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PubMed1976

The problems of sampling and of the statistical evaluation of microbial numbers in mineral waters.

Problems in sampling are considered and the implications of various sampling schemes discussed in terms of the risks involved to the users of the schemes. It is concluded that microbiological testing alone cannot guarantee the "safety" of a product. The reliability of analytical procedures of use in the microbiological examination of water is examined and a method of determining the state of statistical control of the procedure described. Finally control charts available for monitoring a manufacturing process are discussed with particular emphasis on the cumulative sum test and its application to colony counts from water.

Animals↗
PubMed1978

[Method for the stabilization of E-rosettes with glutaraldehyde].

A technically simple method of fixing E-rosettes is represented. Under the influence of glutaraldehyde of 0.5% the E-rosettes being themselves very fragile assume a solid form and may be firmly spread to smears. Comparative examinations made on fresh and panoptically stained preparations showed a good accordance of results. The advantages of this method consist in its easy handling, possible simultaneous or alternative application of two counting procedures and the possibility of having the test results registered in archives.

Aldehydes↗
PubMed1993

[Laboratory diagnosis of immune deficiency].

Highly specialized, state-of-the-art diagnostic tests are available for identifying congenital and acquired immune defects. These methods should only be resorted to when less complicated means have created suspicion of an immune defect. The case history, including the family history, represents the core of the diagnostic procedure. Initially, only simple clinical investigations are indicated. These should enable the physician to exclude or delimit a defect in the immune system which then can be defined more closely by specific tests. Screening includes clinical chemistry (erythrocyte sedimentation rate, total serum protein, serum electrophoresis, C-reactive protein, blood count including differential blood count, ferritin, urine analysis, and a quantitative assay of the immunoglobulins A, G and M), bacteriological, serological, and radiological investigations, and finally skin tests with recall antigens. Thereby, it is usually possible to reliably detect primary B cell defects with humoral antibody deficiency syndromes. Lymphocyte subset counts, immunoelectrophoresis, and bone marrow biopsy are necessary for the differential diagnosis, or for the confirmation, of malignant lymphatic proliferation, especially in adults. IgG subclass defects as well as granulocyte dysfunction and complement defects must be excluded in patients who are susceptible to bacterial infection despite normal immunoglobulin concentrations. In suspected cases of primary or secondary (HIV, cytomegalovirus, Epstein-Barr virus) T cell defects, lymphocyte subset counts and, where applicable, T cell function tests are indicated. The majority of secondary immunodeficiency syndromes, in which the primary disease is known, do not currently require specialized diagnosis. Nevertheless, monitoring of the lymphocyte subsets in HIV-positive patients has already become standard practice in health care (for evaluating the prognosis and deciding on the therapy).

Diagnosis, Differential↗
PubMed1997

Argyrophilic nucleolar organiser regions (AgNORs) in breast lesions.

Nucleolar organiser regions (NORs) demonstrated by argyrophilia of NOR-proteins are indicator of cellular proliferative activity. The NORs can be identified in the nuclei as brown or black dots with silver colloidal staining technique in formalin fixed paraffin sections and in cytology smears. Seventy-five cases including 45 tissue sections and 30 fine needle aspiration cytology (FNAC) smears of benign and malignant lesions of breast have been studied to evaluate the significance and practical application of AgNOR count per nucleus. Out of 45 tissue sections 15 belonged to fibrocystic disease, 10 fibro-adenomas and 20 carcinomas and of the 30 FNAC smears, 10 were fibrocystic disease, 8 fibro-adenomas and 12 carcinomas. In fibrocystic disease the mean AgNOR count was 1.60 (FNAC group-0.75, tissue section-1.61). In fibro-adenomas it was 1.61 (FNAC-1.63, tissue section-1.59). The mean count in carcinoma was 12.10 (FNAC-12.08, tissue section-12.10). The difference in AgNOR count in fibrocystic disease and fibro-adenoma was not significant, but that between benign breast lesion and carcinoma was significant. No difference was observed between FNAC and tissue section groups in benign or malignant lesions. The simple staining technique can be used as an additional criterion to differentiate the benign and malignant lesions of breast.

Biopsy, Needle↗
PubMed1998

Evaluating surrogate markers of clinical outcome when measured with error.

In most clinical trials, markers are measured periodically with error. In the presence of measurement error, the naive method of using the observed marker values in the Cox model to evaluate the relationship between the marker and clinical outcome can produce biased estimates and lead to incorrect conclusions when evaluating a potential surrogate. We propose a two-stage approach to account for the measurement error and reduce the bias of the estimate. In the first stage, an empirical Bayes estimate of the time-dependent covariate is computed at each event time. In the second stage, these estimates are imputed in the Cox proportional hazards model to estimate the regression parameter of interest. We demonstrate through extensive simulations that this methodology reduces the bias of the regression estimate and correctly identifies good surrogate markers more often than the naive approach. An application evaluating CD4 count as a surrogate of disease progression in an AIDS clinical trial is presented.

Acquired Immunodeficiency Syndrome↗
PubMed1981

A neural-counting model incorporating refractoriness and spread of excitation. II. Application to loudness estimation.

In previous paper [Teich and Lachs, J. Acoust. Soc. Am 66, 1738--1749 (1979)] we demonstrated that an energy-based neural counting model incorporating refractoriness and spread of excitation satisfactorily described the results of pure-tone intensity discrimination experiments. In this paper, we show that the identical linear filter refractoriness model (LFRM) also provides proper results for pure-tone loudness estimation experiments at all stimulus levels. In particular, as the stimulus intensity increases from very low to moderate values, the model predicts that the slope of the intensity discrimination curve will climb from 1/2 toward 1, whereas the slope of the loudness function will gradually decline below 1 in this same region. For sufficiently high values of the stimulus intensity, the slopes calculated from a simplified (crude saturation) version of the model are found to be 1--1/4N for the intensity discrimination curve and 1/2N for the loudness function. The quantity N is the number of poles associated with the tuned-filter characteristic of the individual neural channels; it is the only important free parameter in the model. Appropriate values for N appear to lie between 2 and 4, providing an asymptotic slope for the intensity discrimination curve bounded by 7/8 and 15/16 (the near miss to Weber's Law), and an asymptotic slope for the loudness function bounded by 1/4 and 1/8. The results follow from the assumption that the neural concomitant of loudness is the number of impulses observed on a collection of parallel neural channels during a fixed observation time. Our calculations are supported by Hellman and Zwislocki's [J. Acoust. Soc. Am. 33, 687--694 (1961)] observation of unit slope for the loudness function at low intensities and provide a theoretical foundation, based on spread of excitation, for Stevens' power law at high intensities.

Differential Threshold↗
PubMed2006

On counting position weight matrix matches in a sequence, with application to discriminative motif finding.

MOTIVATION AND RESULTS: The position weight matrix (PWM) is a popular method to model transcription factor binding sites. A fundamental problem in cis-regulatory analysis is to "count" the occurrences of a PWM in a DNA sequence. We propose a novel probabilistic score to solve this problem of counting PWM occurrences. The proposed score has two important properties: (1) It gives appropriate weights to both strong and weak occurrences of the PWM, without using thresholds. (2) For any given PWM, this score can be computed while allowing for occurrences of other, a priori known PWMs, in a statistically sound framework. Additionally, the score is efficiently differentiable with respect to the PWM parameters, which has important consequences for designing search algorithms. The second problem we address is to find, ab initio, PWMs that have high counts in one set of sequences, and low counts in another. We develop a novel algorithm to solve this "discriminative motif-finding problem", using the proposed score for counting a PWM in the sequences. The algorithm is a local search technique that exploits derivative information on an objective function to enhance speed and performance. It is extensively tested on synthetic data, and shown to perform better than other discriminative as well as non-discriminative PWM finding algorithms. It is then applied to cis-regulatory modules involved in development of the fruitfly embryo, to elicit known and novel motifs. We finally use the algorithm on genes predictive of social behavior in the honey bee, and find interesting motifs. AVAILABILITY: The program is available upon request from the author.

Algorithms↗
PubMedDate not supplied

Application of pulse mixing method in software coincidence counting.

In recent years the software coincidence counting system, designed for absolute activity measurement, has been developed in the Czech Metrology Institute. In this system a true coincidence count rate is calculated from the records of time and amplitude data of individual pulses and may be determined by two different methods. The first one uses a coincidence resolving time, in a manner similar to a classical coincidence measurement. The second method applies the pulse mixing method formulae, so that it does not use the resolving time and the correction for accidental coincidences. Both methods have been tested on the same data from a 4pibeta (PC)-gamma coincidence measurement of 60Co sources. The difference between the results obtained from both calculation methods applied on the data from the same measurement did not exceed 0.015%. The details of both methods and the results of their comparison are presented.

Algorithms↗
PubMed2003

Development and application of a monoclonal-antibody technique for counting Aureococcus anophagefferens, an alga causing recurrent brown tides in the Mid-Atlantic United States.

A method was developed for the rapid detection and enumeration of Aureococcus anophagefferens, the cause of harmful algal blooms called "brown tides" in estuaries of the Mid-Atlantic United States. The method employs a monoclonal antibody (MAb) and a colorimetric, enzyme-linked immunosorbent assay format. The MAb obtained exhibits high reactivity with A. anophagefferens and very low cross-reactivities with a phylogenetically diverse array of other protists and bacteria. Standard curves are constructed for each 96-well microtiter plate by using known amounts of a preserved culture of A. anophagefferens. This approach allows estimation of the abundance of the alga in natural samples. The MAb method was compared to an existing method that employs polyclonal antibodies and epifluorescence microscopy and to direct microscopic counts of A. anophagefferens in samples with high abundances of the alga. The MAb method provided increased quantitative accuracy and greatly reduced sample processing time. A spatial survey of several Long Island estuaries in May 2000 using this new approach documented a range of abundances of A. anophagefferens in these bays spanning nearly 3 orders of magnitude.

Animals↗
PubMed1976

[Application of a truncated Poisson distribution for the counting of virus plaques by micromethod. Variation of its relative inaccuracy].

The microculture plaque titration of virus shows an important disadvantage : the reduction of the areas observation brings out plaque convergence and prevents from their exact enumeration. Nevertheless, a method, proposed by Moore, enables the estimation of virus title. The influence of the dilution and repetition factors on the title precision has been investigated. Two examples are treated.

Methods↗
PubMedDate not supplied

New stereological methods for counting neurons.

The issue of whether or not neurons die with age is of fundamental importance for understanding senescent decline in motor, sensory, and cognitive functions. Yet after over 100 years of attempts to quantify age-related neuron loss, this fundamental issue is "swirling in controversy" and the results of numerous studies addressing this issue "rife with confusion and seemingly contradictory data" (7). This is in large part due to deficiencies in the way we have thought about what constitutes evidence for neuron loss and deficiencies in the methods that have been available for counting neurons. Over the past several years, a new generation of stereological principles have been developed that have made it possible to identify and eliminate these deficiencies. Although there are now a number of review articles that briefly describe these and other new stereological principles (4,9,13,14,15,18,23), for the most part detailed descriptions of the new principles for counting neurons are found in specialized literature and are accompanied by new terms and concepts that have overwhelmed potential users and inhibited their adoption. In this essay, I describe the principles and concepts that are involved in the new stereological approach to neuron counting and discuss why the data obtained from their application represent improvements over those obtained with previously available techniques. A practical guide to the application of the principles to counting neurons or any other cell, organelle, or object present in sectioned material has been included as an appendix.

Aging↗
PubMed1999

Application and Quantitative Validation of Computer-Automated Three-Dimensional Counting of Cell Nuclei.

: This study provides a quantitative validation of qualitative automated three-dimensional (3-D) analysis methods reported earlier. It demonstrates the applicability and quantitative accuracy of our method to detect, characterize, and count Feulgen stained cell nuclei in two tissues (hippocampus and testes). These methods can provide important insights into the interpretation of biological, pharmacological, pathological, and toxicological events. A laser-scanned confocal light microscope was used to record 3-D images in which our algorithms automatically identified individual nuclei from the optical sections given an estimate of minimum nuclear size. The hippocampal data sets were also manually counted independently by five trained observers using the STERECON 3-D image reconstruction system. The automated and manual counts were compared. The computer counts were lower ( approximately 14%) than the manual counts, mainly because the algorithms counted a nucleus only if it was present in five consecutive optical sections but the human counters included nuclei that were in fewer optical sections. A nucleus-by-nucleus comparison of the manual and automated counts verified that the automated analysis was accurate and reproducible, and permitted additional quantitative analyses not available from manual methods. The algorithms also identified subpopulations of nuclei within the hippocampal samples, and haploid and diploid nuclei in the testes. Our methods were shown to be repeatable, accurate, and more consistent than manual counting. Nuclei in regions of high (hippocampal pyramidal layer) and low (extrapyramidal layer) density were distinguished with equal ease. Haploid and diploid nuclei were distinguished in the testes, demonstrating that our automated method may be useful for ploidy analysis. The results presented here on hippocampus and testis are consistent with other qualitative results from the liver and from immunohistochemically labeled substantia nigra, demonstrating the applicability of our software across tissues and preparation methods.

Journal Article↗