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At least 523 records · Page 29Linked to original sources
PubMed2006

Detection of biofilm formation in Staphylococcus epidermidis from implant infections. Comparison of a PCR-method that recognizes the presence of ica genes with two classic phenotypic methods.

Biofilm-forming ability is increasingly being recognized as an important virulence factor in Staphylococcus epidermidis. This study compares three different techniques for the detection of biofilm-positive strains. The presence of icaA and icaD genes responsible for biofilm synthesis was investigated by a PCR method in a collection of 80 S. epidermidis strains isolated from orthopedic implant infections. The results from molecular analysis were compared with those obtained by two classic phenotypic methods, the Congo red agar (CRA) plate test and the microtiter plate test (MtP). Fifty-seven percent of all the examined strains were found icaA/icaD-positive, of which only three were not positive for CRA test. Differently, by the MtP method, 66% of the strains were found to be biofilm-producers but only a limited agreement with the PCR-method was noticeable because of the observation of (icaA/icaD+)/MtP- strains (8%) and of a surprising ambiguous result of (icaA/icaD-)/MtP+ strains (16%). The category of the weak biofilm-producers provided the highest contribution to these mismatching results (10%). The better agreement between the CRA plate test with the molecular detection of ica genes indicates the former as a reliable test for the phenotypic characterization of virulence of clinical isolates. However, MtP method remains a precious tool for the in vitro screening of different biomaterials for the adhesive properties using a reference strain.

Bacterial Adhesion↗
PubMed2006

Optimized and parallelized implementation of the electronegativity equalization method and the atom-bond electronegativity equalization method.

The most common way to calculate charge distribution in a molecule is ab initio quantum mechanics (QM). Some faster alternatives to QM have also been developed, the so-called "equalization methods" EEM and ABEEM, which are based on DFT. We have implemented and optimized the EEM and ABEEM methods and created the EEM SOLVER and ABEEM SOLVER programs. It has been found that the most time-consuming part of equalization methods is the reduction of the matrix belonging to the equation system generated by the method. Therefore, for both methods this part was replaced by the parallel algorithm WIRS and implemented within the PVM environment. The parallelized versions of the programs EEM SOLVER and ABEEM SOLVER showed promising results, especially on a single computer with several processors (compact PVM). The implemented programs are available through the Web page http://ncbr.chemi.muni.cz/~n19n/eem_abeem.

Journal Article↗
PubMed2003

Fat suppression gradient-echo magnetic resonance imaging of experimental articular cartilage lesions: comparison between phase-contrast method at 0.23T and chemical shift selective method at 1.5T.

PURPOSE: To evaluate the diagnostic performance of a newly developed single-scan phase-contrast water-fat imaging technique for fat suppression at 0.23T open magnet, compared to the conventional chemical shift selective fat suppression method at 1.5T, in the detection of experimental articular cartilage lesions. MATERIALS AND METHODS: Sixty regions of 20 knee joint specimens of pigs with artificially created articular cartilage lesions were examined with 0.23T and 1.5T MR scanners. Sagittal fat-suppressed three-dimensional gradient-echo (3D GRE) images, obtained with the phase-contrast method at 0.23T, and fat-suppressed three-dimensional spoiled gradient recalled echo (3D SPGR) images, obtained with a chemical shift selective method at 1.5T, were evaluated. Diagnostic performance was analyzed. The conspicuity of the lesions, the amount of artifacts, and the uniformity of fat suppression were evaluated. The contrast-to-noise (CNR) values of cartilage-to-bone marrow, and cartilage-to-infrapatellar fat were calculated. RESULTS: At 0.23T, sensitivity and specificity were 80% and 95% for partial cartilage lesions (grade 2), and 91% and 100% for full-thickness lesions (grade 3). At 1.5T, sensitivity and specificity were 85% and 95% for grade 2 lesions, and 96% and 97% for grade 3 lesions. No significant difference was detected in the conspicuity of lesions. The uniformity of fat suppression was more constant with 3D SPGR images compared to 3D GRE images. More susceptibility artifacts, derived from the procedure of creating lesions, were detected at 1.5T. The cartilage-to-fat CNRs were significantly higher with high-field images. CONCLUSION: Phase-contrast method for fat suppression at 0.23T is a useful technique in detecting articular cartilage lesions.

Animals↗
PubMed2004

Development of a capillary zone electrophoretic method to determine six antidepressants in their pharmaceutical preparations. Experimental design for evaluating the ruggedness of method.

A capillary zone electrophoresis method is proposed for the separation of six of the antidepressants most used for the treatment of mental illness (clomipramine, paroxetine, fluoxetine, citalopram, fluvoxamine, and trazodone). Optimum conditions for their separation were investigated. A background electrolyte solution consisting of 50 mM phosphate buffer adjusted to pH 2.0, hydrodynamic injection, and 25 kV as separation voltage were used. Relative standard deviations (RSD) were <0.38% and <2.93% for migration time and corrected peak area (n = 24), respectively. Detection limits obtained for the six antidepressants ranged from 0.03 to 0.11 mg L(-1). Stability of the solutions, linear concentration range, accuracy, and precision were examined during validation of the method. A ruggedness test of this method was performed using the fractional factorial model of Plackett-Burman, requiring in our case design of a matrix of 15 experiments, in which the influence of seven factors at three different levels was tested on different electrophoretic results: efficiency; resolution; and corrected peak area. Statistical evaluation of electrophoretic results was achieved by Youden and Steiner's method. The described method is rapid, sensitive, and rugged and it was tested for the pharmaceutical formulation analysis, giving recoveries between 95.6 and 99.1% with respect to the nominal content.

Antidepressive Agents↗
PubMed1991

The AMeX method: a multipurpose tissue-processing and paraffin-embedding method. III. Extraction and purification of RNA and application to slot-blot hybridization analysis.

RNA was extracted from tissues processed by a new fixation and paraffin-embedding method (the AMeX method) and examined by Northern blot analysis and slot-blot analysis. The RNA extraction method for AMeX-processed tissue sections after the deparaffinization step was the same as that for fresh materials. The total amount of cellular RNA extracted from AMeX-processed mouse liver tissue was slightly less than that extracted from fresh tissue. In tissues of malignant lymphoma, the total amount of cellular RNA extracted from 25 sections each 20 microns thick was about 1.6-1.8 micrograms/mm2, regardless of the histological subtype and period of storage. The extracted RNA was moderately degraded, and usually could not be used for Northern blot hybridization analysis. The intensity of ethidium bromide staining and the hybridization signals of RNA extracted from AMeX-processed tissues were usually reduced in comparison with RNA from fresh material, but specific signals could be detected by slot-blot hybridization analysis. We have demonstrated previously that the AMeX method preserves high-molecular-weight DNA and various antigens. Since the present study showed that information on mRNA can be obtained from AMeX-processed tissue, the versatility and usefulness of this method were further proven.

Animals↗
PubMed2007

MUPRED: a tool for bridging the gap between template based methods and sequence profile based methods for protein secondary structure prediction.

Predicting secondary structures from a protein sequence is an important step for characterizing the structural properties of a protein. Existing methods for protein secondary structure prediction can be broadly classified into template based or sequence profile based methods. We propose a novel framework that bridges the gap between the two fundamentally different approaches. Our framework integrates the information from the fuzzy k-nearest neighbor algorithm and position-specific scoring matrices using a neural network. It combines the strengths of the two methods and has a better potential to use the information in both the sequence and structure databases than existing methods. We implemented the framework into a software system MUPRED. MUPRED has achieved three-state prediction accuracy (Q3) ranging from 79.2 to 80.14%, depending on which benchmark dataset is used. A higher Q3 can be achieved if a query protein has a significant sequence identity (>25%) to a template in PDB. MUPRED also estimates the prediction accuracy at the individual residue level more quantitatively than existing methods. The MUPRED web server and executables are freely available at http://digbio.missouri.edu/mupred.

Algorithms↗
PubMed1993

An ultrafiltration method for the removal of interfering agents and its application to the determination of free ammonia in solutions of oxystarch by the Berthelot reaction method.

Oxystarch was chosen as a model compound for studying biological ammonia-sequestering systems. Ammonia was determined by use of an ion-selective electrode, by L-glutamate dehydrogenase (L-GDH), and by two different Berthelot procedures, in the presence and absence of oxystarch. In the presence of total oxystarch the Berthelot method, particularly when low concentration reagents were used, detected significantly less (P < 0.10) free ammonia than either L-GDH or ion-selective electrode methods. A 0.5-kDa molecular weight cutoff sample ultrafiltration step was added prior to analysis by L-GDH and Berthelot procedures. To facilitate complete removal of oxystarch by the ultrafiltration step, oxystarch was dialyzed before use, yielding a high-molecular-weight fraction (> 1 kDa). Removal of high-molecular-weight oxystarch species and bound ammonia by ultrafiltration of samples prior to assay completely negated discrepancies between ammonia levels measured by L-GDH and both Berthelot methods. The correlation of the levels of measured ammonia, as determined by L-GDH and Berthelot methods, in mixtures with high-molecular-weight oxystarch was significantly improved by the addition of the sample ultrafiltration step. Improved correlation of results from such fundamentally different methods demonstrates the removal of interfering agents as well as the nonperturbatory nature of the improved procedure. The addition of such an ultrafiltration step may be applied to the determination of ammonia by the otherwise interference-prone Berthelot assay in mixtures with any interfering macromolecules, without the inconvenience or potential variabilities associated with distillation or diffusion procedures.

Ammonia↗
PubMed1995

Stereological methods based on point counting and unbiased counting frames for two-dimensional measurements in muscles: comparison with manual and image analysis methods.

Stereological methods, using the principle of point counting and unbiased counting frames, for the estimation of muscle area, total fibre area, number of muscle fibres and mean fibre area are described in detail. Their practical application is demonstrated on cross-sections of the rat soleus muscles. It is shown that the efficiency of these methods is high and their results are comparable with those achieved by the conventional manual and image analysis methods. The main advantages of two-dimensional stereological methods in muscle morphometry are pointed out: measurements are made directly on specimens under the microscope and in the simplest implementation do not require sophisticated and expensive technical equipment. Furthermore, unbiased results are obtained, no segmentation and edge effect problems arise and the quantity of work invested in stereological estimation is reasonable. Based upon the study of the efficiency of used stereological methods, a suitable test system for muscle morphometry is proposed.

Animals↗
PubMed1991

Comparison of the Ruthenium hexammine trichloride method to other methods of chemical fixation for preservation of avian physeal cartilage.

Several methods of chemical fixation of avian physeal cartilage were compared. The Ruthenium hexammine trichloride method was compared to isotonic glutaraldehyde and neutral buffered formalin for light microscopy and paraffin embedment, and to two osmium-ferrocyanide methods and a combination of 1% glutaraldehyde and 4% formaldehyde for electron microscopy. Only the Ruthenium hexammine trichloride method prevented the loss of matrix proteoglycans and shrinkage of chondrocytes. In undecalcified paraffin-embedded cartilage, preservation of matrix and cellular detail was excellent, but Ruthenium hexammine trichloride interfered with Haematoxylin and Eosin staining. Glutaraldehyde gave more intense eosinophilia than neutral buffered formalin. Ultrastructurally, the Ruthenium hexammine trichloride method was the most consistent and gave the best overall fixation. Matrix elements and cellular and nuclear membranes were well preserved. It did result in vacuolation of the cytoplasm and mitochondria, and it increased granularity of the cytoplasm, chromatin, and rough endoplasmic reticulum. Other fixatives produced minimal vacuolation and finer granularity, but preservation was less consistent, cell/matrix contrast was often excessive, and they caused shrinkage of all chondrocytes. Large dilatations of the rough endoplasmic reticulum that appear to be cytoplasmic inclusions by light microscopy are described for the first time in avian cartilage.

Animals↗
PubMed1994

The Lactational Amenorrhea Method (LAM): a postpartum introductory family planning method with policy and program implications.

It is well accepted that breastfeeding contributes significantly to child survival and child nutrition. Healthful child spacing is associated with improved birth outcomes and maternal recovery. On a population basis, breastfeeding may contribute more to birth spacing than all family planning use combined in many countries. However, while breastfeeding does provide a period of infertility, until recently, there was no reliable way for an individual woman to capitalize on this lactational infertility for her own efficacious child spacing. The Lactational Amenorrhea Method (LAM) is a new introductory family planning method that simultaneously promotes child spacing and breastfeeding, with its optimal nutrition and disease preventive benefits for the infant. LAM, as it is called, is based on the utilization of lactational infertility for protection from pregnancy and indicates the time for the introduction of a complementary family planning method. LAM is recommended for up to six months postpartum for women who are fully or nearly fully breastfeeding and amenorrheic, and relies on the maintenance of appropriate breastfeeding practices to prolong lactational infertility, with the concomitant delay in menses return. A recent clinical trial confirmed the theoretical 98% or higher effectiveness of the method and field trials are demonstrating its acceptability. Nonetheless, some demographers and family planning organizations continue to debate its value. The development, efficacy, and sequelae of the method are presented using data from several studies by the authors.

Amenorrhea↗
PubMed2003

Frequencies of the hereditary hemochromatosis allele in different populations. Comparison of previous phenotypic methods and novel genotypic methods.

AIM: The frequencies of the hereditary hemochromatosis allele were compared for different populations assessed by previous phenotypic methods and the present genotypic methods. METHODS: From a literature survey, the calculated hemochromatosis allele frequencies from 16 studies using phenotypic biochemical markers (threshold levels for transferrin saturation [range, 46%-70%] and serum ferritin [range, 164-700 microg/L]) were compared with allele frequencies of the Cys282Tyr mutation of the hemochromatosis gene reported in 19 genotypic studies. RESULTS: Calculated phenotypic allele frequencies are high in Scandinavia: Iceland, 6.1% to 7.4%; Norway, 5.8%; central Sweden, 6.3% to 6.9%; Denmark, 6.1%. Frequencies are similarly high in Wales, Canada, Utah, South Africa, and Australia (range, 5.2%-9.8%). Frequencies are low in Finland (1.9%) and northern Italy (4.5%). Genotypic allele frequencies of the Cys282Tyr mutation are likewise high in Scandinavia. Frequencies are high in the United Kingdom and northern France and low in Finland, central Germany, northern Italy, and Greece. The phenotypic-genotypic ratios of the hemochromatosis homozygosity frequencies for the same geographic area were calculated. A ratio of 1.0 indicates that the 2 methods give similar results. In 3 studies, the ratio was above 1.0, the highest ratio of 1.67 being reported from Italy. In most studies the ratio was slightly below 1.0 (0.71-0.97). The lowest ratio was found in Finland (0.33). CONCLUSION: In most studies there was good agreement between the hemochromatosis allele frequencies determined by phenotypic and genotypic methods. A high ratio (northern Italy) may indicate that phenotypic selection criteria were too loose and/or that causes of iron overload other than the Cys282Tyr mutation are frequent in the region. A low ratio (in Finland) may indicate phenotypic selection criteria that were too stringent and/or a low penetration rate of the mutation.

Biomarkers↗
PubMed1997

Validation of curve-fitting method for blood retention of 99mTc-GSA: comparison with blood sampling method.

We investigated a curve-fitting method for the rate of blood retention of 99mTc-galactosyl serum albumin (GSA) as a substitute for the blood sampling method. Seven healthy volunteers and 27 patients with liver disease underwent 99mTc-GSA scanning. After normalization of the y-intercept as 100 percent, a biexponential regression curve for the precordial time-activity curve provided the percent injected dose (%ID) of 99mTc-GSA in the blood without blood sampling. The discrepancy between %ID obtained by the curve-fitting method and that by the multiple blood samples was minimal in normal volunteers 3.1 +/- 2.1% (mean+/-standard deviation, n = 77 sampling). Slightly greater discrepancy was observed in patients with liver disease (7.5 +/- 6.1%, n = 135 sampling). The %ID at 15 min after injection obtained from the fitted curve was significantly greater in patients with liver cirrhosis than in the controls (53.2 +/- 11.6%, n = 13; vs. 31.9 +/- 2.8%, n = 7, p < 0.0001). There was a highly linear correlation between the %IDs of 99mTc-GSA and the plasma retention rate for indocyanine green (r = -0.869, p < 0.0001, n = 27). These results indicate that the curve-fitting method provides an accurate %ID of 99mTc-GSA and could be a substitute for the blood sampling method.

Adult↗
PubMed1995

Error analysis of table look-up method for cerebral blood flow measurement by 123I-IMP brain SPECT: comparison with conventional microsphere model method.

While N-isopropyl-p-[123I]iodoamphetamine (IMP) is commonly used as a flow tracer, significant clearance from the brain causes underestimation of CBF as compared with true CBF when conventional microsphere model analysis is applied. We previously reported a simple "table look-up" method for CBF measurement using IMP taking into account this clearance effect. The method is based on a two-compartment model, the K1 (corresponding to CBF) and k2 constants being obtained from a table from the ratio of the 1st SPECT (40 min) to the 2nd SPECT (180 min) counts. Arterial input data used were obtained by one point blood sampling 10 min after IMP infusion against the standard input function. In the present study, this approach was compared with conventional microsphere model analysis. For 30 subjects, the latter method entailed 8 min continuous arterial blood sampling after IMP infusion and the use of SPECT data at the end of this period, calibrated by a count ratio of 8 min/40 min planar images of whole brains. A good correlation was observed between the two methods (r = 0.88), but an overestimation of table look-up method CBF as compared with microsphere model CBF was observed contrary to theoretical predictions. Limitations in the estimation of SPECT data at 8 min, obtained with SPECT data at 40 min for calibration of the count ratio of 8 min/40 min whole brain planar images, might be responsible for this.

Amphetamines↗
PubMed2006

Estimation of cardiac output in a pharmacological trial using a simple method based on arterial blood pressure signal waveform: a comparison with pulmonary thermodilution and echocardiographic methods.

OBJECTIVE: Cardiac output (CO) has traditionally been measured using invasive techniques, which involve an element of risk. Thus, a reliable less-invasive method for determining CO would be very valuable for research use. We tested whether simple analysis of the arterial pulse waveform, not requiring large-vessel catheterisation or expensive equipment, could provide an estimate of CO that is accurate enough for pharmacological studies. METHODS: We measured CO in 11 healthy male subjects who received low and high doses of dexmedetomidine (alpha2-adrenoceptor agonist), using pulse contour analysis, echocardiography and pulmonary thermodilution techniques. RESULTS: At baseline, these methods gave the following mean (SD) values of CO: 6.18 (1.59), 5.22 (1.35) and 7.03 (1.54) l/min, respectively. High-dose dexmedetomidine reduced CO to 4.50 (0.68), 3.65 (0.65) and 4.80 (0.89) l/min, corresponding to -25 (14) %, -28 (12) % and -30 (14) % reductions from baseline, respectively. The pulse contour method described these dexmedetomidine-induced changes in CO very similarly to the thermodilution and echocardiographic methods. The limits of agreement [bias (2SD)] were 0.55 (2.55) and -0.10 (2.04) l/min, respectively. CONCLUSION: The minimally invasive pulse contour analysis technique might be suitable for pharmacological studies for the detection of major drug-induced reductions in CO.

Adrenergic alpha-Agonists↗
PubMed1999

Open reduction for congenital dislocation of the hip: comparison of the long-term results of the wide exposure method and Ludloff's method.

We compared the long-term clinical and radiographic results of two methods of open reduction for congenital dislocation of the hip; a wide exposure method (360-degree circumferential capsulotomy) versus Ludloff's method (limited capsulotomy via the medial approach). Thirty-one hips in 24 patients assigned to group A received the wide exposure method and 32 hips in 27 patients assigned to group B had the Ludloff reduction. All patients were surgically reduced at less than 3 years of age. The follow-up averaged 16 years. None of the hips in group A required additional operations; however, 34.4% of the hips in group B did. At the latest review, 26 (83.9%) of the hips in group A were rated as Severin class I or II. Except for one patient, none had pain or a limp. Of the hips in group B, 18 (56.3%) were rated as Severin class I or II. Three patients had pain or Trendelenburg gait. Avascular necrosis occurred in 3.2% of hips in group A and in 21.9% of hips in group B. The wide exposure method is capable of completely releasing the posterosuperior tightness resulting from capsular adhesion to the ilium and the contracted short external rotators. Releasing the posterosuperior tightness from these structures seemed to provide a better chance of achieving an anatomically and functionally satisfactory hip.

Acetabulum↗
PubMed2006

Standard setting in a small scale OSCE: a comparison of the Modified Borderline-Group Method and the Borderline Regression Method.

When setting standards, administrators of small-scale OSCEs often face several challenges, including a lack of resources, a lack of available expertise in statistics, and difficulty in recruiting judges. The Modified Borderline-Group Method is a standard setting procedure that compensates for these challenges by using physician examiners and is easy to use making it a good choice for small scale OSCEs. Unfortunately, the use of this approach may introduce a new challenge. Because a small scale OSCE has a small number of examinees, there may be few examinees in the borderline range, which could introduce an unintentional bias. A standard setting method called The Borderline Regression Method will be described. This standard setting method is similar to the Modified Borderline-Group Method but incorporates a linear regression approach allowing the cut score to be set using the scores from all examinees and not from a subset. The current study uses confidence intervals to analyze the precision of cut scores derived from both approaches when applied to a small scale OSCE.

Bias↗
PubMed1978

An assessment of the radial diffusion method for the measurement of pepsin in gastric secretion and its comparison with the haemoglobin substrate colorimetric method.

The radial diffusion method of pepsin assay has been compared with a modified Anson-Mirsky colorimetric method. Though claimed to measure accurately over a wide range, we found that the assay range of the radial diffusion method was only 10 to 100 mg/l; even with these narrow limits, it was inaccurate. In contrast, the colorimetric method was much more rapid, sensitive and could accurately measure a wide range of 0.5 to 500 mg/l. The colorimetric technique is therefore the superior method.

Diffusion↗
PubMed1987

An improved high performance liquid chromatographic method for determining urinary oxalate, making use of an ID-MS reference method.

With the aid of a newly developed isotope dilution mass spectrometric (ID-MS) measurement of urinary oxalate, an existing HPLC method for assaying this substance was investigated. Results obtained with this method were too high, apparently due to a systematic error. Subsequently, this method was improved by additional prepurification in three different ways: (a) precipitation with CaSO4 to Ca-oxalate, (b) adsorption (and subsequent desorption) to columns supplied with a commercial kit for urinary oxalate and (c) the enzymatic destruction of urinary oxalate present. This work demonstrates the successful use of a reference method in improving a newly developed analytical procedure and presents a reliable and reproducible HPLC method for determining urinary oxalate.

Chromatography, High Pressure Liquid↗