Small kinase assay panels can provide a measure of selectivity

In this Letter, a novel strategy for assessment of ligand promiscuity is described. By using a carefully selected small set of kinases together with multivariate statistical methods, a measure of selectivity can be estimated. This will facilitate an appropriate selection of compounds for further development in lead generation and optimization.     

Levels of viral glycoprotein provide a dose-dependent measure of tumor cell inhibition

A chemosensitivity assay utilizing small replicate Mm5mt/c1 C3H mammary tumor cell cultures was developed to determine whether changes in viral antigen expression and release into culture fluids could be utilized as an in vitro measure of chemotherapeutic drug effect. The 52,000 MW viral envelope glycoprotein (gp52) of the mouse mammary tumor virus (MMTV) was measured in culture fluids of control and drug-treated cultures while cell density was simultaneously determined by cell staining and OD 664 mu determination. While extracellular gp52 levels and cell density both progressively increased over 72 hours for control cultures, treatments with doxorubicin resulted in dose-dependent declines in both parameters at 24, 48, and 72 hours. Comparison of doxorubicin dosages for 50% reduction (ED50s) in both parameters (0.68uM and 1.1uM) revealed a similar coordinate reduction in both cell density and MMTVgp52. When gp52 levels were further examined as a general measure of effect for a broad spectrum of 6 drugs with differing mechanisms of action, coordinate declines in cell density and MMTVgp52 provided a time and dose-dependent dual measure of effect for each of the drugs tested. Coordinate declines resulted in the same following hierarchy of concentration-dependent drug potency: methotrexate greater than 5-fluorouracil greater than doxorubicin greater than N [phosphonacetyl- L aspartic acid] (PALA) greater than cis-platinum greater than cyclophosphamide. The dual measures of therapeutic effect afforded by this assay argue for its use as an in vitro measure of effect for optimizing drug treatments.     

Use of bioelectrical impedance spectroscopy to provide a measure of body composition in sows

The ability to accurately estimate fat mass and fat-free mass (FFM) has the potential to improve the way in which sow body condition can be managed in a breeding herd. Bioelectrical impedance spectroscopy (BIS) has been evaluated as a practical technique for assessment of body composition in several livestock species, but similar work is lacking in sows. Bioelectrical impedance uses population-specific algorithms that require values for the apparent resistivities of body fluids and body proportion factors. This study comprised three major aims: (i) to derive apparent resistivity coefficients for extracellular water (ECW) and intracellular water (ICW) required for validation of BIS predictions of total body water (TBW) in live sows against standard reference tracer dilution methods; (ii) to develop predictions of TBW to body composition prediction algorithms, namely FFM, by developing a body geometry correction factor (Kb) and (iii) to compare the BIS predictions of FFM against existing impedance predictors and published prediction equations for use in sows, based on physical measurements of back-fat depth and BW (P2-based predictors). Whole body impedance measurements and the determination of TBW by deuterium dilution and ECW by bromide dilution were performed on 40 Large White x Landrace sows. Mean apparent resistivity coefficients of body fluids were 431.1 Ω.cm for ECW and 1827.8 Ω.cm for ICW. Using these coefficients, TBW and ECW were over-estimated by 6.5 and 3.3%, respectively, compared to measured reference values, although these differences were not statistically different (P > 0.05). Mean Kb was 1.09 ± 0.14. Fat-free mass predictions were 194.9 kg, which equates to 60.9% of total sow weight, and 183.0 kg for BIS and the deuterium dilution method, respectively. Mean differences between the predicted and measured FFM values ranged from − 8.2 to 32.7%, but were not statistically different (P > 0.05). Method validation (leave-one-out procedure) revealed that mean differences between predicted and measured values were not statistically significant (P > 0.05). Of the impedance-based predictors, equivalence testing revealed that BIS displayed the lowest test bias of 11.9 kg (8.2%), although the P2-based prediction equations exhibited the lowest bias and percentage equivalence, with narrow limits of agreement. Results indicate although differences between mean predicted and measured values were not significantly different, relatively wide limits of agreement suggest BIS as an impractical option for assessing body composition in individual sows compared to the use of existing prediction equations based on BW and back fat.     

Progressive background in moths, and a quantitative measure of crypsis

A method is presented for quantitative estimation of the degree of crypsis of species seen by visual predators against known backgrounds. It is based upon a comparison between transects taken across animal and background colour patterns. The method was applied to day-resting moths in deciduous forest in New Jersey. Each species is found for two to four weeks at characteristic dates, and there is a constant turnover of species. In both moths and backgrounds there is a regular change in the colour pattern parameters from winter through spring to early summer. Moths are on average more cryptic at their normal dates than they would be if present earlier or later in the year. Species with known resting sites are on average more cryptic on their resting sites than other background habitats. Species that rest on more than one background habitat are less cryptic on their preferred habitats than are specialists. Species that rest under leaves and are not visible from above are not very cryptic. Specific v. general resemblance, disruptive coloration, and factors affecting 'aspect diversity' are discussed. The new method of estimating crypsis is useful for studies of crypsis as well as in sexual selection. It is necessary to know much about the resting sites and behaviour of moths, as well as other functions of colour patterns, to understand colour pattern evolution.     

A quantitative measure of migratory connectivity

The study of the extent of the connection between areas where populations of birds breed and areas where they winter has flourished in recent years mainly thanks to the development of new techniques, but also due to traditional ringing and recovery schemes, which allow tracking of individuals or populations linking wintering and breeding distributions. Currently, studies on migratory connectivity focus on retention of breeding population spatial structure on the non-breeding grounds and vice versa.Here we propose a method to quantify migratory connectivity based on Mantel correlation coefficients and to statistically test for deviations of the observed connectivity from a random mix of individuals. In addition, we propose a procedure, based on clustering algorithms, to identify whether observed connectivity depends on aggregation of individuals or on rigid transference of distribution patterns between areas.We applied this method to a large dataset of ringing recoveries of barn swallows (Hirundo rustica L) migrating from their Western Palearctic breeding areas to sub-Saharan winter quarters. We show that migration of barn swallow populations connects specific breeding and wintering areas, and that the “sub-populations” quantitatively identified by our method are consistent with qualitative patterns of migratory connectivity identified by studies of individual geographical populations based on other methods. Finally, we tested the performance of the method by running simulations under different scenarios. Such simulations showed that the method is robust and able to correctly detect migratory connectivity even with smaller datasets and when a strong geographical pattern is not present in the population. Our method provides a quantitative measure of migratory connectivity and allows for the identification of populations showing high connectivity between the breeding and wintering areas. This method is suitable for a generalized application to diverse animal taxa as well as to large scale analyses of connectivity for conservation purposes.     

Temporal changes in phosphoglycerate kinase coding sequences: a quantitative measure.

The ratio of the average of the square of the number of the nucleotides to that of the random sequence of the same strand bias is proposed as a quantitative measure of evolution in some coding DNA sequences. Applying this measure to the phosphoglycerate kinase gene we observe a monotonic rise of the ratio with evolution. We present an interpretation of this data on some bacteria.     

Motor agency: a new and highly sensitive measure to reveal agency disturbances in early psychosis

Background

Early diagnosis of young adults at risk of schizophrenia is essential for preventive approaches of the illness. Nevertheless, classic screening instruments are difficult to use because of the non-specific nature of the signs at this pre-onset phase of illness. The objective of the present contribution was to propose an innovating test that can probe the more specific symptom of psychosis, i.e., the sense of agency, which is defined as being the immediate experience of oneself as the cause of an action. More specifically, we tested whether motor agency is abnormal in early psychosis.

Methods

Thirty-two young symptomatic patients and their age-matched controls participated in the study. 15 of these patients were at ultra high-risk for developing psychosis (UHR), and 17 patients were suffering from first-episode psychosis (FEP). Patients'' neurocognitive capacities were assessed through the use of seven neuropsychological tests. A motor agency task was also introduced to obtain an objective indicator of the degree of sense of agency, by contrasting force levels applied during other and self-produced collisions between a hand-held objet and a pendulum.

Results

As reported in the literature for adult controls, healthy adolescents used more efficient force levels in self than in other-imposed collisions. For both UHR and FEP patients, abnormally high levels of grip force were used for self-produced collisions, leading to an absence of difference between self and other. The normalized results revealed that motor agency differentiated patients from controls with a higher level of sensitivity than the more classic neuropsychological test battery.

Conclusions

This study is in favour of the existence of an abnormal sense of agency early in the psychotic illness. Because it is quick and none verbal, motor agency may be a valuable tool to use in complement to classic interviews, especially when investigating complex ineffable experiences that are difficult to explicitly describe.     

A novel quantitative measure of image quality in fluoroscopy

Assessment of fluoroscopic image quality has not kept pace with technological developments in interventional imaging equipment. Access to ‘for presentation’ data on these systems has motivated this investigation into a novel quantitative method of measuring image quality. We have developed a statistical algorithm as an alternative to subjective assessment using threshold contrast detail detectability techniques. Using sets of uniformity exposed fluoroscopy frames, the algorithm estimates the minimum contrast necessary for conspicuity of a range of virtual target object areas A. Pixel mean value distributions in a central image region are Gaussian, with standard deviation σ Pixel binning produces background distributions with area A. For 95% confidence of conspicuity a target object must exhibit a minimum contrast of 3.29σ. A range of threshold contrasts are calculated for a range of virtual areas. Analysis on a few seconds of fluoroscopy data is performed remotely and no test object is required. In this study Threshold Index and Contrast Detail curves were calculated for different incident air kerma rates at the detector, different levels of electronic magnification and different types of image processing. A limited number of direct comparisons were made with subjective assessments using the Leeds TO.10 test object. Results obtained indicate that the statistical algorithm is not only more sensitive to changes in levels of detector dose rate and magnification, but also to levels of image processing, including edge-enhancement. Threshold Index curves thus produced could be used as an interventional system optimisation tool and to objectively compare image quality between vendor systems.     

Standard line slopes as a measure of a relative matrix effect in quantitative HPLC-MS bioanalysis

A simple experimental approach for studying and identifying the relative matrix effect (for example "plasma-to-plasma" and/or "urine-to-urine") in quantitative analyses by HPLC-MS/MS is described. Using as a database a large number of examples of methods developed in recent years in our laboratories, the relationship between the precision of standard line slopes constructed in five different lots of a biofluid (for example plasma) and the reliability of determination of concentration of an analyte in a particular plasma lot (or subject) was examined. In addition, the precision of standard line slopes was compared when stable isotope-labeled analytes versus analogs were used as internal standards (IS). Also, in some cases, a direct comparison of standard line slopes was made when different HPLC-MS interfaces (APCI versus ESI) were used for the assay of the same compound, using the same IS and the same sample preparation and chromatographic separation conditions. In selected cases, the precision of standard line slopes in five different lots of a biofluid was compared with precision values determined five times in a single lot. The results of these studies indicated that the variability of standard line slopes in different lots of a biofluid [precision of standard line slopes expressed as coefficient of variation, CV (%)] may serve as a good indicator of a relative matrix effect and, it is suggested, this precision value should not exceed 3-4% for the method to be considered reliable and free from the relative matrix effect liability. Based on the results presented, in order to assess the relative matrix effect in bioanalytical methods, it is recommended to perform assay precision and accuracy determination in five different lots of a biofluid, instead of repeat (n=5) analysis in the same, single biofluid lot, calculate standard line slopes and precision of these slopes, and to use <3-4% slope precision value as a guide for method applicability to support clinical studies. It was also demonstrated that when stable isotope-labeled analytes were used as internal standards, the precision of standard line slopes in five different lots of a biofluid was 相似文献   

Faecal egg counts provide a reliable measure of Trichostrongylus tenuis intensities in free-living red grouse Lagopus lagopus scoticus

The reliability of different egg counting methods for estimating the intensity of Trichostrongylus tenuis infections in red grouse, Lagopus lagopus scoticus, was investigated in the autumn, when grouse may harbour high parasite intensities. Possible limitations to the use of these methods were also examined. Faecal egg counts were found to accurately estimate T. tenuis worm intensities, at least up to an observed maximum of c. 8000 worms. Two egg counting methods (smear and McMaster) gave consistent results, although the exact relationship with worm intensity differed according to the method used. Faecal egg counts significantly decreased with increasing length of sample storage time, but egg counts were reliable for estimating worm intensity for three weeks. The concentration of eggs in the caecum was also found to reliably estimate worm intensity. However, egg counts from frozen gut samples cannot be used to estimate worm intensities. These results conclude that, despite some limitations, faecal and caecum egg counts provide useful and reliable ways of measuring T. tenuis intensities in red grouse.     

A quantitative measure of error minimization in the genetic code

Summary We have calculated the average effect of changing a codon by a single base for all possible single-base changes in the genetic code and for changes in the first, second, and third codon positions separately. Such values were calculated for an amino acid's polar requirement, hydropathy, molecular volume, and isoelectric point. For each attribute the average effect of single-base changes was also calculated for a large number of randomly generated codes that retained the same level of redundancy as the natural code. Amino acids whose codons differed by a single base in the first and third codon positions were very similar with respect to polar requirement and hydropathy. The major differences between amino acids were specified by the second codon position. Codons with U in the second position are hydrophobic, whereas most codons with A in the second position are hydrophilic. This accounts for the observation of complementary hydropathy. Single-base changes in the natural code had a smaller average effect on polar requirement than all but 0.02% of random codes. This result is most easily explained by selection to minimize deleterious effects of translation errors during the early evolution of the code.     

Enumeration of lymphokine-secreting cells as a quantitative measure for cellular immune responses in rhesus macaques

Abstract: We investigated whether enumeration of lymphokine-secreting T cells can be used as a quantitative measure to determine the immunogenicity of foreign proteins in rhesus monkeys. In addition, it was assessed whether this approach can supplement and/or substitute for the well-established lymphoproliferation assay. Two candidate vaccine proteins (e.g., HIV-1 gp120 and HSV-2gD) were used as model antigens for immunization. PBMCs from immunized animals were antigenically stimulated and evaluated on their proliferative capacity and lymphokine release at the single cell level. The experiments showed a close quantitative correlation between antigen-triggered proliferative responses and the antigen-induced generation of Il-2 and IFN-gamma producing cells (pc). Il-4pc were found to appear relatively late after the initiation of antigen exposure. The data indicate that ELISPOT assays provide valuable tools for the assessment of the antigenicity of foreign proteins in vivo.     

A quantitative assay to measure chromosome stability in Schizosaccharomyces pombe

Summary The fidelity of mitotic chromosome transmission in Schizosaccharomyces pombe was estimated quantitatively by using cycloheximide resistance as a means to select cells that had undergone chromosome loss or nondisjunction. We aimed to investigate the connection between recombination and mitotic chromosome stability. A number of mutants defective in mitotic recombination such as cdc17-L16, rec59-72, and rec50-25 were tested and in these an approximately ten fold elevation of mitotic haploidization rate was found compared with controls. Our data suggest that recombination is important in controlling the maintenance of chromosomes during mitosis.     

Nutrient induced fluorescence transients (NIFTs) provide a rapid measure of P and C (co-)limitation in a green alga

Nutrient Induced Fluorescence Transients (NIFTs) have been shown to be a possible way of testing for the limiting nutrient in algal populations. In this study we tested the hypothesis that NIFTs can be used to detect a (co-)limitation for inorganic phosphorus (Pi) and CO₂ in the green alga Chlamydomonas acidophila and that the magnitude of the NIFTs can be related to cellular P:C ratios. We show a co-limitation response for Pi and CO₂ via traditional nutrient enrichment experiments in natural phytoplankton populations dominated by C. acidophila. We measured NIFT responses after a Pi- or a CO₂-spike in C. acidophila batch cultures at various stages of Pi and inorganic C limitation. Significant NIFTs were observed in response to spikes in both nutrients. The NIFT response to a Pi-spike showed a strong negative correlation with cellular P:C ratio that was pronounced below 3 mmol P: mol C (equivalent to 0.2 pg P cell^–1). Both cellular P and C content influenced the extent of the Pi-NIFT response. The NIFT response to a CO₂-spike correlated to low CO₂ culturing conditions and also had a negative correlation with cellular P content. A secondary response within the Pi-NIFT response was related to the CO₂ concentration and potentially reflected co-limitation. In conclusion, NIFTs provided a quick and reliable method to detect the growth-limiting nutrient in an extremophile green alga, under Pi-, CO_2- and Pi/CO₂ (co-)limited growth conditions.     

Eimeria tenella: parasite-specific incorporation of 3H-uracil as a quantitative measure of intracellular development

An assay has been developed using parasite-specific incorporation of 3H-uracil to assess the intracellular growth of Eimeria tenella in vitro. As shown by both scintillation counts and autoradiography, 3H-uracil was incorporated specifically into intracellular parasites from the onset of infection and continued throughout development of the first generation schizonts. Mature schizonts and first generation merozoites did not continue to incorporate additional 3H-uracil, indicating that RNA synthesis had halted in these stages. Based on these findings, a semi-automated microscale uracil incorporation assay was developed to determine parasite viability. This method should be useful for biochemical studies with intracellular parasites and for screening compounds for anticoccidial activity. The ease, rapidity, and quantitative nature of this assay contrasts favorably with standard morphometric approaches of determining parasite development. In addition, parallel studies using host cell incorporation of 3H-uridine have been introduced as a method of determining whether antiparasitic activity is direct or indirect in relation to effects on the host cell.