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PubMed1995

The cytopathology of proliferative breast disease. Comparison with features of ductal carcinoma in situ.

Epithelial hyperplasia, a component of proliferative breast disease (PBD), is a known risk factor for the development of breast carcinoma. To determine if criteria established for tissue biopsy could be used to more precisely define cytologic criteria for diagnosis of PBD, 37 breast fine-needle aspirates with biopsy diagnoses of PBD were studied. In cases with adequate cellularity, the following findings were consistently observed: (1) three-dimensional cell clusters with outlying myoepithelial cells, swirling intralumenal masses and peripheral, slit-like, irregular sublumens (65% of cases); (2) convoluted sheets of ductal epithelium with outlying myoepithelial cells and bulbous projections tethered to the ductal lining (29%); and (3) a background of discohesive small frayed groups of ductal cells (32%). Of the 15 cases that did not meet these criteria, most were paucicellular (87%), which suggested sampling error. Other cytologic features that were observed included: moderately increased cellularity (20 cases), moderate-to-marked nuclear overlap (14 cases), minimal nuclear atypia, and few single epithelial cells. Fifteen cases of confirmed ductal carcinoma in situ were studied for comparison. In these cases, cellularity, nuclear overlap, and atypia were increased, but swirling intralumenal masses, prominent myoepithelial cells and slit-like lumens were absent. In conclusion, the features of PBD established for tissue biopsy can be applied to cytologic specimens, and may provide useful clues to the diagnosis of epithelial hyperplasia in breast fine-needle aspiration specimens.

Adult↗
PubMed1996

Secondary pericardial malignancies: a critical appraisal of the role of cytology, pericardial biopsy, and DNA ploidy analysis.

The authors studied 112 pericardial fluids (45 malignant, and 67 benign) from 63 men and 33 women. All cytologic (n = 112) and histologic (n = 61) specimens were reviewed. Statistical analysis was conducted in 61 paired cytology and histology specimens (45 malignant and 16 benign) and correlated with available ploidy analysis of fluid specimens (n = 34). In cases of malignancy (41 patients), the primary site was known in 34 patients, whereas no origin for metastatic disease was apparent in 3 patients. Pericardial cytology yielded the initial diagnosis in four patients. After careful review of all cytology and histology specimens, seven truly discrepant cases were noted, six of which had positive cytology. Tissue biopsy sampling error was the cause for such discrepancies. DNA diploidy obtained by flow cytometry correlated with benign cytology, whereas aneuploidy was associated with malignant cytology in a total of 32 of 34 cases (94%). Cytologically malignant effusions rendered diploid DNA in 2 of 10 cases (20%). In conclusion, cytology is the single most important parameter in the evaluation of secondary pericardial malignancy and should be considered the gold standard. Causes for false-negative cytologic diagnoses include scant cellularity and obscuring blood. Hence, careful screening is recommended. The low sensitivity of flow cytometric DNA analysis does not favor its routine use.

Adolescent↗
PubMed1998

Diagnostic value of brush cytology in the diagnosis of duodenal, biliary, and ampullary neoplasms.

Endoscopy is a valuable tool in the diagnosis and management of duodenal lesions and biliary strictures. We assessed the value of cytology in the evaluation of these lesions and analyzed the causes of discrepancy among clinical, histologic, and cytologic parameters. The study included 118 patients with duodenal ulcers, ampullary neoplasms, or biliary strictures who were examined between 1975 and 1995; 120 cytologic examinations were performed. The specimens included brushings of the duodenum (DB, n = 50), ampulla (AB, n = 32), and biliary ducts (BB, n = 38). Endoscopic biopsies performed concurrently included the duodenum (n = 37), the ampulla (n = 22), and the biliary ducts (n = 23). Comparison of cytologic and histologic results showed the following sensitivity and specificity: DB, 40% and 97%, respectively; AB, 100% each; BB, 75% and 93%, respectively. The DB, AB, and BB revealed malignant neoplasms in 2 of 5, 7 of 7, and 6 of 8 cases, respectively. Twenty-three duodenal neoplasms were diagnosed by either modality and included 11 adenocarcinomas, 9 villous tumors, 2 metastatic renal cell carcinomas, and 1 large cell non-Hodgkin's lymphoma. Endoscopic brush cytology is an effective means of diagnosing ampullary neoplasms, and it complements tissue biopsy in cases of bile duct stricture. Location, predominance of tumor-induced stroma, an extramucosal growth pattern, sampling error, and interpretative experience influence the diagnostic evaluation. Cytologic diagnosis of an adenoma does not exclude an underlying malignant neoplasm in ampullary tumors. In some instances, it may be difficult to distinguish between villous tumors with severe dysplasia and adenocarcinomas by cytology alone.

Adenocarcinoma↗
PubMed1999

How reliable is histologic examination of bone marrow trephine biopsy specimens for the staging of non-Hodgkin lymphoma? A study of hairy cell leukemia and mantle cell lymphoma involvement of the bone marrow trephine specimen by histologic, immunohistochemical, and polymerase chain reaction techniques.

Analysis of non-Hodgkin lymphoma (NHL) involvement of bone marrow trephine biopsy specimens by morphologic features and immunohistochemistry is often difficult, and the criteria for involvement are ill defined. We compared the morphologic and immunohistochemical analysis of B-cell NHL involvement with immunoglobulin heavy chain gene (IgH) rearrangement analysis by polymerase chain reaction (PCR) amplification of the complementarity determining region 3 (CDR3) in bone marrow biopsy specimens from patients with mantle cell lymphoma (n = 53) or hairy cell leukemia (n = 71). By combing morphologic features and phenotype, 54 specimens were considered positive, 62 negative, and 8 inconclusive. PCR analysis showed clonal IgH rearrangements in 46 positive and 6 inconclusive specimens. No clonal IgH rearrangements were present in 61 negative specimens. The 1 false-positive and most false-negative PCR results were likely due to sampling error or DNA degradation of the fixed tissues. In most cases, bone marrow involvement by NHL can be identified by histologic and immunohistochemical examination. Furthermore, clonality of the B-cell population can be detected by amplification of the IgH CDR3 on DNA extracted from bone marrow trephine biopsy sections, which can be helpful in cases diagnosed as inconclusive.

Bone Marrow Examination↗
PubMed1979

In-vitro methods for determining minimal lethal concentrations of antimicrobial agents.

To determine the minimal lethal concentration of an antimicrobial agent, broth dilution tests may be performed and then a sample from each tube showing no visible growth may be subcultured onto a drug-free agar medium. By counting the number of viable cells recovered from each tube, the minimal concentration of drug required to kill 99.9% of the cells in the initial inoculum can be determined. Studies were undertaken to determine the circumstances under which false-negative tests could occur as a result of continued inhibition of growth by the antimicrobic carried over in the sample. Drug carryover did significantly reduce the number of viable cells recovered from broth containing relatively high concentrations of antimicrobic: the larger the sample, the greater the effect of drug carryover. The effect was minimal with samples of 10 microliter or less. Furthermore, the effect of drug carryover was reduced by spreading the sample over the surface of an agar medium. The relative precisions of four methods for performing subcultures with such small-volume samples were determined; coefficients of variation were 16-25%. Sampling errors inherent in the procedure for subculturing broth tubes should be taken into consideration when interpreting results of individual tests, and replicate subcultures will improve the reliability of the colony counts.

Enterococcus faecalis↗
PubMed1984

Transthoracic fine-needle aspiration cytology. Analysis of 82 patients with detailed verification criteria and evaluation of false-negative cases.

The authors herein report a series of transthoracic fine-needle aspiration cytology studies performed over a ten-year period at a medical center. The verification criteria they utilized for "positive" and " nonpositive " results are unique to the TFNA literature, as is the authors' detailed analysis of false-negative cases. The authors' statistical findings included specificity, 100%; sensitivity, 79.0%; and overall accuracy, 83.0%. Eleven of 13 false-negative studies (84.6%) were consequent to sampling error; the remaining two cases (both "suspects") were the result of cytopathologist judgment error. In those patients with tissue corroboration of their lung disease, the authors obtained a 93.8% concordance rate between cytology and histology results. They conclude that uniform verification criteria, as well as careful analysis of "suspects" and false negatives, can lead to better patient care through improved quality control.

Adult↗
PubMed1987

Detection of estrogen receptors with monoclonal antibodies in routinely processed formalin-fixed paraffin sections of breast carcinoma. Use of DNase pretreatment to enhance sensitivity of the reaction.

This study describes an improved immunohistochemical method for the sensitive and specific identification of estrogen receptors (ERs) in paraffin sections from formalin-fixed and routinely processed breast carcinoma tissues, using DNase pretreatment to expose nuclear antigenic sites and commercially available immunoreagents (including monoclonal antibody) in kit form. Results were compared with dextran-coated charcoal cytosolic assay (DCC) and with conventional immunohistochemistry on frozen sections. Sensitivity and specificity for determinations on paraffin sections were 88% and 86%, respectively, and statistical analysis showed very good agreement between DCC and paraffin sections (kappa = 0.805). The DNase technic on paraffin sections allows excellent correlation between histologic characteristics and ER status and reduces DCC sampling error resulting from stromal dilution and tumor variability. This method offers a reliable and reproducible alternative when tissue is not suitable or unavailable for DCC or frozen tissue analysis and can be used for retrospective studies on stored tissue blocks.

Antibodies, Monoclonal↗
PubMed1990

A prospective comparison of DNA quantitation by image and flow cytometry.

Advances in computer and video technology suggest that image analysis may be practical method of measuring DNA that also allows visual confirmation of cell type. The purpose of this study was to prospectively compare DNA quantitation from 92 solid tumors in which DNA indices had been measured by image analysis of touch preparations (CAS 100) and flow cytometry of cell suspensions (FACScan). For 81 cases, there was excellent correlation between the two methods. For nine cases, however, an aneuploid population, usually near tetraploid, was identified by image but not by flow cytometry. Three cases had aneuploid peaks by flow cytometry that were not identified by image. Although these methods show good correlation, rare populations may be missed by CAS, presumably because of sampling errors in the touch preparation. Aneuploid populations may also be missed by flow cytometry, either because of cell loss during processing or because visual identification by image can increase sensitivity.

Adenocarcinoma↗
PubMed1994

Effect of atrial natriuretic hormone on hypertonic saline-induced suppression of the renin-aldosterone system.

To evaluate the effect of physiologic doses of atrial natriuretic hormone (ANH) on hypertonic saline-induced renin-aldosterone system suppression, nine healthy subjects were studied three times: 1) on a low-salt (LS) diet with a 2 h placebo infusion; 2) on LS with 2 h infusion of human Ser-Tyr28 ANH (0.6 pmol/kg/min)(LS+ANH); and 3) on a high-salt (HS) diet with a 2 h placebo infusion. On each study day during the second hour of infusion, subjects also received 3% saline (0.1 mL/kg/min) infusion. Data from eight subjects were used for analysis because of a sampling error in one subject. During ANH infusion, plasma ANH levels increased about twofold and reached levels similar to ANH levels on HS. Serum sodium increased by 3-4 mEq/L, and serum osmolality increased by 7-8 mOsm/L during 3% saline infusion on all study days. ANH levels remained stable during 3% saline infusion. During the first hour of ANH infusion, plasma renin activity (PRA) decreased by about 24% and aldosterone levels by about 27%. Hypertonic saline caused further suppression of PRA and aldosterone. The extent of the suppression was similar under each condition, and the levels at the end of hypertonic saline infusion reached about 60% of the levels at the beginning of the saline infusion. We conclude that low-dose ANH infusion does not seem to have any major influence on PRA and aldosterone response to hypertonic saline.

Adult↗
PubMed1989

Adipose dysplasia of the right ventricle: is endomyocardial biopsy useful?

Right ventricular dysplasia (RVD) is a cardiac anomaly characterized by replacement of right ventricular myocardium by adipose and fibrous tissue that was first described at autopsy, and is now being recognized pre-mortem. Sudden death and ventricular arrhythmias are the most common clinical manifestation of the condition. This paper reviews the literature on myocardial biopsies performed in patients with idiopathic arrhythmias who had pathologic findings consistent with RVD, and the results of biopsies from patients suspected of having RVD. The significance of sampling error in myocardial biopsies, possible familial associations, and other conditions associated with myocardial adipose infiltration are also discussed. Based on the review, the possibility is raised that RVD may represent the end result of an unusual healing process, whereby genetically susceptible individuals recover from a variety of RV insults by deposition of adipose tissue. These fatty scars may then be the focus for arrhythmias which remain the major clinical manifestation of the syndrome.

Adipose Tissue↗
PubMed1988

The use of endomyocardial biopsy in heart failure.

Endomyocardial biopsy in this study of 1250 biopsied patients (mean of five samples/patient) proved to be a remarkably safe technique with no lethal complications. It may help to detect the underlying cause of heart failure but is handicapped by sampling error in focal disease processes (such as myocarditis and sarcoid heart disease) when conventional light and electron microscopy are used. In this biopsy series 123 patients (9.8%) suffered from severe heart failure; lymphocytic infiltrates were found in only 10 (8%). Immunohistological data suggested a secondary humoral immunopathogenesis in all patients with myocarditis and perimyocarditis, in 75% of patients with postmyocarditic heart muscle disease and in 48% of patients with primary dilated cardiomyopathy. There may thus be a need for a new classification of heart muscle diseases that includes immunological parameters of humoral and cellular autoreactivity.

Biopsy↗
PubMed1985

Gene conversion at the gray locus of Sordaria fimicola: fit of the experimental data to a hybrid DNA model of recombination.

A hybrid DNA (hDNA) model of recombination has been algebraically formulated, which allows the prediction of frequencies of postmeiotic segregation and conversion of a given allele and their probability of being associated with a crossing over. The model considered is essentially the "Aviemore model." In contrast to some other interpretations of recombination, it states that gene conversion can only result from the repair of heteroduplex hDNA, with postmeiotic segregation resulting from unrepaired heteroduplexes. The model also postulates that crossing over always occurs distally to the initiation site of the hDNA. Eleven types of conversion and postmeiotic segregation with or without associated crossover were considered. Their theoretical frequencies are given by 11 linear equations with ten variables, four describing heteroduplex repair, four giving the probability of hDNA formation and its topological properties and two giving the probability that crossing over occurs at the left or right of the converting allele. Using the experimental data of Kitani and coworkers on conversion at the six best studied gray alleles of Sordaria fimicola, we found that the model considered fit the data at a P level above or very close (allele h4) to the 5% level of sampling error provided that the hDNA is partly asymmetric. The best fitting solutions are such that the hDNA has an equal probability of being formed on either chromatid or, alternatively, that both DNA strands have the same probability of acting as the invading strand during hDNA formation. The two mismatches corresponding to a given allele are repaired with different efficiencies. Optimal solutions are found if one allows for repair to be more efficient on the asymmetric hDNA than on the symmetric one. In the case of allele g1, our data imply that the direction of repair is nonrandom with respect to the strand on which it occurs.

Alleles↗
PubMed1990

Analysis of the inheritance, selection and evolution of growth trajectories.

We present methods for estimating the parameters of inheritance and selection that appear in a quantitative genetic model for the evolution growth trajectories and other "infinite-dimensional" traits that we recently introduced. Two methods for estimating the additive genetic covariance function are developed, a "full" model that fully fits the data and a "reduced" model that generates a smoothed estimate consistent with the sampling errors in the data. By decomposing the covariance function into its eigenvalues and eigenfunctions, it is possible to identify potential evolutionary changes in the population's mean growth trajectory for which there is (and those for which there is not) genetic variation. Algorithms for estimating these quantities, their confidence intervals, and for testing hypotheses about them are developed. These techniques are illustrated by an analysis of early growth in mice. Compatible methods for estimating the selection gradient function acting on growth trajectories in natural or domesticated populations are presented. We show how the estimates for the additive genetic covariance function and the selection gradient function can be used to predict the evolutionary change in a population's mean growth trajectory.

Animals↗
PubMed1995

Methodology and accuracy of estimation of quantitative trait loci parameters in a half-sib design using maximum likelihood.

Maximum likelihood methods were developed for estimation of the six parameters relating to a marker-linked quantitative trait locus (QTL) segregating in a half-sib design, namely the QTL additive effect, the QTL dominance effect, the population mean, recombination between the marker and the QTL, the population frequency of the QTL alleles, and the within-family residual variance. The method was tested on simulated stochastic data with various family structures under two genetic models. A method for predicting the expected value of the likelihood was also derived and used to predict the lower bound sampling errors of the parameter estimates and the correlations between them. It was found that standard errors and confidence intervals were smallest for the population mean and variance, intermediate for QTL effects and allele frequency, and highest for recombination rate. Correlations among standard errors of the parameter estimates were generally low except for a strong negative correlation (r = -0.9) between the QTL's dominance effect and the population mean, and medium positive and negative correlations between the QTL's additive effect and, respectively, recombination rate (r = 0.5) and residual variance (r = -0.6). The implications for experimental design and method of analysis on power and accuracy of marker-QTL linkage experiments were discussed.

Alleles↗
PubMed1996

Molecular genetics of rust resistance in poplars (Melampsora larici-populina Kleb/Populus sp.) by bulked segregant analysis in a 2 x 2 factorial mating design.

With random amplified polymorphic DNA (RAPD) markers, we have tagged a genomic region in Populus sp. involved in qualitative resistance to Melampsora larici-populina. Our approach was based on three steps: use of RAPD markers that can be quickly and efficiently researched: application of "bulked segregant analysis" technique on individuals of one interspecific family P. trichocarpa x P. deltoides to search for RAPD markers linked to resistance; and validation of these markers in two other families linked with the first one in a 2 x 2 factorial mating design. Of five detected markers, only one marker M03/04_480 was polymorphic in the three segregating families, involving 89 individuals and four different parents. We have estimated the recombination value of 1 cM with 1 cM sampling error.

Basidiomycota↗
PubMed1996

On the potential for estimating the effective number of breeders from heterozygote-excess in progeny.

The important parameter of effective population size is rarely estimable directly from demographic data. Indirect estimates of effective population size may be made from genetic data such as temporal variation of allelic frequencies or linkage disequilibrium in cohorts. We suggest here that an indirect estimate of the effective number of breeders might be based on the excess of heterozygosity expected in a cohort of progeny produced by a limited number of males and females. In computer simulations, heterozygote excesses for 30 unlinked loci having various numbers of alleles and allele-frequency profiles were obtained for cohorts produced by samples of breeders drawn form an age-structured population and having known variance in reproductive success and effective number. The 95% confidence limits around the estimate contained the true effective population size in 70 of 72 trials and the Spearman rank correlation of estimated and actual values was 0.991. An estimate based on the heterozygote excess might have certain advantages over the previous estimates, requiring only single-locus and single-cohort data, but the sampling error among individuals and the effect of departures from random union of gametes still need to be explored.

Breeding↗
PubMed2004

Laboratory testing policies and their effects on routine surveillance of community antimicrobial resistance.

OBJECTIVE: To investigate the effects of laboratory testing policies, particularly selective testing, rule-based reporting and isolate identification, on estimates of community antimicrobial resistance. MATERIALS AND METHODS: Antibiotic resistance estimates were analysed from an all-Wales dataset for approximately 300 000 community isolates of common pathogens. RESULTS: Selective testing policies were often associated with markedly increased resistance, particularly for second-line testing. Site-specific testing tended to yield variant resistance estimates for eye and ear isolates. Estimates from rule-based reporting deviated markedly from test-result-based reporting. Urinary isolates reported as Escherichia coli showed greater susceptibility than those reported as undifferentiated urinary 'coliforms'. The proportion of isolates tested for an antibiotic by a laboratory was a useful indicator of selective testing in this dataset. Selective testing policies had invariably been applied where the proportion of isolates of a species tested against an antibiotic was <90%. As this proportion fell with increasingly selective policies, divergence from pooled-all-Wales non-selective estimates tended to increase, with a bias to increased resistance. CONCLUSIONS: Selective testing, rule-based reporting and urinary coliform identification policies all had significant effects upon resistance estimates. Triage based upon the proportion of isolates tested seemed a useful tool in assigning analysis resources. Where <20% of isolates were tested, selective policies with inherent bias to increased resistance were common, the low number of isolates gave high potential sampling errors, and little confidence could be placed in the resistance estimate. Where 20-90% of isolates were tested, detailed analysis sometimes revealed resistance estimates that might be usefully retrieved. Where >/=90% of isolates were tested, there was no evidence of selective testing, and inter-laboratory variation in estimates appeared to be safely ascribable to other effects, e.g. methodology or real variation in resistance levels.

Anti-Bacterial Agents↗
PubMed2005

Bayes empirical bayes inference of amino acid sites under positive selection.

Codon-based substitution models have been widely used to identify amino acid sites under positive selection in comparative analysis of protein-coding DNA sequences. The nonsynonymous-synonymous substitution rate ratio (d(N)/d(S), denoted omega) is used as a measure of selective pressure at the protein level, with omega > 1 indicating positive selection. Statistical distributions are used to model the variation in omega among sites, allowing a subset of sites to have omega > 1 while the rest of the sequence may be under purifying selection with omega < 1. An empirical Bayes (EB) approach is then used to calculate posterior probabilities that a site comes from the site class with omega > 1. Current implementations, however, use the naive EB (NEB) approach and fail to account for sampling errors in maximum likelihood estimates of model parameters, such as the proportions and omega ratios for the site classes. In small data sets lacking information, this approach may lead to unreliable posterior probability calculations. In this paper, we develop a Bayes empirical Bayes (BEB) approach to the problem, which assigns a prior to the model parameters and integrates over their uncertainties. We compare the new and old methods on real and simulated data sets. The results suggest that in small data sets the new BEB method does not generate false positives as did the old NEB approach, while in large data sets it retains the good power of the NEB approach for inferring positively selected sites.

Alleles↗