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PubMed2005

Comparison of disk diffusion method and broth microdilution method for antifungal susceptibility testing of dermatophytes.

The use of the agar diffusion Neo-Sensitabs method to determine antifungal susceptibility of 59 isolates of dermatophytes, namely Epidermophyton floccosum, Microsporum canis, M. gypseum, Trichophyton mentagrophytes, T. rubrum and T. tonsurans to Clotrimazole (CLZ), Itraconazole (ITZ) and Terbinafine (TBF) is described. Results obtained are compared to the minimum inhibitory concentrations (MIC) determined by an adaptation of the NCCLS-M38-A procedure. Using the diffusion method, all strains showed a broad zone of inhibition at the first available reading time (3 or 7 days). Using the broth microdilution method, the geometric mean MIC (microg/ml) with regard to all isolates was < or = 0.03 for TBF, < or = 0.069 for CLZ and < or = 0.919 for ITZ. In both methods, TBF was the most active antifungal agent against all isolates tested. The two methods evaluated were able to detect the resistance of the quality control strains of Aspergillus fumigatus to ITZ. Even though a reference method for testing dermatophytes still has not been developed, our data suggest that the Neo-Sensitabs diffusion method could provide a simple procedure for the antifungal susceptibility testing of dermatophytes in the routine clinical laboratory.

Antifungal Agents↗

PubMed1978

Comparison of the conventional lecture method and the self-instruction method for teaching clinical pathology.

Two separate courses in clinical pathology were presented to two groups of second-year medical students. The first (large) group was taught by the conventional lecture method; the other (small) group, by a self-instructional method for roughly half of the course, followed by the conventional lecture method for the second half of the course. The effectivenesses of the two methods were compared, based on performances on the final written examination. It was found that the self-instructional method was as effective as the conventional method in teaching clinical pathology, at least in teaching basic principles and interpretive clinical chemistry, as judged by the performances of the two groups. Surprisingly, the two groups differed significantly in performances on the portion of the course taught by similar methods.

Education, Medical, Undergraduate↗

PubMed2004

Recognition of multiple patterns in unaligned sets of sequences: comparison of kernel clustering method with other methods.

MOTIVATION: Transcription factor binding sites often differ significantly in their primary sequence and can hardly be aligned. Often one set of sites can contain several subsets of sequences that follow not just one but several different patterns. There is a need for sensitive methods to reveal multiple patterns in unaligned sets of sequences. RESULTS: We developed a novel method for analysis of unaligned sets of sequences based on kernel estimation. The method is able to reveal 'multiple local patterns'-a set of weight matrices. Every weight matrix characterizes a pattern that can be found in a significant subset of sequences under analysis. The method developed has been compared with several other methods of pattern discovery such as Gibbs sampling, MEME, CONSENSUS, MULTIPROFILER and PROJECTION. The kernel method showed the best performance in terms of how close the revealed weight matrices are to the original ones. We applied the kernel method to analyze three samples of promoters (cell-cycle, T-cells and muscle-specific). We compared the multiple patterns revealed with the TRANSFAC library of weight matrices and found a strong similarity to several weight matrices for transcription factors known to be involved in the mentioned specific gene regulation. AVAILABILITY: The program is available for on-line use at: http://www.biobase.de/cgi-bin/biobase/cbs2/bin/template.cgi?template=cbscall.html

Algorithms↗

PubMed2004

A comparative study of the disc diffusion method with the broth microdilution and Etest methods for voriconazole susceptibility testing of Aspergillus spp.

OBJECTIVE: The activity of voriconazole against Aspergillus spp. (n = 77) was tested by the Etest, disc diffusion and the NCCLS M38-A methods. METHODS: Four Rhizomucor spp. isolates were included to study the suitability of the three susceptibility testing methods to detect isolates resistant to voriconazole. The disc diffusion method performed on Mueller-Hinton agar (Difco) supplemented with 2% glucose and Methylene Blue (0.5 mg/L) gave zone diameters with very clear border edges. RESULTS: The disc diffusion method showed excellent correlation with the Etest and the NCCLS methods. CONCLUSION: On the basis of our results, it appears that the disc diffusion test is a useful method for testing the activity of voriconazole against Aspergillus spp.

Antifungal Agents↗

PubMed1998

Percutaneous dilational tracheostomy: the Ciaglia method versus the Portex [correction of Rapitrach] method.

UNLABELLED: In a prospective study, we performed percutaneous dilational tracheostomy (PDT) using either the Ciaglia method (gradual dilation) or the Portex [corrected] method (single dilation) in 80 patients. We encountered difficulty in dilating the tracheal stoma of three (7.5%) patients in the Ciaglia group because of tight pretracheal fascia. It was difficult to insert the tracheostomy tube in four (10%) patients in the Portex [corrected] group even after appropriate tracheal dilation. However, the tracheal cannulation was successfully completed in all patients in subsequent attempts. The mean time for completion of the procedures, from skin incision to insertion of the tracheostomy tube, was 14+/-5.5 min with the Ciaglia method and 6.5+/-3.5 min with the Portex [corrected] method. PDT with either method has not been associated with clinically significant hemorrhage, infection at the stoma site, or cosmetic deformity. In a follow-up period of 9 mo, none of our decannulated patients presented with clinical tracheal stenosis. Our results indicate that PDT with both methods is as safe and easy to organize and perform as a bedside procedure, obviating the need to transport critically ill patients from the critical care unit. IMPLICATIONS: The tracheas of 80 patients were cannulated through an artificial opening using either the Ciaglia (gradual dilation) or the Portex [corrected] (single dilation) method. Both techniques were successful with no significant complications. After 9 mo of closure of this opening, none of the survivors had significant scarring or narrowing of the trachea.

Adolescent↗

PubMed2000

Producing a full-scale model from computed tomographic data with the rapid prototyping technique using the binder jet method: a comparison with the laser lithography method using a dry skull.

Rapid prototyping using the binder jet method has recently been established and has already produced excellent results in industrial applications. The authors recently developed a technique for producing a full-scale model from computed tomographic (CT) data with the binder jet method as an approach to overcome the shortcomings of the laser lithography method, which is already widely used in medicine. They conducted a comparative investigation of full-scale models made with both techniques using a dry skull to determine the accuracy of the models. It was clearly demonstrated that the accuracy of the binder jet method was high enough to be used in craniomaxillofacial surgery because it was the same as the laser lithography method. This study employed data from the latest helical volume scan computed tomography device using a multidetector. The study showed that the new rapid prototyping technique was satisfactory in terms of speed, cost, installation environment, and accuracy of models, and that detailed shapes and structures can be reproduced well. Because this technique has many advantages over the laser lithography method, it should play a major role in craniomaxillofacial surgery and in other medical fields in combination with advances in CT devices. Although plaster is a more suitable fixation material when the emphasis is on the reproducibility of detailed structures, the binder jet method using starch is extremely useful for simulating operations and determining implant shapes because it allows for the prompt production of models.

Analog-Digital Conversion↗

PubMedDate not supplied

Comparison of test-injection method and fixed-time method for depiction of hepatocellular carcinoma using dynamic steady-state free precession magnetic resonance imaging.

OBJECTIVE: The purpose of this study was to clarify the usefulness of the test-injection method as compared with the fixed-time method in dynamic magnetic resonance (MR) imaging of hepatocellular carcinoma (HCC). METHODS: Ninety-seven patients with a total of 118 hepatocellular carcinomas underwent 3-dimensional fast imaging with steady-state free precession (3D-FISP) for dynamic study of the liver as well as catheter-assisted computed tomography hepatic angiography (CTHA) for preoperative evaluation. In 42 cases, the fixed-time method (30-second scan time delay in the hepatic arterial phase [HAP]) was performed (group 1), and in 55 cases, the test-injection method was performed (group 2). The following parameters were evaluated: 1) the adequacy of the HAP, 2) tumor vascularity using CTHA findings as a gold standard, and 3) the contrast-to-noise ratio (CNR) of the HCC during the HAP of dynamic MR imaging. RESULTS: In group 1, 79% (33 of 42) of the cases were obtained at the optimal HAP; the percentage in group 2 was 98% (54 of 55) of the cases. This difference was statistically significant (P < 0.05). The vascularity of 82% of the tumors in group 1 and 89% of those in group 2 was diagnosed correctly. Regarding hypervascular tumors, correct evaluation of tumor vascularity was made in 87% of group 1 cases and 95% of group 2 cases. No significant difference was present between the 2 groups (total: P = 0.43, hypervascular HCC: P = 0.29). 3) The CNR calculated for all HCCs in group 2 (mean +/- SD: 8.66 +/- 11.0) was significantly higher than that for HCCs in group 1 (4.29 +/- 9.44; P < 0.05). As for the hypervascular tumors, the CNR calculated for group 2 (mean +/- SD: 9.89 +/- 10.6) was also significantly higher than that for group 1 (5.52 +/- 9.81; P < 0.05). CONCLUSION: The 3D-FISP dynamic MR imaging using the test-injection method resulted in better demonstration of HCC than the 3D-FISP using the fixed-time method.

Adult↗

PubMed1996

A comparison between a PCR method and a conventional culture method for detecting pathogenic Yersinia enterocolitica in food.

The aim of this study was to develop a polymerase chain reaction (PCR) method for the detection of pathogenic Yersinia enterocolitica and to compare it with an official culture method (NMKL-117). Primers were selected for nested PCR directed at the attachment invasion locus, ail, on the bacterial chromosome, as well as at a sequence on the pathogenic marker plasmid, termed virulence factor, virF. The final results obtained by the two methods were similar. However, while the conventional method yielded contradictory data for some steps the PCR method provided unambiguous results. Considerable advantages, i.e. higher sensitivity and specificity of the PCR method, compared with the conventional method for detecting pathogenic Y. enterocolitica, were demonstrated in this study.

Bacterial Outer Membrane Proteins↗

PubMed1996

Comparison of the Equil2 program and other methods for estimating the ion-activity product of urinary calcium oxalate: a new simplified method is proposed.

BACKGROUND: We aimed to develop a new simplified method to determine the urinary calcium-oxalate saturation. METHODS: The ion-activity product (AP) of urinary calcium oxalate was estimated in 345 clinical urine specimens (all 2.5 hour collections) using the Equil2 computer program and several other methods, and the results were compared. A new index using 4 parameters was created using multiple regression analysis. RESULTS: Our new simplified method (the AP(CaOx) index EQ2) provided a better approximation to the Equil2 method (r = 0.9897) than other conventional methods. CONCLUSION: This new method requiring 4 factors (urinary calcium, magnesium, oxalate, and citrate concentrations) is simple and clinically usable.

Calcium Oxalate↗

PubMed1996

A regression method including chronological and bone age for predicting final height in Turner's syndrome, with a comparison of existing methods.

A total of 235 measurement points of 57 Dutch women with Turner's syndrome (TS), including women with spontaneous menarche and oestrogen treatment, served to develop a new Turner-specific final height (FH) prediction method (PTS). Analogous to the Tanner and Whitehouse mark 2 method (TW) for normal children, smoothed regression coefficients are tabulated for PTS for height (H), chronological age (CA) and bone age (BA), both TW RUS and Greulich and Pyle (GP). Comparison between all methods on 40 measurement points of 21 Danish TS women showed small mean prediction errors (predicted minus observed FH) and corresponding standard deviation (ESD) of both PTSRUS and PTSGP, in particular at the "younger" ages. Comparison between existing methods on the Dutch data indicated a tendency to overpredict FH. Before the CA of 9 years the mean prediction errors of the Bayley and Pinneau and TW methods were markedly higher compared with the other methods. Overall, the simplest methods--projected height (PAH) and its modification (mPAH)--were remarkably good at most ages. Although the validity of PTSRUS and PTSGP remains to be tested below the age of 6 years, both gave small mean prediction errors and a high accuracy. FH prediction in TS is important in the consideration of growth-promoting therapy or in the evaluation of its effects.

Adolescent↗

PubMed1992

Serum lipase determination in the dog: a comparison of a titrimetric method with an automated kinetic method.

An enzymatic, kinetic method for determining serum lipase activity was evaluated and compared to a standard manual method for use in dogs. The kinetic method was a commercial kit adapted for use on a tandem access clinical chemistry analyzer and utilized a series of coupled enzymatic reactions based on the hydrolysis of 1,2-diglyceride by lipase. The manual method was the Cherry-Crandall technique based on the titration of base against the acid formed by hydrolysis of an olive oil substrate by lipase. The correlation between the two methods was very good (r = 0.94). The reference range for 56 clinically healthy dogs assayed by the kinetic method was 90 to 527 U/L. Diseases associated with a greater than twofold elevation in serum lipase activity as determined by the kinetic method included pancreatitis, gastritis with liver disease, and oliguric renal failure with metabolic acidosis. In some cases, pancreatitis was seen with other clinical problems, such as gastroenteritis, diabetic ketoacidosis, duodenal mass, disseminated intravascular coagulation, and septic peritonitis. Diseases associated with serum lipase activity within the reference range or elevated less than twofold included gastritis, gastric ulcer, cholestasis, phenobarbital-induced hepatopathy, colitis, copper hepatopathy, abdominal hematoma, apocrine gland adenocarcinoma, and thrombocytopenia with pneumonia.

Journal Article↗

PubMed1999

Fluconazole susceptibilities of bloodstream Candida sp. isolates as determined by National Committee for Clinical Laboratory Standards method M27-A and two other methods.

The in vitro activity of fluconazole against 143 Candida spp. obtained from the bloodstreams of 143 hospitalized patients from 1995 to 1997 was studied. Susceptibility tests were carried out by two macrodilution methods, the M27-A and a modified M27-A method (0. 165 M, pH 7/morpholinepropanesulfonic acid-buffered RPMI 1640 medium supplemented with 20 g of D-dextrose per liter), and by the agar diffusion method (with 15-microg fluconazole [Neo-Sensitab] tablets). With 2 microg of fluconazole per ml, 96.92% of 65 C. albicans isolates, 86.2% of 58 C. parapsilosis isolates 7 of 8 C. tropicalis isolates, and 1 of 6 C. glabrata isolates were inhibited. Only one strain of C. albicans and one strain of C. tropicalis were resistant. The agreement between the two macrodilution methods was greater than 90% within +/-2 log2 dilutions for all strains except C. glabrata (83.3%) and C. tropicalis (87.5%). Generally, MICs were 1 log2 dilution lower in glucose-supplemented RPMI 1640 medium. No correlation between zone sizes and MICs was found. All strains susceptible by the diffusion test were susceptible by the dilution method, but the converse was not necessarily true. Interestingly, inhibition zones were smaller for C. albicans, for which the geometric mean MIC was 0.29 microg/ml and the mean inhibition zone diameter was 25.7 mm, while for C. parapsilosis the geometric mean MIC was 0.96 microg/ml and the mean inhibition zone diameter was 31. 52 mm. In conclusion, the two macrodilution methods give similar results. The modified M27-A method with 2% dextrose has the advantage of shortening the incubation time and simplifying the endpoint determination.

Antifungal Agents↗

PubMedDate not supplied

Comparison of erythrocyte sedimentation rate measurement by the automated SEDIsystem and conventional Westergren method using the Bland and Altman statistical method.

OBJECTIVES: To compare the performance of SEDIsystem(TM), a fully automated analyzer for the measurement of the erythrocyte sedimentation rate (ESR), with the manual Westergren method. MATERIALS AND METHODS: Both methods were applied to 150 randomly selected subjects. The linear regression and Bland and Altman data analysis methods were used to measure the agreement between the automated and manual methods. RESULTS: The regression analysis showed a good correlation between the two methods (r=0.91). The Bland and Altman data analysis showed no systematic bias (95% confidence interval for mean difference); however, limits of agreement were between 11.52 and -37.88. This indicates that ESR values measured by the SEDIsystem may be 11.52 mm/h above or 37.88 mm/h below the reference method. A greater scatter of data was also observed with abnormally high (>25 mm/h) ESR results (mean of difference=-21.4 and limits of agreement=-45.2 and 2.26) compared with normal (<25 mm/h) readings (mean of difference=-3.9 and limits of agreement=-13.5 and 5.7). CONCLUSION: The Bland and Altman statistical analysis showed a wide degree of scatter between results obtained by the two ESR techniques that was not clearly demonstrated using the linear regression analysis. The automated system was found to underestimate ESR with the Bland and Altman statistical analysis, and therefore a correction factor is recommended.

Autoanalysis↗

PubMed1976

A comparative study of the Bessey method and Hausamen method for serum alkaline phosphatase determination.

The methods of Bessey et al. and Hausamen et al. for serum alkaline phosphatase determination were compared. Determinations were carried out using sera from healthy blood donors and sera from patients suffering from different hepatobiliary diseases. A high reproducibility of values obtained using both methods was noted. The sensitivity of the method of Hausamen et al. is about four times greater than that of the method of Bessey et al., even though the former method employed a lower reaction temperature. A high degree of correlation exists between the two methods and the data reported indicate that both methods are completely valid.

Adult↗

PubMed2005

Evaluation of methods for predicting the topology of beta-barrel outer membrane proteins and a consensus prediction method.

BACKGROUND: Prediction of the transmembrane strands and topology of beta-barrel outer membrane proteins is of interest in current bioinformatics research. Several methods have been applied so far for this task, utilizing different algorithmic techniques and a number of freely available predictors exist. The methods can be grossly divided to those based on Hidden Markov Models (HMMs), on Neural Networks (NNs) and on Support Vector Machines (SVMs). In this work, we compare the different available methods for topology prediction of beta-barrel outer membrane proteins. We evaluate their performance on a non-redundant dataset of 20 beta-barrel outer membrane proteins of gram-negative bacteria, with structures known at atomic resolution. Also, we describe, for the first time, an effective way to combine the individual predictors, at will, to a single consensus prediction method. RESULTS: We assess the statistical significance of the performance of each prediction scheme and conclude that Hidden Markov Model based methods, HMM-B2TMR, ProfTMB and PRED-TMBB, are currently the best predictors, according to either the per-residue accuracy, the segments overlap measure (SOV) or the total number of proteins with correctly predicted topologies in the test set. Furthermore, we show that the available predictors perform better when only transmembrane beta-barrel domains are used for prediction, rather than the precursor full-length sequences, even though the HMM-based predictors are not influenced significantly. The consensus prediction method performs significantly better than each individual available predictor, since it increases the accuracy up to 4% regarding SOV and up to 15% in correctly predicted topologies. CONCLUSIONS: The consensus prediction method described in this work, optimizes the predicted topology with a dynamic programming algorithm and is implemented in a web-based application freely available to non-commercial users at http://bioinformatics.biol.uoa.gr/ConBBPRED.

Algorithms↗

PubMed1991

Collagen-gel-embedded three-dimensional culture of human thyroid epithelial cells: comparison between the floating sandwich method and the dispersed embedding method.

Human thyroid epithelial cells were isolated from surgically resected human thyroid gland with collagenase and cultured for one week under EGF-supplemented conditions to allow them to proliferate. Then the cells were transferred to the following three-dimensional culture systems. One was a culture of isolated cells between floating double layers of collagen gel, designated the "floating sandwich method." The other was a culture of isolated cells mixed with collagen gel, designated the "dispersed embedding method." Many folliclelike structures with lumina of appreciable size were obtained by the former method. The cells cultured by the floating sandwich method exhibited a distinct polarity shown by the presence of numerous microvilli at the apical surface and close contact with collagen gels at the basal surface. On the other hand, only a few folliclelike structures were obtained by the dispersed embedding method, in which the folliclelike structures were small in size and the cells showed less distinct polarity than those observed in the floating sandwich method. Thus, the floating sandwich method appears to be suitable for studying the process and mechanism of in vitro organization of follicular structures by human thyroid epithelial cells.

Cell Division↗

PubMed1990

Particle design of tolbutamide by the spherical crystallization technique. III. Micromeritic properties and dissolution rate of tolbutamide spherical agglomerates prepared by the quasi-emulsion solvent diffusion method and the solvent change method.

With the objective of modifying the micromeritic properties of tolbutamide (i.e., to manufacture a highly functional powder form), particle design was attempted using a quasi-emulsion solvent diffusion (QESD) method, and the micromeritic properties and dissolution rate of the obtained spherical agglomerates were evaluated by comparison with agglomerates prepared by the solvent change (SC) method. For the production of tolbutamide agglomerates by the QESD method, a necessary condition was the addition of a sucrose fatty acid ester to the system as an emulsifying agent. The particle diameter of the agglomerates obtained by the QESD method depended on the size of the initially formed quasi-emulsion droplets, which in turn depended on the viscosity of the solution. In addition, the agglomerates were nearly perfectly spherical in shape. In the QESD method, the quasi-emulsion droplets crystallized instantaneously from the droplet surface inward. The resultant agglomerates were dense, had great mechanical strength and showed excellent flowability due to their perfect spherical shape. On the other hand, the agglomerates produced by the SC method were conglomerates of primary crystals, and fine, needle-like crystals formed on their surface. As a result, these agglomerates had a large specific surface area, and they therefore showed greater solubility than the agglomerates prepared by the QESD method.

Chemistry, Pharmaceutical↗

PubMed2003

Appropriate methods for analyzing the effect of method choice on contraceptive discontinuation.

The contraceptive method chosen is an important determinant of contraceptive discontinuation. However, method choice is endogenous to contraceptive discontinuation. Using data from the 1997 Indonesia Demographic and Health Survey, we apply a multilevel multi-process model to examine the impact of method choice on three types of contraceptive discontinuation. We confirm that method choice is endogenous to the processes of contraceptive abandonment and method switching, but not failure. Ignoring the endogeneity of contraceptive choice leads to various biases in the magnitude of estimated effects of method choice on abandonment and method switching, but the general conclusions are robust to these biases.

Adult↗