungi
Lutzoni, François M.
Syst. Biol. 49(2):278305, 2000 278 Phylogenetic Relationships of Agaric Fungi Based on Nuclear groups within the order. The earliest classification system for agar- ics and other basidiomycetes to the solution of problems. Singer, (1986:viii) Whence cometh the Agarics? Miller and Watling (1987) 1Present
NASA Astrophysics Data System (ADS)
Zendejas, Gerardo; Chiasson, Mike
This paper will propose and explore a method to enhance focal actors' abilities to enroll and control the many social and technical components interacting during the initiation, production, and diffusion of innovations. The reassembling and stabilizing of such components is the challenging goal of the focal actors involved in these processes. To address this possibility, a healthcare project involving the initiation, production, and diffusion of an IT-based innovation will be influenced by the researcher, using concepts from actor network theory (ANT), within an action research methodology (ARM). The experiences using this method, and the nature of enrolment and translation during its use, will highlight if and how ANT can provide a problem-solving method to help assemble the social and technical actants involved in the diffusion of an innovation. Finally, the paper will discuss the challenges and benefits of implementing such methods to attain widespread diffusion.
Lattice simulation method to model diffusion and NMR spectra in porous materials
NASA Astrophysics Data System (ADS)
Merlet, Céline; Forse, Alexander C.; Griffin, John M.; Frenkel, Daan; Grey, Clare P.
2015-03-01
A coarse-grained simulation method to predict nuclear magnetic resonance (NMR) spectra of ions diffusing in porous carbons is proposed. The coarse-grained model uses input from molecular dynamics simulations such as the free-energy profile for ionic adsorption, and density-functional theory calculations are used to predict the NMR chemical shift of the diffusing ions. The approach is used to compute NMR spectra of ions in slit pores with pore widths ranging from 2 to 10 nm. As diffusion inside pores is fast, the NMR spectrum of an ion trapped in a single mesopore will be a sharp peak with a pore size dependent chemical shift. To account for the experimentally observed NMR line shapes, our simulations must model the relatively slow exchange between different pores. We show that the computed NMR line shapes depend on both the pore size distribution and the spatial arrangement of the pores. The technique presented in this work provides a tool to extract information about the spatial distribution of pore sizes from NMR spectra. Such information is difficult to obtain from other characterisation techniques.
NASA Astrophysics Data System (ADS)
García-Ruiz, J. M.; Novella, M. L.; Otálora, F.
1999-01-01
We present experimental observation of the spatio-temporal pattern of supersaturation in counter-diffusion methods. These complex patterns were recorded by dynamical interferometric analysis using a Mach-Zehnder configuration. Tetragonal hen egg white lysozyme crystals were grown inside APCF (advanced protein crystallisation facility) reactors. Salt and protein diffusion profiles were obtained independently by performing duplicated experiments with and without protein in the protein chamber; salt gradients were observed directly while protein concentration profiles are computed from the differences in refractive index between the two experiments. As expected from computer simulations, the time evolution of supersaturation shows a maximum about 45 h after activation (although this value can change as a function of the starting conditions and the geometry of the reactor). Nucleation takes place before this maximum supersaturation is reached. This explains the trend of the growth rate versus time curves for experiments performed within APCF reactors (both on ground and in space) and in capillaries by the gel acupuncture technique. By using very low concentration agarose gel in the protein chamber, sedimentation and buoyancy effects are eliminated so that the effects of gravity on fluid dynamics and hence on the spatio-temporal evolution of supersaturation can be assessed. These results confirm experimentally the predicted behaviour of counter-diffusion systems and support their use in growing large high-quality protein single crystals.
A method to analyze the diffuse gamma-ray emission with the Fermi Large Area Telescope
Ackermann, Markus; Johannesson, Gueolaugur; Digel, Seth; Moskalenko, Igor V.; Reimer, Olaf; Porter, Troy; Strong, Andrew
2008-12-24
The Fermi Gamma-Ray Space Telescope with its main instrument the LAT is the most sensitive {gamma}-ray telescope in the energy region between 30 MeV and 100 GeV. One of the prime scientific goals of this mission is the measurement and interpretation of the diffuse Galactic and extragalactic {gamma}-ray emission. While not limited by photon statistics, this analysis presents several challenges: Instrumental response functions, residual background from cosmic rays as well as resolved and unresolved foreground {gamma}-ray sources have to be taken carefully into account in the interpretation of the data. Detailed modeling of the diffuse {gamma}-ray emission is being performed and will form the basis of the investigations. We present the analysis approach to be applied to the Fermi LAT data, namely the modeling of the diffuse emission components and the background contributions, followed by an all-sky maximum-likelihood fitting procedure. We also report on the performance of this method evaluated in tests on simulated Fermi LAT and real EGRET data.
[Evaluation of the apical seal of endodontically treated teeth by the ion-diffusion method].
Chen, B F; Hsieh, C C; Wu, S J; Liu, C C
1993-06-01
It is generally accepted that improper preparation of the post space in endodontically treated teeth may damage sealing of the filling and cause treatment failure. Conventional method of detecting the sealing ability of endodontically treated teeth are quite complicated and inconvenient. To avoid the shortcomings of these traditional methods, the law of diffusion was adopted in this experimental design, and the results were compared with those of the traditional dye penetration method. Fifty sound molar teeth were treated by routine endodontic procedures, and were instrumented to 35# endodontic file. In 20 teeth in the control group, half were treated as a positive control by leaving the apical foramen open, and the remaining half were used as a negative control by sealing the foramen with two layers of nail polish. The other 30 experimental teeth were filled with gutta-percha points and sealer Canals by the lateral condensation method. Two weeks later, the filling material was removed to apical 3 mm, then 60 microL 2915 mM KCl solution was placed into the pulp cavity. The root was immersed into 1 mL 24.17 mM KCl solution. During the following 30 days, the concentration of the potassium ions in the outer solution was monitored by an ion-selective electrode. Finally, all 50 teeth were immersed in 1% methylene blue for 24 hours, sectioned with Isomet, and the extent of dye penetration was measured under a stereomicroscope with a digital caliper. The results of both methods were compared by means of regression analysis. There was a good correlation between the dye penetration method and the newly designed ion-diffusion method (r = 0.812).(ABSTRACT TRUNCATED AT 250 WORDS) PMID:7904201
cAMP diffusion in Dictyostelium discoideum: A Green's function method
NASA Astrophysics Data System (ADS)
Calovi, Daniel S.; Brunnet, Leonardo G.; de Almeida, Rita M. C.
2010-07-01
A Green’s function method is developed to approach the spatiotemporal equations describing the cAMP production in Dictyostelium discoideum, markedly reducing numerical calculations times: cAMP concentrations and gradients are calculated just at the amoeba locations. A single set of parameters is capable of reproducing the different observed behaviors, from cAMP synchronization, spiral waves and reaction-diffusion patterns to streaming and mound formation. After aggregation, the emergence of a circular motion of amoebas, breaking the radial cAMP field symmetry, is observed.
3D modeling for solving forward model of no-contact fluorescence diffuse optical tomography method
NASA Astrophysics Data System (ADS)
Nouizi, F.; Chabrier, R.; Torregrossa, M.; Poulet, P.
2009-07-01
This paper presents detailed computational aspects of a new 3D modeling for solving the direct problem in a no-contact time-resolved Fluorescent Diffuse Optical Tomography (FDOT) method that rely on near-infrared scattered and fluorescent photons to image the optical properties and distribution of fluorescent probes in small laboratory animals. An optical scanner allowing performing in-vivo measurements in no-contact scheme was built in our laboratory and is presented. We use the three-dimensional Finite Element Method (FEM) to solve the coupled diffusion equations of excitation and fluorescence photons in highly scattering objects. The computed results allowed yielding photon density maps and the temporal profiles of photons on the surface of the small animal. Our 3D modeling of propagation of photons in the void space between the surface of the object and the detectors allows calculating the quantity of photons reaching the optodes. Simulations were carried-out on two test objects: a resin cylinder and a mouse phantom. The results demonstrate the potential applications of the method to pre-clinical imaging.
NASA Astrophysics Data System (ADS)
He, Z. H.; Cao, H. Z.; He, Z. Y.
In this paper, analytical solutions of 2-D double-diffusive convection induced by g-jitter are obtained. The model problem in consideration is a square cavity filled with a binary liquid metal. The upper and lower walls are adiabatic, and the left side is fixed at a higher temperature. Double-diffusive melt convection is driven by buoyancy forces, which caused by the time-varying gravity perturbation and temperature gradient. To get the velocity field by analytical method, nonlinear term is ignored in N-S equation and energy equation. By introducing the stream function, the nondimensional equations of flow field can be written in the form of stream-function. The expression of velocity field can be obtained by taking the derivative of stream function. Then boundary collocation method is adopted to get analytical solution of the velocity. Substituting the analytical solutions of velocity into the energy equation and considering the nonlinear term in the energy equation, the small perturbation method was carried out to get the temperature field.
A comparison between the fission matrix method, the diffusion model and the transport model
Dehaye, B.; Hugot, F. X.; Diop, C. M.
2013-07-01
The fission matrix method may be used to solve the critical eigenvalue problem in a Monte Carlo simulation. This method gives us access to the different eigenvalues and eigenvectors of the transport or fission operator. We propose to compare the results obtained via the fission matrix method with those of the diffusion model, and an approximated transport model. To do so, we choose to analyse the mono-kinetic and continuous energy cases for a Godiva-inspired critical sphere. The first five eigenvalues are computed with TRIPOLI-4{sup R} and compared to the theoretical ones. An extension of the notion of the extrapolation distance is proposed for the modes other than the fundamental one. (authors)
NASA Astrophysics Data System (ADS)
Fernandes, Ryan I.; Fairweather, Graeme
2012-08-01
An alternating direction implicit (ADI) orthogonal spline collocation (OSC) method is described for the approximate solution of a class of nonlinear reaction-diffusion systems. Its efficacy is demonstrated on the solution of well-known examples of such systems, specifically the Brusselator, Gray-Scott, Gierer-Meinhardt and Schnakenberg models, and comparisons are made with other numerical techniques considered in the literature. The new ADI method is based on an extrapolated Crank-Nicolson OSC method and is algebraically linear. It is efficient, requiring at each time level only O(N) operations where N is the number of unknowns. Moreover, it is shown to produce approximations which are of optimal global accuracy in various norms, and to possess superconvergence properties.
NSDL National Science Digital Library
Khalsa, Amrit
2009-08-15
Fully biodegradable green composites were prepared using natural sisal fiber and soy flour (SF) resin modified with sorbitol, agar, and NB416 microfiber. The SF resin modified with agar and NB416 microfibers had a higher Tensile Stress and Young’s Modulus, 8.73 + 0.60 MPa, 232.61 + 25.44 MPa, and 12.15 + 1.53 MPa, 327.87 + 27.62 respectively, compared to the Tensile Stress and Young’s Modulus of the sorbitol modified SF resin. The composites fabricated with sorbitol modified SF resin showed the highest Tensile Stress of 141.45 + 16.72 MPa which was significantly greater than the Tensile Stress of the pure SF resin. Problems arose in preparing the composites with the resins modified with agar and NB416. The method for coating the fibers with the more viscous resin solutions was not an adequate way to prepare the composite. The mechanical properties of the SF resins modified with agar and NB416 microfibers suggests that if the resin was equally dispersed in the composites then the composite properties would be very high. These composites are very useful in replacing some of the petroleum based composites in use today and reducing the amount of plastics in the landfills.
NASA Astrophysics Data System (ADS)
Marchetti, M.; Robinson, B. H.; Evangelou, M. W. H.; Vachey, A.; Schwitzguebel, J. P.; Bernier-Latmani, R.; Schulin, R.
2009-04-01
Trace elements (TE) are essential for humans and plants, but they may be toxic if their concentration is too high. For this reason, the management of TE in soils is very important. In some cases it may be necessary to increase the uptake of nutrients or TE by plants, for example in a biofortification perspective. Conversely, in some other cases TE uptake by plants should be decreased, for instance to avoid heavy metals entering the food chain via edible crops. Microorganisms living in the rhizosphere affect trace element (TE) uptake by plants. However, due to the complexity of this space and the variety of microorganisms that occur there, it is difficult to isolate the effect of any particular strain. To overcome this hurdle, we developed a system in which we grew plants under sterile conditions in agar and inoculated their rhizosphere with a single, well-defined microbial strain. For many years, agar has been used as a growth substrate for microorganisms and plant tissues. It is cheap, easy to use, and can be autoclaved to ensure its sterility. Because of its widespread use, an experiment conducted using this substrate can be reproduced under the same conditions in any laboratory. In contrast to soil, there is little interaction between the trace elements and the agar matrix. There are many studies investigating the influence of microorganisms on TE uptake by plants. However, so far only a small variety of microorganisms has been tested on few plant species. Therefore, the first objective of our research was to develop a method to rapidly screen a large variety of microorganisms on various plant species. Once this goal was achieved, we sought to study the effect of single, well-defined microbial strains on TE uptake by sunflower and wheat. The substrate for plants growth was a 10% agar solution prepared with modified Hoagland's solution and a TE solution containing 1 mg/kg Pb and molar equivalents of Cu, Ni and Zn. The agar solution was autoclaved and poured into sterile, transparent plastic boxes, whose lid was equipped with a filter allowing gas exchanges without contamination by external microorganisms. The seed surface was sterilised and the plants grew one week in agar before their rhizosphere was inoculated with LB broth containing a pure bacterial strain or agar plugs colonized by fungal hyphae. We tested 14 strains, with 5 replicates per treatment and a control where the system was inoculated with sterile LB broth. The plants grew for 2 weeks in a climate chamber and their shoots were analysed for their TEs by ICP-OES. Samples of agar and roots were collected to confirm microbial colonization of the rhizosphere, respectively sterile conditions in the control treatments. Concerning the method development, the plants grew without visible toxicity in all the boxes, and the analysis of root and agar samples indicated that the controls were sterile and the strains inoculated were growing along the roots. More than 90% of the TE and nutrients added to the system were in the liquid fraction of the agar medium, thus available for root uptake. The screening showed that the microorganisms in general decreased TE uptake by wheat and sunflower, although some of them had an opposite effect on the plants. However, with the same plant species, the microorganisms had a consistent effect on all TE tested, i.e. a given single strain caused the same effect (increase or decrease of TE uptake) on all TE tested. In sunflower, 3 microorganisms (Paenibacillus polymyxa, Pythium ultimum and Rhizoctonia solani) decreased Cu and Zn uptake by 50% compared to the control treatment. These three species are common soil microorganisms. All three are known to exude auxin, a phytohormone. This hormone can modify root morphology and physiology and thus may affect TE uptake by plants. R. solani and P. ultimum are root pathogens. Their effect was opposite to what we expected. If roots are damaged, TE should have flooded into the plant and accumulate in the tissues, but this was not the case. One explanation could be the biosorption of TE by these mi
J. VAN ELDERE; L. JOOSTEN; A. VERHAEGHE
A comparative study offluconazole and amphotericin B susceptibility testing was performed with 68 clinical Candidaspecies isolates and three test methods. The methods used were an agar diffusion method (E-test) and two broth dilution methods, the National Committee for Clinical Laboratory Standards (NCCLS) reference broth macrodilution method and an in-house-prepared semiautomated broth microdilution method based on the Bioscreen turbidometer. In the
A new method for apportionnement of diffuse nutrient sources of surface water contamination
NASA Astrophysics Data System (ADS)
Groenendijk, Piet; Mulder, Martin; Van Boekel, Erwin; Van der Bolt, Frank; Hendriks, Rob; Renaud, Leo
2014-05-01
Surface water quality has improved slightly in many regions of the Netherlands during the last decades, due to a reduction of the nutrient loads from point sources, but in most areas the concentrations do not meet the targets to comply with the objectives of the Water Framework Directive. Leaching from agricultural soils is currently the largest source. Quantitative insight into the contribution of the various land management related sources is necessary to discuss the responsibility of different authorities to further improve the quality. Such an understanding is also needed to assess the effects of mitigation measures. The STONE model was developed in 1998- 2000 aiming at the assessment of the effectiveness of Dutch policy measures to reduce nutrient loads to groundwater and surface waters from agricultural land. The process oriented model simulates the carbon, nitrogen and phosphorus cycles in soil and is capable to calculate N and P fluxes to surface waters. Due to the nature of the interdependent soil transformation processes, straight forward model runs don't yield in the relative contribution of the use of fertilizers and other diffuse sources to the total diffuse loads to surface waters. A new method was developed to reveal the relative contribution to surface water contamination of resp. the actual fertilization practise, the historical fertilizer excesses, the atmospheric deposition rates, the inputs by upward seeping water flow, the inputs by infiltrated surface water during summer time in polders and the natural soil release. The method is based on a linear proxy model of the STONE model. The coefficients were derived from the results of a sensitivity analysis. At the national level, the diffuse nitrogen and phosphorus load on surface waters due to the actual fertilization practise amounts to resp. 64% and 48% of the total diffuse loads from agricultural land. Deposition, the input by upward seeping water and the input by infiltrated surface water in polders amounts to less than 5% each. The release from soils, including the effect of historical nutrient surpluses, amounts to resp. 27% and 45% of nitrogen and phosphorus load from agricultural land. The method allows for a further distinction in the relative source contributions per land use, soil type and groundwater regime class. Although agriculture is one of the main contributors to surface water contamination, diminishing manure and fertilizer inputs will not result to a short time contamination reduction due to the long memory of the soil.
Borelli's lactritmel agar induces conidiation in rare-macroconidia producing dermatophytic fungi.
Ilkit, Macit; Gümral, Ramazan; Dö?en, Aylin
2012-10-01
Macroconidia are among the most important indicators used to identify dermatophytic fungi, but several do not usually sporulate and/or produce macroconidia on Sabouraud glucose agar. Specifically, Microsporum audouinii, M. ferrugineum, Trichophyton concentricum, T. schoenleinii, T. verrucosum, and T. violaceum (including T. soudanense and T. yaoundei) rarely form macroconidia and, therefore, cannot be easily identified. In this study, we investigated the production of macroconidia on nine common laboratory media, including Borelli's lactritmel agar (BLA), modified Borelli's lactritmel agar (MBLA), brain heart infusion agar (BHIA), Christensen's urease agar in Petri dishes (UPA), cornmeal dextrose agar (CMDA), Lowenstein-Jensen agar (LJA), malt extract agar (MEA), oatmeal agar (OA), and potato dextrose agar (PDA). The performance of these media was evaluated using 18 rare-macroconidia producing isolates, including representative of the six species mentioned above. All cultures in this study were incubated at 26°C on the bench, and conidia formation on each was investigated at 5, 10, 15, 20, 25, and 30 days of incubation. BLA apparently improved macroconidia production after 15 days and was the most useful nutrient agar medium to induce these phenotypic characters in daily practice, closely followed by OA, PDA, and MBLA. PMID:22563856
Method and apparatus for determining minority carrier diffusion length in semiconductors
Moore, Arnold R. (Princeton, NJ)
1984-01-01
Method and apparatus are provided for determining the diffusion length of minority carriers in semiconductor material, particularly amorphous silicon which has a significantly small minority carrier diffusion length using the constant magnitude surface-photovoltage (SPV) method. Steady or modulated illumination at several wavelengths provides the light excitation on the surface of the material to generate the SPV. A manually controlled or automatic servo system maintains a constant predetermined value of the SPV for each wavelength. A drop of a transparent electrolyte solution containing redox couples (preferably quinhydrone) having an oxidation-reduction potential (E) in the order of +0.6 to -1.65 volts couples the SPV to a measurement system. The drop of redox couple solution functions to create a liquid Schottky barrier at the surface of the material. Illumination light is passed through a transparent rod supported over the surface and through the drop of transparent electrolyte. The drop is held in the gap between the rod and the surface. Steady red light is also used as an optical bias to reduce deleterious space-charge effects that occur in amorphous silicon.
Method and apparatus for determining minority carrier diffusion length in semiconductors
Moore, Arnold R. (Princeton, NJ)
1984-02-21
Method and apparatus are provided for determining the diffusion length of minority carriers in semiconductor material, particularly amorphous silicon, which has a significantly small minority carrier diffusion length using the constant magnitude surface-photovoltage (SPV) method. Steady or modulated illumination at several wavelengths provides the light excitation on the surface of the material to generate the SPV. A manually controlled or automatic servo system maintains a constant predetermined value of the SPV for each wavelength. A probe electrode immersed in an electrolyte solution containing redox couples (preferably quinhydrone) having an oxidation-reduction potential (E) in the order of +0.6 to -1.65 volts couples the SPV to a measurement system. The redox couple solution functions to create a liquid Schottky barrier at the surface of the material. The Schottky barrier is contacted by merely placing the probe in the solution. The redox solution is placed over and in contact with the material to be tested and light is passed through the solution to generate the SPV. To compensate for colored redox solutions a portion of the redox solution not over the material is also illuminated for determining the color compensated light intensity. Steady red light is also used as an optical bias to reduce deleterious space-charge effects that occur in amorphous silicon.
A Simple and Efficient Diffuse Interface Method for Compressible Two-Phase Flows
Ray A. Berry; Richard Saurel; Fabien Petitpas
2009-05-01
In nuclear reactor safety and optimization there are key issues that rely on in-depth understanding of basic two-phase flow phenomena with heat and mass transfer. For many reasons, to be discussed, there is growing interest in the application of two-phase flow models to provide diffuse, but nevertheless resolved, simulation of interfaces between two immiscible compressible fluids – diffuse interface method (DIM). Because of its ability to dynamically create interfaces and to solve interfaces separating pure media and mixtures for DNS-like (Direct Numerical Simulation) simulations of interfacial flows, we examine the construction of a simple, robust, fast, and accurate numerical formulation for the 5-equation Kapila et al. [1] reduced two-phase model. Though apparently simple, the Kapila et al. model contains a volume fraction differential transport equation containing a nonlinear, non-conservative term which poses serious computational challenges. To circumvent the difficulties encountered with the single velocity and single pressure Kapila et al. [1] multiphase flow model, a 6-equation relaxation hyperbolic model is built to solve interface problems with compressible fluids. In this approach, pressure non-equilibrium is first restored, followed by a relaxation to an asymptotic solution which is convergent to the solutions of the Kapila et al. reduced model. The apparent complexity introduced with this extended hyperbolic model actually leads to considerable simplifications regarding numerical resolution, and the various ingredients used by this method are general enough to consider future extensions to problems involving complex physics.
NASA Astrophysics Data System (ADS)
Al, T. A.; Marica, F.; Mayer, K. U.; Rasouli, P.; Balcom, B.; Subudhi, R.; Hussein, E.
2009-05-01
Determination of the porosity and diffusion properties of porous sedimentary rocks is an important prerequisite for quantification of diffusive mass transfer between fractures and the matrix in fractured porous rock flow systems. Porosity may be measured in a variety of ways, but few methods are available to provide quantitative, spatially-resolved measurements in heterogeneous porous media. Similarly, most of the common techniques for measuring diffusion coefficients are not able to provide spatially-resolved information on the diffusion properties of heterogeneous porous media. We have developed and tested X-ray radiography, ?-ray transmission, and magnetic resonance imaging (MRI) techniques for quantifying the porosity and tracer-concentration distributions in rock samples. These are non-destructive techniques and are therefore capable of acquiring spatially and temporally resolved concentration distributions for a single sample. Diffusion coefficients for a specific tracer in the porous medium can then be obtained by fitting the observed concentration distributions with a quantitative diffusion model. Examples of spatially-resolved distributions of porosity are provided in 1D, 2D and 3D for common rock types at scales from ?m to cm. Spatially-resolved tracer concentration distributions are demonstrated, and diffusion coefficients are derived by fitting a diffusion model to the tracer concentration data. In addition, we test the applicability of an established Archie's-Law relationship between porosity and the effective diffusion coefficient at a scale of several tens of ?m. These methods have the potential to provide a means for quantifying the feedback between geochemical reactions and the physical properties of the porous media, such as porosity and diffusion coefficient.
Satti, Luqman; Ikram, Aamer; Palomino, Juan Carlos; Martin, Anandi; Khan, Farooq Ahmad
2013-05-01
In this study we evaluated the performance of colorimetric nitrate reductase assay (NRA) on Middlebrook 7H11 agar instead of Lowenstein-Jensen medium for detection of isoniazid (INH) and rifampin (RIF) resistance directly on 114 smear positive sputum specimens and compared the results with direct proportion method on LJ medium. The results of both methods were in 100% agreement for detection of RIF resistance while agreement for INH was 96.4%. The average turnaround time for NRA was 18.6 days and majority of the specimens gave positive results within 21 days. Thus direct NRA testing on smear positive sputum specimens by using 7H11 agar could be used as a fast, reliable and inexpensive method in resource starved settings. PMID:23507185
Efficient method for near real-time diffuse optical tomography of the human brain
NASA Astrophysics Data System (ADS)
Wu, Xue; Eggebrecht, Adam T.; Ferradal, Silvina L.; Culver, Joseph P.; Dehghani, Hamid
2015-07-01
Previous studies have showed only regions with a sensitivity higher that 1% of the maximum value can affect the recovery result for diffuse optical tomography (DOT). Two methods of efficient sensitivity map generation based on Finite Element Models (FEM) are developed based on (1) reduced sensitivity matrix and (2) parallelisation process. Time and memory efficiency of these processes are evaluated and compared with conventional methods. It is shown that the computational time for a full head model containing 200k nodes is reduced from 3 hours to 48 minutes and the required memory is reduced from 5.5 GB to 0.5 GB. For a range of mesh densities up to 320k nodes, the required memory is improved by ~1000% and computational time by ~400% to allow near real-time image recovery.
Janik, Paulina; Tylko, Grzegorz; Ostachowicz, Beata; Turnau, Katarzyna
2010-12-01
The elemental composition of spores, peridium walls, and lime nodes of Physarum compressum sporocarps, cultivated on rabbit dung as a natural growing environment for the slime mold and on artificial agar medium, was compared to evaluate differences that may be dependent on substrates. Whole fruiting bodies and samples of both experimental media were extracted with nitric acid or Parr digest bomb, respectively, and analyzed by means of total X-ray reflection fluorescence (TXRF). Electron probe microanalysis (EPMA) of spores, peridium walls, and lime nodes structure was carried out with the scanning electron microscope equipped with energy-dispersive spectrometer. Because of minute sizes and roughness of investigated structures, Monte Carlo simulations were utilized to establish analytical conditions of EPMA. Biological and geological standards were used in the quantification of element concentrations. According to TXRF, the fruiting bodies from agar medium revealed lower concentrations of K, Ca, Cr, Mn, and Fe in relation to fruiting bodies from the dung, reflecting elemental relationships in the experimental media. According to EPMA, the highest Ca concentration was found in the lime nodes followed by the peridium and the spores. Culturing of the slime molds on the rabbit dung indicated higher concentration of Ca in the lime nodes and peridium walls when compared with those obtained from the sporocarps grown on agar media. The opposite relation was found for the spores. The concentration of Na, Mg, P, S, and Cl was generally lower in all structures of the sporocarps harvested from the dung than from the agar medium. K was in higher concentration in analyzed structures from dung than from agar. Different element uptake (except for Ca and K) was revealed by the two methods: TXRF and EPMA. PMID:20981759
Convergence of methods for coupling of microscopic and mesoscopic reaction-diffusion simulations
Mark B Flegg; Stefan Hellander; Radek Erban
2013-04-27
In this paper, three multiscale methods for coupling of mesoscopic (compartment-based) and microscopic (molecular-based) stochastic reaction-diffusion simulations are investigated. Two of the three methods that will be discussed in detail have been previously reported in the literature; the two-regime method (TRM) and the compartment-placement method (CPM). The third method that is introduced and analysed in this paper is the ghost cell method (GCM). Presented is a comparison of sources of error. The convergent properties of this error are studied as the time step $\\Delta t$ (for updating the molecular-based part of the model) approaches zero. It is found that the error behaviour depends on another fundamental computational parameter $h$, the compartment size in the mesoscopic part of the model. Two important limiting cases, which appear in applications, are considered: (i) \\Delta t approaches 0 and h is fixed; and (ii) \\Delta t approaches 0 and h approaches 0 such that \\Delta t/h^2 is fixed. The error for previously developed approaches (the TRM and CPM) converges to zero only in the limiting case (ii), but not in case (i). It is shown that the error of the GCM converges in the limiting case (i). Thus the GCM is superior to previous coupling techniques if the mesoscopic description is much coarser than the microscopic part of the model.
NASA Astrophysics Data System (ADS)
Li, Zhenhua; Lai, Jiancheng; Wang, Chunyong; He, Anzhi
2003-12-01
In this paper, a mathematical expression of reflectance point-spread-function, that is defined as the spatial distribution of light diffuse-reflected from biological tissues irradiated by pencil light, is derived from the diffusion approximation (DA) theory. Through calculating partial derivative of the reflectance point-spread function with respect to effective scattering coefficient, we proposed a quantitative criterion for the applicability of diffuse approximation. Moreover, by the introduction of the reflectance point-spread-function, we can use convolution method to calculate the spatial resolved reflectance from dense and thick tissues irradiated by photon beams with finite diameter. We called this method DA based convolution method. Numerical calculations show that the DA based convolution method has much higher computing efficiency compared with the Monte Carlo method.
Identifying human microRNA-disease associations by a new diffusion-based method.
Liao, Bo; Ding, Sumei; Chen, Haowen; Li, Zejun; Cai, Lijun
2015-08-01
Identifying the microRNA-disease relationship is vital for investigating the pathogenesis of various diseases. However, experimental verification of disease-related microRNAs remains considerable challenge to many researchers, particularly for the fact that numerous new microRNAs are discovered every year. As such, development of computational methods for disease-related microRNA prediction has recently gained eminent attention. In this paper, first, we construct a miRNA functional network and a disease similarity network by integrating different information sources. Then, we further introduce a new diffusion-based method (NDBM) to explore global network similarity for miRNA-disease association inference. Even though known miRNA-disease associations in the database are rare, NDBM still achieves an area under the ROC curve (AUC) of 85.62% in the leave-one-out cross-validation in improving the prediction accuracy of previous methods significantly. Moreover, our method is applicable to diseases with no known related miRNAs as well as new miRNAs with unknown target diseases. Some associations who strongly predicted by our method are confirmed by public databases. These superior performances suggest that NDBM could be an effective and important tool for biomedical research. PMID:26004789
NASA Astrophysics Data System (ADS)
Ilas, Germina
In the first part, an accurate and fast computational method is presented as an alternative to the Monte Carlo or deterministic transport theory codes currently used to determine the subcriticality of spent fuel storage lattices. The method is capable of analyzing storage configurations with simple or complex lattice cell geometry. It is developed based on two-group nodal diffusion theory, with the nodal cross sections and discontinuity factors determined from continuous-energy Monte Carlo simulations of each unique node (spent fuel assembly type). Three different approaches are developed to estimate the node-averaged diffusion coefficient. The applicability and the accuracy of the nodal method are assessed in two-dimensional geometry through several benchmark configurations typical at Savannah River Site. It is shown that the multiplication constant of the analyzed configurations is within 1% of the MCNP results. In the second part, the high-order cross section homogenization method, recently developed by McKinley and Rahnema, is implemented in the context of two-group nodal diffusion theory. The method corrects the generalized equivalence theory homogenization parameters for the effect of the core environment. The reconstructed fine-mesh (fuel pin) flux and power distributions are a natural byproduct of this method. The method was not tested for multigroup problems, where it was assumed that the multigroup flux expansion in terms of the perturbation parameter is a convergent series. Here the applicability of the method to two-group problems is studied, and it is shown that the perturbation expansion series converges for the multigroup case. A two-group nodal diffusion code with a bilinear intra-nodal flux shape is developed for the implementation of the high-order homogenization method in the context of the generalized equivalence theory. The method is tested by using as a benchmark a core configuration typical of a BWR in slab geometry, which has large variations in the flux distribution across the core. There is a very good agreement between the nodal calculation and the fine-mesh reference calculation: the node-integrated group flux is within 0.5% of the reference solution in all nodes. The reconstructed fine-mesh flux (or equivalently the power distribution) in the core approximates the reference value very well.
Higher-order boundary condition perturbation methods in transport and diffusion theory
NASA Astrophysics Data System (ADS)
McKinley, Michael Scott
Boundary condition perturbation techniques have primarily been limited to first-order analysis in flux and eigenvalue. The purpose of this research is to develop higher-order boundary condition perturbation techniques in diffusion and transport theory. The formalisms presented require two adjoint functions to be solved to compute all the higher-order terms. One of the adjoint functions is a Green's function and requires special techniques for a solution. Several examples are provided to verify the validity of the formalisms presented. Analytical and numerical examples are provided for the diffusion approximation examples. Due to the complexity of transport theory, only numerical examples are shown. Special numerical techniques needed for the solution of the higher-order terms will be discussed. A nodal code that has its homogenization parameters and discontinuity factors corrected by the higher-order perturbation methods is developed for a monoenergetic, one-dimensional slab. This code demonstrates that this theory can increase the accuracy of a coarse mesh code with little additional computational time added.
NASA Astrophysics Data System (ADS)
Nagasaka, Y.; Hatakeyama, T.; Okuda, M.; Nagashima, A.
1988-07-01
This article is devoted to the theory and experiment of the forced Rayleigh scattering method for measurement of thermal diffusivity of liquids which can be employed in the form of an instrument operated optically in a contact-free manner. The theoretical considerations included are: (1) effect of cell wall, (2) effect of dye, (3) effect of Gaussian beam intensity distribution, (4) effect of heating duration time, and (5) effect of coupled dye and wall for a heavily absorbing sample. The errors caused by inadequate setting of optical conditions are also analyzed: (1) effects of grating thickness and (2) effects of initial temperature amplitude. Experimental verifications of the theory have been carried out through the measurements on toluene and water as standard reference substances. As a result of these experiments and theory, the criteria for optimum measuring conditions became available. To demonstrate the applicability of the present theory and the apparatus, the thermal diffusivities of toluene and methanol have been measured near room temperature under atmospheric pressure. The accuracy of the present measurement is estimated to be ±3%.
Evaluation of eight agar media for the isolation of shiga toxin-Producing Escherichia coli.
Gill, Alexander; Huszczynski, George; Gauthier, Martine; Blais, Burton
2014-01-01
The growth characteristics of 96 shiga toxin-producing Escherichia coli (STEC) strains representing 36 different O-types (including priority O types O26, O45, O103, O111, O121, O145 and O157) on commercial and in-house agar media were studied. The ability of the strains to grow on agar media with varying selective supplement formulations was evaluated using MacConkey Agar (MAC); Rainbow® Agar O157 (RBA); Rainbow® Agar O157 with manufacturer-recommended selective supplements (RBA-NT); Rainbow® Agar O157 with USDA-recommended selective supplements (RBA-USDA); CHROMagar STEC™ (CH STEC); Tryptone Bile agar containing cefixime and tellurite (TBA-CT); Tryptone Bile agar containing cefixime, tellurite, eosin and methylene blue (TBA-EM); and VTEC agar. All of the strains were able to grow on MAC, RBA and VTEC agar, whereas a number of strains (including some non-O157 priority O types) were unable to grow on the highly selective media CH STEC, RBA-NT, RBA-USDA, TBA-EM and TBA-CT. Only RBA-NT and CH STEC exhibited significant inhibition of background flora from ground beef enrichment. Significant inhibition of background flora from beef trim enrichment was observed with RBA-NT, RBA-USDA, CH STEC, TBA-EM and VTEC agar. With exception of E. coli O157, several different colony morphologies were observed on the differential plating media among strains of the same O type, indicating that this colony morphology is not a reliable means of identifying target STEC. These results suggest that an approach to maximize the recovery of target STEC from beef enrichment cultures is dual plating on lesser (RBA, MAC, VTEC agar) and more highly (RBA-NT, CH STEC) selective agars. PMID:24211606
NASA Astrophysics Data System (ADS)
Ge, Hong-Xia; Cheng, Rong-Jun
2014-04-01
Fractional diffusion equations have been the focus of modeling problems in hydrology, biology, viscoelasticity, physics, engineering, and other areas of applications. In this paper, a meshfree method based on the moving Kriging interpolation is developed for a two-dimensional time-fractional diffusion equation. The shape function and its derivatives are obtained by the moving Kriging interpolation technique. For possessing the Kronecker delta property, this technique is very efficient in imposing the essential boundary conditions. The governing time-fractional diffusion equations are transformed into a standard weak formulation by the Galerkin method. It is then discretized into a meshfree system of time-dependent equations, which are solved by the standard central difference method. Numerical examples illustrating the applicability and effectiveness of the proposed method are presented and discussed in detail.
Visualization of Biosurfactant Film Flow in a Bacillus subtilis Swarm Colony on an Agar Plate.
Kim, Kyunghoon; Kim, Jung Kyung
2015-01-01
Collective bacterial dynamics plays a crucial role in colony development. Although many research groups have studied the behavior of fluidic swarm colonies, the detailed mechanics of its motion remains elusive. Here, we developed a visualization method using submicron fluorescent beads for investigating the flow field in a thin layer of fluid that covers a Bacillus subtilis swarm colony growing on an agar plate. The beads were initially embedded in the agar plate and subsequently distributed spontaneously at the upper surface of the expanding colony. We conducted long-term live cell imaging of the B. subtilis colony using the fluorescent tracers, and obtained high-resolution velocity maps of microscale vortices in the swarm colony using particle image velocimetry. A distinct periodic fluctuation in the average speed and vorticity of flow in swarm colony was observed at the inner region of the colony, and correlated with the switch between bacterial swarming and growth phases. At the advancing edge of the colony, both the magnitudes of velocity and vorticity of flow in swarm colony were inversely correlated with the spreading speed of the swarm edge. The advanced imaging tool developed in this study would facilitate further understanding of the effect of micro vortices in swarm colony on the collective dynamics of bacteria. PMID:26343634
M. Sitaram Kumar; Pallapothu Mahendra Kumar; Hemant M Sarnaik; A. K Sadhukhan
2000-01-01
The success of strain improvement programme depends on the number of isolates that can be screened after mutagenic treatment. A technique to rapidly screen large number of high-yielding isolates was developed. The ‘agar plug’ method that utilizes the anti-fungal property of lovastatin to produce a zone of inhibition against Neurospora crassa was not only economical but also less labour-intensive. We
Evaluation of rigid registration methods for whole head imaging in diffuse optical tomography.
Wu, Xue; Eggebrecht, Adam T; Ferradal, Silvina L; Culver, Joseph P; Dehghani, Hamid
2015-07-01
Functional brain imaging has become an important neuroimaging technique for the study of brain organization and development. Compared to other imaging techniques, diffuse optical tomography (DOT) is a portable and low-cost technique that can be applied to infants and hospitalized patients using an atlas-based light model. For DOT imaging, the accuracy of the forward model has a direct effect on the resulting recovered brain function within a field of view and so the accuracy of the spatially normalized atlas-based forward models must be evaluated. Herein, the accuracy of atlas-based DOT is evaluated on models that are spatially normalized via a number of different rigid registration methods on 24 subjects. A multileveled approach is developed to evaluate the correlation of the geometrical and sensitivity accuracies across the full field of view as well as within specific functional subregions. Results demonstrate that different registration methods are optimal for recovery of different sets of functional brain regions. However, the "nearest point to point" registration method, based on the EEG 19 landmark system, is shown to be the most appropriate registration method for image quality throughout the field of view of the high-density cap that covers the whole of the optically accessible cortex. PMID:26217675
NDRC: A Disease-Causing Genes Prioritized Method Based on Network Diffusion and Rank Concordance.
Fang, Minghong; Hu, Xiaohua; Wang, Yan; Zhao, Junmin; Shen, Xianjun; He, Tingting
2015-07-01
Disease-causing genes prioritization is very important to understand disease mechanisms and biomedical applications, such as design of drugs. Previous studies have shown that promising candidate genes are mostly ranked according to their relatedness to known disease genes or closely related disease genes. Therefore, a dangling gene (isolated gene) with no edges in the network can not be effectively prioritized. These approaches tend to prioritize those genes that are highly connected in the PPI network while perform poorly when they are applied to loosely connected disease genes. To address these problems, we propose a new disease-causing genes prioritization method that based on network diffusion and rank concordance (NDRC). The method is evaluated by leave-one-out cross validation on 1931 diseases in which at least one gene is known to be involved, and it is able to rank the true causal gene first in 849 of all 2542 cases. The experimental results suggest that NDRC significantly outperforms other existing methods such as RWR, VAVIEN, DADA and PRINCE on identifying loosely connected disease genes and successfully put dangling genes as potential candidate disease genes. Furthermore, we apply NDRC method to study three representative diseases, Meckel syndrome 1, Protein C deficiency and Peroxisome biogenesis disorder 1A (Zellweger). Our study has also found that certain complex disease-causing genes can be divided into several modules that are closely associated with different disease phenotype. PMID:26080386
Modeling diffusion and phase transitions by a uniform-acceptance force-bias Monte Carlo method
NASA Astrophysics Data System (ADS)
Timonova, Maria; Groenewegen, Jasper; Thijsse, Barend J.
2010-04-01
The uniform-acceptance force-bias Monte Carlo (UFMC) method [G. Dereli, Mol. Simul. 8, 351 (1992)] is a little-used atomistic simulation method that has strong potential as alternative or complementary technique to molecular dynamics (MD). We have applied UFMC to surface diffusion, amorphization, melting, glass transition, and crystallization, mainly of silicon. The purpose is to study the potential and the limitations of the method: to investigate its applicability, determine safe and effective values of the two UFMC parameters—a temperature and a maximum allowed atomic displacement per iteration step—that lead to reliable results for different types of simulations, assess the computational speed increase relative to MD, discover the microscopic mechanisms that make UFMC work, and show in what kind of simulations it can be useful and preferable over MD. It is found that in many simulations, UFMC can be a very efficient alternative to MD: it leads to analogous results in much fewer iteration steps. Due to the straightforward formalism of UFMC, it can be easily implemented in any MD code. Thus both methods can be combined and applied in turn, using UFMC for the acceleration of certain processes and MD for keeping precision and monitoring individual atom trajectories.
George Wright; Bruce Tan; Andreas Rosenwald; Elaine H. Hurt; Adrian Wiestner; Louis M. Staudt
2003-01-01
To classify cancer specimens by their gene expression profiles, we created a statistical method based on Bayes' rule that estimates the probability of membership in one of two cancer subgroups. We used this method to classify diffuse large B cell lymphoma (DLBCL) biopsy samples into two gene expression subgroups based on data obtained from spotted cDNA microarrays. The germinal center
Wareing, T.A.; Morel, J.E.; McGhee, J.M.
1999-09-27
A diffusion synthetic acceleration method is developed for the time dependent S{sub N} equations with linear discontinuous finite element time differencing and discontinuous finite element spatial differencing on unstructured grids. Both theoretical and computational results are given which demonstrate the effectiveness and efficiency of the method.
A. Bodalal; J. S. Zhang; E. G. Plett
2000-01-01
An experimental method for the determination of the internal diffusion coefficient (D) and partition coefficient (ke) of volatile organic compounds (VOCs) is developed for dry building materials (such as carpet, vinyl flooring, plywood, etc.). The method is used to determine D and ke for four VOCs (toluene, nonane, decane, and undecane ) through the backing material of a carpet specimen,
Wetting dynamics of colloidal dispersions on agar gel surfaces.
Seino, Eri; Chida, Shigeki; Mayama, Hiroyuki; Hotta, Jun-ichi; Nonomura, Yoshimune
2014-10-01
The effects of silica particle addition on the wetting velocity on flat and fractal agar gel surfaces were analyzed along with the applicability of such particles for controlling the wetting dynamics of water. The contact angles (?D) of the colloidal dispersions obeyed the power law, i.e., ?D?t(-x), where t is time and x is a constant. Wetting was inhibited by the addition of a suitable amount of 20-nm-diameter silica particles. Specifically, the exponent x reached a minimum value for a silica composition of 0.1wt%. However, such inhibition effects were not observed upon the addition of silica particles with diameters of 100, 550, and, 1000nm. The mechanism of the inhibition of the liquid wetting on gel surfaces may be attributed to a slight increase in local viscosity around the contact line during wetting. PMID:25016539
Gas immersion laser diffusion - A new method for making efficient Si solar cells
NASA Astrophysics Data System (ADS)
Turner, G. B.; Tarrant, D.; Aldrich, D.; Pressley, R.; Press, R.
In the present method for the fabrication of both p(+)/n and n(+)/p junction solar cells, a silicon wafer is immersed in a transparent dopant gas and irradiated at 0.73 microns with a laser. The surface of the silicon wafer melts for less than a microsecond, allowing dopant from the gas to be dissolved before epitaxial regrowth is possible. This technique has been designated 'gas immersion laser diffusion' (GILD). Using PH3 or B2H6 dopant, junctions have been formed in 3 x 3 mm squares by single, 200-nsec, 2 J/sq cm pulses. Efficiencies of 9.2 percent have been achieved by means of GILD in both types of junction, without antireflection coatings or back surface fields. Substrates are not heated except at the surface.
A Lagged Diffusivity Method for Computing Total Variation Regularized Fluid Flow
Basnayake, R.; Luttman, A.; Bollt, E.
2013-03-01
There is a great deal of recent work using optical flow methods for analyzing the dynamics of fluids, and much attention has been paid to developing regularization schemes for variational approaches that are consistent with the physics of fluid flow. In this work we show that using total variation to regularize two different kinds of optical flow functionals leads to very good flow field reconstructions for the kinds of dynamical structures that appear in fluid flow. The first optical flow functional is the classical component-based conservation of intensity, and the second approach is to reconstruct the potential of the flow, rather than the flow components. In the two cases, total variation regularization corresponds to imposing different scientific priors on the solution, which we compute using a variation of the Lagged Diffusivity Fixed Point Iteration. Numerical details are presented, and the results are demonstrated on synthetic data and on a data-driven oceanic flow model.
Wang, Yangyang; Sun, Che-Nan; Fan, Fei; Sangoro, Joshua R; Berman, Marc; Greenbaum, Steve; Zawodzinski, Thomas; Sokolov, Alexei P
2013-01-01
Electrode polarization analysis is frequently used to determine free-ion diffusivity and number density in ionic conductors. In the present study, this approach is critically examined in a wide variety of electrolytes, including aqueous and nonaqueous solutions, polymer electrolytes, and ionic liquids. It is shown that the electrode polarization analysis based on theMacdonald-Trukhan model [J. Chem. Phys. 124, 144903 (2006); J. Non-Cryst. Solids 357, 3064 (2011)] progressively fails to give reasonable values of free-ion diffusivity and number density with increasing salt concentration. This should be expected because the original model of electrode polarization is designed for dilute electrolytes. An empirical correction method which yields ion diffusivities in reasonable agreement with pulsed-field gradient nuclear magnetic resonance measurements is proposed. However, the analysis of free-ion diffusivity and number density from electrode polarization should still be exercised with great caution because there is no solid theoretical justification for the proposed corrections.
Nakayama, M; Tanishita, K
1994-01-01
This study propose a new simple method of measuring the thermal diffusivity of living tissue by thermal pulse decay technique with focused ultrasonic beam, which does not require the accurate knowledge of Gaussian variance within the focal region. The measurement of temperatures at two different locations outside the focal region replaces the elaborate measurement of the size of the focal region and gives a thermal diffusivity with reasonable accuracy and automatically avoids the artifact due to beam-thermocouple interaction. The focused ultrasound was generated by the bowl-shaped ceramic piezoelectric transducer with the diameter of 30 mm. The focal lengths of transducer were 40 mm and 60 mm and the frequencies 1.7 and 3.6 MHz. The values of thermal diffusivity of biological tissues obtained in this method are fairly close to the previously published values and are also compared to the values obtained by heated thermistor method. PMID:7920196
A reaction-diffusion model of the Darien Gap Sterile Insect Release Method
NASA Astrophysics Data System (ADS)
Alford, John G.
2015-05-01
The Sterile Insect Release Method (SIRM) is used as a biological control for invasive insect species. SIRM involves introducing large quantities of sterilized male insects into a wild population of invading insects. A fertile/sterile mating produces offspring that are not viable and the wild insect population will eventually be eradicated. A U.S. government program maintains a permanent sterile fly barrier zone in the Darien Gap between Panama and Columbia to control the screwworm fly (Cochliomyia Hominivorax), an insect that feeds off of living tissue in mammals and has devastating effects on livestock. This barrier zone is maintained by regular releases of massive quantities of sterilized male screwworm flies from aircraft. We analyze a reaction-diffusion model of the Darien Gap barrier zone. Simulations of the model equations yield two types of spatially inhomogeneous steady-state solutions representing a sterile fly barrier that does not prevent invasion and a barrier that does prevent invasion. We investigate steady-state solutions using both phase plane methods and monotone iteration methods and describe how barrier width and the sterile fly release rate affects steady-state behavior.
Effect of Different Commerical Agar Preparations on the Inhibitory Activities of Phenols
Sands, J. G.; Bennett, E. O.
1966-01-01
The minimal inhibitory concentrations of 11 phenolic inhibitors were compared in five commercial agars and in nutrient broth. It was found that the brand of agar affected the end point obtained for a particular inhibitor, and that the degree of antagonism varied with each compound studied. The results indicate that there are at least two deleterious factors present in agar, one of which is water-soluble and one which is not. The major portion of the total antagonism was due to the water-soluble factor, which could be removed by washing the agar in warm distilled water prior to use in the test medium. PMID:5959856
Lawrence, R.D.
1984-01-01
This paper describes two new nodal methods for solving the multigroup neutron diffusion and transport equations in three-dimensional Cartesian geometry. These methods have been developed for the global analysis of fast-reactor critical experiments once cell-averaged multigroup cross sections for each matrix position or drawer have been computed using appropriate cell-homogenization procedures. Brief descriptions of the nodal diffusion and transport schemes are presented, along with results of two- and three-dimensional calculations for a current Zero Power Plutonium Reactor (ZPPR) configuration.
Coban, Ahmet Yilmaz; Cayci, Yeliz Tanriverdi; Deveci, Aydin; Akgunes, Alper; Uzun, Meltem; Durupinar, Belma
2011-05-01
The susceptibility of 49 Mycobacterium tuberculosis clinical isolates to isoniazid (INH) and rifampisin (RIF) (28 multi-drug resistant-tuberculosis samples) was determined by a nitrate reductase assay (NRA) on blood agar. Agreement between the NRA and other testing methods was found to be 93.8% for both INH and RIF. The sensitivity, specificity, positive predictive value and negative predictive value for INH were 92.8%, 94.2%, 86.6% and 97%, respectively. The sensitivity, specificity, positive predictive value and negative predictive value for RIF were 90.4%, 96.4%, 95% and 93.1%. In conclusion, we show here that blood agar can be used effectively for the NRA test. PMID:21655831
Diffuse Attenuation Coefficient of Downwelling Irradiance: An Evaluation of Remote Sensing Methods
NASA Technical Reports Server (NTRS)
Lee, Zhong-Ping; Darecki, Miroslaw; Carder, Kendall L.; Davis, Curtiss O.; Stramski, Dariusz; Rhea, W. Joseph
2005-01-01
The propagation of downwelling irradiance at wavelength lambda from surface to a depth (z) in the ocean is governed by the diffuse attenuation coefficient, K(sup -)(sub d)(lambda). There are two standard methods for the derivation of K(sup -)(sub d)(lambda) in remote sensing, which both are based on empirical relationships involving the blue-to-green ratio of ocean color. Recently, a semianalytical method to derive K(sup -)(sub d)(lambda) from reflectance has also been developed. In this study, using K(sup -)(sub d)(490) and K(sup -)(sub d)(443) as examples, we compare the K(sup -)(sub d)(lambda) values derived from the three methods using data collected in three different regions that cover oceanic and coastal waters, with K(sup -)(sub d)(490) ranging from approximately 0.04 to 4.0 per meter. The derived values are compared with the data calculated from in situ measurements of the vertical profiles of downwelling irradiance. The comparisons show that the two standard methods produced satisfactory estimates of K(sup -)(sub d)(lambda) in oceanic waters where attenuation is relatively low but resulted in significant errors in coastal waters. The newly developed semianalytical method appears to have no such limitation as it performed well for both oceanic and coastal waters. For all data in this study the average of absolute percentage difference between the in situ measured and the semianalytically derived K(sup -)(sub d) is approximately 14% for lambda = 490 nm and approximately 11% for lambda = 443 nm.
Alemani, Davide; Chopard, Bastien; Galceran, Josep; Buffle, Jacques
2006-09-21
This paper studies the optimisation of a numerical model and a computer code to solve numerically reaction-diffusion processes in environmental or biological systems with complicated geometries and mixtures of reactions including time and spatial scales extending over several order of magnitude. In particular, we consider different grid refinement techniques in the framework of a lattice Boltzmann solver for reaction-diffusion systems. Two new grid refinement methods are proposed, which are both quantitatively good. The first method is based on the matching of the concentration profiles and fluxes across two adjacent sub-domains, while the second method is based on nested subgrids. The focus of our study is the trade off between accuracy and CPU time. We show how the different parameters of the method, such as the refinement factors, the location of the boundary between different grids or coupling methods at the interface affect the quality of the numerical solution and the efficiency of the method. PMID:17028701
NASA Astrophysics Data System (ADS)
Mittelstaedt, Eric; Davaille, Anne; van Keken, Peter E.; Gracias, Nuno; Escartin, Javier
2010-10-01
Diffuse flow velocimetry (DFV) is introduced as a new, noninvasive, optical technique for measuring the velocity of diffuse hydrothermal flow. The technique uses images of a motionless, random medium (e.g., rocks) obtained through the lens of a moving refraction index anomaly (e.g., a hot upwelling). The method works in two stages. First, the changes in apparent background deformation are calculated using particle image velocimetry (PIV). The deformation vectors are determined by a cross correlation of pixel intensities across consecutive images. Second, the 2-D velocity field is calculated by cross correlating the deformation vectors between consecutive PIV calculations. The accuracy of the method is tested with laboratory and numerical experiments of a laminar, axisymmetric plume in fluids with both constant and temperature-dependent viscosity. Results show that average RMS errors are ˜5%-7% and are most accurate in regions of pervasive apparent background deformation which is commonly encountered in regions of diffuse hydrothermal flow. The method is applied to a 25 s video sequence of diffuse flow from a small fracture captured during the Bathyluck'09 cruise to the Lucky Strike hydrothermal field (September 2009). The velocities of the ˜10°C-15°C effluent reach ˜5.5 cm/s, in strong agreement with previous measurements of diffuse flow. DFV is found to be most accurate for approximately 2-D flows where background objects have a small spatial scale, such as sand or gravel.
NASA Technical Reports Server (NTRS)
Yang, T.-T.; Nelson, C. D.
1979-01-01
Contoured wall diffusers are designed by using an inverse method. The prescribed wall velocity distribution(s) was taken from the high lift airfoil designed by A. A. Griffith in 1938; therefore, such diffusers are named Griffith diffusers. First the formulation of the inverse problem and the method of solution are outlined. Then the typical contour of a two-dimensional diffuser and velocity distributions across the flow channel at various stations are presented. For a Griffith diffuser to operate as it is designed, boundary layer suction is necessary. Discussion of the percentage of through-flow required to be removed for the purpose of boundary layer control is given. Finally, reference is made to the latest version of a computer program for a two-dimensional diffuser requiring only area ratio, nondimensional length and suction percentage as inputs.
L. Ambrosone; A. Ceglie; G. Colafemmina; G. Palazzo
A method based on the minimization of the variance is developed for the analysis of the pulsed field gradient NMR echo decays\\u000a in emulsion systems. The method has been applied successfully to margarines and water-in-olive oil emulsions. Our tests suggest\\u000a the method might be used in all experimental situations of restricted diffusion in emulsions. For normal and light margarine\\u000a a
Kavuri, Venkaiah C.; Liu, Hanli
2015-01-01
The inclusion of anatomical prior information in reconstruction algorithms can improve the quality of reconstructed images in near-infrared diffuse optical tomography (DOT). Prior literature on possible locations of human prostate cancer from trans-rectal ultrasound (TRUS), however, is limited, and has led to biased reconstructed DOT images. In this work, we propose a hierarchical clustering method (HCM) to improve the accuracy of image reconstruction with limited prior information. HCM reconstructs DOT images in three steps: After the initial step of reconstructing the human prostate, we divide the prostate region into geometric clusters to search for anomalies in finer clusters. The geometric segmentation is continued within found anomalies for improved reconstruction. We demonstrated this hierarchical clustering method using computer simulations and laboratory phantom experiments. Computer simulations were performed using combined TRUS/DOT probe geometry with a multi-layered model; experimental demonstration was performed with a single-layer, tissue-simulating phantom. In computer simulations, two hidden absorbers without prior location information were reconstructed with a recovery rate of 100% in their locations and 95% in their optical properties. In experiments, a hidden absorber without prior location information was reconstructed with a recovery rate of 100% in its location and 83% in its optical property. PMID:24439338
KERR, REX A.; BARTOL, THOMAS M.; KAMINSKY, BORIS; DITTRICH, MARKUS; CHANG, JEN-CHIEN JACK; BADEN, SCOTT B.; SEJNOWSKI, TERRENCE J.; STILES, JOEL R.
2010-01-01
Many important physiological processes operate at time and space scales far beyond those accessible to atom-realistic simulations, and yet discrete stochastic rather than continuum methods may best represent finite numbers of molecules interacting in complex cellular spaces. We describe and validate new tools and algorithms developed for a new version of the MCell simulation program (MCell3), which supports generalized Monte Carlo modeling of diffusion and chemical reaction in solution, on surfaces representing membranes, and combinations thereof. A new syntax for describing the spatial directionality of surface reactions is introduced, along with optimizations and algorithms that can substantially reduce computational costs (e.g., event scheduling, variable time and space steps). Examples for simple reactions in simple spaces are validated by comparison to analytic solutions. Thus we show how spatially realistic Monte Carlo simulations of biological systems can be far more cost-effective than often is assumed, and provide a level of accuracy and insight beyond that of continuum methods. PMID:20151023
Bifurcation analysis of brown tide by reaction-diffusion equation using finite element method
Kawahara, Mutsuto; Ding, Yan [Chuo Univ., Tokyo (Japan)] [Chuo Univ., Tokyo (Japan)
1997-03-01
In this paper, we analyze the bifurcation of a biodynamics system in a two-dimensional domain by virtue of reaction-diffusion equations. The discretization method in space is the finite element method. The computational algorithm for an eigenspectrum is described in detail. On the basis of an analysis of eigenspectra according to Helmholtz`s equation, the discrete spectra in regards to the physical variables are numerically obtained in two-dimensional space. In order to investigate this mathematical model in regards to its practical use, we analyzed the stability of two cases, i.e., hydranth regeneration in the marine hydroid Tubularia and a brown tide in a harbor in Japan. By evaluating the stability according to the linearized stability definition, the critical parameters for outbreaks of brown tide can be theoretically determined. In addition, results for the linear combination of eigenspectrum coincide with the distribution of the observed brown tide. Its periodic characteristic was also verified. 10 refs., 8 figs., 5 tabs.
NASA Astrophysics Data System (ADS)
Xu, Jing; Wu, Jian; Feng, Daming; Cui, Zhiming
Serious types of vascular diseases such as carotid stenosis, aneurysm and vascular malformation may lead to brain stroke, which are the third leading cause of death and the number one cause of disability. In the clinical practice of diagnosis and treatment of cerebral vascular diseases, how to do effective detection and description of the vascular structure of two-dimensional angiography sequence image that is blood vessel skeleton extraction has been a difficult study for a long time. This paper mainly discussed two-dimensional image of blood vessel skeleton extraction based on the level set method, first do the preprocessing to the DSA image, namely uses anti-concentration diffusion model for the effective enhancement and uses improved Otsu local threshold segmentation technology based on regional division for the image binarization, then vascular skeleton extraction based on GMM (Group marching method) with fast sweeping theory was actualized. Experiments show that our approach not only improved the time complexity, but also make a good extraction results.
Kerr, Rex A; Bartol, Thomas M; Kaminsky, Boris; Dittrich, Markus; Chang, Jen-Chien Jack; Baden, Scott B; Sejnowski, Terrence J; Stiles, Joel R
2008-10-13
Many important physiological processes operate at time and space scales far beyond those accessible to atom-realistic simulations, and yet discrete stochastic rather than continuum methods may best represent finite numbers of molecules interacting in complex cellular spaces. We describe and validate new tools and algorithms developed for a new version of the MCell simulation program (MCell3), which supports generalized Monte Carlo modeling of diffusion and chemical reaction in solution, on surfaces representing membranes, and combinations thereof. A new syntax for describing the spatial directionality of surface reactions is introduced, along with optimizations and algorithms that can substantially reduce computational costs (e.g., event scheduling, variable time and space steps). Examples for simple reactions in simple spaces are validated by comparison to analytic solutions. Thus we show how spatially realistic Monte Carlo simulations of biological systems can be far more cost-effective than often is assumed, and provide a level of accuracy and insight beyond that of continuum methods. PMID:20151023
Holographic method for investigating the diffusion of dye molecules in the polymer host
NASA Astrophysics Data System (ADS)
Wang, C. H.; Xia, J. L.
1990-02-01
Laser induced holographic grating relaxation studies of thymoquinone dissolved in amorphous poly(?-methyl styrene) have been carried out. The Onsager theory of mutual diffusion for binary and tertiary systems are utilized to analyze the shape of the diffraction intensity curve. Different line shapes that are associated with the relaxation of the diffraction intensity are interpreted in terms of the diffusion processes. Diffusion coefficients are obtained as a function of thymoquinone concentration from 0.3 to 20 wt. % at various temperatures. It is shown that at very low concentrations (less than 0.5%), the self-diffusion coefficients of the dye molecule and its photoproduct are obtained. Above 0.5% concentrations the diffusion coefficient rapidly increases with increasing dye concentration. The temperature dependence of the self-diffusion coefficient follows the Williams-Landel-Ferry equation, whereas the mutual diffusion coefficient at higher dye concentrations follows the Arrhenius equation. The self-diffusion coefficient rapidly decreases as the sample temperature is traversed across the glass transition temperature (Tg). However at finite dye concentrations there is no detectable effect owing to the onset of Tg on the mutual diffusion coefficient. The difference is attributed to the plasticizing effect of the dye molecules.
Adaptive meshless local maximum-entropy finite element method for convection-diffusion problems
NASA Astrophysics Data System (ADS)
Wu, C. T.; Young, D. L.; Hong, H. K.
2014-01-01
In this paper, a meshless local maximum-entropy finite element method (LME-FEM) is proposed to solve 1D Poisson equation and steady state convection-diffusion problems at various Peclet numbers in both 1D and 2D. By using local maximum-entropy (LME) approximation scheme to construct the element shape functions in the formulation of finite element method (FEM), additional nodes can be introduced within element without any mesh refinement to increase the accuracy of numerical approximation of unknown function, which procedure is similar to conventional p-refinement but without increasing the element connectivity to avoid the high conditioning matrix. The resulted LME-FEM preserves several significant characteristics of conventional FEM such as Kronecker-delta property on element vertices, partition of unity of shape function and exact reproduction of constant and linear functions. Furthermore, according to the essential properties of LME approximation scheme, nodes can be introduced in an arbitrary way and the continuity of the shape function along element edge is kept at the same time. No transition element is needed to connect elements of different orders. The property of arbitrary local refinement makes LME-FEM be a numerical method that can adaptively solve the numerical solutions of various problems where troublesome local mesh refinement is in general necessary to obtain reasonable solutions. Several numerical examples with dramatically varying solutions are presented to test the capability of the current method. The numerical results show that LME-FEM can obtain much better and stable solutions than conventional FEM with linear element.
Nguyen, Dang Van; Li, Jing-Rebecca; Grebenkov, Denis; Le Bihan, Denis
2014-04-15
The complex transverse water proton magnetization subject to diffusion-encoding magnetic field gradient pulses in a heterogeneous medium can be modeled by the multiple compartment Bloch–Torrey partial differential equation (PDE). In addition, steady-state Laplace PDEs can be formulated to produce the homogenized diffusion tensor that describes the diffusion characteristics of the medium in the long time limit. In spatial domains that model biological tissues at the cellular level, these two types of PDEs have to be completed with permeability conditions on the cellular interfaces. To solve these PDEs, we implemented a finite elements method that allows jumps in the solution at the cell interfaces by using double nodes. Using a transformation of the Bloch–Torrey PDE we reduced oscillations in the searched-for solution and simplified the implementation of the boundary conditions. The spatial discretization was then coupled to the adaptive explicit Runge–Kutta–Chebyshev time-stepping method. Our proposed method is second order accurate in space and second order accurate in time. We implemented this method on the FEniCS C++ platform and show time and spatial convergence results. Finally, this method is applied to study some relevant questions in diffusion MRI.
Huang, Yang; Chapman, Belinda; Wilson, Mark; Hocking, Ailsa D
2009-07-31
The concept of water activity (a(w)) does not differentiate between water status resulting from the interaction of water with solutes, and that from interaction of water with matrices, which is termed matric potential (psi(m)). This study reports the effect of agar concentration (1.5, 3.0, 4.5, 6.0, and 7.5%, w/w) on matric potential of glycerol agar media (GA) and the germination and growth of xerophilic fungi (Eurotium herbariorum and E. rubrum) and non-xerophilic fungi (Aspergillus niger, A. flavus, and Penicillium roqueforti) on GA with or without sorbic acid (0.1-0.4%, w/w) at 0.90 a(w) and 0.95 a(w). The matric potential of GA decreased when the agar concentration increased from 1.5 to 7.5%. When the agar concentration increased at each a(w), the radial growth rate of the xerophilic fungi generally increased but the biomass density (biomass per unit area) decreased, whereas the radial growth rate of the non-xerophilic fungi generally decreased but the biomass density was unchanged. In the absence of sorbic acid, the time to germination of each species was similar for all agar concentrations. In the presence of sorbic acid, the time to germination of some species was significantly longer at higher agar concentrations (4.5%-7.5%) than 1.5% agar. This study demonstrated the inhibition effect on germination and growth of non-xerophilic fungi and xerophilic fungi by decreased matric potential resulting from increased agar concentrations, and the different responses of non-xerophilic fungi and xerophilic fungi to water stress from solutes and matrices. The concept of matric potential may be useful in food microbiology to provide a better understanding of fungal growth in complex food matrices. PMID:19520449
CELINE COSTELLO DALY; IRVING HOFFMAN; MARCIA HOBBS; MARTIN MAIDA; DICK ZIMBA; RACHAEL DAVIS; G. MUGHOGHO; MYRON S. COHEN
Susceptibility of Neisseria gonorrhoeae to gentamicin, the primary treatment for gonorrhea in Malawi since 1993, was determined by using agar dilution MICs, E-test MICs, disc diffusion, and clinical cure rate. Agar dilution MICs were slightly higher in 1996 than in 1993 isolates, with a concomitant drop in the clinical cure rate. E-test MICs were substantially lower than agar dilution determinations,
Stimulating growth and xylindein production of Chlorociboria aeruginascens in agar-based systems.
Robinson, Sara C; Tudor, Daniela; Snider, Hilary; Cooper, Paul A
2012-01-01
Four isolates of Chlorociboria aeruginascens were tested for possible stimulatory effects when grown on malt agar media containing wood additives. The addition of any of the four types of test wood (Acer saccharum, Populus tremuloides, spalted P. tremuloides, and Ailanthus altissima), stimulated colony growth and xylindein production in C. aeruginascens. Addition of any amount of wood produced more growth than no wood additions, while ground wood produced more growth than chopped wood. Of the wood types tested, A. saccharum wood stimulated all four isolates, while spalted Populus tremuloides stimulated three of the four isolates. High glucose and sucrose amounts may be partially responsible for the greater stimulatory affect of some woods over others. The development of this simple and reliable method for growth and pigment stimulation of C. aeruginascens in laboratory conditions will allow for further development of this fungus for decorative and commercial use. PMID:22409931
Stimulating growth and xylindein production of Chlorociboria aeruginascens in agar-based systems
2012-01-01
Four isolates of Chlorociboria aeruginascens were tested for possible stimulatory effects when grown on malt agar media containing wood additives. The addition of any of the four types of test wood (Acer saccharum, Populus tremuloides, spalted P. tremuloides, and Ailanthus altissima), stimulated colony growth and xylindein production in C. aeruginascens. Addition of any amount of wood produced more growth than no wood additions, while ground wood produced more growth than chopped wood. Of the wood types tested, A. saccharum wood stimulated all four isolates, while spalted Populus tremuloides stimulated three of the four isolates. High glucose and sucrose amounts may be partially responsible for the greater stimulatory affect of some woods over others. The development of this simple and reliable method for growth and pigment stimulation of C. aeruginascens in laboratory conditions will allow for further development of this fungus for decorative and commercial use. PMID:22409931
Algebraic Methods for Direct and Feature Based Registration of Diffusion Tensor Images
Vidal, René
molecules in human and animal tissues. As the directional dependence of water diffusion rates is closely Tensor Imaging (DTI) is a relatively new 3-D imaging technique that measures the diffusion of water in a direction v R3 as vT Dv. Since the image data live on a 6-dimensional space with nontrivial geometry
A Simple Educational Method for the Measurement of Liquid Binary Diffusivities
ERIC Educational Resources Information Center
Rice, Nicholas P.; de Beer, Martin P.; Williamson, Mark E.
2014-01-01
A simple low-cost experiment has been developed for the measurement of the binary diffusion coefficients of liquid substances. The experiment is suitable for demonstrating molecular diffusion to small or large undergraduate classes in chemistry or chemical engineering. Students use a cell phone camera in conjunction with open-source image…
NASA Technical Reports Server (NTRS)
Stoker, Carol R.; Rages, Kathy
2002-01-01
We correct spectra of Yogi to remove diffuse illumination and show that the part of Yogi facing the wind is less red than other faces of the rock. Our method eliminates ambiguity in interpreting spectra obtained under Mars illumination conditions. Additional information is contained in the original extended abstract.
Technology Transfer Automated Retrieval System (TEKTRAN)
Thermal conductivity and thermal diffusivity are two important physical properties essential for designing any food engineering processes. Recently a new transient plane-source method was developed to measure a variety of materials, but its application in foods has not been documented. Therefore, ...
NASA Astrophysics Data System (ADS)
Espejo, A.; Giráldez, J. V.; Vanderlinden, K.; Taguas, E. V.; Pedrera, A.
2014-08-01
Despite the well-accepted value of soil hydraulic properties for describing and modeling matter and energy fluxes in the unsaturated zone, their accurate measurement across scales is still a daunting task. The increasing availability of continuous soil water content measurements at discrete points in space, as provided by sensor networks, offers still unexplored possibilities for evaluating soil physical properties across landscapes. In this study, we propose a new method, based on the Bruce and Klute equation, to estimate effective soil water diffusivity from soil water profile data observed during continuous desiccation periods. An analytical expression is proposed for the diffusion-soil water relationship, assuming an exponential relationship between soil water content and the Boltzmann variable. The method has been evaluated using soil water profile data observed at inter-row and under canopy locations across a rainfed olive orchard in SW Spain. The spatial variability of the effective soil water diffusivity across the orchard was estimated. Different soil conditions under the tree canopies as compared to inter-row areas resulted in significantly different effective diffusivity relationships, reflecting the effect of trees on soil physical properties and water dynamics across olive orchards. The proposed method offers a suitable alternative to traditional laboratory methods and can be easily extended to estimate soil hydraulic conductivity and water retention curves.
ERIC Educational Resources Information Center
Artun, Huseyin; Costu, Bayram
2013-01-01
The aim of this study was to explore a group of prospective primary teachers' conceptual understanding of diffusion and osmosis as they implemented a 5E constructivist model and related materials in a science methods course. Fifty prospective primary teachers' ideas were elicited using a pre- and post-test and delayed post-test survey consisting…
The solid-phase diffusion coefficient (Dm) and material-air partition coefficient (Kma) are key parameters for characterizing the sources and transport of semivolatile organic compounds (SVOCs) in the indoor environment. In this work, a new experimental method was developed to es...
Effect of refrigerated storage on cefaclor in Mueller-Hinton agar.
Surprenant, A M; Preston, D A
1985-01-01
Cefaclor is less stable than most cephalosporins in media at 35 degrees C. We demonstrated that the activity of cefaclor in Mueller-Hinton agar diminishes continuously at 4 degrees C, resulting in a loss of two-thirds of the activity within 21 days. We recommend that agar dilution plates for this cephalosporin be prepared on the day of their use. PMID:3968200
Marinho-Soriano, E; Bourret, E
2003-12-01
The effect of season on yield and physical properties of agars extracted from Gracia gracilis and G. bursa-pastoris were determined. The agar yield from G. gracilis was maximum during spring (30%) and minimum during autumn (19%). In G. bursa-pastoris, the agar yield was greatest in summer (36%) and lowest in winter (23%). Agar yield from G. bursa-pastoris was positively correlated with temperature (r=0.94; P<0.01) and salinity (r=0.97; P<0.01) and negatively with nitrogen content (r=-0.93; P<0.01). Agar gel strengths fluctuated from 229 to 828 gcm(-2) and 23 to 168 gcm(-2) for G. gracilis and G. bursa-pastoris, respectively. The gelling temperature showed significant seasonal variation for both species. Chemical analysis of agar from the two seaweeds indicated variation in 3,6-anhydrogalactose and sulfate content (P<0.01). Furthermore, there was an inverse correlation between the two chemical variables. In general, agar extracted from G. gracilis possessed better qualities than agar extracted from G. bursa-pastoris and can be considered a candidate for industrial use. PMID:14575957
Development of novel agar media for isolating guaiacol producing Alicyclobacillus spp.
Chang, S S; Park, S H; Kang, D H
2013-06-01
The purpose of this study is to develop a selective and differential medium (SK2 agar) for isolating guaiacol producing Alicyclobacillus. Forty-one selected dyes and vanillic acid were incorporated in SK agar for screening selective and differential agents. Two guaiacol producing (1016, 1101) and two non-guaiacol producing (19220, C-GD 1-1) Alicyclobacillus isolates were streaked onto media and color differentiation of the isolates was assessed. Among 41 tested dyes, Chrome Azurol S (CAS) allowed color differentiation of the two types of Alicyclobacillus. Colonies of guaiacol producing Alicyclobacillus isolates appeared as dark purple to royal blue color with yellow background, whereas non-guaiacol producing Alicyclobacillus isolates produced cream colored colonies with yellow background. Vanillic acid not only served as a precursor for guaiacol formation but also inhibited non-guaiacol producing Alicyclobacillus. Non-guaiacol producing isolates did not grow on SK agar containing more than 70 ppm vanillic acid, whereas the recovery of guaiacol producing isolates was unaffected. When compared with other Alicyclobacillus isolation media, not only was SK2 agar capable of selectively recovering guaiacol-producing Alicyclobacillus, the degree of growth was also approximately equal if not better than orange serum agar, potato dextrose agar, and K agar. The development of SK2 agar provides the fruit juice industry with an inexpensive, simple to use alternative for the detection of guaiacol producing Alicyclobacillus. PMID:23587706
Sengul, Mustafa; Ergin, Ca?r?; Kartal, Tu?ba
2014-04-01
Cryptococcus neofomans is an encapsulated yeast-like fungus that causes life-threatening infections, especially in immunosuppresive patients. C.neoformans infection is believed to be acquired via inhalation of aerosolized particles from the environment. Avian guano, decaying tree hollows and soil are the related known environmental niches. Brown pigmented yeast growth from the precursors in growth media is an important step for the identification and isolation of C.neoformans. Seeds of plants in nature are preferred owing to easy accessibility and low costs for the preparation of such media. Guizotia abysinicca (Niger seed) as Staib agar, Helianthus annus (Sunflower) as Pal's medium, Brassica nigra (Mustard) agar, tobacco agar, Mucuna pruriens (Velvet bean) seed agar, Perilla frutescens (Beefsteak plant) seed agar, Rubus fruticosus (Blackberry) agar and ground red hot pepper agar are pigment-based selective media for the differentiation of C.neoformans. The aim of this study was to observe the pigment production of C.neoformans in a new medium based on eggplant (Solanum melongena) and also to compare its performance with the simplified Staib, Pal's and tobacco agar for isolation from the environment. Three different eggplant-based medium (S.melongena Melanzaza viserba, S.melongena Pinstripe F1 and S.ovigerum Ivory F1) were included in the study. Pigment-forming eggplant medium, simplified Staib agar, Pal's agar and tobacco agar were used for the cultivation of the environmental swabbed samples from 19 Eucalyptus camaldulensis trunk hollows in continuous colonization region. While pigment formation were observed with S.melongena Melanzaza viserba and S.melongena Pinstripe F1 containing media, S.ovigerum Ivory F1 medium was found to be non-reactive. In colonization area (Gökova-Akyaka, Turkey), 11 (57.9%) out of 19 E.camaldulensis samples were positive with simplified Staib agar, Pal's agar and eggplant agar while 10 (52.6%) of them are positive with tobacco agar. C.neoformans colony forming unit (cfu) per plate were found as 51, 57 and 48 (median values) on simplified Staib agar, Pal's agar and eggplant agar, respectively, while tobacco agar has lower performance with 33 cfu/petri. No statistically significant difference were found between simplified Staib agar, Pal's agar and eggplant agar's performances for C.neoformans isolations from the nature (p=0.71). In conclusion, easily prepared eggplant agar is as functional as widely used media such as simplified Staib agar and Pal's agar for the isolation of C.neoformans from the natural environment. PMID:24819266
Rule, Toby D. [II-VI Incorporated; Cai, Wei [ORNL; Wang, Hsin [ORNL
2013-01-01
Because of its extremely high thermal conductivity, measuring the thermal conductivity or diffusivity of optical-grade diamond can be challenging. Various methods have been used to measure the thermal conductivity of thick diamond films. For the purposes of commercial quality control, the AC laser calorimetry method is appealing because it enables fairly rapid and convenient sample preparation and measurement. In this paper, the method is used to measure the thermal diffusivity of optical diamond. It is found that sample dimensions and measurement parameters are critical, and data analysis must be performed with great care. The results suggest that the method as it is applied to optical-grade diamond could be enhanced by a more powerful laser, higher frequency beam modulation, and post-processing based on 2D thermal simulation.
Thickness mapping of eleven retinal layers segmented using the diffusion maps method in normal eyes.
Kafieh, Raheleh; Rabbani, Hossein; Hajizadeh, Fedra; Abramoff, Michael D; Sonka, Milan
2015-01-01
This study was conducted to determine the thickness map of eleven retinal layers in normal subjects by spectral domain optical coherence tomography (SD-OCT) and evaluate their association with sex and age. Mean regional retinal thickness of 11 retinal layers was obtained by automatic three-dimensional diffusion map based method in 112 normal eyes of 76 Iranian subjects. We applied our previously reported 3D intraretinal fast layer segmentation which does not require edge-based image information but rather relies on regional image texture. The thickness maps are compared among 9 macular sectors within 3 concentric circles as defined by ETDRS. The thickness map of central foveal area in layers 1, 3, and 4 displayed the minimum thickness. Maximum thickness was observed in nasal to the fovea of layer 1 and in a circular pattern in the parafoveal retinal area of layers 2, 3, and 4 and in central foveal area of layer 6. Temporal and inferior quadrants of the total retinal thickness and most of other quadrants of layer 1 were significantly greater in the men than in the women. Surrounding eight sectors of total retinal thickness and a limited number of sectors in layers 1 and 4 significantly correlated with age. PMID:25960888
Zaidan, M R S; Noor Rain, A; Badrul, A R; Adlin, A; Norazah, A; Zakiah, I
2005-12-01
Medicinal plants have many traditional claims including the treatment of ailments of infectious origin. In the evaluation of traditional claims, scientific research is important. The objective of the study was to determine the presence of antibacterial activity in the crude extracts of some of the commonly used medicinal plants in Malaysia, Andrographis paniculata, Vitex negundo, Morinda citrifolia, Piper sarmentosum, and Centella asiatica. In this preliminary investigation, the leaves were used and the crude extracts were subjected to screening against five strains of bacteria species, Methicillin Resistant Staphylococcus aureus (MRSA), Staphylococcus aureus, Klebsiella pneumoniae, Pseudomonas aeruginosa and Escherichia coli, using standard protocol of Disc Diffusion Method (DDM). The antibacterial activities were assessed by the presence or absence of inhibition zones and MIC values. M. citrifolia, P. sarmentosum and C. asiatica methanol extract and A. paniculata (water extract) have potential antibacterial activities to both gram positive S. aureus and Methicillin Resistant S. aureus (MRSA). None of the five plant extracts tested showed antibacterial activities to gram negative E. coli and K. pneumoniae, except for A. paniculata and P. sarmentosum which showed activity towards P. aeruginosa. A. paniculata being the most potent at MIC of 2 g/disc. This finding forms a basis for further studies on screening of local medicinal plant extracts for antibacteria properties. PMID:16883283
Optimal Analysis Method for Dynamic Contrast-Enhanced Diffuse Optical Tomography
Ghijsen, Michael; Lin, Yuting; Hsing, Mitchell; Nalcioglu, Orhan; Gulsen, Gultekin
2011-01-01
Diffuse Optical Tomography (DOT) is an optical imaging modality that has various clinical applications. However, the spatial resolution and quantitative accuracy of DOT is poor due to strong photon scatting in biological tissue. Structural a priori information from another high spatial resolution imaging modality such as Magnetic Resonance Imaging (MRI) has been demonstrated to significantly improve DOT accuracy. In addition, a contrast agent can be used to obtain differential absorption images of the lesion by using dynamic contrast enhanced DOT (DCE-DOT). This produces a relative absorption map that consists of subtracting a reconstructed baseline image from reconstructed images in which optical contrast is included. In this study, we investigated and compared different reconstruction methods and analysis approaches for regular endogenous DOT and DCE-DOT with and without MR anatomical a priori information for arbitrarily-shaped objects. Our phantom and animal studies have shown that superior image quality and higher accuracy can be achieved using DCE-DOT together with MR structural a priori information. Hence, implementation of a combined MRI-DOT system to image ICG enhancement can potentially be a promising tool for breast cancer imaging. PMID:21811492
Roberts, Elijah; Stone, John E.; Luthey-Schulten, Zaida
2013-01-01
Spatial stochastic simulation is a valuable technique for studying reactions in biological systems. With the availability of high-performance computing, the method is poised to allow integration of data from structural, single-molecule, and biochemical studies into coherent computational models of cells. Here we introduce the Lattice Microbes software package for simulating such cell models on high-performance computing systems. The software performs either well-stirred or spatially resolved stochastic simulations with approximated cytoplasmic crowding in a fast and efficient manner. Our new algorithm efficiently samples the reaction-diffusion master equation using NVIDIA GPUs and is shown to be two orders of magnitude faster than exact sampling for large systems while maintaining an accuracy of ?0.1%. Display of cell models and animation of reaction trajectories involving millions of molecules is facilitated using a plug-in to the popular VMD visualization platform. The Lattice Microbes software is open source and available for download at http://www.scs.illinois.edu/schulten/lm. PMID:23007888
A grey diffusion acceleration method for time-dependent radiative transfer calculations
Nowak, P.F.
1991-07-01
The equations of thermal radiative transfer describe the emission, absorption and transport of photons in a material. As photons travel through the material they are absorbed and re-emitted in a Planckian distribution characterized by the material temperature. As a result of these processes, the material can change resulting in a change in the Planckian emission spectrum. When the coupling between the material and radiation is strong, as occurs when the material opacity or the time step is large, standard iterative techniques converge very slowly. As a result, nested iterative algorithms have been applied to the problem. One algorithm, is to use multifrequency DSA to accelerate the convergence of the multifrequency transport iteration and a grey transport acceleration (GTA) followed by a single group DSA. Here we summarize a new method which uses a grey diffusion equation (GDA) to directly solve the multifrequency transport (S{sub N}) problem. Results of Fourier analysis for both the continuous and discretized equations are discussed and the computational efficiency of GDA is compared with the DSA and GTA nested algorithms. 5 refs., 1 fig., 1 tab.
A modified method to estimate eddy diffusivity in the North Pacific using altimeter eddy statistics
NASA Astrophysics Data System (ADS)
Zhang, Zhiwei; Li, Yaru; Tian, Jiwei
2013-07-01
The method proposed by Stammer (1998) is modified using eddy statistics from altimeter observation to obtain more realistic eddy diffusivity ( K) for the North Pacific. Compared with original estimates, the modified K has remarkably reduced values in the Kuroshio Extension (KE) and North Equatorial Counter Current (NECC) regions, but slightly enhanced values in the Subtropical Counter Current (STCC) region. In strong eastward flow areas like the KE and NECC, owing to a large difference between mean flow velocity and propagation velocity of mesoscale eddies, tracers inside the mesoscale eddies are transported outside rapidly by advection, and mixing length L is hence strongly suppressed. The low eddy probability ( P) is also responsible for the reduced K in the NECC area. In the STCC region, however, L is mildly suppressed and P is very high, so K there is enhanced. The zonally-averaged K has two peaks with comparable magnitudes, in the latitude bands of the STCC and KE. In the core of KE, because of the reduced values of P and L, the zonally-averaged K is a minimum. Zonally-integrated eddy heat transport in the KE band, calculated based on the modified K, is much closer to the results of previous independent research, indicating the robustness of our modified K. The map of modified K provides useful informationfor modeling studies in the North Pacific.
Comparison of dialysis membrane diffusion samplers and two purging methods in bedrock wells
Imbrigiotta, T.E.; Ehlke, T.A.; Lacombe, P.J.; Dale, J.M.
2002-01-01
Collection of ground-water samples from bedrock wells using low-flow purging techniques is problematic because of the random spacing, variable hydraulic conductivity, and variable contamination of contributing fractures in each well's open interval. To test alternatives to this purging method, a field comparison of three ground-water-sampling techniques was conducted on wells in fractured bedrock at a site contaminated primarily with volatile organic compounds. Constituent concentrations in samples collected with a diffusion sampler constructed from dialysis membrane material were compared to those in samples collected from the same wells with a standard low-flow purging technique and a hybrid (high-flow/low-flow) purging technique. Concentrations of trichloroethene, cis-1,2-dichloroethene, vinyl chloride, calcium, chloride, and alkalinity agreed well among samples collected with all three techniques in 9 of the 10 wells tested. Iron concentrations varied more than those of the other parameters, but their pattern of variation was not consistent. Overall, the results of nonparametric analysis of variance testing on the nine wells sampled twice showed no statistically significant difference at the 95-percent confidence level among the concentrations of volatile organic compounds or inorganic constituents recovered by use of any of the three sampling techniques.
Thickness Mapping of Eleven Retinal Layers Segmented Using the Diffusion Maps Method in Normal Eyes
Kafieh, Raheleh; Rabbani, Hossein; Abramoff, Michael D.; Sonka, Milan
2015-01-01
This study was conducted to determine the thickness map of eleven retinal layers in normal subjects by spectral domain optical coherence tomography (SD-OCT) and evaluate their association with sex and age. Mean regional retinal thickness of 11 retinal layers was obtained by automatic three-dimensional diffusion map based method in 112 normal eyes of 76 Iranian subjects. We applied our previously reported 3D intraretinal fast layer segmentation which does not require edge-based image information but rather relies on regional image texture. The thickness maps are compared among 9 macular sectors within 3 concentric circles as defined by ETDRS. The thickness map of central foveal area in layers 1, 3, and 4 displayed the minimum thickness. Maximum thickness was observed in nasal to the fovea of layer 1 and in a circular pattern in the parafoveal retinal area of layers 2, 3, and 4 and in central foveal area of layer 6. Temporal and inferior quadrants of the total retinal thickness and most of other quadrants of layer 1 were significantly greater in the men than in the women. Surrounding eight sectors of total retinal thickness and a limited number of sectors in layers 1 and 4 significantly correlated with age. PMID:25960888
Secure Multicast Tree Structure Generation Method for Directed Diffusion Using A* Algorithms
NASA Astrophysics Data System (ADS)
Kim, Jin Myoung; Lee, Hae Young; Cho, Tae Ho
The application of wireless sensor networks to areas such as combat field surveillance, terrorist tracking, and highway traffic monitoring requires secure communication among the sensor nodes within the networks. Logical key hierarchy (LKH) is a tree based key management model which provides secure group communication. When a sensor node is added or evicted from the communication group, LKH updates the group key in order to ensure the security of the communications. In order to efficiently update the group key in directed diffusion, we propose a method for secure multicast tree structure generation, an extension to LKH that reduces the number of re-keying messages by considering the addition and eviction ratios of the history data. For the generation of the proposed key tree structure the A* algorithm is applied, in which the branching factor at each level can take on different value. The experiment results demonstrate the efficiency of the proposed key tree structure against the existing key tree structures of fixed branching factors.
NASA Astrophysics Data System (ADS)
Park, S.; Hong, J.; Lee, J.; Cho, S.
2006-12-01
Recent study has demonstrated that the use of combustion appliances in indoor environments, e.g., gas stoves and heaters, results in significant concentrations of NO2 and nitrous acid (HONO). Indoor HONO is formed by both direct emissions from combustion processes and the heterogeneous reaction of NO2 with water vapor on surfaces present indoors. In this study in-situ instrument was constructed for measuring HONO concentration in both indoor and outdoor environments, utilizing diffusion scrubber and peroxynitrite-induced luminol chemiluminescent methods. We measured the HONO concentration under the conditions existing in living room of an apartment, along with NO, NO2, temperature, and relative humidity, to investigate the sources, chemical transformation, and lifetimes of nitrogen oxides and HONO. Some experiments investigated the emissions and transformations of nitrogen species from operation of unvented or vented gas appliance. Measurement data of NO, NO2, and HONO will be reported, and formation pathway of the HONO under the experimental conditions will also be discussed. In addition to measurement of indoor HONO, comparison of HONO measurements by luminol chemiluminescence and annular denuder integrated samples was made in outdoor environment. HONO in ambient air was sampled with annular denuders (Teflon-coated PM2.5 cyclone inlet followed by two Na2CO3-coated denuders coupled in series) operated at 16.7 L/min. Acknowledgement This study was supported by grant No. (# R01-2005-000-10775-0) from the Basic Research Program of the Korea Science and Engineering Foundation (KOSEF).
Method of coating the interior surface of hollow objects with a diffusion coating
Knowles, Shawn D.; Senor, David J.; Forbes, Steven V.; Johnson, Roger N.; Hollenberg, Glenn W.
2005-03-15
A method for forming a diffusion coating on the interior of surface of a hollow object wherein a filament, extending through a hollow object and adjacent to the interior surface of the object, is provided, with a coating material, in a vacuum. An electrical current is then applied to the filament to resistively heat the filament to a temperature sufficient to transfer the coating material from the filament to the interior surface of the object. The filament is electrically isolated from the object while the filament is being resistively heated. Preferably, the filament is provided as a tungsten filament or molybdenum filament. Preferably, the coating materials are selected from the group consisting of Ag, Al, As, Au, Ba, Be, Bi, Ca, Cd, Co, Cr, Cu, Dy, Er, Eu, Fe, Ga, Ge, Hg, In, K, Li, Mg, Mn, Na, Ni P, Pb, Pd, Pr, S, Sb, Sc, Se, Si, Sn, Sr, Te, Tl, Y, Yb, Zn, and combinations thereof. The invention additionally allows for the formation of nitrides, hydrides, or carbides of all the possible coating materials, where such compounds exist, by providing a partial pressure of nitrogen, hydrogen, hydrocarbons, or combination thereof, within the vacuum.
Rheological and structural characterization of agar/whey proteins insoluble complexes.
Rocha, Cristina M R; Souza, Hiléia K S; Magalhães, Natália F; Andrade, Cristina T; Gonçalves, Maria Pilar
2014-09-22
Complex coacervation between whey proteins and carboxylated or highly sulphated polysaccharides has been widely studied. The aim of this work was to characterise a slightly sulphated polysaccharide (agar) and whey protein insoluble complexes in terms of yield, composition and physicochemical properties as well as to study their rheological behaviour for better understanding their structure. Unlike other sulphated polysaccharides, complexation of agar and whey protein at pH 3 in the absence of a buffering agent resulted in a coacervate that was a gel at 20°C with rheological properties and structure similar to those of simple agar gels, reinforced by proteins electrostatically aggregated to the agar network. The behaviour towards heat treatment was similar to that of agar alone, with a high thermal hysteresis and almost full reversibility. In the presence of citrate buffer, the result was a "flocculated solid", with low water content (75-81%), whose properties were governed by protein behaviour. PMID:24906765
Archfield, Stacey A.; LeBlanc, Denis R.
2005-01-01
To evaluate diffusion sampling as an alternative method to monitor volatile organic compound (VOC) concentrations in ground water, concentrations in samples collected by traditional pumped-sampling methods were compared to concentrations in samples collected by diffusion-sampling methods for 89 monitoring wells at or near the Massachusetts Military Reservation, Cape Cod. Samples were analyzed for 36 VOCs. There was no substantial difference between the utility of diffusion and pumped samples to detect the presence or absence of a VOC. In wells where VOCs were detected, diffusion-sample concentrations of tetrachloroethene (PCE) and trichloroethene (TCE) were significantly lower than pumped-sample concentrations. Because PCE and TCE concentrations detected in the wells dominated the calculation of many of the total VOC concentrations, when VOC concentrations were summed and compared by sampling method, visual inspection also showed a downward concentration bias in the diffusion-sample concentration. The degree to which pumped- and diffusion-sample concentrations agreed was not a result of variability inherent within the sampling methods or the diffusion process itself. A comparison of the degree of agreement in the results from the two methods to 13 quantifiable characteristics external to the sampling methods offered only well-screen length as being related to the degree of agreement between the methods; however, there is also evidence to indicate that the flushing rate of water through the well screen affected the agreement between the sampling methods. Despite poor agreement between the concentrations obtained by the two methods at some wells, the degree to which the concentrations agree at a given well is repeatable. A one-time, well-bywell comparison between diffusion- and pumped-sampling methods could determine which wells are good candidates for the use of diffusion samplers. For wells with good method agreement, the diffusion-sampling method is a time-saving and cost-effective alternative to pumped-sampling methods in a long-term monitoring program, such as at the Massachusetts Military Reservation.
Secular resonant dressed orbital diffusion - I. Method and WKB limit for tepid discs
NASA Astrophysics Data System (ADS)
Fouvry, Jean-Baptiste; Pichon, Christophe; Prunet, Simon
2015-05-01
The equation describing the secular diffusion of a self-gravitating collisionless system induced by an exterior perturbation is derived while assuming that the time-scale corresponding to secular evolution is much larger than that corresponding to the natural frequencies of the system. Its two-dimensional formulation for a tepid galactic disc is also derived using the epicyclic approximation. Its Wentzel-Kramers-Brillouin (WKB) limit is found while assuming that only tightly wound transient spirals are sustained by the disc. It yields a simple quadrature for the diffusion coefficients which provides a straightforward understanding of the loci of maximal diffusion within the disc.
Secular resonant dressed orbital diffusion I : method and WKB limit for tepid discs
Fouvry, Jean-Baptiste; Prunet, Simon
2015-01-01
The equation describing the secular diffusion of a self-gravitating collisionless system induced by an exterior perturbation is derived while assuming that the timescale corresponding to secular evolution is much larger than that corresponding to the natural frequencies of the system. Its two dimensional formulation for a tepid galactic disc is also derived using the epicyclic approximation. Its WKB limit is found while assuming that only tightly wound transient spirals are sustained by the disc. It yields a simple quadrature for the diffusion coefficients which provides a straightforward understanding of the loci of maximal diffusion within the disc.
Driessen, B.J.; Dohner, J.L.
1998-08-01
In this paper a hybrid, finite element--boundary element method which can be used to solve for particle advection-diffusion in infinite domains with variable advective fields is presented. In previous work either boundary element, finite element, or difference methods have been used to solve for particle motion in advective-diffusive domains. These methods have a number of limitations. Due to the complexity of computing spatially dependent Green`s functions, the boundary element method is limited to domains containing only constant advective fields, and due to their inherent formulation, finite element and finite difference methods are limited to only domains of finite spatial extent. Thus, finite element and finite difference methods are limited to finite space problems for which the boundary element method is not, and the boundary element method is limited to constant advection field problems for which finite element and finite difference methods are not. In this paper it is proposed to split a domain into two sub-domains, and for each of these sub domains, apply the appropriate solution method; thereby, producing a method for the total infinite space, variable advective field domain.
Swenson, Jana M.; Killgore, George E.; Tenover, Fred C.
2004-01-01
Although both broth microdilution (BMD) and disk diffusion (DD) are listed by NCCLS as acceptable methods for testing Acinetobacter spp. for antimicrobial susceptibility, few studies have compared the results generated by the two methods. We tested 196 isolates of Acinetobacter spp. from nine U.S. hospitals and from the Centers for Disease Control culture collection by using BMD and DD and clinically appropriate antimicrobial agents. Categorical results for amikacin, ciprofloxacin, gatifloxacin, gentamicin, imipenem, levofloxacin, meropenem, tobramycin, and trimethoprim-sulfamethoxazole were comparable for the two methods: there was only one very major (VM) error, with tobramycin, and only one major (M) error, with meropenem, when DD results were compared with BMD results. However, VM errors were frequent with the ?-lactams and ?-lactam-?-lactam inhibitor combinations, while M errors were often observed with tetracyclines. For BMD, tests frequently exhibited subtle growth patterns that were difficult to interpret, especially for ?-lactams. If subtle growth (i.e., granular, small button, or “starry” growth) was considered positive, error rates between BMD and DD were unacceptably high for ampicillin-sulbactam (VM error, 9.8%; minor [m] error, 16.1%), piperacillin (VM error, 5.7%; m error, 13.5%), piperacillin-tazobactam (VM error, 9.3%; m error, 12.9%), ceftazidime (VM error, 6.2%; m error, 11.4%), cefepime (VM error, 6.2%; m error, 13.0%), cefotaxime (m error, 21.2%), ceftriaxone (m error, 23.3%), tetracycline (M error, 11.4%; m error, 32.1%), and doxycycline (M error, 2.6%). When subtle growth patterns were ignored, the agreement still did not achieve acceptable levels. To determine if the problems with BMD testing occurred in other laboratories, we sent frozen BMD panels containing ?-lactam drugs and nine isolates to six labs with experience in performing BMD and DD. Among these laboratories, cefepime MICs ranged from ?8 to ?32 ?g/ml for four of the nine strains, confirming the problem in interpreting BMD results. Discrepancies between the categorical interpretations of BMD and DD tests were noted primarily with cefepime and piperacillin, for which the BMD results were typically more resistant. Clinical laboratories should be aware of these discrepancies. At present, there are no data to indicate which method provides more clinically relevant information. PMID:15528702
E. coli swimming over agar in a thin aqueous film
NASA Astrophysics Data System (ADS)
Berg, Howard
2010-11-01
When cells of Escherichia coli are grown in a rich medium over somewhat soft agar (0.45%) they elongate, produce more flagella, and swarm (or flock). Their behavior is dominated by collisions: an individual cell's velocity is randomized in about 0.2 s [1]. However, cells do not swim in spirals, as they do when in a thick layer of fluid near a solid boundary [2]. This suggests that the surface of the swarm is stationary, i.e., that the cells swim in a thin film of fluid between two fixed surfaces. We showed that this is the case by following the motion of MgO smoke particles deposited at the fluid-air interface [3]. By visualizing flagella of cells in swarms, we found that cells can escape from a confined environment by swimming back through the flagellar bundle, without changing the orientation of the cell body. This maneuver involves normal-to-curly and curly-to-normal polymorphic transformations [4]. These phenomena will be illustrated.[4pt] [1] Darnton NC, Turner L, Rojevsky S, & Berg HC (2010) Dynamics of bacterial swarming. Biophys. J. 98:2082-2090.[0pt] [2] Lauga E, DiLuzio WR, Whitesides GM, & Stone HA (2006) Swimming in circles: motion of bacteria near solid boundaries. Biophys. J. 90:400-412.[0pt] [3] Zhang R, Turner L, & Berg HC (2010) The upper surface of an Escherichia coli swarm is stationary. Proc. Natl. Acad. Sci. USA 107:288-290.[0pt] [4] Turner L, Zhang R, Darnton NC, & Berg HC (2010) Visualization of flagella during bacterial swarming. J. Bacteriol. 192:3259-3267.
Bougoffa, Lazhar
2014-01-01
This paper begins by giving the results obtained by the Crank-Gupta method and Gupta-Banik method for the oxygen diffusion problem in absorbing tissue, and then we propose a new resolution method for this problem by the Adomian decomposition method. An approximate analytical solution is obtained, which is demonstrated to be quite accurate by comparison with the numerical and approximate solutions obtained by Crank and Gupta. The study confirms the accuracy and efficiency of the algorithm for analytic approximate solutions of this problem. PMID:25165743
Bougoffa, Lazhar
2014-01-01
This paper begins by giving the results obtained by the Crank-Gupta method and Gupta-Banik method for the oxygen diffusion problem in absorbing tissue, and then we propose a new resolution method for this problem by the Adomian decomposition method. An approximate analytical solution is obtained, which is demonstrated to be quite accurate by comparison with the numerical and approximate solutions obtained by Crank and Gupta. The study confirms the accuracy and efficiency of the algorithm for analytic approximate solutions of this problem. PMID:25165743
DEVELOPMENT OF SPLIT-OPERATOR, PETROV-GALERKIN METHODS TO STIMULATE TRANSPORT AND DIFFUSION PROBLEMS
The rate at which contaminants in groundwater undergo sorption and desorption is routinely described using diffusion models. uch approaches, when incorporated into transport models, lead to large systems of coupled equations, often nonlinear. his has restricted applications of co...
A comparison of implicit numerical methods for solving the transient spherical diffusion equation
NASA Technical Reports Server (NTRS)
Curry, D. M.
1977-01-01
Comparative numerical temperature results obtained by using two implicit finite difference procedures for the solution of the transient diffusion equation in spherical coordinates are presented. The validity and accuracy of these solutions are demonstrated by comparison with exact analytical solutions.
Investigation to develop a method to apply diffusion barrier to high strength fibers
NASA Technical Reports Server (NTRS)
Veltri, R. D.; Paradis, R. D.; Douglas, F. C.
1975-01-01
A radio frequency powered ion plating process was used to apply the diffusion barriers of aluminum oxide, yttrium oxide, hafnium oxide and titanium carbide to a substrate tungsten fiber. Each of the coatings was examined as to its effect on both room temperature strength and tensile strength of the base tungsten fiber. The coated fibers were then overcoated with a nickel alloy to become single cell diffusion couples. These diffusion couples were exposed to 1093 C for 24 hours, cycled between room temperature and 1093 C, and given a thermal anneal for 100 hours at 1200 C. Tensile testing and metallographic examinations determined that the hafnium oxide coating produced the best high temperature diffusion barrier for tungsten of the four coatings.
DEVELOPMENT OF SPLIT-OPERATOR, PETROV-GALERKIN METHODS TO SIMULATE TRANSPORT AND DIFFUSION PROBLEMS
The rate at which contaminants in groundwater undergo sorption and desorption is routinely described using diffusion models. Such approaches, when incorporated into transport models, lead to large systems of coupled equations, often nonlinear. This has restricted applications of ...
NASA Astrophysics Data System (ADS)
Nii, N.
1998-03-01
A new analytical formulation is proposed to solve the diffusion equation under Approximation B in electron-photon cascade theory. The Suzuki-Trotter formula, analytical continuation of the hypergeometric function, and product integration are introduced. By using these methods the usual series solutions are obtained, and summation of the infinite series for arbitrary values of the energy E is performed by using the method of Prony's interpolation. As E --> 0, the infinite sum for the electron component turns out to be the function of K1(s, -s) used in the usual cascade theory, and a logarithmic divergence arises for the photon component. Use of Prony's method makes it possible to derive the energy spectra as well as the track length distributions and the transition curves. Our numerical results agree well with previous authors' as expected. Our analytical approach provides a general framework for solving other diffusion equations containing non-commutative operators in different contexts.
NASA Astrophysics Data System (ADS)
van der Kamp, G.; Van Stempvoort, D. R.; Wassenaar, L. I.
A new method is described for the determination of the isotopic composition and chemistry of groundwater in aquitards. The effective porosities for each component can be determined concurrently. The method is based on diffusive exchange of water and solutes between groundwater in a cylindrical core of aquitard material and water in a reservoir placed along the axis of the cylinder. The method was tested for 2H, Cl, and SO4 in an aquitard consisting of clay-rich glacial till. The ?2H in aquitard core samples as determined by radial diffusion agreed closely with ?2H in groundwater obtained from corresponding piezometers installed in the aquitard. For the concentrations of Cl and SO4 the agreement was less close but still satisfactory. The effective porosities were equal to the total porosities for 2H and were less than the total porosities for Cl and SO4 ions.
Varela, Norma P.; Friendship, Robert; Dewey, Cate; Valdivieso, Alfonso
2008-01-01
The primary aim of this study was to evaluate the level of agreement of the E-test for in vitro antimicrobial susceptibility testing of Campylobacter coli using the agar dilution technique, which is the approved method. A convenience sample of 80 Ontario swine farms was chosen for this study; each farm was visited from January to June 2004. A total of 233 isolates of C. coli were tested for susceptibility to 10 antimicrobials by agar dilution and the E-test. Performance of the tests was evaluated using 7 quality control strains: Escherichia coli ATCC 25922, Staphylococcus aureus ATCC 29213, Campylobacter jejuni ATCC 33560, and Campylobacter coli ATCC 33559 for the E-test and E. coli ATCC 25922, Pseudomonas aeruginosa ATCC 27853, and C. jejuni ATCC 33560 for the agar dilution test. Weighted Cohen’s kappa and prevalence-adjusted bias-adjusted kappa (PABAK) tests were used for statistical analysis. The E-test and agar dilution test results had a strong agreement when resistance to streptomycin and tetracycline were evaluated (weighted kappa: 0.68 and 0.66, respectively). However, marked disagreement was detected when testing susceptibility to nalidixic acid and ampicillin (0.15 and 0.22, respectively). Almost perfect agreement was detected by PABAK when testing susceptibility to gentamicin (0.99). Agreement was found to be moderate for ciprofloxacin, azithromycin, clindamycin, erythromycin, and chloramphenicol. Although the level of agreement between the E-test and agar dilution depended on the antimicrobial being tested, the E-test always detected a lower proportion of resistant isolates compared to agar dilution. PMID:18505206
A time-dependent method for characterizing the diffusion of 222Rn in concrete.
Zapalac, G H
1983-08-01
The porosity and diffusion length of concrete have been determined by measuring the time-dependent diffusion of radon through a thin slab of the material. One surface of the slab is exposed to a large, fixed radon concentration beginning at t = 0. The radon that diffuses out of a portion of the opposite surface is collected during several contiguous time intervals. The total activity collected over a set of intervals beginning at t = 0 and the steady-state flux of activity are used to calculate the porosity and diffusion length. As a test of these parameters, they are then used to predict the activity collected during other time intervals and for other sample thicknesses. Samples from two types of concrete were tested: one type yielded a porosity of 0.068 and a diffusion length of 12.6 cm; the respective values for the other were 0.32 and 16.9 cm. The predicted and experimental results agreed well, thereby verifying the assumption that concrete may be treated as a homogenous diffusion medium for radon. PMID:6885437
Cowan, K M; Graves, J H
1968-03-01
Agar gel diffusion precipitin reactions obtained with foot-and-mouth disease virus antigens were examined by an acridine orange staining procedure. After treatment with 0.01% acridine orange, precipitin bands produced by the virus particles (140 S antigen) fluoresced flame red when examined under ultraviolet light and with 0.001% to 0.0001% acridine orange, a yellow green. Treatment with RNase prior to staining inhibited the reaction, whereas, treatment with DNase did not. This was in accord with the known RNA nature of foot-and-mouth disease virus. Precipitin bands formed by the 75 S, 12 S, and infection-associated (VIA) antigenic components did not take up acridine orange, an indication that they do not contain detectable amounts of nucleic acid. PMID:18614127
da Silva, Agnes Soares; Cardoso, Maria Regina; Meliefste, Kees; Brunekreef, Bert
2006-01-01
Background Air pollution in São Paulo is constantly being measured by the State of Sao Paulo Environmental Agency, however there is no information on the variation between places with different traffic densities. This study was intended to identify a gradient of exposure to traffic-related air pollution within different areas in São Paulo to provide information for future epidemiological studies. Methods We measured NO2 using Palmes' diffusion tubes in 36 sites on streets chosen to be representative of different road types and traffic densities in São Paulo in two one-week periods (July and August 2000). In each study period, two tubes were installed in each site, and two additional tubes were installed in 10 control sites. Results Average NO2 concentrations were related to traffic density, observed on the spot, to number of vehicles counted, and to traffic density strata defined by the city Traffic Engineering Company (CET). Average NO2concentrations were 63?g/m3 and 49?g/m3 in the first and second periods, respectively. Dividing the sites by the observed traffic density, we found: heavy traffic (n = 17): 64?g/m3 (95% CI: 59?g/m3 – 68?g/m3); local traffic (n = 16): 48?g/m3 (95% CI: 44?g/m3 – 52?g/m3) (p < 0.001). Conclusion The differences in NO2 levels between heavy and local traffic sites are large enough to suggest the use of a more refined classification of exposure in epidemiological studies in the city. Number of vehicles counted, traffic density observed on the spot and traffic density strata defined by the CET might be used as a proxy for traffic exposure in São Paulo when more accurate measurements are not available. PMID:16772044
Urbán-Morlán, Zaida; Ganem-Rondero, Adriana; Melgoza-Contreras, Luz María; Escobar-Chávez, José Juan; Nava-Arzaluz, María Guadalupe; Quintanar-Guerrero, David
2010-01-01
Solid lipid nanoparticles (SLNs) have been used for carrying different therapeutic agents because they improve absorption and bioavailability. The aim of the study was to prepare lipidic nanoparticles containing cyclosporine (CyA) by the emulsification-diffusion method and to study their physicochemical stability. Glyceryl behenate (Compritol® ATO 888) and lauroyl macrogolglycerides (Gelucire® 44/14) were used as carrier materials. Nanoparticles with good stability were obtained with Gelucire®, while it was difficult to obtain stable systems with Compritol®. Systems with Gelucire® were characterized by particle size, Z-potential, differential scanning calorimetry (DSC), scanning electron microscopy (SEM), entrapment efficiency and in vitro release. Particle size and Z-potential were evaluated for at least three months. With a high CyA content (?60 mg) in Gelucire® SLNs, variations in size were greater and particle size also increased over time in all batches; this effect may have been caused by a probable expulsion of the drug due to the lipid’s partial rearrangement. While the Z-potential decreased 10 mV after three months, this effect may be explained by the superficial properties of the drug that make the molecules to be preferably oriented at the solid-liquid interface, causing a change in the net charge of the particle. SEM confirmed size and shape of the nanoparticles. DSC studies evidenced that CyA affects the lipid structure by a mechanism still unknown. The entrapment efficiency was higher than 92%, and CyA release from SLNs was relatively fast (99.60% in 45 min). PMID:20856836
NASA Astrophysics Data System (ADS)
Hamdi, Amine; Miller, Eric L.; Boas, David; Franceschini, Maria A.; Kilmer, Misha E.
2005-03-01
Analysis of the quasi-sinusoidal temporal signals measured by a Diffuse Optical Tomography (DOT) instrument can be used to determine both quantitative and qualitative characteristics of functional brain activities arising from visual and auditory simulations, motor activities, and cognitive tasks performances. Once the activated regions in the brain are resolved using DOT, the temporal resolution of this modality is such that one can track the spatial evolution (both the location and morphology) of these regions with time. In this paper, we explore a state-estimation approach using Extended Kalman Filters to track the dynamics of functionally activated brain regions. We develop a model to determine the size, shape, location and contrast of an area of activity as a function of time. Under the assumption that previously acquired MRI data has provided us with a segmentation of the brain, we restrict the location of the area of functional activity to the thin, cortical sheet. To describe the geometry of the region, we employ a mathematical model in which the projection of the area of activity onto the plane of the sensors is assumed to be describable by a low dimensional algebraic curve. In this study, we consider in detail the case where the perturbations in optical absorption parameters arising due to activation are confined to independent regions in the cortex layer. We estimate the geometric parameters (axis lengths, rotation angle, center positions) defining the best fit ellipse for the activation area's projection onto the source-detector plane. At a single point in time, an adjoint field-based nonlinear inversion routine is used to extract the activated area's information. Examples of the utility of the method will be shown using synthetic data.
Large DNA separation using field alternation agar gel electrophoresis.
Dawkins, H J
1989-08-11
The techniques for large DNA separation have developed from a seminal idea for field alternation which has transformed the field of DNA electrophoresis. This single innovation of pulsed field-gradient electrophoresis (PFGE) and the subsequent modifications have made a significant impact on molecular biology, eukaryote genetics, biopolymer research and diagnostic research. The apparatus types used for large DNA separation are depicted and critically compared with relation to molecular mass separation capabilities, straight-lane migration of samples, band sharpness and ease of operation. With these criteria in mind PFGE and orthogonal field alternation gel electrophoresis systems had a number of drawbacks, the principle one being the inability of these systems to give straight-lane migration. To a large extent this has restricted the widespread use of these systems. Field inversion gel electrophoresis produces straight-lane migration but was subject to an upper molecular mass limitation of 2 megabase pairs and tended to produce broader bands in the higher-molecular-mass areas. Transverse alternating field electrophoresis, rotating gel electrophoresis and contour-clamped homogeneous electric field electrophoresis systems where superior to all the other systems. They gave straight-lane migration, separation of chromosomes up to 10 megabase pairs, good resolution of bands and were all relatively simple to operate. Very little was found to separate these three electrophoresis systems. Field alternation electrophoresis has enabled a 500-fold increase in the size of DNA molecules that can be resolved in agar gels. Consequently, electrophoretic karyotypes of a number of organisms have been produced, while genome maps, gene locations and sequences of large areas of mammalian genomes are now being undertaken. The ability to separate entire chromosomes or large DNA fragments has, in conjunction with novel molecular biology techniques, enabled scientists to work backwards from large purified fragments or entire chromosomes to construct long-range genetic maps. The time saving alone when compared with the old techniques of using very small fragments to construct a picture of the gene or gene complex is commendable. The diagnostic role of large DNA separation and electrophoretic karyotyping is beginning to be explored, while the use of this technique for clinical studies of genetic disorders is well advanced. Very few innovations in nucleic acid separation have had as marked an influence on as many areas as field alternation electrophoresis. These techniques have brought mapping of the mammalian genome into the realms of possibility and is contributing in many sphere PMID:2671005
Xanthan gum: an economical substitute for agar in plant tissue culture media.
Jain, R; Babbar, S B
2006-03-01
Xanthan gum, a microbial desiccation-resistant polysaccharide prepared commercially by aerobic submerged fermentation from Xanthomonas campestris, has been successfully used as a solidifying agent for plant tissue culture media. Its suitability as a substitute to agar was demonstrated for in vitro seed germination, caulogenesis and rhizogenesis of Albizzia lebbeck, androgenesis in anther cultures of Datura innoxia, and somatic embryogenesis in callus cultures of Calliandra tweedii. Culture media used for eliciting these morphogenic responses were gelled with either 1% xanthan gum or 0.9% agar. Xanthan gum, like agar, supported all these responses. PMID:16331459
Leonenko, Nikolai N.; Meerschaert, Mark M.
2013-01-01
Pearson diffusions are governed by diffusion equations with polynomial coefficients. Fractional Pearson diffusions are governed by the corresponding time-fractional diffusion equation. They are useful for modeling sub-diffusive phenomena, caused by particle sticking and trapping. This paper provides explicit strong solutions for fractional Pearson diffusions, using spectral methods. It also presents stochastic solutions, using a non-Markovian inverse stable time change. PMID:23626377
Tsapalov, Andrey; Gulabyants, Loren; Livshits, Mihail; Kovler, Konstantin
2014-04-01
The mathematical apparatus and the experimental installation for the rapid determination of radon diffusion coefficient in various materials are developed. The single test lasts not longer than 18 h and allows testing numerous materials, such as gaseous and liquid media, as well as soil, concrete and radon-proof membranes, in which diffusion coefficient of radon may vary in an extremely wide range, from 1·10(-12) to 5·10(-5) m(2)/s. The uncertainty of radon diffusion coefficient estimation depends on the permeability of the sample and varies from about 5% (for the most permeable materials) to 40% (for less permeable materials, such as radon-proof membranes). PMID:24412813
Manzini, Gianmarco; Cangiani, Andrea; Sutton, Oliver
2014-10-02
This document describes the conforming formulations for virtual element approximation of the convection-reaction-diffusion equation with variable coefficients. Emphasis is given to construction of the projection operators onto polynomial spaces of appropriate order. These projections make it possible the virtual formulation to achieve any order of accuracy. We present the construction of the internal and the external formulation. The difference between the two is in the way the projection operators act on the derivatives (laplacian, gradient) of the partial differential equation. For the diffusive regime we prove the well-posedness of the external formulation and we derive an estimate of the approximation error in the H^{1}-norm. For the convection-dominated case, the streamline diffusion stabilization (aka SUPG) is also discussed.
A. G. Makeev; N. L. Semendyaeva
2009-01-01
The matrix-free Newton-Krylov method that uses the GMRES algorithm (an iterative algorithm for solving systems of linear algebraic\\u000a equations) is used for the parametric continuation of the solitary traveling pulse solution in a three-component reaction-diffusion\\u000a system. Using the results of integration on a short time interval, we replace the original system of nonlinear algebraic equations\\u000a by another system that has
NASA Astrophysics Data System (ADS)
Wang, Yangyang; Sun, Che-Nan; Fan, Fei; Sangoro, Joshua R.; Berman, Marc B.; Greenbaum, Steve G.; Zawodzinski, Thomas A.; Sokolov, Alexei P.
2013-04-01
Electrode polarization analysis is frequently used to determine free-ion diffusivity and number density in ionic conductors. In the present study, this approach is critically examined in a wide variety of electrolytes, including aqueous and nonaqueous solutions, polymer electrolytes, and ionic liquids. It is shown that the electrode polarization analysis based on the Macdonald-Trukhan model [J. Chem. Phys.JCPSA60021-960610.1063/1.2186638 124, 144903 (2006); J. Non-Cryst. SolidsJNCSBJ0022-309310.1016/j.jnoncrysol.2011.04.012 357, 3064 (2011)] progressively fails to give reasonable values of free-ion diffusivity and number density with increasing salt concentration. This should be expected because the original model of electrode polarization is designed for dilute electrolytes. An empirical correction method which yields ion diffusivities in reasonable agreement with pulsed-field gradient nuclear magnetic resonance measurements is proposed. However, the analysis of free-ion diffusivity and number density from electrode polarization should still be exercised with great caution because there is no solid theoretical justification for the proposed corrections.
NASA Astrophysics Data System (ADS)
Taha, M. P. M.; Drew, G. H.; Tamer Vestlund, A.; Aldred, D.; Longhurst, P. J.; Pollard, S. J. T.
Actinomycetes are the dominant bacteria isolated from bioaerosols sampled at composting facilities. Here, a novel method for the isolation of actinomycetes is reported, overcoming masking of conventional agar plates, as well as reducing analysis time and costs. Repeatable and reliable actinomycetes growth was best achieved using a soil compost media at an incubation temperature of 44 °C and 7 days' incubation. The results are of particular value to waste management operators and their advisors undertaking regulatory risk assessments that support environmental approvals for compost facilities.
A one-level FETI method for the drift-diffusion-Poisson system with discontinuities at an interface
NASA Astrophysics Data System (ADS)
Baumgartner, Stefan; Heitzinger, Clemens
2013-06-01
A 3d FETI method for the drift-diffusion-Poisson system including discontinuities at a 2d interface is developed. The motivation for this work is to provide a parallel numerical algorithm for a system of PDEs that are the basic model equations for the simulation of semiconductor devices such as transistors and sensors. Moreover, discontinuities or jumps in the potential and its normal derivative at a 2d surface are included for the simulation of nanowire sensors based on a homogenized model. Using the FETI method, these jump conditions can be included with the usual numerical properties and the original Farhat-Roux FETI method is extended to the drift-diffusion-Poisson equations including discontinuities. We show two numerical examples. The first example verifies the correct implementation including the discontinuities on a 2d grid divided into eight subdomains. The second example is 3d and shows the application of the algorithm to the simulation of nanowire sensors with high aspect ratios. The Poisson-Boltzmann equation and the drift-diffusion-Poisson system with jump conditions are solved on a 3d grid with real-world boundary conditions.
Pyrak-Nolte, Laura J.
The effect of mixing conditions on the material properties of an agar gel January 2005 Abstract The effect of mixing on the properties of agar gels was investigated Calorimetry. Agar gels of 1 and 3% concentrations were prepared. The gels were subjected to three different
Hardboiled eggs petri dishes for growing tooth microbes (find proper agar)
Materials Hardboiled eggs cola OJ Water petri dishes for growing tooth microbes (find proper agar) activities: roleplay egg in acid grow microbes Intro so just a little about myself; name; Im a Chemist I go
Role of Protein A in the Serum-Soft Agar Technique
Forsum, Urban; Forsgren, Arne; Hjelm, Eva
1972-01-01
Formation of compact colonies of Staphylococcus aureus in serum-soft agar is mainly a result of a reaction between protein A and the Fc-part of immunoglobulin G and not a clumping factor-fibrinogen reaction. PMID:4117800
Gruner, Susan V.; Slone, Daniel H.
2014-01-01
Forensically important calliphorids can be reared on a mixture of beef liver and agar. Small pieces of meat, especially fresh or frozen beef liver, will desiccate in 2–6 h, but this simple-to-make feeding substrate remains moist for at least 12 h at 25 and 30°C without desiccation, even in small (5 g) amounts. We determined the survivorship of small numbers of Chrysomya megacephala (F.) (first-instar larvae to adult eclosion) raised on 5 g of liver agar and fresh beef liver. We found that all larvae raised on 5 g of liver died due to desiccation, but survivorship on 5 g of liver agar was equivalent to that on larger (50 g) pieces of either liver agar or beef liver.
Bistatic passive mapping of the field distribution of single element transducer in agar phantom
Illinois at Urbana-Champaign, University of
1 Bistatic passive mapping of the field distribution of single element transducer in agar phantom with the tissue [1], [2]. When the HIFU transducer and the passive listening array are not co-located, a bistatic
R. R. Coifman; S. Lafon; A. B. Lee; M. Maggioni; B. Nadler; F. Warner; S. W. Zucker
2005-01-01
In the companion article, a framework for structural multiscale geometric organization of subsets of and of graphs was introduced. Here, diffusion semigroups are used to generate multiscale analyses in order to organize and represent complex structures. We emphasize the multiscale nature of these problems and build scaling functions of Markov matrices (describing local transitions) that lead to macroscopic descriptions at
New method to diffusion bond superalloys A. A. Shirzadi and E. R. Wallach
Cambridge, University of
of Materials, Minerals and Mining. BACKGROUND Nickel base and cobalt base superalloys are especially suitable, such as brazing and transient liquid phase (TLP) diffusion bonding, normally require long bonding times and interface. There are several hypotheses which have been proposed to suggest how a bond is formed
M Persson; J.-I Flock; J van der Linden
2003-01-01
Postoperative wound infections are often a result of peri-operative contamination by Staphylococcus aureus. With a new insufflation device, a gas diffuser, it has become possible to establish a local micro-environment of almost 100% carbon dioxide in an open surgical wound. The device enables ventilation of the wound with an antiseptic agent, which in gaseous form can be delivered as a
Hosseinbor, Ameer Pasha; Kim, Won Hwa; Adluru, Nagesh; Acharya, Amit; Vorperian, Houri K; Chung, Moo K
2014-01-01
Recently, the HyperSPHARM algorithm was proposed to parameterize multiple disjoint objects in a holistic manner using the 4D hyperspherical harmonics. The HyperSPHARM coefficients are global; they cannot be used to directly infer localized variations in signal. In this paper, we present a unified wavelet framework that links Hyper-SPHARM to the diffusion wavelet transform. Specifically, we will show that the HyperSPHARM basis forms a subset of a wavelet-based multiscale representation of surface-based signals. This wavelet, termed the hyperspherical diffusion wavelet, is a consequence of the equivalence of isotropic heat diffusion smoothing and the diffusion wavelet transform on the hypersphere. Our framework allows for the statistical inference of highly localized anatomical changes, which we demonstrate in the first-ever developmental study on the hyoid bone investigating gender and age effects. We also show that the hyperspherical wavelet successfully picks up group-wise differences that are barely detectable using SPHARM. PMID:25320783
NASA Astrophysics Data System (ADS)
Damberg, Peter; Jarvet, Jüri; Gräslund, Astrid
2001-02-01
For NMR probes equipped with pulsed field gradient coils, which are not optimized for gradient linearity, the precision and accuracy of experimentally measured translational diffusion coefficients are limited by the linearity of the gradient pulses over the sample volume. This study shows that the accuracy and precision of measured diffusion coefficients by the Stejskal-Tanner spin-echo pulsed field gradient experiment can be significantly improved by mapping the gradient z-profile and by using the mapped calibration parameters in the data analysis. For practical applications the gradient distribution may be approximated by a truncated linear distribution defined by minimum and maximum values of the gradient. By including the truncated linear gradient distribution function in the Stejskal-Tanner equation, the systematic deviation between the fitted curve and the experimental attenuation curve decreases by an order of magnitude. The gradient distribution may be calibrated using an intense NMR signal from a sample with a known diffusion coefficient. The diffusion coefficient of an unknown sample may then be determined from a two-parameter fit, using the known gradient distribution function.
Kirk, B.L.; Azmy, Y.
1994-09-01
A modified scheme is developed for solving the two-dimensional nodal diffusion equations on distributed memory computers. The scheme is aimed at minimizing the volume of communication among processors while maximizing the tasks in parallel. Results show a significant improvement in parallel efficiency on the Intel iPSC/860 hypercube compared to previous algorithms.
Numerical simulation of diffusion MRI signals using an adaptive time-stepping method
Li, Jing-Rebecca
in biological tissues in the presence of applied magnetic field gradient pulses can be modeled by a multiple of this equation by coupling a standard Cartesian spatial discretization with an adaptive time discretization plus the extra-cellular space being Gaussian with an effective diffusion tensor. #12;Numerical
NASA Astrophysics Data System (ADS)
Kolesov, Yu S.
2001-08-01
Although we consider only the concrete problem indicated in the title (the proofs of general theorems would be bulky), our arguments can be adapted for a wide class of singularly perturbed systems of reaction-diffusion type with time-delay in the ordinary part.
Development of a rapid, reliable and quantitative method - "SPOTi" for testing antifungal efficacy.
Rizi, Khalida; Murdan, Sudaxshina; Danquah, Cynthia A; Faull, Jane; Bhakta, Sanjib
2015-10-01
A reference method for the antimicrobial susceptibility testing of common fungal pathogens such as dermatophytes, is currently lacking. In this study, we report the successful adaptation of solid agar-based spot culture growth inhibition assay (SPOTi) for dermatophytes, currently being used as a gold-standard in the anti-tubercular drug discovery field. The fungal-SPOTi assay correlated with the disc-diffusion method, and is validated using mycelial plugs. We propose the fungal-SPOTi as a high-throughput alternative to the disc-diffusion and broth micro-dilution anti-fungal assays to screen novel anti-fungals. PMID:26183763
Forgrave, R; Donaghy, J A; Fisher, A; Rowe, M T
2014-10-01
Reports have highlighted the absence of contemporary peer reviewed publications pertaining to Mycobacterium bovis culture from raw milk and cheese. By replicating traditional methods, cheese-making methodology and equipment were devised to produce Cheddar (n = 6) and Caerphilly (n = 3) artificially contaminated with M. bovis (three genotypes) under stringent laboratory-containment guidelines for handling hazardous microbiological material. Middlebrook 7H11, modified for M. bovis isolation, was assessed for capacity to enumerate M. bovis despite changing cheese microflora and prolonged M. bovis exposure to the cheese matrix using maturing cheese test portions (n = 63; up to 16 weeks). Malachite green (MG) containing media isolated M. bovis at significantly (P < 0·05) lower levels than unmodified Middlebrook 7H11 agar despite MG being a common adjunct of Middlebrook 7H11 agar modified for M. bovis growth. Subsequently, a selective MG-free Middlebrook 7H11 agar modified using haemolysed red cells and calf serum was demonstrated as the best performing (P < 0·05) medium for recovery of M. bovis from typical UK cheese types, Cheddar and Caerphilly. Significance and impact of the study: Following increased M. bovis infection of UK cattle, the risk posed to consumers from consumption of unpasteurized milk and dairy products has changed. Furthermore, published methods for the culture and molecular detection of M. bovis in raw milk products are limited. Cheese-making protocols and M. bovis culture media reported here provide tools for further investigation of M. bovis survival during all stages of cheese manufacture and could inform future assessment of the risk to consumers from M. bovis contamination of unpasteurized dairy products. PMID:24888395
Varshosaz, Jaleh; Zaki, Mohammad Reza; Minaiyan, Mohsen; Banoozadeh, Jaafar
2015-01-01
Bupropion is an atypical antidepressant drug. Fluctuating in its serum levels following oral administration of immediate release dosage forms leads to occasional seizure. The aim of the present work was designing of sustained release bupropion HCl nanospheres suited for pulmonary delivery. Agar nanospheres were prepared by transferring the w/o emulsion to solid in oil (s/o) suspension. Calcium chloride was used as cross-linking agent and hydroxypropyl ?-cyclodextrin (HP?CD) was used as permeability enhancer. A response surface D-optimal design was used for optimization of nanospheres. Independent factors included in the design were calcium chloride percent, speed of homogenization, agar percent, and HP?CD percent. Optimum condition was predicted to be achieved when the calcium chloride was set at 7.19%, homogenization speed at 8500?rpm, agar content at 2%, and HP?CD at 0.12%. The optimized nanoparticles showed particle size of 587?nm, zeta potential of -30.9?mV, drug loading efficiency of 38.6%, and release efficiency of 51% until 5?h. The nanospheres showed high degree of bioadhesiveness. D-optimal response surface method is a satisfactory design to optimize the fabrication of bupropion HCl loaded agar nanospheres and these nanospheres can be successively exploited to deliver bupropion in a controlled manner for a sufficiently extended period. PMID:26090423
Influence of the extraction process on the rheological and structural properties of agars.
Sousa, Ana M M; Borges, João; Silva, A Fernando; Gonçalves, Maria P
2013-07-01
Agars obtained by traditional hot-water (TWE) and microwave-assisted (MAE) extractions were compared in terms of their rheological and physicochemical properties and molecular self-association in solutions of low (0.05%, w/w) and high (1.5%, w/w) polymer concentrations. At low concentration, thin gelled layers were imaged by AFM. Slow or rapid cooling of the solutions influenced structure formation. In each case, TWE and MAE agar structures were different and apparently larger for MAE. At high concentration, progressive structural reinforcement was seen; while TWE agar showed a more open and irregular 3D network, MAE agar gel imaged by cryoSEM was denser and fairly uniform. The rheological (higher thermal stability and consistency) and mechanical (higher gel strength) behaviors of MAE agar seemed consistent with a positive effect of molecular mass and 3,6-anhydro-?-l-galactose content. MAE produced non-degraded agar comparable with commercial ones and if properly monitored, could be a promising alternative to TWE. PMID:23688466
Broth versus solid agar culture of swab samples of cadaveric allograft musculoskeletal tissue.
Varettas, Kerry
2013-12-01
As part of the donor assessment protocol, bioburden assessment must be performed on allograft musculoskeletal tissue samples collected at the time of tissue retrieval. Swab samples of musculoskeletal tissue allografts from cadaveric donors are received at the microbiology department of the South Eastern Area Laboratory Services (Australia) to determine the presence of bacteria and fungi. This study will review the isolation rate of organisms from solid agar and broth culture of swab samples of cadaveric allograft musculoskeletal tissue over a 6-year period, 2006-2011. Swabs were inoculated onto horse blood agar (anaerobic, 35 °C) and chocolate agar (CO2, 35 °C) and then placed into a cooked meat broth (aerobic, 35 °C). A total of 1,912 swabs from 389 donors were received during the study period. 557 (29.1 %) swabs were culture positive with the isolation of 713 organisms, 249 (34.9 %) from solid agar culture and an additional 464 (65.1 %) from broth culture only. This study has shown that the broth culture of cadaveric allograft musculoskeletal swab samples recovered a greater amount of organisms than solid agar culture. Isolates such as Clostridium species and Staphylococcus aureus would not have been isolated from solid agar culture alone. Broth culture is an essential part of the bioburden assessment protocol of swab samples of cadaveric allograft musculoskeletal tissue in this laboratory. PMID:23378168
Complex impedance and conductivity of agar-based ion-conducting polymer electrolytes
NASA Astrophysics Data System (ADS)
Nwanya, A. C.; Amaechi, C. I.; Udounwa, A. E.; Osuji, R. U.; Maaza, M.; Ezema, F. I.
2015-04-01
Agar-based electrolyte standing films with different salts and weak acids as ion and proton conductors were prepared and characterized by X-ray diffraction, UV-visible spectrophotometry, photoluminescence emission spectroscopy and electrochemical impedance spectroscopy. The salts used are lithium perchlorate (LiClO4) and potassium perchlorate (KClO4), while the weak acids used are acetic acid (CH3COOH) and lactic acid (C3H6O3). The values of the ion conductivity obtained for the agar-based polymer films are 6.54 × 10-8, 9.12 × 10-8, 3.53 × 10-8, 2.24 × 10-8 S/cm for the agar/acetic acid, agar/lactic acid, agar/LiClO4 and agar/KClO4 polymer films, respectively. As a function of temperature, the ion conductivity exhibits an Arrhenius behavior and the estimated activation energy is ?0.1 eV for all the samples. The samples depicted high values of dielectric permittivity toward low frequencies which is due mostly to electrode polarization effect. The samples showed very high transparency (85-98 %) in the visible region, and this high transparency is one of the major requirements for application in electrochromic devices (ECD). The values of conductivity and activation energy obtained indicate that the electrolytes are good materials for application in ECD.
NASA Technical Reports Server (NTRS)
Horai, K.-I.
1981-01-01
A theory of the measurement of the thermal diffusivity of a sample by the modified Angstrom method is developed for the case in which radiative heat loss from the end surface of the sample is not negligible, and applied to measurements performed on lunar samples. Formulas allowing sample thermal diffusivity to be determined from the amplitude decay and phase lag of a temperature wave traveling through the sample are derived for a flat disk sample for which only heat loss from the end surface is important, and a sample of finite diameter and length for which heat loss through the end and side surfaces must be considered. It is noted that in the case of a flat disk, measurements at a single angular frequency of the temperature wave are sufficient, while the sample of finite diameter and length requires measurements at two discrete angular frequencies. Comparison of the values of the thermal diffusivities of two lunar samples of dimensions approximately 1 x 1 x 2 cm derived by the present methods and by the Angstrom theory for a finite bar reveals them to differ by not more than 5%, and indicates that more refined data are required as the measurement theory becomes more complicated.
NASA Astrophysics Data System (ADS)
Ivanauskas, Remigijus; Samardokas, Linas; Mikolajunas, Marius; Virzonis, Darius; Baltrusaitis, Jonas
2014-10-01
Composite materials based on III-VI elements are promising in designing efficient photoelectronic devices, such as thin film organic-inorganic solar cells. In this work, TlSe composite materials were synthesized on a model polymer polyamide using temperature and pH controlled adsorption-diffusion method via (a) selenization followed by (b) the exposure to the group III metal (Tl) salt solution and their surface morphological, chemical and crystalline phase information was determined with particular focus on their corresponding structure-optical property relationship. XRD analysis yielded a complex crystalline phase distribution which correlated well with the optical and surface morphological properties measured. pH 11.3 and 80 °C yielded well defined, low structural disorder composite material surface. After annealing in N2 at 100 °C, polycrystalline PA-TlxSey composite materials yielded a single TlSe phase due to the enhanced diffusion and reaction of thallium ions into the polymer. The method described here can be used to synthesize variety of binary III-VI compounds diffused into the polymer at relatively low temperatures and low overall cost, thus providing for a flexible synthesis route for novel composite solar energy harvesting materials.
Diffusion Geometry Diffusion Geometry
Hirn, Matthew
Diffusion Geometry Diffusion Geometry for High Dimensional Data Matthew J. Hirn July 3, 2013 #12;Diffusion Geometry Introduction Embedding of closed curve Figure: Left: A closed, non-self-intersecting curve in 3 dimensions. Right: Its embedding as a circle. #12;Diffusion Geometry Introduction Cartoon
Valdes, Claudia P.; Varma, Hari M.; Kristoffersen, Anna K.; Dragojevic, Tanja; Culver, Joseph P.; Durduran, Turgut
2014-01-01
We introduce a new, non-invasive, diffuse optical technique, speckle contrast optical spectroscopy (SCOS), for probing deep tissue blood flow using the statistical properties of laser speckle contrast and the photon diffusion model for a point source. The feasibility of the method is tested using liquid phantoms which demonstrate that SCOS is capable of measuring the dynamic properties of turbid media non-invasively. We further present an in vivo measurement in a human forearm muscle using SCOS in two modalities: one with the dependence of the speckle contrast on the source-detector separation and another on the exposure time. In doing so, we also introduce crucial corrections to the speckle contrast that account for the variance of the shot and sensor dark noises. PMID:25136500
NASA Astrophysics Data System (ADS)
Pang, Miao; Rong, Jian; Yuan, Xuewen; Gao, Xueyan; Hu, Xiaoyang; Zhou, Shan
2013-12-01
The intensity distribution of a laser beam (laser beam profile) is one of its most important characteristics because it yields information on the non-uniformity, centroid, centroid jitter and beam quality. A novel measurement method for obtaining a large laser beam intensity distribution based on CCD diffuse transmission imaging is proposed. The measurement principle is presented. The measurement components of the system have been designed. The layout of the system and the design of a diffuse transmission sampling target are emphasized. The methods of correcting geometric and intensity distortion of the spot are described in detail. The method to calibrate the power coefficient is also given. After the laser spot correction, we can obtain the precise laser beam intensity profile as well as the laser power. The presented test results validate the method. In the measurement field of large laser beams, the method can measure the profile with a non-uniformity of less than 1%, and laser power within 2% error compared with the calibration power meter. The measurement system can be used as a standard measurement instrument after being calibrated when manufactured.
Schwartz, L M; Bergman, D J; Dunn, K J; Mitra, P P
1996-01-01
Random walk computer simulations are an important tool in understanding magnetic resonance measurements in porous media. In this paper we focus on the description of pulsed field gradient spin echo (PGSE) experiments that measure the probability, P(R,t), that a diffusing water molecule will travel a distance R in a time t. Because PGSE simulations are often limited by statistical considerations, we will see that valuable insight can be gained by working with simple periodic geometries and comparing simulation data to the results of exact eigenvalue expansions. In this connection, our attention will be focused on (1) the wavevector, k, and time dependent magnetization, M(k, t); and (2) the normalized probability, Ps(delta R, t), that a diffusing particle will return to within delta R of the origin after time t. PMID:8970076
Intrauterine device for laser light diffusion and method of using the same
Tadir, Y.; Berns, M.W.; Svaasand, L.O.; Tromberg, B.J.
1995-12-26
An improved device for delivery of photoenergy from a light source, such as a laser, into a uterine cavity for photodynamic therapy is comprised of a plurality of optic fibers, which are bundled together and inserted into the uterine cavity by means of a uterine cannula. The cannula is positioned within the uterine cavity at a preferred location and then withdrawn thereby allowing the plurality of optic fibers to splay or diverge one from the other within the cavity. Different portions of the distal tip of the optic fiber is provided with a light diffusing tip, the remainder being provided with a nondiffusing tip portion. The fiber optic shape, as well as the segment which is permitted to actively diffuse light through the tip, is selected in order to provide a more uniform exposure intensity of the photo energy or at least sufficient radiation directed to each segment of the uterine walls. 5 figs.
NASA Astrophysics Data System (ADS)
Jin, Shi; Xiu, Dongbin; Zhu, Xueyu
2015-05-01
In this paper we develop a set of stochastic numerical schemes for hyperbolic and transport equations with diffusive scalings and subject to random inputs. The schemes are asymptotic preserving (AP), in the sense that they preserve the diffusive limits of the equations in discrete setting, without requiring excessive refinement of the discretization. Our stochastic AP schemes are extensions of the well-developed deterministic AP schemes. To handle the random inputs, we employ generalized polynomial chaos (gPC) expansion and combine it with stochastic Galerkin procedure. We apply the gPC Galerkin scheme to a set of representative hyperbolic and transport equations and establish the AP property in the stochastic setting. We then provide several numerical examples to illustrate the accuracy and effectiveness of the stochastic AP schemes.
An Approximate Method of Estimating Soil Water Diffusivity For Different Soil Bulk Densities
NASA Astrophysics Data System (ADS)
Libardi, P. L.; Reichardt, K.; Jose, C.; Bazza, M.; Nielsen, D. R.
1982-02-01
The effect of soil bulk density on soil water diffusivity and on infiltration is studied using data from 13 soils, widely ranging in texture. It is shown for horizontal infiltration of water into initially air dry soil that although changes in the slopes of plots of the distance to the wetting front as a function of square root of infiltration time corresponding to different bulk density values actually depend on soil type, they may be considered independent. Hence a generalized exponential equation is developed which expresses the soil water diffusivity of any soil as a function of soil water content and soil bulk density, knowing only the rate at which the wetting front advances for only one value of the bulk density.
Determination of the Solute Diffusion Coefficient by the Droplet Migration Method
Shan Liu; Jing Teng; Jeongyun Choi
2007-07-01
Further analysis of droplet migration in a temperature gradient field indicates that different terms can be used to evaluate the solute diffusion coefficient in liquid (D{sub L}) and that there exists a characteristic curve that can describe the motion of all the droplets for a given composition and temperature gradient. Critical experiments are subsequently conducted in succinonitrile (SCN)-salol and SCN-camphor transparent alloys in order to observe dynamic migration processes of a number of droplets. The derived diffusion coefficients from different terms are the same within experimental error. For SCN-salol alloys, D{sub L} = (0.69 {+-} 0.05) x 10{sup -3} mm{sup 2}/s, and for SCN-camphor alloys, D{sub L} = (0.24 {+-} 0.02) x 10{sup -3} mm{sup 2}/s.
Winston, Gavin P; Mancini, Laura; Stretton, Jason; Ashmore, Jonathan; Symms, Mark R; Duncan, John S; Yousry, Tarek A
2011-11-01
The optic radiation is a key white matter structure at risk during epilepsy surgery involving the temporal, parietal or occipital lobes. It shows considerable anatomical variability, cannot be delineated on clinical MRI sequences and damage may cause a disabling visual field deficit. Diffusion tensor imaging tractography allows non-invasive mapping of this pathway. Numerous methods have been published but direct comparison is difficult as patient, acquisition and analysis parameters differ. Two methods for delineating the optic radiation were applied to 6 healthy controls and 4 patients with epileptogenic lesions near the optic radiation. By comparing methods with the same datasets, many of the parameters could be controlled. The first method was previously developed to accurately identify Meyer's loop for planning anterior temporal lobe resection. The second aimed to address limitations of this method by using a more automated technique to reduce operator time and to depict the entire optic radiation. Whilst the core of the tract was common to both methods, there was significant variability between the methods. Method 1 gave a more consistent depiction of Meyer's loop with fewer spurious tracts. Method 2 gave a better depiction of the entire optic radiation, particularly in more posterior portions, but did not identify Meyer's loop in one patient. These results show that whilst tractography is a promising technique, there is significant variability depending on the method chosen even when the majority of parameters are fixed. Different methods may need to be chosen for surgical planning depending on the individual clinical situation. PMID:21885257
A numerical method for the diffusion equation with nonlocal boundary specifications
NASA Astrophysics Data System (ADS)
Wang, Shingmin; Lin, Yanping
An implicit Crank-Nicolson scheme is used as the foundation for the numerical solution of a diffusion equation subject to nonlocal boundary specifications. The treatment has two desirable features: first, it is a nonlocal treatment that serves as a faithful description of the model, and, secondly, it utilizes Simpson's rule, which is highly accurate, numerically stable, and error-absorbing. Numerical experiments are presented which confirm the stability and second-order accuracy of the solutions.
Bertolotti, M. [Dipartimento di Energetica, Universita di Roma ``La Sapienza,`` Via Scarpa 16, 00161 Roma (Italy)] [Dipartimento di Energetica, Universita di Roma ``La Sapienza,`` Via Scarpa 16, 00161 Roma (Italy); [GNEQP of CNR (Italy); [INFM (Italy); Liakhou, G. [Technical University of Moldova, Stephan Cel Mare, 277012 Kishinev, Moldova (??)] [Technical University of Moldova, Stephan Cel Mare, 277012 Kishinev, Moldova (??); Li Voti, R.; Paoloni, S.; Sibilia, C. [Dipartimento di Energetica, Universita di Roma ``La Sapienza,`` Via Scarpa 16, 00161 Roma (Italy)] [Dipartimento di Energetica, Universita di Roma ``La Sapienza,`` Via Scarpa 16, 00161 Roma (Italy); [GNEQP of CNR (Italy); [INFM (Italy); Sparvieri, N. [ALENIA, Via Tiburtina Km 12.4, 00131 Roma (Italy)] [ALENIA, Via Tiburtina Km 12.4, 00131 Roma (Italy)
1995-12-01
A cryostatic setup is described to perform photothermal deflection measurements from room temperature to 77 K. The setup uses gaseous nitrogen as a medium where the photodeflection is produced. The ability of the system to work is demonstrated presenting some measurements of thermal diffusivity of high-temperature superconductor samples and of yttrium-iron garnets with variable aluminum content. {copyright} {ital 1995} {ital American} {ital Institute} {ital of} {ital Physics}.
Lattice Boltzmann method for diffusion-limited partial dissolution of fluids
NASA Astrophysics Data System (ADS)
Aursjø, Olav; Pride, Steven R.
2015-07-01
A lattice Boltzmann model for two partially miscible fluids is developed. By partially miscible we mean that, although there is a definite interfacial region separating the two fluids with a surface tension force acting at all points of the transition region, each fluid can nonetheless accept molecules from the other fluid up to a set solubility limit. We allow each fluid to diffuse into the other with the solubility and diffusivity in each fluid being input parameters. The approach is to define two regions within the fluid: one interfacial region having finite width, across which most of the concentration change occurs, and in which a surface tension force and color separation step are allowed for and one miscible fluid region where the concentration of the binary fluids follows an advection-diffusion equation and the mixture as a whole obeys the Navier-Stokes incompressible flow equations. Numerical examples are presented in which the algorithm produces results that are quantitatively compared to exact analytical results as well as qualitatively examined for their reasonableness. The model has the ability to simulate how bubbles of one fluid flow through another while dissolving their contents as well as to simulate a range of practical invasion problems such as injecting supercritical CO2 into a porous material saturated with water for sequestration purposes.
Lattice Boltzmann method for diffusion-limited partial dissolution of fluids.
Aursjø, Olav; Pride, Steven R
2015-07-01
A lattice Boltzmann model for two partially miscible fluids is developed. By partially miscible we mean that, although there is a definite interfacial region separating the two fluids with a surface tension force acting at all points of the transition region, each fluid can nonetheless accept molecules from the other fluid up to a set solubility limit. We allow each fluid to diffuse into the other with the solubility and diffusivity in each fluid being input parameters. The approach is to define two regions within the fluid: one interfacial region having finite width, across which most of the concentration change occurs, and in which a surface tension force and color separation step are allowed for and one miscible fluid region where the concentration of the binary fluids follows an advection-diffusion equation and the mixture as a whole obeys the Navier-Stokes incompressible flow equations. Numerical examples are presented in which the algorithm produces results that are quantitatively compared to exact analytical results as well as qualitatively examined for their reasonableness. The model has the ability to simulate how bubbles of one fluid flow through another while dissolving their contents as well as to simulate a range of practical invasion problems such as injecting supercritical CO_{2} into a porous material saturated with water for sequestration purposes. PMID:26274306
Alman, David E. (Corvallis, OR); Wilson, Rick D. (Corvallis, OR); Davis, Daniel L. (Albany, OR)
2011-03-08
This invention relates to a method for producing components with internal architectures, and more particularly, this invention relates to a method for producing structures with microchannels via the use of diffusion bonding of stacked laminates. Specifically, the method involves weakly bonding a stack of laminates forming internal voids and channels with a first generally low uniaxial pressure and first temperature such that bonding at least between the asperites of opposing laminates occurs and pores are isolated in interfacial contact areas, followed by a second generally higher isostatic pressure and second temperature for final bonding. The method thereby allows fabrication of micro-channel devices such as heat exchangers, recuperators, heat-pumps, chemical separators, chemical reactors, fuel processing units, and combustors without limitation on the fin aspect ratio.
Li, Liang; Du, Wenbin; Ismagilov, Rustem F.
2010-08-04
This paper describes two SlipChip-based approaches to protein crystallization: a SlipChip-based free interface diffusion (FID) method and a SlipChip-based composite method that simultaneously performs microbatch and FID crystallization methods in a single device. The FID SlipChip was designed to screen multiple reagents, each at multiple diffusion equilibration times, and was validated by screening conditions for crystallization of two proteins, enoyl-CoA hydratase from Mycobacterium tuberculosis and dihydrofolate reductase/thymidylate synthase from Babesia bovis, against 48 different reagents at five different equilibration times each, consuming 12 {micro}L of each protein for a total of 480 experiments using three SlipChips. The composite SlipChip was designed to screen multiple reagents, each at multiple mixing ratios and multiple equilibration times, and was validated by screening conditions for crystallization of two proteins, enoyl-CoA hydratase from Mycobacterium tuberculosis and dihydrofolate reductase/thymidylate synthase from Babesia bovis. To prevent cross-contamination while keeping the solution in the neck channels for FID stable, the plates of the SlipChip were etched with a pattern of nanowells. This nanopattern was used to increase the contact angle of aqueous solutions on the surface of the silanized glass. The composite SlipChip increased the number of successful crystallization conditions and identified more conditions for crystallization than separate FID and microbatch screenings. Crystallization experiments were scaled up in well plates using conditions identified during the SlipChip screenings, and X-ray diffraction data were obtained to yield the protein structure of dihydrofolate reductase/thymidylate synthase at 1.95 {angstrom} resolution. This free-interface diffusion approach provides a convenient and high-throughput method of setting up gradients in microfluidic devices and may find additional applications in cell-based assays.
LaBombardi, Vincent J; Urban, Carl M; Kreiswirth, Barry N; Chen, Liang; Osorio, Giuliana; Kopacz, Joanna; Labaze, Georges; Segal-Maurer, Sorana
2015-09-01
We compared the Remel Spectra CRE agar plate to CDC standard methodology for the isolation of carbapenem-resistant Enterobacteriaceae (CRE) from 300 rectal swab specimens obtained from patients residing in a long-term-care facility (LTCF). Multiplex PCR experiments were performed on isolates to identify specific Klebsiella pneumoniae carbapenemases (KPC) and additional ?-lactamases. Of the 300 patients, 72 (24%) harbored CRE and were PCR positive for KPC enzymes. The Remel Spectra CRE plates detected KPC-type CRE in isolates from 70 of 72 patients (97.2%), while the CDC method detected CRE in 56 of 72 (77.8%). CRE identification results were available in 18 h compared to 36 h for the CDC method. Remel Spectra CRE agar plates can provide useful means for a fast and reliable method for detecting KPC-type CRE and for accelerated institution of appropriate infection control precautions. PMID:26085613
NASA Astrophysics Data System (ADS)
Delage, D.; Roca, R.; Bertin, F.; Delcourt, J.; CréMieu, A.; Massebeuf, M.; Ney, R.; van Velthoven, P.
1997-03-01
The capability of Stratosphere-Troposphere radars for estimating the energy dissipation rate ? and eddy diffusivity Kz is still strongly questioned because the methods proposed in the literature generally make use of assumptions not yet fully justified. In order to clarify this point, two assessment campaigns, using the high-resolution UHF PROUST radar, have been performed. Results obtained with both "width" and "power" methods are systematically compared with a statistical approach proposed by Dewan [1979] and Woodman and Rastogi [1984], using the thickness and lifetime of the turbulent layers. The ? and Kz derived from these three methods in observed turbulent fields near the tropopause level are found to be reasonably similar for turbulent layers whose thickness LT is smaller than 300 m. For the thicker turbulent patches (LT>300 m), the statistical approach using turbulent thickness tends to give eddy diffusivity values greater than those obtained with width and power methods. This discrepancy could be due to the nonhomogeneity of the turbulence in these large turbulent structures.
Wind, Carolien M; de Vries, Henry J C; van Dam, Alje P
2015-03-01
In response to antimicrobial resistance of Neisseria gonorrhoeae to last-resort extended-spectrum cephalosporins, combination therapy of azithromycin+ceftriaxone is now recommended. Dual therapy can be effective to treat monoresistant strains as well as multidrug-resistant strains, preferably employing the effect of in vitro synergy. As reports on in vitro synergy of azithromycin+ceftriaxone in N. gonorrhoeae are conflicting, in this study an evaluation of this combination was performed using a cross-wise Etest method and agar dilution. Synergy was defined as a fractional inhibitory concentration index (FICI) of ?0.5. To identify other dual treatment options for gonorrhoea, in vitro synergy was evaluated for 65 dual antimicrobial combinations using Etest. Azithromycin, cefixime, ceftriaxone, colistin, ertapenem, fosfomycin, gentamicin, minocycline, moxifloxacin, rifampicin, spectinomycin and tigecycline were screened for synergy in all possible combinations. No synergy or antagonism was found for any of the 65 combinations. The geometric mean FICI ranged from 0.82 to 2.00. The mean FICI of azithromycin+ceftriaxone was 1.18 (Etest) and 0.55 (agar dilution). The difference between both methods did not result in a difference in interpretation of synergy. Ceftriaxone-resistant strain F89 was tested in all combinations and no synergy was found for any of them. Most importantly, the ceftriaxone minimum inhibitory concentration of F89 was not decreased below the breakpoint with any concentration of azithromycin. PMID:25532741
Shawar, R; Paetznick, V; Witte, Z; Ensign, L G; Anaissie, E; LaRocco, M
1992-08-01
A study was performed in two laboratories to evaluate the effect of growth medium and test methodology on inter- and intralaboratory variations in the MICs of amphotericin B (AMB), flucytosine (5FC), fluconazole (FLU), itraconazole (ITRA), and the triazole Sch 39304 (SCH) against 14 isolates of Candida albicans. Testing was performed by broth microdilution and semisolid agar dilution with the following media, buffered to pH 7.0 with morpholinepropanesulfonic acid (MOPS): buffered yeast nitrogen base (BYNB), Eagle's minimal essential medium (EMEM), RPMI 1640 medium (RPMI), and synthetic amino acid medium for fungi (SAAMF). Inocula were standardized spectrophotometrically, and endpoints were defined by the complete absence of growth for AMB and by no more than 25% of the growth in the drug-free control for all other agents. Comparative analyses of median MICs, as determined by each test method, were made for all drug-medium combinations. Both methods yielded similar (+/- 1 twofold dilution) median MICs for AMB in EMEM and RPMI, 5FC in all media, and FLU in EMEM, RPMI, and SAAMF. In contrast, substantial between-method variations in median MICs were seen for AMB in BYNB and SAAMF, FLU In BYNB, and ITRA and SCH in all media. Interlaboratory concordance of median MICs was good for AMB, 5FC, and FLU but poor for ITRA and SCH in all media. Endpoint determinations were analyzed by use of kappa statistical analyses for evaluating the strength of observer agreement. Moderate to almost perfect interlaboratory agreement occurred with AMB and 5FC in all media and with FLU in EMEM, RPMI, and SAAMF, irrespective of the test method. Slight to almost perfect interlaboratory agreement occurred with ITRA and SCH in EMEM, RPMI, and SAAMF when tested by semisolid agar dilution but not broth microdilution. Kappa values assessing intralaboratory agreement between methods were high for 5FC in all media, for AMB in BYNB, ENEM, and RPMI, and for FLU in EMEM, RPMI, and SAAMF. One laboratory, but not the other, reported substantial to almost perfect agreement between methods for ITRA, and SCH in EMEM, RPMI, and SAAMF. Both laboratories reported poor agreement between methods for the azoles in BYNB. Discrepancies noted in azole-BYNB combinations were largely due to the greater inhibitory effect of these agents in BYNB than in other media. These results indicate that the semisolid agar dilution and broth microdilution methods with EMEM or RPMI yield equivalent and reproducible MICs for AMB, 5FC, and FLU but not ITRA and SCH. PMID:1500502
Heal, Mathew R
2008-01-01
A few studies have suggested that the precision and accuracy of measurement of NO2 by Palmes-type passive diffusion tube (PDT) are affected by the method of preparation of the triethanolamine (TEA) absorbent coating on the ...
Functional properties of edible agar-based and starch-based films for food quality preservation.
Phan, The D; Debeaufort, F; Luu, D; Voilley, A
2005-02-23
Edible films made of agar (AG), cassava starch (CAS), normal rice starch (NRS), and waxy (glutinous) rice starch (WRS) were elaborated and tested for a potential use as edible packaging or coating. Their water vapor permeabilities (WVP) were comparable with those of most of the polysaccharide-based films and with some protein-based films. Depending on the environmental moisture pressure, the WVP of the films varies and remains constant when the relative humidity (RH) is >84%. Equilibrium sorption isotherms of these films have been measured; the Guggenheim-Anderson-de Boer (GAB) model was used to describe the sorption isotherm and contributed to a better knowledge of hydration properties. Surface hydrophobicity and wettability of these films were also investigated using the sessile drop contact angle method. The results obtained suggested the migration of the lipid fraction toward evaporation surface during film drying. Among these polysaccharide-based films, AG-based film and CAS-based film displayed more interesting mechanical properties: they are transparent, clear, homogeneous, flexible, and easily handled. NRS- and WRS-based films were relatively brittle and have a low tension resistance. Microstructure of film cross section was observed by environmental scanning electron microscopy to better understand the effect of the structure on the functional properties. The results suggest that AG-based film and CAS-based films, which show better functional properties, are promising systems to be used as food packaging or coating instead of NRS- and WRS-based films. PMID:15713008
NASA Astrophysics Data System (ADS)
Chai, Zhenhua; Zhao, T. S.
2014-07-01
In this paper, we propose a local nonequilibrium scheme for computing the flux of the convection-diffusion equation with a source term in the framework of the multiple-relaxation-time (MRT) lattice Boltzmann method (LBM). Both the Chapman-Enskog analysis and the numerical results show that, at the diffusive scaling, the present nonequilibrium scheme has a second-order convergence rate in space. A comparison between the nonequilibrium scheme and the conventional second-order central-difference scheme indicates that, although both schemes have a second-order convergence rate in space, the present nonequilibrium scheme is more accurate than the central-difference scheme. In addition, the flux computation rendered by the present scheme also preserves the parallel computation feature of the LBM, making the scheme more efficient than conventional finite-difference schemes in the study of large-scale problems. Finally, a comparison between the single-relaxation-time model and the MRT model is also conducted, and the results show that the MRT model is more accurate than the single-relaxation-time model, both in solving the convection-diffusion equation and in computing the flux.
NASA Astrophysics Data System (ADS)
Abdulagatov, I. M.; Abdulagatova, Z. Z.; Kallaev, S. N.; Bakmaev, A. G.; Ranjith, P. G.
2015-04-01
The well-known contact-free, laser-flash method was used for measurement of the thermal diffusivity of natural sandstone samples. The experimental procedure was conducted using the microflash apparatus (LFA 457). The measurements have been made over the temperature range from (302.9 to 774.3) K. The isobaric heat capacities of the same sample were measured over the temperature range from (308 to 763) K using DSC 204 F1. Uncertainties are 3 % and 1 % for and , respectively. Measured values of and together with density data were used to calculate the thermal conductivity of sandstone. Theoretically based correlations for the thermal diffusivity (damped harmonic oscillator, DHO) and heat capacity (Debye and Einstein theories) were adopted to accurately represent the measured data. Correlation equations for the thermal diffusivity and heat capacity have been developed using the well-known theoretical asymptotic behavior of and for various temperature ranges (low- and high-temperature limits). The microscopic nature of the effect of temperature on and behavior of sandstone is discussed. Detailed interpretation and testing of the measured property data for sandstone using various existing theoretical and empirical models, in order to check their accuracy, predictive capability, and applicability, are provided.
Su, Jonathan T; Duncan, P Brent; Momaya, Amit; Jutila, Arimatti; Needham, David
2010-01-28
While the Stokes-Einstein (SE) equation predicts that the diffusion coefficient of a solute will be inversely proportional to the viscosity of the solvent, this relation is commonly known to fail for solutes, which are the same size or smaller than the solvent. Multiple researchers have reported that for small solutes, the diffusion coefficient is inversely proportional to the viscosity to a fractional power, and that solutes actually diffuse faster than SE predicts. For other solvent systems, attractive solute-solvent interactions, such as hydrogen bonding, are known to retard the diffusion of a solute. Some researchers have interpreted the slower diffusion due to hydrogen bonding as resulting from the effective diffusion of a larger complex of a solute and solvent molecules. We have developed and used a novel micropipette technique, which can form and hold a single microdroplet of water while it dissolves in a diffusion controlled environment into the solvent. This method has been used to examine the diffusion of water in both n-alkanes and n-alcohols. It was found that the polar solute water, diffusing in a solvent with which it cannot hydrogen bond, closely resembles small nonpolar solutes such as xenon and krypton diffusing in n-alkanes, with diffusion coefficients ranging from 12.5x10(-5) cm(2)/s for water in n-pentane to 1.15x10(-5) cm(2)/s for water in hexadecane. Diffusion coefficients were found to be inversely proportional to viscosity to a fractional power, and diffusion coefficients were faster than SE predicts. For water diffusing in a solvent (n-alcohols) with which it can hydrogen bond, diffusion coefficient values ranged from 1.75x10(-5) cm(2)/s in n-methanol to 0.364x10(-5) cm(2)/s in n-octanol, and diffusion was slower than an alkane of corresponding viscosity. We find no evidence for solute-solvent complex diffusion. Rather, it is possible that the small solute water may be retarded by relatively longer residence times (compared to non-H-bonding solvents) as it moves through the liquid. PMID:20113048
NASA Astrophysics Data System (ADS)
Tønning, Erik; Polders, Daniel; Callaghan, Paul T.; Engelsen, Søren B.
2007-09-01
This paper demonstrates how the multi-linear PARAFAC model can with advantage be used to decompose 2D diffusion-relaxation correlation NMR spectra prior to 2D-Laplace inversion to the T2- D domain. The decomposition is advantageous for better interpretation of the complex correlation maps as well as for the quantification of extracted T2- D components. To demonstrate the new method seventeen mixtures of wheat flour, starch, gluten, oil and water were prepared and measured with a 300 MHz nuclear magnetic resonance (NMR) spectrometer using a pulsed gradient stimulated echo (PGSTE) pulse sequence followed by a Carr-Purcell-Meiboom-Gill (CPMG) pulse echo train. By varying the gradient strength, 2D diffusion-relaxation data were recorded for each sample. From these double exponentially decaying relaxation data the PARAFAC algorithm extracted two unique diffusion-relaxation components, explaining 99.8% of the variation in the data set. These two components were subsequently transformed to the T2- D domain using 2D-inverse Laplace transformation and quantitatively assigned to the oil and water components of the samples. The oil component was one distinct distribution with peak intensity at D = 3 × 10 -12 m 2 s -1 and T2 = 180 ms. The water component consisted of two broad populations of water molecules with diffusion coefficients and relaxation times centered around correlation pairs: D = 10 -9 m 2 s -1, T2 = 10 ms and D = 3 × 10 -13 m 2 s -1, T2 = 13 ms. Small spurious peaks observed in the inverse Laplace transformation of original complex data were effectively filtered by the PARAFAC decomposition and thus considered artefacts from the complex Laplace transformation. The oil-to-water ratio determined by PARAFAC followed by 2D-Laplace inversion was perfectly correlated with known oil-to-water ratio of the samples. The new method of using PARAFAC prior to the 2D-Laplace inversion proved to have superior potential in analysis of diffusion-relaxation spectra, as it improves not only the interpretation, but also the quantification.
Nicol, Ginger E; Morrato, Elaine H; Johnson, Mark C; Campagna, Elizabeth; Yingling, Michael D; Pham, Victor; Newcomer, John W
2011-01-01
There is public health interest in the identification and treatment of modifiable cardiometabolic risk factors among patients treated with antipsychotic medications. However, best-practice screening recommendations endorsed by multiple medical organizations have not translated into real-world clinical practice. Quality improvement strategies may help to address the gap between policy and implementation. This column describes the successful implementation of a best-practice glucose screening program in a large network of community mental health centers that was based on Six Sigma and diffusion of innovation theory. PMID:21209293