The transducer model for contrast detection and discrimination: formal relations, implications, and an empirical test

The transducer function mu for contrast perception describes the nonlinear mapping of stimulus contrast onto an internal response. Under a signal detection theory approach, the transducer model of contrast perception states that the internal response elicited by a stimulus of contrast c is a random variable with mean mu(c). Using this approach, we derive the formal relations between the transducer function, the threshold-versus-contrast (TvC) function, and the psychometric functions for contrast detection and discrimination in 2AFC tasks. We show that the mathematical form of the TvC function is determined only by mu, and that the psychometric functions for detection and discrimination have a common mathematical form with common parameters emanating from, and only from, the transducer function mu and the form of the distribution of the internal responses. We discuss the theoretical and practical implications of these relations, which have bearings on the tenability of certain mathematical forms for the psychometric function and on the suitability of empirical approaches to model validation. We also present the results of a comprehensive test of these relations using two alternative forms of the transducer model: a three-parameter version that renders logistic psychometric functions and a five-parameter version using Foley's variant of the Naka-Rushton equation as transducer function. Our results support the validity of the formal relations implied by the general transducer model, and the two versions that were contrasted account for our data equally well.     

The role of temporal generalization in a temporal discrimination task

Two experiments trained rats to discriminate two or three stimulus durations using a temporal discrimination task. A standard peak shift effect was observed when training was administered with short versus long signals in Experiment 1. Both discrimination accuracy scores and the generalization gradients revealed that shorter intervals were discriminated more accurately, which may be due to the scalar property of timing. In Experiment 2, three signals (short, medium, and long) were associated with three different responses, or two of the intervals were associated with one response (short and long or short and medium) and the other interval with a different response. Here, the short/medium versus long discrimination was learned most readily of the three tasks. The results of both experiments indicated a strong contribution of learning of individual durations combined with scalar generalization gradients, but Experiment 2 indicated that categorical encoding of durations may have also been operating.     

Spatial and temporal analysis of disease occurrence for detection of clustering

Data on disease occurrence often consist of the number of cases recorded in a set of regions during each of several time periods. In this paper a method of analysis of such data is proposed which allows one to distinguish and test for spatial clustering, temporal clustering, and space-time clustering of cases. Departures of case numbers from expectation are partitioned into region and time period main effects and region-by-time interactions. Spatial and temporal relationships among regions and time periods are incorporated by pooling estimates over neighborhoods. In addition to providing tests for clustering, the analysis identifies the contributions to clustering made by individual neighborhoods. Data on Creutzfeldt-Jakob disease in France are used to illustrate the approach.     

The resolution and discrimination of images in the visual system

We analysed the conformity of optic and retinal cones anatomy factors by the two-point test. Obtained by F. Campbell and R. W. Gubish, the point spread function has a width of about 1 arc min. Cones sizes are equal to 0.5 arc min in the fovea. Functional pixel consists of 3-5 cones under the point spread function. Such an organisation in very useful in decreasing the samping noise of receptors. We carried out psychophysical investigations to show a consensus among the optic, receptors', and neuronal levels. In experiments we studied changes of the two-point pattern perception in respect to the points separation, measured the orientation threshold of small size stimuli. Data were compared with optical point-spread function, the hexagonal mosaic of cones, and line spread function of spatial elements, which form spatial frequency channels at the cortical level.     

Testing for microscopic reversibility in the gating of maxi K+ channels using two-dimensional dwell-time distributions.

An assumption usually made when developing kinetic models for the gating of ion channels is that the transitions among the various states involved in the gating obey microscopic reversibility. If this assumption is incorrect, then the models and estimated rate constants made with the assumption would be in error. This paper examines whether the gating of a large conductance Ca-activated K+ channel in skeletal muscle is consistent with microscopic reversibility. If microscopic reversibility is obeyed, then the number of forward and backward transitions per unit time for each individual reaction step will, on average, be identical and, consequently, the gating must show time reversibility. To look for time reversibility, two-dimensional dwell-time distributions of the durations of open and closed intervals were obtained from single-channel current records analyzed in the forward and in the backward directions. Two-dimensional dwell-time distributions of pairs of open intervals and of pairs of closed intervals were also analyzed to extend the resolution of the method to special circumstances in which intervals from different closed (or open) states might have similar durations. No significant differences were observed between the forward and backward analysis of the two-dimensional dwell-time distributions, suggesting time reversibility. Thus, we find no evidence to indicate that the gating of the maxi K+ channel violates microscopic reversibility.     

Acquisition, extinction and temporal discrimination in human conditioned avoidance

Two experiments were conducted with the aim of designing a videogame for the study of human conditioned avoidance. Participants had to destroy enemy spaceships with the goal of increasing the score in a counter. Coloured signals might announce the launching of a bomb that could hit participant's spaceship producing a 30 points decrease in participant's score. Three groups of participants were trained in discriminating between a warning signal (W) and a safety signal (S) in Experiment 1. Instrumental group could avoid the loss of points by hiding the spaceship before the offset of W. Participants in the Yoked group received the same treatment received by their instrumental partners, regardless of their behaviour. In the Pavlovian group, W was always followed by the loss of points, regardless of participant's behaviour. Discrimination between W and S was better in the Instrumental groups than in the Yoked and Pavlovian control groups. Experiment 2 found extinction of avoidance when the warning signal was not followed by the bomb. Temporal discrimination was found within the participants that received the instrumental contingency in both experiments, with higher avoidance response towards the end of the warning signal. Temporal discrimination disappeared after extinction in Experiment 2.     

Methods for increasing the resolution of two-dimensional protein electrophoresis

A two-dimensional gel elctrophoresis protocol has been developed which provides for a 1.5-to 3-fold increase in the resolution of proteins compared to other frequently used methods. The major variations from previous protocols include increased pore size in the isoelectric focusing gels; cholamidopropyldimethylhydroxypropanesulfonate, a zwitterionic detergent, replaces most of the Nonidet P-40, a nonionic detergent, in the isoelectric focusing gels; no equilibration step is employed between the first and second dimensional separation. The use of a stacking gel in the second dimension has been eliminated; a more efficient and evenly distributed cooling system has been designed for the molecular mass separation, allowing faster migration with higher current. Finally, the crosslinker diacrylylpiperazine is employed which improves protein separation and detection with ammoniacal silver staining. Silver-stained two-dimensional gel electrophoretograms of human plasma and hamster brain tissues and autoradiographs of rat liver cells are compared to the results obtained from previous methods.     

A simple photoactivation and image analysis module for visualizing and analyzing axonal transport with high temporal resolution

We describe a strategy for analyzing axonal transport of cytosolic proteins (CPs) using photoactivatable GFP-PAGFP-with modifications of standard imaging components that can be retroactively fitted to a conventional epifluorescence microscope. The photoactivation and visualization are nearly simultaneous, allowing studies of proteins with rapidly mobile fractions. Cultured hippocampal neurons are transfected with PAGFP-tagged constructs, a discrete protein population within axons is photoactivated, and then the activated population is tracked by live imaging. We show the utility of this method in analyzing axonal transport of CPs that have inherent diffusible pools and distinguish this transport modality from passive diffusion and vesicle transport. The analytical tools used to quantify the motion are also described. Aside from the time needed for preparation of neuronal cultures/transfection, the experiment takes 2-3 h, during which time several axons can be imaged and analyzed. These methods should be easy to adopt by most laboratories and may also be useful for monitoring CP movement in other cell types.     

Adenine and guanine 8CH exchange in nucleic acids: resolution and measurement by Raman optical multichannel analysis

Deuterium exchange of 8C protons of adenine and guanine in nucleic acids is conveniently monitored by laser Raman spectrophotometry, and the average exchange rate so determined [kA + kG] can be exploited as a dynamic probe of the secondary structure of DNA or RNA [J. M. Benevides and G. J. Thomas, Jr. (1985) Biopolymers 24, 667-682]. The present work describes a rapid Raman procedure, based upon optical multichannel analysis, which permits discrimination of the different 8CH exchange rates, kA of adenine and kG of guanine, in a single experimental protocol. For this procedure, simultaneous measurements are made of the intensity decay or frequency shift in separately resolved Raman bands of adenine and guanine, each of which is sensitive only to 8C deuteration of its respective purine. Resolution of the rates kA and kG is demonstrated for the mononucleotide mixtures, 5'-rAMP + 5'-rGMP and 5'-dAMP + 5'-dGMP, for the polynucleotides poly(dA-dT).poly(dA-dT) and poly(dG-dC).poly(dG-dC), for calf thymus DNA, and for the 17 base-pair operator OR3. We show that the different exchange rates of adenine and guanine, in nucleotide mixtures and in DNA, may also be calculated independently from intensity decay of the composite 1481-cm-1 band, comprising overlapped adenine and guanine components, over a time domain that encompasses two distinct regimes: (1) a relatively more rapid exchange of guanine, and (2) a concurrent slower exchange of adenine. Both methods developed here yield consistent results. We find, first, that exchange of guanine is approximately twofold more rapid than that of adenine when both purines are present in the same structure and solvent environment, presumably a consequence of the greater basicity of the 7N site of guanine. Second, we find that adenine suffers greater retardation of exchange than guanine when both purines are incorporated into a "classical" B-DNA secondary structure, such as that of calf thymus DNA. This finding suggests different microenvironments at the 7N-8C loci of adenine and guanine in aqueous B-DNA. We also confirm that adenine residues of B-form poly(dA-dT).poly(dA-dT) exchange much more slowly than those of other B-DNA sequences, implying a secondary structure for the alternating-AT sequence with unusual stereochemistry in the major groove. The greater resistance of adenine than guanine to 8CH exchange in the B-DNA secondary structure is more evident in high molecular weight calf thymus DNA and in the alternating AT and GC copolymer duplexes than in the smaller 17 base-pair operator OR3.(ABSTRACT TRUNCATED AT 400 WORDS)     

The myth of automated, high-throughput two-dimensional gel analysis

Many software packages have been developed to process and analyze 2-D gel images. Some programs have been touted as automated, high-throughput solutions. We tested five commercially available programs using 18 replicate gels of a rat brain protein extract. We determined computer processing time, approximate spot editing time, time required to correct spot mismatches, as well as total processing time. We also determined the number of spots automatically detected, number of spots kept after manual editing, and the percentage of automatically generated correct matches. We also determined the effect of increasing the number of replicate gels on spot matching efficiency for two of the programs. We found that for all programs tested, less than 3% of the total processing time was automated. The remainder of the time was spent in manual, subjective editing of detected spots and computer generated matches. Total processing time for 18 gels varied from 22 to 84 h. The percentage of correct matches generated automatically varied from 1 to 62%. Increasing the number of gels in an experiment dramatically reduced the percentage of automatically generated correct matches. Our results demonstrate that these 2-D gel analysis programs are not automatic or rapid, and also suggest that matching accuracy decreases as experiment size increases.     

Molecular discrimination and ploidy level determination for elite willow cultivars

Willow (Salix spp.), a woody plant in forms of tree, sub-tree, or shrub, has long been cultivated as an important fiber resource and for environmental protection. To manage commercial willow plantations, there is an increasing demand for the genetic discrimination of willow cultivars based on molecular markers. In this study, based on the genomic sequences of Salix suchowensis, a core set of 16 highly polymorphic simple sequence repeat (SSR) primer pairs were selected for the molecular discrimination of different willow cultivars. Using these primer pairs, DNA fingerprints of a collection of 25 elite willow cultivars were generated and their genetic identities were analyzed based on the SSR genotyping profiles and the UPGMA clustering. Subsequently, we examined the ploidy levels of these cultivars by combining SSR marker genotyping with flow cytometry measurements. It was found that, in this collection, the shrub cultivars were mainly presented as diploids, while cultivars in tree form mainly existed as polyploids. This study established a reference DNA fingerprinting database for managing the commercial willow cultivars, and the determination of their ploidy levels provided critical information for aiding the polyploid breeding programs in willows.     

Bioinformatics describes novel Loci for high resolution discrimination of leptospira isolates

Background

Leptospirosis is one of the most widespread zoonoses in the world and with over 260 pathogenic serovars there is an urgent need for a molecular system of classification. The development of multilocus sequence typing (MLST) schemes for Leptospira spp. is addressing this issue. The aim of this study was to identify loci with potential to enhance Leptospira strain discrimination by sequencing-based methods.

Methodology and Principal Findings

We used bioinformatics to evaluate pre-existing loci with the potential to increase the discrimination of outbreak strains. Previously deposited sequence data were evaluated by phylogenetic analyses using either single or concatenated sequences. We identified and evaluated the applicability of the ligB, secY, rpoB and lipL41 loci, individually and in combination, to discriminate between 38 pathogenic Leptospira strains and to cluster them according to the species they belonged to. Pairwise identity among the loci ranged from 82.0–92.0%, while interspecies identity was 97.7–98.5%. Using the ligB-secY-rpoB-lipL41 superlocus it was possible to discriminate 34/38 strains, which belong to six pathogenic Leptospira species. In addition, the sequences were concatenated with the superloci from 16 sequence types from a previous MLST scheme employed to study the association of a leptospiral clone with an outbreak of human leptospirosis in Thailand. Their use enhanced the discriminative power of the existing scheme. The lipL41 and rpoB loci raised the resolution from 81.0–100%, but the enhanced scheme still remains limited to the L. interrogans and L. kirschneri species.

Conclusions

As the first aim of our study, the ligB-secY-rpoB-lipL41 superlocus demonstrated a satisfactory level of discrimination among the strains evaluated. Second, the inclusion of the rpoB and lipL41 loci to a MLST scheme provided high resolution for discrimination of strains within L. interrogans and L. kirschneri and might be useful in future epidemiological studies.     

Principal component analysis of ensemble recordings reveals cell assemblies at high temporal resolution

Simultaneous recordings of many single neurons reveals unique insights into network processing spanning the timescale from single spikes to global oscillations. Neurons dynamically self-organize in subgroups of coactivated elements referred to as cell assemblies. Furthermore, these cell assemblies are reactivated, or replayed, preferentially during subsequent rest or sleep episodes, a proposed mechanism for memory trace consolidation. Here we employ Principal Component Analysis to isolate such patterns of neural activity. In addition, a measure is developed to quantify the similarity of instantaneous activity with a template pattern, and we derive theoretical distributions for the null hypothesis of no correlation between spike trains, allowing one to evaluate the statistical significance of instantaneous coactivations. Hence, when applied in an epoch different from the one where the patterns were identified, (e.g. subsequent sleep) this measure allows to identify times and intensities of reactivation. The distribution of this measure provides information on the dynamics of reactivation events: in sleep these occur as transients rather than as a continuous process.     

Influence of taxonomic and numerical resolution on the analysis of temporal changes in phytoplankton communities

From December 2003 to November 2005, we analyzed the phytoplankton community of four streams located in Central Brazil (Goiás State) to evaluate if the temporal changes in phytoplankton community structure were dependent on the taxonomic/numerical resolution used to represent the data. Classification based on functional criteria was also contrasted with taxonomic classification to assess whether these classification schemes produce different ordination patterns. Procrustean analyses indicated that ordination patterns generated with data based on the presence or absence of genera correlated significantly with the patterns generated by species density. Temporal trajectories of scores derived from functional groups significantly matched those derived from analyses based on quantitative data (density or biovolume) for genus or family. In general, the results indicated that some simplifications are justifiable, mainly when one takes into account the need for uninterrupted biomonitoring programs over large spatial scales in a continent-sized country with increasing environmental problems and with a relative paucity of scientists.     

The QUEST system for quantitative analysis of two-dimensional gels

The strategies and methods used by the QUEST system for two-dimensional gel analysis are described, and the performance of the system is evaluated. Radiolabeled proteins, resolved on two-dimensional gels and detected using calibrated exposures to film, are quantified in units of disintegrations per minute or as a fraction of the total protein radioactivity applied to the gel. Spot quantitation and resolution of overlapping spots is performed by two-dimensional gaussian fitting. Pattern matching is carried out for groups of gels called matchsets, and within each matchset every gel is matched to every other gel. During the matching process, spots are automatically added to each pattern at positions where unmatched spots were detected in other patterns. This results in enhanced accuracy for both spot detection and for matching. The spot fitting procedure is repeated after matching. Tests show that up to 97% of spots in each pattern can be matched and that fewer than 1% of the spots are matched inconsistently. Approximately 2000 proteins are detected from typical gels. Of these 1600 are high quality spots. Tests to measure the coefficient of variation of spot quantitation versus spot quality show that the average coefficient of variation for high quality spots is 21%. The intensities of the detected proteins range from 4 to 20,000 ppm of total protein synthesis. The QUEST analysis system has been used to build a quantitative database for the proteins of normal and transformed REF52 cells, as presented in the accompanying reports (Garrels, J., and Franza, B. R., Jr. (1989) J. Biol. Chem. 264, 5283-5298, 5299-5312).     

Conditions when statistical tests for model discrimination have high power. Some examples from pharmacokinetics, ligand binding, transient and steady-state enzyme kinetics

The situation where data pairs xi, yi are actually generated by a true model, f(delta, x), but erroneously fitted by a deficient model, g(phi, x), is explored. A function, Q(delta), is described which is the average squared distance between f(delta, x) and the best-fit false model, g(phi, x). For a range of x covering 5-95% 'saturation' of f(delta, x), Q(delta) is calculated numerically for sums of exponentials, binding functions and rational functions. In each case, the region of delta when the second model in the series can be reliably differentiated from the first by statistical tests is described.     

Quantitative analysis of the local rates of growth of dicot leaves at a high temporal and spatial resolution,using image sequence analysis

A new technique is presented for quantitative mapping of dicot leaf growth at high spatial and temporal resolution, at a speed making online-mapping feasible. Time lapse video sequences of growing leaves are captured by a personal computer (PC) with a frame-grabber board and a standard CCD camera, and evaluated using algorithms that have been recently developed to analyse motion in dynamic image sequences. Growth can be detected at under 1% per hour, with a time resolution of minutes and a spatial resolution of a few millimeters. The new technique has been verified by comparing it with classical approaches to map integrated growth. Diurnal courses of leaf growth of Ricinus communis and tobacco are presented to demonstrate the localised character of growth in leaves. Expansion growth is restricted to the base of the leaf and is restricted to a few hours at the end of the night and the start of the day. The high resolution of the method is illustrated by mapping the responses to step-changes in leaf turgor. A 3 bar turgor jump led to a rapid transient expansion over the entire length of the leaf that was partially reversed when the turgor was relaxed.     

A method for the analysis of temporal changes in vegetation pattern at the landscape level

A new approach to study temporary changes in small landscape units is proposed, based on vegetation-complex relevés (sigma relevés). The method is introduced using extensively grazed or abandoned heathland and Nardus-sward landscapes in the Black Forest as examples. Thirty-six sigma relevés of the years 1979–80 are compared with those of 1989–90. Each of the compared plot areas covers on the average 2–4 hectares, and has a diversity of about 20 different vegetation types. The vegetation complex relevés can be ordered to 3 different types which characterize landscape ecological zones dependant on former rural management.As a result of the comparison 2 main developments which have a spatial differentiation in the Black Forest are confirmed and documentated: