MTD Method Research Articles

Correction of The MTD Program and Methods of Its Utilization

Correction of The MTD Program and Methods of Its Utilization

Diagnostic value of nine nucleic acid amplification test systems for Mycobacterium tuberculosis complex

Objective: In this study, nine commercial Nucleic Acid Amplification Test Systems (NAATs) were evaluated for diagnostic performance of Mycobacterium tuberculosis complex (MTBC) from smear positive sputum species (SPss) and smear negative sputum specimens (SNss). Methods: Sixty SPss and 55 SNss were examined microscopically by Ehrlich Ziehl Neelsen (EZN) staining method, and also inoculated on Lowenstein Jensen (LJ) medium for culture. The sensitivity and specificity of nine NAATs were calculated according to LJ culture method accepted as gold standard. Results: When LJ culture results were taken as gold standard; the sensitivity rates of method COBAS Amplicor MTB (Method A), GenProbe MTD (Method B), Cobas TaqMan MTB PCR (Method C), iCycler iQ RT PCR (Method D), TaqMan PCR AB 5700 (Method E), TaqMan PCR AB7700 (Method F), LightCycler® 480 RT PCR (Method G), Rotor Gene RT PCR (Method H) and the AdvanSure TB/NTM RT PCR (Method I) for SPss were 98.3 %, 93.3 %, 96.7 %, 100 %, 93.3 %, 100 %, 100 %, 100 % and 100 %, respectively. The sensitivity was 53.84% for the methods A, B, D, E, G and I; 38.46% for the method C and H; 61.5% for the method F for the method I in SNss. There were no statistical significant differences between the nine NAATs (p≥0.05). The specificity was 100% for all nine NAATs in SNss. The positivity rates of methods were 53.8% for methods A, B, D, E, G, I; 38.5% for methods C and H, and 61.5% for method F in SNss. These rates were 100% for D, F, G, H and I; 98.3% for method A; 96.7% for method C; 93,3% for methods B and E in SPss. Statistical analysis showed that there was no statistically significant differences among the nine NAATs (p≥0.05). Conclusion: It is concluded that the nine NAATs might be useful for detecting MTBC from SPss, but not effective for SNss. J Microbiol Infect Dis 2015;5(3): 103-109 Key words: Tuberculosis, polymerase chain reaction, nucleic acid amplification test, smear positive, smear negative, sputum

RADAR Signal Parameters Estimation in the MTD Tasks

RADAR Signal Parameters Estimation in the MTD Tasks The MTD method adaptive to current target speed, in which suboptimal iterative algorithms for the reflected signal parameters estimation are synthesized, is suggested. This method allows to detect a slowly moving targets with radial speed 3-4 times less, than for pulse-pair subtraction (PPS).

A Combined Metadynamics and Umbrella Sampling Method for the Calculation of Ion Permeation Free Energy Profiles.

Free energy calculations are one of the most useful methods for the study of ion transport mechanisms through confined spaces such as protein ion channels. Their reliability depends on a correctly defined reaction coordinate (RC). A straight line is usually not a proper RC for such complicated processes so in this work a combined metadynamics/umbrella sampling (MTD/US) method is proposed. In the combined method, the ion transport pathway is first identified by the MTD method and then the free energy profile or potential of mean force (PMF) along the path is calculated using umbrella sampling. This combined method avoids the discontinuity problem often associated with normal umbrella sampling calculations that assume a straight line RC and it provides a more physically accurate PMF for such processes. The method is demonstrated for the proton transport process through the protein channel of aquaporin-1.

ACUTE BACTERIAL MENINGITIS IN ADULTS: TEMPORAL ASSOCIATION BETWEEN INITIATION OF PARENTERAL ANTIBIOTIC THERAPY AND CEREBROSPINAL FLUID STERILISATION

negative in all cases. In five patientswas performed a laparoscopic abdomen examination. It showed peritoneal thickening and multiple whitish nodules. Hystologic examination of parietal peritoneum and lymph nodes biopsies showed necrotizing granulomas in all cases. Auramin stains of tissue biopsies detected bacilli in three cases. Nucleic acid amplification (NAA) through MTD method to detect Mycobacterium Tuberculosis genome was done n fove patients. It showed positive results in four cases. Culture made on Coletsos and Lowenstein Jensen of tissue biopsies, ascites or pleural effusion was positive in three cases. Tuberculostatic multidrug therapy was started in all patients. On a regular basis, fever withdrew in the first week and progressive general improvement began after 4 weeks of treatment. All patients had a good clinical outcome, except one who died due to urine Gram-negative sepsis. Conclusions: acute abdominal tenderness and fever should be considered as an initial manifestation of tuberculous peritonitis. In young patients who came from endemic areas with abdominal tenderness, fever and ascites, tuberculous peritonitis should be early ruled out. The inland patients are most commonly elders. CT imaging described appropriately main features of this disease (ascites, omental caking, lymph nodes). Laparoscopic exploration of the abdomen and puncture under radiological control are the most reliable techniques to both microbiological and pathological diagnosis. Pleural effusion is the most affected site of disease extension. Good clinical outcome could be achieved in immunocompetent patients affected by tuberculous peritonitis, on the basis of an early and accurate diagnosis.

The capacity of MTD method for distinguishing Mycobacterium tuberculosis and nontuberculosis mycobacteria

目的 应用结核分枝杆菌直接检测(MTD)试剂盒对临床痰液样本及分离的结核分枝杆菌复合群,进行检出率和常规菌型鉴定法符合率的比较和评价.方法 将10株标准菌种(其中1株为H37Rv、9株为非结核分枝杆菌)、94株临床分离菌株(其中48株经常规生化方法分型鉴定为结核分枝杆菌,46株分型法鉴定为非结核分枝杆菌)和40份临床痰标本分别用法国生物梅里埃公司生产的AMPLIFIED-MTD试剂盒进行检测.结果 结核分枝杆菌复合群检测均呈阳性,非结核分枝杆菌检测均呈阴性,符合率均达到100%.临床痰标本用MTD检测的阳性检出率为65%(26/40),明显高于直接涂片法的12%(5/40)、培养方法的12%(5/40)、集菌涂片法的25%(10/40).结论 MTD试验是一套新的生物学检测技术,具有快速、灵敏的特点。

Evaluation of a Modified Gen-Probe Amplified Direct Test for Detection of Mycobacterium tuberculosis Complex Organisms in Cerebrospinal Fluid

Laboratory evidence for tuberculous meningitis is difficult to acquire due to the low numbers of organisms present in cerebrospinal fluid (CSF) and the presence of nucleic acid amplification inhibitors. The Amplified Mycobacterium tuberculosis Direct Test (MTD) is sensitive and specific for the direct detection of M. tuberculosis complex in respiratory samples but has not been approved for CSF. We evaluated a modified version of the current MTD, optimized for use with CSF samples. Samples were prepared by spiking CSF with various numbers of M. tuberculosis complex organisms. The modified MTD performance was compared with results obtained using a purified RNA sample extracted using the Qiagen RNeasy Protect Bacteria Mini Kit. By use of CSF artificially spiked with M. tuberculosis complex, the sensitivity of the modified MTD was 100% (six of six) for CSF samples containing approximately 600 CFU/ml, 78% (seven of nine) for approximately 60 CFU/ml, 50% (three of six) for 6 CFU/ml, and 17% (one of six) for samples with <1 CFU/ml. The specificity of the modified MTD method was 100% (22 of 22). The sensitivity of the Qiagen MTD method was 100% for CSF samples containing approximately 600 CFU/ml (six of six) and approximately 60 CFU/ml (nine of nine), 50% for samples with approximately 6 CFU/ml (three of six), and 50% for samples with <1 CFU/ml (three of six). The specificity of the Qiagen MTD method was 86% (19 of 22). With the Qiagen MTD method, however, initial results were equivocal for 14 of the 27 (52%) positive samples, requiring repeat analysis, whereas with the modified MTD, only 1 of 27 (4%) was equivocal. The modified MTD for CSF samples was less time-consuming and less expensive and resulted in considerably fewer equivocal results than the Qiagen MTD method did.

Miliary Tuberculosis with Endometrial Spread in a Pregnant Woman: A Case Report

Miliary Tuberculosis with Endometrial Spread in a Pregnant Woman: A Case Report

MTD‐PLS: A PLS‐Based Variant of the MTD Method. Part 2. Mapping Ligand—Receptor Interactions. Enzymatic Acetic Esters Hydrolysis.

MTD‐PLS: A PLS‐Based Variant of the MTD Method. Part 2. Mapping Ligand—Receptor Interactions. Enzymatic Acetic Esters Hydrolysis.

QSAR for Cycloaliphatic Alcohols with Qualitatively Defined Sandalwood Odour Characteristics

QSAR's are set up for a series of up to 53 cycloaliphatic alcohols with qualitatively defined sandalwood odour characteristics: i-inactive, w-weak, s-strong, and vs-very strong. “Central” values (0, 1, 2, and 3) were attached to these qualitative characteristics, as well as intervals (<0.5; 0.5–1.5; 1.5–2.5; >2.5). The superposition procedure of the MTD method was used to define the probable active conformation. Conformational energies and log Poct values were also calculated using HyperChem-2 and Chemicalc-2. A correlational equations were set up using δ, D and D2–with δ=1 for OH groups in favourable position and D–the distance between the gravity centre of the hydrophobic moiety and the osmophoric OH-group. The MTD method was used only for a series of N=15 rigid molecules, because a too large number of vertices for the whole series appear. Eighter central values or intervals were used as biologic activities. The δ, D and D2–equations set up for N=31 molecules allow a good classification of the training set and also of the rest of molecules, considered as test set. An osmophoric receptor with a hydrophylic part (2 or 3 OH-groups) and a relatively large hydrophobic pocket is suggested, which produces also some steric misfit with regard to these molecules.

Evaluation of two commercial diagnostic kits for Mycobacterium tuberculosis completely based on bacterial DNA and rRNA amplification for direct detection of tubercle bacilli in sputum specimens.

The Roche Amplicor Mycobacterium Tuberculosis Kit (Amplicor PCR) and Gen-Probe Amplified Mycobacterium Tuberculosis Direct Test (MTD) were compared for efficiency in the direct detection of tubercle bacilli in sputum specimens. In total, 72 sputum specimens obtained from patients with active tuberculosis were examined with the Amplicor PCR and MTD kits. Of the 72 test specimens, 45 and 41 samples were positive by the Amplicor PCR and MTD methods, respectively. These values were larger than those obtained by the culture method (Septi-Chek) and acid-fast bacilli-smear test, yielding 37 and 20 positive results, respectively, and the sensitivities were as follows: smear, 39.2%; culture, 72.5%; Amplicor PCR, 88.2%; MTD, 80.4%. Amplicor PCR was similarly or somewhat more sensitive in direct detection of M. tuberculosis in sputum samples from patients with clinically active tuberculosis than was MTD.

QSARs with Orthogonal Descriptors on Psychotomimetic Phenylalkylamines

AbstractMultiple linear regressions have been obtained for 49 psychotomimetic phenylalkylamines. The MTD method has been applied and the MTD parameter was used as steric descriptor. The energy of the lowest unoccupied molecular orbital and the net charges on the phenyl ring atoms (from AMI calculations) have been used as electronic descriptors and logPow, or average electrostatic field as lipophilicity descriptor. Hall and Kier electrotopological state indices were also tested. The descriptors have been scaled to unit and orthogonalized by Randic method. The predictability of the regressions obtained from MTD method have been checked by a method similar to cross‐validation from CoMFA method. MTD has been identified as the dominant descriptor by Randic orthogonalization. The best model has been obtained with MTD and electrotopological state indices, showing the importance of the steric and electronic properties for the interaction at the receptor site level.

Clinical evaluation of a reagent for detection of DNA of Mycobacterium tuberculosis complex using the ligase chain reaction (LCR) method

We evaluated the clinical efficacy of LCR MTB, a reagent developed by Abbott in the USA, in the full automatic ligase chain reaction (LCR) for detection of DNA of M. tuberculosis complex using a thermostable ligase. Using 458 samples isolated from patients with tuberculosis, LCR was compared with a smear method and with a culture method, and was also compared with two other methods of gene amplification, MTD and Amplicor, using 340 and 200 of the 458 samples, respectively. The LCR method detected M. tuberculosis in 49.8% (228/458) of the samples, and was superior to the smear method (31.9%, 146/458) and the culture method (39.1%, 179/458) in sensitivity. The LCR method was also superior to the MTD and Amplicor methods; sensitivity were 37.9% (129/340) for MTD vs. 47.6% (162/340) for LCR, and 56.5% (113/200) for Amplicor vs. 59.5% (119/200) for LCR. These favorable results and the convenience of the LCR method, which enables rapid detection of target genes with a high degree of sensitivity, strongly suggest that LCR MTB is useful as a reagent for detection of M. tuberculosis using nucleic acid amplification.

Comparative QSAR study with electronic and steric parameters for cAMP derivatives with large substituents in positions 2, 6 and 8

In order to discern structural characteristics for specific activation of four sites, AI and BI on cAK-I and AII and BII on cAK-II, an extended study on a series of cAMP derivatives with large substituents in positions 2, 6 and 8, has been performed. The effect of charged (at pH ≈ 7) substituents upon the corresponding receptor affinities has also been investigated. The MTD method was used together with the estimated hydrophobicities of the base moiety and the charge on the substituent at the 6-(purinic)-position (calculated by the AM1 method) as supplementary structural parameters. For the multiparametric correlations, r values between 0.73 and 0.98 were obtained, while in a cross-validation-like procedure, the r CV 2 values are between 0.36 and 0.64.

Comparative Structure‐Affinity Relations by MTD for Binding of Cycloadenosine Monophosphate Derivatives to Protein Kinase Receptors

AbstractA “testkit” series of 27 derivatives of cAMP with various substituents in position 1, 2, 6 and 8 and within the purine cycle, thiophosphoric acid derivatives (with equatorial or axial S‐atom) also included, were used to map four receptor sites of the R‐subunit of cAMP dependent phosphokinases I and II, namely labile and stable receptors AI, BI, AII and BII. A QSAR by the MTD method was applied for the four series of activities, together with the relative nitrogen base hydrophobicity (lgKw), electric charge of the position 6‐substituent (qN) and an indicator variable (δ = 1 for equatorial thiophosphoric derivatives). Correlation coefficients between r = 0.836 and 0.948 were obtained and the reliability of QSAR results was tested by a cross validation‐like procedure. Characteristic steric features (concerning the effects of substituents in different nitrogen‐base positions) were separately obtained for each receptor. For AI and BI receptor there is a negatively charged receptor group interacting with substituents in position 6 of cAMP derivatives. BI and BII receptors are of a marked hydrophobic character. Thiophosphoric acid derivatives, especially those with equatorial S‐atom, have a decreased affinity for all four receptors. The results are compared with other QSAR studies of our group, concerning different series of cAMP derivatives.

A QSAR study of the adsorption by cellulose fibre of anthraquinone vat dyes

The affinity of a series of 46 anthraquinone vat dyes to cellulose fibre was analysed by multiple regression analysis and the MTD method of QSAR. The main structural feature responsible for fibre binding is the number (n) of bonds of the conjugated chain along the main axis of the molecules (correlation coefficient r = 0.914). Hydrophobic interactions and hydrogen bonding, especially by proton donor groups of the dye molecule are also important (r = 0.943 for a correlation with four structural parameters). The optimized receptor map of the MTD method suggests binding to both crystalline and amorphous regions of the cellulose fibre.

Multiconformational Minimal Steric Difference. Structure‐Acetylcholinesterase Hydrolysis Rates Relations for Acetic Acid Esters

AbstractThis note presents the multiconformational MTD method and its application in a QSAR for acetylcholinesterase catalysed hydrolysis rates of a series of 25 acetic acid esters. Multiconformational MTD allows consideration of molecules with several low energy conformations, as the mostly aliphatic alcohol esters of this series, for QSAR. Conformations were selected for the QSAR study according to their energies calculated by the COSMIC modelling program. Information from an X‐ray crystallography study, together with results of conformational energy calculations was used in constructing the hypermolecule for the 25 acetic acid ester molecules. A classical Hansch QSAR, with σ*‐Taft constants, π‐hydrophobicities and Es‐steric constants yields r2 = 0.779 and r2cv = 0.577 in a crossvalidation procedure. The multiconformational MTD, with σ* and MTD as structural parameters yields, for the corelational equation r2 = 0.868 and r2cv = 0.661 in a cross validation procedure. Both correlational equations indicate an appreciable positive effect of electron withdrawing ester groups. The optimised receptor map indicates a receptor cavity with certain similarities to acetylcholine, but somewhat larger. QSAR studies are able, thus, to yield supplementary details to those given by X‐ray studies.

Structure‐activity Relations in Gestagenic Steroids by the MTD Method. The Case of Hard Molecules and Soft Receptors

AbstractA QSAR is obtained for affinity towards the gestagenic receptor for a series of 55 progesterone derivatives (r = 0.935), using the MTD‐method, with MTD for steric misfit and f a corrected relative hydrophobicity. Acceptable stability of regression coefficients of vertex attributions are obtained when this QSAR is compared with previous QSAR's for a reduced series of progesterone derivatives and for testosterone derivatives. Acceptable predicted activities for test molecules (r2 = 0.71) and acceptable results in a cross validation‐like procedure (r2 = 0.76) were obtained. These are strong arguments that our MTD results correspond to some real features of the gestagenic receptor site. In order to explain relative success of the MTD‐method in QSAR's for steroids, as compared to other methods, molecular aspects of the receptor‐effector interaction are discussed in relation to QSAR‐methodology. Recent computational chemistry approaches are based upon drug molecule‐receptor site energy calculations, assuming a fixed conformation for the receptor site. If the drug molecules are “hard” (rigid), the steric misfit with a “soft” (conformationally flexible) receptor site may be avoided by induction of different local conformational changes in the latter.