Method For Quantitative Comparison Research Articles

Triggering of Human Parainfluenza Virus 3 Fusion Protein (F) by the Hemagglutinin-Neuraminidase (HN) Protein: an HN Mutation Diminishes the Rate of F Activation and Fusion

For human parainfluenza virus type 3 and many other paramyxoviruses, membrane fusion mediated by the fusion protein (F) has a stringent requirement for the presence of the homotypic hemagglutinin-neuraminidase protein (HN). With the goal of gaining further insight into the role of HN in the fusion process, we developed a simple method for quantitative comparison of the ability of wild-type and variant HNs to activate F. In this method, HN/F-coexpressing cells with red blood cells (RBC) bound to them at 4 degrees C are transferred to 22 degrees C, and at different times after transfer 4-guanidino-neu5Ac2en (4-GU-DANA) is added; this inhibitor of the HN-receptor interaction then releases all reversibly bound RBC but not those in which F insertion in the target membrane or fusion has occurred. Thus, the amount of irreversibly bound (nonreleased) RBC provides a measure of F activation, and the use of fluorescently labeled RBC permits microscopic assessment of the extent to which F insertion has progressed to fusion. We studied two neuraminidase-deficient HN variants, C28a, which has two mutations, P111S and D216N, and C28, which possesses the D216N mutation only. C28a but not C28 exhibits a slow fusion phenotype, although determination of the HNs' receptor-binding avidity (with our sensitive method, employing RBC with different degrees of receptor depletion) showed that the receptor-binding avidity of C28a or C28 HN was not lower than that of the wild type. The F activation assay, however, revealed fusion-triggering defects in C28a HN. After 10 and also 20 min at 22 degrees C, irreversible RBC binding was significantly less for cells coexpressing wild-type F with C28a HN than for cells coexpressing wild-type F with wild-type HN. In addition, F insertion progressed to fusion more slowly in the case of C28a HN-expressing cells than of wild-type HN-expressing cells. Identical defects were found for P111S HN, whereas for C28 HN, representing the 216 mutation of C28a, F activation and fusion were as rapid as for wild-type HN. The diminished fusion promotion capacity of C28a HN is therefore attributable to P111S, a mutation in the stalk region of the molecule that causes no decrease in receptor-binding avidity. C28a HN is the first parainfluenza virus variant found so far to be specifically defective in HN's F-triggering and fusion promotion functions and may contribute to our understanding of transmission of the activating signal from HN to F.

Infrared and Raman spectra of bicyclic molecules using scaled noncorrelated and correlated ab initio force fields

This paper reports the application of a scaled ab initio calculated harmonic force field to predict the frequencies, infrared intensities, Raman intensities, and depolarization ratios of benzofuran, benzothiophene, indole, benzothiazole, and benzoxazole. The theoretical calculations were made using the Hartree–Fock HF/3-21G* and HF/6-31G* basis sets and density-functional theory (DFT)B3-LYP/6-31G* levels. The equilibrium calculated force constants are scaled according to the method of Pulay and compared with the experimentally determined frequencies, intensities, and depolarization ratios to assess the accuracy and fit of the theoretical calculation. Methods for quantitative comparison of intensities were developed. The double numerical differentiation algorithm of Komornicki and McIver was analyzed and used to calculate the Raman intensities for the (DFT)B3-LYP/6-31G* model. The (DFT)B3-LYP/6-31G* model is approaching the harmonic limit in the planar and nonplanar refinement of these bicyclics with wave number fits of 5 and 4 cm−1, respectively. It reduces the need for scale factors and increases their transfer accuracy, largely because the scale factors values cluster near unity. The Komornicki and McIver algorithm is still a viable method for calculating Raman intensity information for methods that do not have analytic routines programmed. The main shortcoming to this method may lie in the tighter self-consistent field (SCF) convergence criterion possibly needed to calculate Raman intensities for the totally symmetric modes of large molecules. The (DFT)B3-LYP/6-31G* model was superior for calculating the planar intensities, but equal to the HF methods for predicting the nonplanar intensities.

A residual analysis method for quantitative comparison of spatial data from the Iceland-Faeroes Front

A spatial statistical method has been developed from the well-known Kriging technique in geostatistics, as a way of providing quantitative comparison between a pair of spatial data sets, and a measure for such a comparison. This residual analysis method is applied to oceanographic data in order to compare Iceland-Faeroes Front (IFF) model predictions against appropriate field observations, with an aim to assess the IFF model performance and its prediction accuracy. The method is also used to evaluate the model-generated dynamical variability within the model predictions, as well as the natural variability within the frontal observations. From the results, it has been found that the IFF model is highly robust, and gives better predictions at depth 150–350 m than elsewhere. Within such a depth (i.e. 250–350 m), there is also evidence to suggest that the main frontal region is most active above the IF Ridge. The natural variability obtained from the observations appears to be comparable to the model-generated dynamical variability after 20 days of integration, indicating a certain degree of accuracy in the model predictions. The method reported in this paper could also be extended for further use in model data assimilation. Thus, the work not only demonstrates how spatial statistics can be applied to oceanographic data, but also opens up new statistical tools for data handling in ocean modelling.

Computational sequence analysis of matrix metalloproteinases.

Matrix metalloproteinases (MMP) play a cardinal role in the breakdown of extracellular matrix involved in a variety of biological and pathological processes. Research on MMPs has classified and characterized these enzymes according to their matrix substrate specificity, gene and protein domain structure, and regulation of activity and expression. However, the discovery of new MMPs has introduced a need for a more comprehensive and systematic method of classification and quantitative comparison of known and newly discovered members. This study compiles a sequence alignment, constructs a dendrogram, and calculates physical data and homology percentage assignments in order to obtain further insight into MMP structure-function relationships. Thorough analysis of MMP primary sequence domains, physical data patterns, and statistical analysis of sequence homology yields higher resolution in the similarities and differences that group MMP members.

Is Consensus Reproducible?

The authors evaluated the reproducibility of a clinical algorithm consensus development process across three different physician panels at a health maintenance organization. Physician groups were composed of primary care internists, who were provided with identical selections from the medical literature and first-draft "seed" algorithms on the management of two common clinical problems: acute sinusitis and dyspepsia. Each panel used nominal group process and a modified Delphi method to create final algorithm drafts. To compare the clinical logic in the final algorithms, the authors applied a new qualitative and quantitative comparison method, the Clinical Algorithm Patient Abstraction (CAPA). Dyspepsia algorithms from all physician groups recommended empiric anti-acid therapy for most patients, favored endoscopy over barium swallow, and had very similar indications for endoscopy. The average CAPA comparison score among final physician algorithms was 6.1 on a scale of 0 (different) to 10 (identical). Sinusitis algorithms from all groups proposed empiric antibiotic therapy for most patients. Indications for sinus radiographs were similar between two algorithms (CAPA = 4.9), but differed significantly in the third, resulting in lower CAPA scores (average CAPA = 1.9, P < 0.03). The clinical similarity of the algorithms produced by these physician panels suggests a high level of reproducibility in this consensus-driven algorithm development process. However, the difference among the sinusitis algorithms suggests that physician consensus groups using a consensus process that a health maintenance organization can do with limited resources will produce some guidelines that vary due to differences in interpretation of evidence and physician experience.

Resolution of pace mapping stimulus site separation using body surface potentials.

Several studies have related 12-lead ECG waveform during ventricular tachycardia to ECG waveform during ventricular pacing to identify ablation sites for therapy of ventricular tachycardia. QRS isopotential maps and QRS isointegral maps derived from body surface isopotential maps have also been correlated with left ventricular pacing sites with the same objective. The comparison process used is subjective and only semiquantitative. Improved accuracy of catheter placement may improve success rates of ablation therapy. This animal study was performed to determine the spatial resolution with which left ventricular pacing sites could be distinguished by body surface isopotential mapping. Potentials were recorded from 64 evenly spaced thoracic leads. Hexapolar or octapolar pacing catheters with 2-mm interelectrode spacing were placed percutaneously in the left ventricle in each of six dogs, and bipolar endocardial pacing was performed using each pair of adjacent electrodes. QRS isopotential maps of each pacing site for each catheter placement were cross-correlated by computer. Difference maps for each pair of pacing sites were calculated lead by lead and time instant by time instant, and root-mean-square voltage differences were calculated. Results indicated that correlation coefficients and root-mean-square error of voltage differences monotonically decrease and increase, respectively, with stimulus site separation. Both measures were significantly different (P < .05) for separations of 4 mm or more. A method of quantitative comparison of body surface potential maps can be used in normal hearts to localize ventricular pacing sites within a 4-mm range. The method may have utility in determining potential ablation sites for therapy of ventricular tachycardia or preexcitation syndromes.

Structures of the lovozerite type – a quantitative investigation

The structure of lovozerite is derived from perovskite. For 24 members of the lovozerite family an aristotype is postulated. The method of quantitative comparison using the concept of mappings is applied to the lovozerite family using the aristotype as a «structural unit». The method is extended to relationships of symmetry-type II, i.e. the derived structure and the aristotype have only a common subgroup, the remaining non-common symmetry of the derived structure is used as distribution symmetry for the structural unit. The numerical results are discussed in detail

Quantitative gated blood pool tomographic assessment of regional ejection fraction: Definition of normal limits

Objective. Our aim was to select a method of analysis for gated blood pool tomography that reduced variability in a group of normal subjects, allowed comparison with normal limit files and displayed results in the bull's-eye format.Background. Abnormalities in left ventricular function may not be accurately detected by measures of global function because hyperkuiesia in normal regions may compensate for abnormal regional function. Gated blood pool tomography acquires threedimensional data and offers advantages over other noninvasive modalities Tor quantitative assessment of global and regional function.Methods. Alternative methods for selecting the ventricular axis, calculating regional ejection fraction and choosing the number of ventricular divisions were studied In 15 normal volunteers to select the combination of parameter that produced the lowest variability in quantitative regional ejection fraction. Methods for quantitative comparison, of regional ejection fraction with normal limit files and for display in the bull's-eye format were also examined.Results. A fixed axis (the geometric center of the ventricle defined for end-diastole and used for end-systole) gave ejection fractions that were significantly higher in the lateral wall versus in the septum, 82 ± 8 (mean ± 1 SD) versus 39 ± 17 (p < 0.001) at the midcavity and 66 ± 11 versus 21 ± 20 (p < 0.001) at the base. A floating axis system (axis defined individually for end-diastole and end-systole and realigned at the center) gave more uniform regional ejection fraction: 63 ±6 versus 64 ± 8 (p = NS) at the midcavity and 44 ± 16 versus 45 ± 15 (p = NS) at the base. The coefficient of variability for regional ejection fraction was consistently lower using a floating axis. Calculating regional ejection fraction by dividing the regional stroke volume by the enddiastollc volume of the region gave a lower coefficient of variability and a more easily understood value than dividing the regional stroke volume by the total end-diastolic volume of the ventricle. Although the variability was lower using five versus nine ventricular divisions, nine regions offer greater spatial resolution. Comparison of regional ejection fraction with normal data identified regions > 2.5 SD below the mean as abnormal. We described the two-dimensional bull's-eye format as a method for displaying the regional three-dimensional data and illustrated abnormalities in patients with prior myocardial infarction.Conclusions. Gated blood pool tomography performed using a floating axis system, regional stroke volume calculation of ejection fraction and nine regions uses all the three-dimensional blood pool data to calculate regional ejection fraction, allow quantitative comparison with normal limit tiles, display the functional data in the two-dimensional bull's-eye format and demonstrate abnormalities in patients with myocardial infarction.

Quantitative method for comparison of skeletal muscle architectural properties

A numerical method is presented which calculates the architectural difference index between two muscles. This index is based upon the parameters, identified using statistical discriminant analysis, which best characterize the various muscles. This index can be used to reduce multiple architectural properties into a single value and may be useful in selecting donor muscles which are required to perform a substitute function for another muscle which has been lost or injured.

Quantitative Determination of IL-1α-Induced IL-8 mRNA Levels in Cultured Human Keratinocytes, Dermal Fibroblasts, Endothelial Cells, and Monocytes

The presence of the leukocyte chemotactic cytokine interleukin 8 (IL-8) in psoriatic scales and in epidermal tissue overlying allergic patch test reactions suggests a role for this cytokine in certain inflammatory skin diseases. IL-8 can be produced by several cell types present in the skin. Their relative potentials for IL-8 expression has, however, not yet been studied, due to the lack of convenient methods for quantitative comparison of specific mRNA amounts in different cell types. Using a new method for quantification, we compared specific IL-8 mRNA amounts in cultures of keratinocytes, dermal fibroblasts, endothelial cells, and monocytes, stimulated with interleukin 1 alpha (IL-1 alpha). Endothelial cells produced very high, fibroblasts and monocytes intermediate, and keratinocytes low amounts of IL-8 mRNA. We also studied the time course of IL-8 mRNA levels in the four cell types following IL-1 alpha stimulation, and found a clear difference both in onset and stability of the response. We discuss the different strength of the response at different time points in the cell types analyzed in relation to their possible role in regulation of the normal response to stimulation.

Some morphometric evidence of hepatoprotective effects of (+)-cyanidanol-3

The (+)-cyanidanol-3 is used as an antihepatotoxic and hepatoprotective drug in both men and animals against alcoholic and experimental liver injury. Histologic staining techniques give mostly qualitative or semiquantitative description of liver damages. Experiments have been carried out to determine the hepatoprotective effects of (+)-cyanidanol-3 on alcoholic liver damage (i.e., fatty liver and hepatomegaly) by morphometric measurement of the liver tissue sections. Ethanol was administered ad lib to CFY rats to cause mild alcoholic liver damage together with 200 mg/kg/day (+)-cyanidanol-3 to prevent the tissue deterioration. The changes of hepatic lobule and hepatocytes were measured morphometrically. The chronic ethanol consumption results in hepatocellular hypertrophy, a significant increase in size of the hepatocytes and a mild increase of the intralobular extrahepatocytic space as well when compared with controls. The volume of cytoplasm was increased while the parameters of nuclei were unchanged. The (+)-cyanidanol-3 prevents changes and the morphometric parameters in the treated group were almost the same as in the controls. The treatment with (+)-cyanidanol-3 alone does not affect the hepatic tissue parameters. The results show the hepatoprotective effect of (+)-cyanidanol-3 and the suitability of the morphometric method for quantitative comparison of normal and experimentally-altered liver cells.

Clonal analysis of chimaeric patterns in aortic endothelium

The mosaicism in aortic endothelium of mouse aggregation chimaeras is demonstrated using the lectin Dolichos biflorus agglutinin as a strain-specific marker. The general fragmentary appearance and considerable size range of patches suggests that endothelial cells do not proliferate in a highly coherent manner. The developmental significance of the observed patterns is investigated by means of a quantitative statistical analysis-the Greig-Smith analysis of variance. This method examines the spatial distribution of patches and is able to detect and characterize pattern at various scales. The results show that (1) patches are non-randomly distributed at all scales examined and (2) 'clusters of clusters' occur at one small and one large scale, defining territories of 'primary' and 'secondary' descendent clones, which arose respectively during early and late periods in the development of the endothelium. We conclude from this analysis that (1) cell mixing is never complete, even in the early embryo and (2) cell mingling is not uniform during development. A different pattern was previously demonstrated for intestinal epithelium (Schmidt, Wilkinson & Ponder, 1985c) indicating the potential value of the method for quantitative comparison of mosaicism between tissues and also different developmental stages. Our results suggest that the analysis of patch sizes is likely to be less informative in terms of developmental mechanisms, than the analysis of the spatial arrangement of patches.

MICROFLUOROMETRIC MEASUREMENT OF DNA IN EUDORINA ELEGANS AND E. CALIFORNICA (CHOROPHYCEAE)1

ABSTRACTThe fluorescent dye 2,5‐bis (4′‐aminophenyl (1′))‐1,3,4‐oxidiwle (BAO) was compared to the Feulgen procedure as a method for quantitative comparison of DNA levels in two species of Eudorina. The BAO procedure proved to be specific and as quantitative as the Feulgen procedure, and was more convenient and rapid. The DNA level of the nuclei of gonidial cells of Eudorina elegans Ehrenberg and E. californica (Shaw) Goldstein doubled prior to each division. The DNA level of the somatic, usually non‐dividing nuclei of E. californica did not vary from the IC (haploid) level.

Ribosomal Translocation Assayed by the Matrix‐Bound Poly(uridylic acid) Column Technique

The system of translation of cellulose-bound poly(uridylic acid) by Escherichia coli ribosomes has been used for preparation of pre-translocation state ribosomes in columns. Translocation has been induced by passing the elongation factor G (EF-G) with GTP or its non-cleavable analog (guanosine 5'-[beta, gamma-methylene]triphosphate) through the column. A method for quantitative comparison of translocation rates, and thus of effectiveness of translocation-inducing factors, has been proposed. The method is based on an analysis of the profile of deacylated tRNA elution resulting from translocation in the column. The determination of the rate and amount of translocation has been done under different ionic conditions. It has been found that the Mg2+ concentration is a decisive factor of translocation in vitro: at high Mg2+ (30 mM) EF-G cannot induce translocation, and lowering the Mg2+ concentration (to 10 mM) is required for EF-G to become effective. Sufficiently low Mg2+ (3 mM) itself has proved to induce fast and complete translocation, without EF-G.

Ecological studies of ixodid ticks (Acari, Ixodidae) in Zambia. I. Cattle as hosts of the larvae ofAmblyomma variegatum(F.) andRhipicephalus appendiculatusneum.

AbstractThe roles of cattle and alternative hosts in maintaining the immature stages ofAmblyomma variegatum(F.) andRhipicephalus appendiculatusNeum. are unknown. Weekly collections of ticks from cattle in two herds in Zambia indicated an apparently higher nymph-adult ratio in the annual totals forA. variegatumthan forR. appendiculatus. The larva-nymph ratios for these herds were estimated by a patch-sampling method in which all larvae and nymphs on 100 cm2areas on the cheek, neck, dewlap, shoulder, ribs, abdomen and lower-foreleg were collected. The overall annual ratios of larvae to nymphs on the two herds were:A. variegatum5:1 and 14:1,R. appendiculatus1·5:1 in both herds. The ratios suggest that cattle themselves feed larvae ofA. variegatumin sufficient numbers to maintain their nymphal infestation level. The numbers of cattle-fed larvae ofR. appendiculatusmay not be adequate for this, and alternative hosts may play an important part in maintaining the population at existing levels. There was negligible evidence of significant shift of distribution of the immature stages over the body with advancing season, and it is suggested that patch-sampling affords a method of quantitative comparison of the relative infestations by the immature stages of ticks.

Nonbonded interactions in membrane active cyclic biopolymers. I. Valinomycin-potassium ion complex

A method for quantitative comparison of various conformers of cyclic macromolecules in terms of nonbonded interaction energy terms is proposed. The first step in the procedure is an analytical evaluation of a set of Cartesian atomic coordinates consistent with the ring closure condition and prescribed values for internal parameters. A variant of the same technique enables different conformations of the macromolecule to be generated. Nonbonded interactions of the electrostatic, polarization and dispersion type and van der Waals repulsion are calculated using the generated coordinates, empirical bond polarizability data and results of simple molecular orbital calculations. An application of the proposed techniques to the closed symmetric conformation of valinomycin indicates that the macromolecule by itself is somewhat constrained in this state but that its affinity for a potassium ion is very strong—much stronger than the hydration energy of the latter.

Catalysis of the Reduction of Hydroperoxides by Triphenylphosphine

The reaction of hydroperoxides with triphenylphosphine is catalyzed by the addition of strong acid. Likewise in hydroxylic solvents, the log of the bimolecular rate constant increases linearly with the solvents' autoprotolysis constants. Soluble salts of molybdenum or vanadium are 104 to 105 times more effective catalysts than H+. The reaction shows promise as a method for quantitative comparison of the effectiveness of these compounds in augmenting the electrophilic character of hydroperoxides.

Thermoluminescence of LiF: A statistical analysis of the influence of pre-annealing on the precision of measurement

The standard deviation of the signals recorded from thermoluminescent LiF as a function of the thermal treatment before irradiation (pre-annealing) has been investigated (see preceding abstr). For pre-annealing temperatures higher than -50 degrees C, the standard deviation increases with pre-annealing temperature and time. A consequence is that in pre-annealing, high temperatures should be used for periods as short as possible. If the thermal treatment during the readout (a few seconds at approximately 300 degrees C) is the only high temperature treatment of the dosimeter between repeated irradiations, a standard deviation of 0.22% in the measured signals can be obtained. Different factors contributing to the standard deviation are analysed and, in consequence, a sensitive method for quantitative comparison between different readout instruments is given.

Application of Life-Table Analyses to Tree Seedlings in Quetico Provincial Park, Ontario

Data for numbers of living seedlings by two-year age-classes under old-growth forests permit examination of life-table analysis as a tool for following seedling population relationships. The population depletion curves for white pine, balsam fir and red maple are compared. The negative exponential depletion model is demonstrated as a potentially sensitive method for quantitative comparison of silvical response characteristics.

Variations in drawings of "a person" and "myself" by hearing-impaired and normal children.

Summary. Study of drawings of ‘a person’ and ‘myself’ by hearing‐impaired children suggested the existence of consistent patterns of qualitative difference between the two. A simple method of quantitative comparison was devised and comparisons made with drawings by a control group of normally hearing children. Analysis of results showed significant variations between the hearing‐impaired and normal groups in terms of direction and degree of person/self differences for the two types of drawing. These results, together with those relating to possible sex differences, are discussed and a wider investigation proposed to consider the possible relevance of these trends to conceptual development and psycho‐social adjustment.