Comparison of the dye method with the thermocouple psychrometer for measuring leaf water potentials

The dye method for measuring water potential was examined and compared with the thermocouple psychrometer method in order to evaluate its usefulness for measuring leaf water potentials of forest trees and common laboratory plants. Psychrometer measurements are assumed to represent the true leaf water potentials. Because of the contamination of test solutions by cell sap and leaf surface residues, dye method values of most species varied about 1 to 5 bars from psychrometer values over the leaf water potential range of 0 to −30 bars. The dye method is useful for measuring changes and relative values in leaf potential. Because of species differences in the relationships of dye method values to true leaf water potentials, dye method values should be interpreted with caution when comparing different species or the same species growing in widely different environments. Despite its limitations the dye method has a usefulness to many workers because it is simple, requires no elaborate equipment, and can be used in both the laboratory and field.     

Estimation of lipids in marine animals and tissues: Detailed investigation of the sulphophosphovanilun method for ‘total’ lipids

A reliable and simple method for the estimation of ‘total’ lipids in the tissue of marine animals is much needed for biochemical-ecological work. As a result of the present investigations the phosphosulphovanillin method used, hitherto, only for blood serum samples, is recommended. The method depends on using a cholesterol standard which has previously been related to gravimetric values obtained on blood sera. The colorimetric values have been compared with gravimetric results on a variety of marine tissues — largely of invertebrates.The data given in the tables may be used to convert colorimetric values, using a cholesterol standard to total lipids. For extended investigations, however, it is recommended that the cholesterol values are first calibrated against gravimetric values for the particular tissue under investigation.A summary of the preparation of reagents and procedure is given.     

A comparison of three methods for the determination of available lysine in barley

The protein quality of barley was determined by the measurement of the protein efficiency ratio (PER). Available lysine in the same samples was determined chemically and by microbiological assay, and relationships were obtained between PER and either total or available lysine content.In the PER test, groundnut meal was found to be a suitable protein supplement to barley for the purpose of detecting differences in the protein quality of barley. The method was sufficiently sensitive to detect a reduction in protein quality of one variety as a result of micronization. Available lysine values obtained by the modified Tetrahymena method were significantly correlated (r = 0.99) with PER values; there was no significant correlation between total lysine content and the PER value.The available lysine values measured by the two chemical methods were higher than the Tetrahymena values. The Silcock method gave results better correlated (r = 0.93) with the Tetrahymena values than did the Carpenter method (r = 0.82). The results of chemical methods were not significantly related with PER values, but the methods ranked the barleys in an order similar to that obtained with the PER and Tetrahymena tests.     

Bagging GLM: Improved generalized linear model for the analysis of zero-inflated data

Species-occurrence data sets tend to contain a large proportion of zero values, i.e., absence values (zero-inflated). Statistical inference using such data sets is likely to be inefficient or lead to incorrect conclusions unless the data are treated carefully. In this study, we propose a new modeling method to overcome the problems caused by zero-inflated data sets that involves a regression model and a machine-learning technique. We combined a generalized liner model (GLM), which is widely used in ecology, and bootstrap aggregation (bagging), a machine-learning technique. We established distribution models of Vincetoxicum pycnostelma (a vascular plant) and Ninox scutulata (an owl), both of which are endangered and have zero-inflated distribution patterns, using our new method and traditional GLM and compared model performances. At the same time we modeled four theoretical data sets that contained different ratios of presence/absence values using new and traditional methods and also compared model performances. For distribution models, our new method showed good performance compared to traditional GLMs. After bagging, area under the curve (AUC) values were almost the same as with traditional methods, but sensitivity values were higher. Additionally, our new method showed high sensitivity values compared to the traditional GLM when modeling a theoretical data set containing a large proportion of zero values. These results indicate that our new method has high predictive ability with presence data when analyzing zero-inflated data sets. Generally, predicting presence data is more difficult than predicting absence data. Our new modeling method has potential for advancing species distribution modeling.     

Very fast empirical prediction and rationalization of protein pKa values

A very fast empirical method is presented for structure-based protein pKa prediction and rationalization. The desolvation effects and intra-protein interactions, which cause variations in pKa values of protein ionizable groups, are empirically related to the positions and chemical nature of the groups proximate to the pKa sites. A computer program is written to automatically predict pKa values based on these empirical relationships within a couple of seconds. Unusual pKa values at buried active sites, which are among the most interesting protein pKa values, are predicted very well with the empirical method. A test on 233 carboxyl, 12 cysteine, 45 histidine, and 24 lysine pKa values in various proteins shows a root-mean-square deviation (RMSD) of 0.89 from experimental values. Removal of the 29 pKa values that are upper or lower limits results in an RMSD = 0.79 for the remaining 285 pKa values.     

A practical graphical method for estimating the fraction of cells in S in DNA histograms from clinical tumor samples containing aneuploid cell populations

A graphical method for the analysis of unperturbed DNA histograms is presented in which the area of the normalized histogram subtended by the fraction of cells in S is represented by a trapezoid whose dimensions are dependent on features common to all such histograms. The technique takes measurement variability into account. This method was applied to a variety of synthetic DNA histograms. Overall, calculated values for the fraction of cells in S correlated well with actual values. This method was applied to 36 diploid cases of non-Hodgkin lymphoma; results correlated well with those obtained by a computer-based method. The results of the graphical-method were also highly reproducible between different observers. The graphical method can be used in the presence of aneuploid cell populations. Techniques for calculating S fractions in the presence of aneuploidy in clinical samples are described. These techniques were applied to synthetic histograms of mixed diploid and aneuploid populations. Calculated values correlated well with actual values.     

Heat resistance of Campylobacter and Yersinia strains by three methods

Two methods of determining the heat resistance of bacteria, a glass cup and a test tube method, were compared with a method using capillary tubes. Three strains of Yersinia enterocolitica, one of Campylobacter jejuni and two of C. coli were tested in physiological saline. The differences between the results obtained by the glass cup method and the reference method were not statistically significant for five strains and were small also for the other, a Yersinia strain. D values obtained by the glass cup method at 58, 60 and 62 degrees C were 1.4-1.8, 0.40-0.51 and 0.15-0.19 min (zeta values 4.00-4.52 degrees C) for the Yersinia strains, and 0.42, 0.13 and 0.07 min (zeta value 5.07 degrees C) for one C. coli strain. For the other Campylobacter strains, D values of 0.71-0.78, 0.24-0.28 and 0.12-0.14 min (zeta values 4.94 and 5.60 degrees C) were recorded at 56, 58 and 60 degrees C. D values obtained at 60 degrees C by the test tube method were 2.7-5.0 min and were considered to be unrealistic.     

Measuring the successes and deficiencies of constant pH molecular dynamics: a blind prediction study

A constant pH molecular dynamics method has been used in the blind prediction of pK(a) values of titratable residues in wild type and mutated structures of the Staphylococcal nuclease (SNase) protein. The predicted values have been subsequently compared to experimental values provided by the laboratory of García-Moreno. CpHMD performs well in predicting the pK(a) of solvent-exposed residues. For residues in the protein interior, the CpHMD method encounters some difficulties in reaching convergence and predicting the pK(a) values for residues having strong interactions with neighboring residues. These results show the need to accurately and sufficiently sample conformational space in order to obtain pK(a) values consistent with experimental results.     

Evaluation of two devices for point-of-care testing of haemoglobin in neonatal pigs

In veterinary medicine, point-of-care testing (POCT) techniques have become popular, since they provide immediate results and only small amounts of blood are needed. However, their accuracy is controversial. Pigs are often used for research purposes and accurate measurement of haemoglobin (Hb) is important during invasive procedures. The aim of this study was to evaluate two different Hb POCT devices in neonatal pigs. A prospective study with 57 pigs of 3-6 weeks of age, weighing 4.1-6.2 kg (median 5.1 kg) was performed. Fifty-seven blood samples were analysed for Hb using a conductivity-based and a photometrical POCT device and compared with a photometrical reference method. Statistical analysis was performed with Bland-Altman analysis, Spearman correlation and Passing-Bablok regression analysis. Hb values ranged from 32 to 108 g/L (median 80 g/L) using the reference method. The bias of the photometrical method (HemoCue(?)) to the reference method was -1 g/L, with limits of agreement (LOA) of -7 to 6 g/L. The conductivity-based method (i-STAT(?)) had a bias of -15 g/L with LOA from -24 to -6 g/L. There was a significant association between protein values and the bias of i-STAT versus CellDyn (r(2) = 0.27, P < 0.05) but not with the bias of HemoCue versus CellDyn (r(2) = 0.001, P = 0.79). The lower the protein values were, the lower the Hb values were measured by the i-STAT. The conductivity-based measurement of Hb constantly underestimated Hb values, whereas the photometrical method demonstrated a better accuracy and is therefore more reliable for on-site measurement of Hb in pigs.     

Estimation of pK(a) values using microchip capillary electrophoresis and indirect fluorescence detection

Microchip capillary electrophoresis (CE), coupled with indirect fluorescence detection was investigated for estimating the pK(a) values of non-fluorescent compounds. The CE method is based on the differences in electrophoretic mobility of the analyte as a function of the pH of the running buffer. Nine compounds were tested, including several of pharmaceutical importance, with pK(a) values from 10.3 to 4.6. All buffers contained 5-TAMRA as the fluorescent probe for indirect detection. Calculated pK(a) values agreed well with literature values obtained by traditional methods, differing not more than 0.2 from the literature value. The current work on single lane chips demonstrates the principle of microchip CE with indirect detection as a viable method for estimating pK(a) values. However, increased throughput will be required using a multilane chip to enable the approach to be used practically.     

Heat resistance of Campylobacter and Yersinia strains by three methods

Two methods of determining the heat resistance of bacteria, a glass cup and a test tube method, were compared with a method using capillary tubes. Three strains of Yersinia enterocolitica , one of Campylobacter jejuni and two of C. coli were tested in physiological saline. The differences between the results obtained by the glass cup method and the reference method were not statistically significant for five strains and were small also for the other, a Yersinia strain. D values obtained by the glass cup method at 58, 60 and 62°C were 1.4–1.8, 0.40–0.51 and 0.15–0.19 min ( z values 4.00–4.52°C) for the Yersinia strains, and 0.42, 0.13 and 0.07 min ( z value 5.07°C) for one C. coli strain. For the other Campylobacter strains, D values of 0.71–0.78, 0.24–0.28 and 0.12–0.14 min ( z values 4.94 and 5.60°C) were recorded at 56, 58 and 60°C. D values obtained at 60°C by the test tube method were 2.7–5.0 min and were considered to be unrealistic.     

The use of an enzymatic kit to measure plasma creatinine in the mouse and three other species

Plasma creatinine concentrations were determined in mice, rats, dogs and humans using a kinetic alkaline picrate method and an enzymatic method with a centrifugal analyser. Lower creatinine values were obtained for all four species using the enzymatic method, but the differences between methods were greater for mice and rats. Removal of creatininase from the enzymatic method reagents gave proportionally higher values for non-creatinine chromogens in mice and rats. A single enzymatic method was not specific for creatinine when used for these species.     

Extending the method of mathematically controlled comparison to include numerical comparisons

MOTIVATION: The method of mathematically controlled comparison has been used for some time to determine which of two alternative regulatory designs is better according to specific quantitative criteria for functional effectiveness. In some cases, the results obtained using this technique are general and independent of parameter values and the answers are clear-cut. In others, the result might be general, but the demonstration is difficult and numerical results with specific parameter values can help to clarify the situation. In either case, numerical results with specific parameter values can also provide an answer to the question of how much larger the values might be. In contrast, a more ambiguous result is obtained when either of the alternatives can have the larger value for a given systemic property, depending on the specific values of the parameters. In any case, introduction of specific values for the parameters reduces the generality of the results. Therefore, we have been motivated to develop and apply statistical methods that would permit the use of numerical values for the parameters and yet retain some of the generality that makes mathematically controlled comparison so attractive. RESULTS: We illustrate this new numerical method in a step-by-step application using a very simple didactic example. We also validate the results by comparison with the corresponding results obtained using the previously developed analytical method. The analytical approach is briefly present for reference purposes, since some of the same key concepts are needed to understand the numerical method and the results are needed for comparison. The numerical method confirms the qualitative differences between the systemic behavior of alternative designs obtained from the analytical method. In addition, the numerical method allows for quantification of the differences and it provides results that are general in a statistical sense. For example, the older analytical method showed that overall feedback inhibition in an unbranched pathway makes the system more robust whereas it decreases the stability margin of the steady state. The numerical method shows that the magnitudes of these differences are not comparable. The differences in stability margins (1-2% on average) are small when compared to the differences in robustness (50-100% on average). Furthermore, the numerical method shows that the system with overall feedback responds more quickly to change than the otherwise equivalent system without overall feedback. These results suggest reasons why overall feedback inhibition is such a prevalent regulatory pattern in unbranched biosynthetic pathways.     

Estimation of economic values and financial losses associated with clinical mastitis and somatic cell score in Holstein dairy cattle

The objective of this study was to develop a method for calculating economic values of clinical mastitis (CM) and somatic cell score (SCS) for inclusion in a dairy cattle breeding goal in the context of a country where farm production and economic data are scarce. In order to calculate the costs and derive economic values for SCS, a new model, 'milk collection method', has been developed and was compared with the Meijering model with individual and average SCS distributions. For the population, estimated economic values using the milk collection method were 1.3 and 2.4 times higher than those of Meijering method with average and individual SCS, respectively. The milk collection method needs no assumptions about normality of the distribution of SCS and because of a lack of normality in Iranian data for SCS, the Meijering method resulted in economic values that were biased downwards. Failing to account for the fact that milk price penalties for SCS are applied at milk collection rather than individual cow level resulted in a further large downward bias in the economic value of SCS. When the distribution of data is unknown or difficult to approximate or when a transformation to normality is not straightforward, the milk collection method would be preferable. Inclusion of SCS and CM in the breeding goal for Iranian dairy cattle is justified based on these results. The model to calculate mastitis costs proposed here could be used to estimate economic values for CM in other developing countries where farm production and economic data are generally poor.     

A Comparison of the British Pharmacopoeia (1973) and United States Pharmacopeia (1975) Methods for Detecting Pseudomonads

The British Pharmacopoeia (Anon. 1973) test for contamination by pseudomonads and the United States Pharmacopeia (Anon. 1975) test for the detection of Pseudomonas aeruginosa have been evaluated using type cultures representative of a wide spectrum of Pseudomonas spp. Media containing cetrimide are recommended by both Pharmacopoeias for the detection of pseudomonads. Of the 28 strains tested only five were detected by the BP method and 11 by the USP method. However, only one strain of P. aeruginosa failed to be detected using the USP method. A correlation between m.i.c. values for cetrimide and detection of the organisms was noted. The BP method failed to detect organisms with m.i.c. values of ± 0.03% whilst the USP method did not detect strains with m.i.c. values ± 0.015%.     

Determination of Apparent Ileal Amino Acid Digestibility in Rapeseed Meal and Cake Processed at Different Temperatures Using the Direct and Difference Method with Growing Pigs

Studies were conducted with ten barrows, average initial body weight 34.5 ± 2.1kg, fitted with a T-cannula at the distal ileum, to study the accuracy of determination of the apparent ileal digestibility (AID) values of crude protein (CP) and amino acids (AA) in rapeseed meal and cake and the effects of processing, using the difference method. Five corn starch-based diets in the studies were formulated to contain 17.7% CP and based on soybean meal, prepress-extraction rapeseed meal, prepress-extraction rapeseed meal plus soybean meal, high-temperature press rapeseed cake plus soybean meal, or low-temperature press rapeseed cake plus soybean meal as the sole source of dietary protein. The design was an incomplete Latin Square involving two three-week periods and five-treatments. It was found that the AID values of CP and most AA determined with the difference or direct method were significantly lower in rapeseed meal or cakes than soybean meal. The AID values of CP and most AA in prepress-extraction rapeseed meal, high-temperature press or low-temperature cakes determined with the difference method were no difference from those in prepress-extraction rapeseed meal determined with the direct method. The AID values of CP and AA in rapeseed meal and cake determined with the difference method were accurate, when the contribution of CP and AA from rapeseed was more than 50%. The AID values of CP and AA (especially lysine) were lower in the high-temperature press rapeseed cake than in the low-temperature press cake or the prepress-extraction meal.     

Determination of cation exchange capacity of woody plant roots using ammonium acetate extractant

Summary A rapid exchange procedure using ammonium acetate as an extractant was developed for measurement of cation exchange capacity (CEC) of plant roots. The CEC values obtained with 1∶100 and 1∶200 root/solution ratios were almost equal, though the values increased with length of the time of immersion in both the root/solution ratios. The method gave higher CEC values with fresh roots as compared to dried roots. However, dried milled and dried unmilled roots gave identical values.     

The principle of interval constraints: a generalization of the symmetric Dirichlet distribution.

A structure for representing problems in decision analysis and in expert systems, which reason under uncertainty, is the influence diagram or causal network. A causal network consists of an underlying joint probability distribution and a directed acyclic graph in which a propositional variable that represents a marginal distribution is stored at each vertex in the graph. This paper is concerned with two of the problems in applications that use causal networks. The first problem is the determination of the conditional probabilities of the values of remaining propositional variables in the network given that certain variables are instantiated for particular values. This is called probability propagation. The second problem is the determination of the most probable, second most probable, third most probable, and so on sets of values of a particular set of variables (called the explanation set) given that certain variables are instantiated for particular values. This problem is called abductive inference. There exists a class of causal networks in which each variable has only two parents, for which the time is required, by any known method, for probability propagation is exponential relative to the number of vertices in the network. The determination of a new method that would be efficient for all causal networks appears unlikely, because probability propagation has been shown to be #P-complete. In many medical applications, networks are often large and not sparsely connected. Therefore a method for the exact determination of probability values appears unlikely for such applications, and the development of approximation methods seems to be the best solution. The current approximation methods obtain interval bounds for the probability values. When such intervals are obtained, it is not possible in general to rank the alternatives. In this paper, a method is developed for obtaining expected values for the point probabilities from interval constraints on the probabilities. The method is based on an application of the principle of indifference to the probability values themselves. The distributions obtained with the principle of indifference are a generalization of the symmetric Dirichlet distribution in which prior ignorance is assumed.     

Modification of Lofland's colorimetric semiautomated serum triglyceride determination, assessed by an enzymatic glycerol determination

Erroneously high values for serum triglyceride levels obtained with the semiautomated method of Lofland were found to be due to contamination of the isopropanol extracts with glucose or other carbohydrate. Treatment of the isopropanol extracts with a mixture of copper sulfate and calcium hydroxide removed the contaminating glucose. Analysis of the glucose-free extracts by either the semiautomated or manual colorimetric method gave values in good agreement with each other and with those obtained by a new specific enzymatic method. The simple modification described in this paper obviates the necessity for the more expensive automated fluorometric apparatus.     

I-STOD: a new standardization method for analysing indirect-ELISA results of a schistosomiasis field study

Variability among samples analysed using the same ELISA protocol generates ambiguity in deciding which assay best quantifies the protein concentration. In this study, we propose a standardization method, called I-STOD (Improved STandardization method for Optical Density), for the transformation of OD values on different plates into relative concentrations of the antibody levels being assessed. We derived an equation relating OD values of different test samples to antibody levels according to the multi-stage reaction dynamics of the indirect-ELISA. Using serum samples from a Schistosomiasis japonica endemic area, we evaluated the fitness of the I-STOD model to experimental data of a standard reference serum in comparison with 5 other models. Calibration curves fitted by the I-STOD method judged to be superior, based on adjusted R2 (adjusted R2>0.99 on 22 out of 26 plates) values. The CV (coefficient of variation) value of the results between multi-well plates and the number of plates with OD values beyond the control range in Shewhart charts also demonstrate that the I-STOD method is a powerful tool which can greatly improve the comparability of results on different multi-well ELISA plates. We conclude that a standardization method is certainly necessary for antibody levels detected in order to properly illustrate clinical differences.