Reproducibility of coccolith morphometry: Evaluation of spraying and smear slide preparation techniques

It is of great importance to assess the internal accuracy and reproducibility of coccolith morphometry, and to understand any systematic differences between various sample preparation techniques, so that data obtained with different methods can be adequately compared. Here, we performed a comparative study between two techniques regularly used to prepare nannofossil microscope slides, the standard smear slide and spraying methods. With each technique, ten replicate slides were prepared and morphometric measurements were carried out on the coccolith genus Calcidiscus as well as full assemblage counts to determine the reproducibility of coccolith size measurements and relative species abundances for each method.For either method, two significant sources of variance are related to the morphometric data, the variance between replicate slides and the variance within slides. Thus, in order to reduce the total variance of the estimate of mean coccolith size, it is beneficial to increase the number of replicate slides as well as the number of measurements on each slide. If the aim of the morphometric study is to address the mean size of a coccolith taxon or species complex (a group of closely related sub-species), one could rely on either preparation technique, since no significant difference in (log-normalised) mean size between the two tested methodologies was found. Likewise, the 10th percentiles are statistically equal for both methods. However, the 90th percentile values are significantly larger in the sprayed slides than in the smear slides, indicating that the spraying method may either favour larger coccoliths or better resolve the full extent of size variability present in the sample. Future tests are needed to investigate whether, and if so, how, size-fractionation may occur when using the spraying method. Nevertheless, the spraying method is preferred based on the reproducibility of proportion estimates since no significant difference between replicate samples was observed, in stark contrast to the smear slide series with 3–4 times higher variance. It appears that information gained from one sprayed slide requires counting at least three replicate smear slides.     

Minimal sample requirement for highly multiplexed protein quantification in cell lines and tissues by PCT‐SWATH mass spectrometry

The amount of sample available for clinical and biological proteomic research is often limited and thus significantly restricts clinical and translational research. Recently, we have integrated pressure cycling technology (PCT) assisted sample preparation and SWATH‐MS to perform reproducible proteomic quantification of biopsy‐level tissue samples. Here, we further evaluated the minimal sample requirement of the PCT‐SWATH method using various types of samples, including cultured cells (HeLa, K562, and U251, 500 000 to 50 000 cells) and tissue samples (mouse liver, heart, brain, and human kidney, 3–0.2 mg). The data show that as few as 50 000 human cells and 0.2–0.5 mg of wet mouse and human tissues produced peptide samples sufficient for multiple SWATH‐MS analyses at optimal sample load applied to the system. Generally, the reproducibility of the method increased with decreasing tissue sample amounts. The SWATH maps acquired from peptides derived from samples of varying sizes were essentially identical based on the number, type, and quantity of identified peptides. In conclusion, we determined the minimal sample required for optimal PCT‐SWATH analyses, and found smaller sample size achieved higher quantitative accuracy.     

Effect of sample size on reproducibility of behavioral teratological study results: a computer simulation experiment using data from the Collaborative Behavioral Teratology Study of the National Center for Toxicological Research

A computer simulation experiment which attempted to examine the effect of sample size on reproducibility of the effect of treatment was performed on the basis of actual data obtained from the Collaborative Behavioral Teratology Study of the National Center for Toxicological Research. The degree of the treatment effect was assessed in terms of the strength of the association (eta square). The results indicate that sample size has a large effect on the reproducibility of results which are assessed with the magnitude of SD for eta squares obtained from replication experiments. Suitable sample sizes to obtain relatively consistent results across studies were discussed, pointing out that not enough attention has been paid to the effect of sample size in the issue of reproducibility of results in some behavioral teratology studies.     

Comparison of two preparation methods for endocervical evaluation

OBJECTIVE: To assess the validity of SurePath liquid-based preparation method for examination of endocervical brush specimens as a substitute for conventionally prepared cytology methods for evaluating the endocervical canal during colposcopic examination and biopsy. STUDY DESIGN: Paired SurePath liquid-based test slides and conventional smears were obtained using an endocervical brush in a split sample protocol before biopsy at the time of colposcopy. The level of agreement between cytologic results obtained was assessed. Accuracy and operating characteristics were evaluated compared to histologic follow-up. RESULTS: Agreement between cytology results for the methods was excellent. The overall kappa was 0.924 (p = 0.0000). There was exact agreement on interpretation between the methods in 283 of 299 cases (94.6%). Cytohistologic follow-up results correlation were: SurePath liquid-based Pap test results and conventional smear results agreed with histology results in 47.8% and 49.2% of cases, respectively. Allowing for a discrepancy within 1 level of severity of cytologic grade, agreements were 76.6% and 77.2%, respectively. CONCLUSION: This study demonstrates that the SurePath method is equivalent to conventional endocervical brush cytology preparation and performs well for detection of cervical intraepithelial lesions and cancer. SurePath is acceptable for endocervical evaluation as a substitute for endocervical curettage at colposcopic biopsy.     

Rapid stereology based quantitative immunohistochemistry of dendritic cells in lymph nodes: a methodological study.

This study was done to arrive at a fast and reliable protocol for assessment of fractional volumes of immunohistochemically stained dendritic cells in lymph nodes. Twenty axillary lymph nodes of patients with locally advanced breast cancer were immuno-histochemically stained with an S100 antibody. Fractional volumes of dendritic cells were assessed by stereology based quantitative immunohistochemistry using an interactive video overlay system including an automated microscope. The gold standard percentage of dendritic cells was the fractional volume of S100 stained cells in 500 fields systematically spread over the whole lymph node. Then, in a computer simulation, different sample sizes (1-200 fields of vision) were tested and the coefficient of variation (CV) for each sample size was calculated. The CV dropped with increasing sample size. A sample size of 100 fields of vision appeared to be optimal. Intra- and interobserver reproducibility appeared to be good (correlation coefficients of 0.95 and 0.86, respectively) when re-analyzing the cases with the established protocol.In conclusion, a fast and reliable assessment of the fractional volume of dendritic cells in lymph nodes is possible with semi-automated quantitative immuno-histochemistry. This method will form the base for further clinical studies into the immunological response in lymph nodes of patients with locally advanced breast cancer.     

Flow cytometric and histomorphometric analysis of limitations of clinical breast cytomorphometry

The clinical value and limitations of a previously described cytomorphometric method, based on nuclear size and anisonucleosis, for evaluation of routine fine-needle aspiration of the breast were assessed in a series of 313 histologically investigated primary breast lesions. Limitations were analyzed by histomorphometry and DNA flow cytometry in 116 consecutive cases of histologically confirmed breast carcinoma. Eighty per cent of histologically proven malignant tumours were classified cytomorphometrically as malignant and no false-positive results were encountered. For benign lesions a benign cytomorphometric classification was reached in 66% of the cases. Histomorphometry showed that on the whole the assignment of histologically malignant tumours to a non-malignant cytomorphometric classification was determined by smaller nuclei and not by sampling error. Tumours assigned to a malignant cytomorphometric classification had on average significantly higher DNA indices than did tumours not assigned to a malignant cytomorphometric classification (P less than 0.001). The mean-nuclear areas in cytomorphometry and histomorphometry were strongly correlated with DNA indices indicated by DNA flow cytometry (P less than 0.001 for both). The present findings show that this cytomorphometric method is appropriate for routine quality control of a cytological diagnosis of malignancy in FNA of the breast. However, an inconclusive result in 15-25% of the tumours is inevitable.     

Use of High-Frequency In-Home Monitoring Data May Reduce Sample Sizes Needed in Clinical Trials

Background

Trials in Alzheimer’s disease are increasingly focusing on prevention in asymptomatic individuals. This poses a challenge in examining treatment effects since currently available approaches are often unable to detect cognitive and functional changes among asymptomatic individuals. Resultant small effect sizes require large sample sizes using biomarkers or secondary measures for randomized controlled trials (RCTs). Better assessment approaches and outcomes capable of capturing subtle changes during asymptomatic disease stages are needed.

Objective

We aimed to develop a new approach to track changes in functional outcomes by using individual-specific distributions (as opposed to group-norms) of unobtrusive continuously monitored in-home data. Our objective was to compare sample sizes required to achieve sufficient power to detect prevention trial effects in trajectories of outcomes in two scenarios: (1) annually assessed neuropsychological test scores (a conventional approach), and (2) the likelihood of having subject-specific low performance thresholds, both modeled as a function of time.

Methods

One hundred nineteen cognitively intact subjects were enrolled and followed over 3 years in the Intelligent Systems for Assessing Aging Change (ISAAC) study. Using the difference in empirically identified time slopes between those who remained cognitively intact during follow-up (normal control, NC) and those who transitioned to mild cognitive impairment (MCI), we estimated comparative sample sizes required to achieve up to 80% statistical power over a range of effect sizes for detecting reductions in the difference in time slopes between NC and MCI incidence before transition.

Results

Sample size estimates indicated approximately 2000 subjects with a follow-up duration of 4 years would be needed to achieve a 30% effect size when the outcome is an annually assessed memory test score. When the outcome is likelihood of low walking speed defined using the individual-specific distributions of walking speed collected at baseline, 262 subjects are required. Similarly for computer use, 26 subjects are required.

Conclusions

Individual-specific thresholds of low functional performance based on high-frequency in-home monitoring data distinguish trajectories of MCI from NC and could substantially reduce sample sizes needed in dementia prevention RCTs.     

The preparation of additional smears from a cervical scrape: impact on the rate of detection of cervical neoplasia

The preparation of additional smears from a cervical scrape: impact on the rate of detection of cervical neoplasia It has been known for some time that only a proportion of the cells on the smear-taking device is transferred to the slide. This can give rise to errors in reporting although the smear may have been taken correctly. This study was undertaken to identify a quick and simple method of improving the accuracy of the Papanicolaou test. A conventional smear and five additional smears were obtained from 62 women attending a Genito-Urinary Medicine clinic. The cell content of the conventional smears and the additional smears was compared. Dyskaryotic cells were detected both in the conventional smear and in the first and second additional smears from 22 women. Dyskaryotic cells were detected in the first and second additional smears only in five women. Thus, the conventional smear failed to detect biopsy-confirmed cervical abnormality in these women. A cell count of the first additional smear in the five cases where the conventional smear was negative showed that they contained, on average, 310 dyskaryotic cells. The preparation of one additional cervical smear per cervical scrape could significantly increase the accuracy of the cervical smear test by 11% (P=0.025, McNemar's test).     

Induced sputum is a reproducible method to assess airway inflammation in asthma

To evaluate the reproducibility of induced sputum analysis, and to estimate the sample size required to obtained reliable results, sputum was induced by hypertonic saline inhalation in 29 asthmatic subjects on two different days. The whole sample method was used for analysis, and inflammatory cells were counted on cytospin slides. Reproducibility, expressed by intra-class correlation coefficients, was good for macrophages (+0.80), neutrophils (+0.85), and eosinophils (+0.87), but not for lymphocytes (+0.15). Detectable differences were 5.5% for macrophages, 0.6% for lymphocytes, 5.2% for neutrophils, and 3.0% for eosinophils. We conclude that analysis of induced sputum is a reproducible method to study airway inflammation in asthma. Sample sizes greater than ours give little improvement in the detectable difference of eosinophil percentages.     

Profile-likelihood inference for highly accurate diagnostic tests

We consider profile-likelihood inference based on the multinomial distribution for assessing the accuracy of a diagnostic test. The methods apply to ordinal rating data when accuracy is assessed using the area under the receiver operating characteristic (ROC) curve. Simulation results suggest that the derived confidence intervals have acceptable coverage probabilities, even when sample sizes are small and the diagnostic tests have high accuracies. The methods extend to stratified settings and situations in which the ratings are correlated. We illustrate the methods using data from a clinical trial on the detection of ovarian cancer.     

Mapping quantitative-trait loci in humans by use of extreme concordant sib pairs: selected sampling by parental phenotypes.

In two previous articles, we have considered sample sizes required to detect linkage for mapping quantitative-trait loci in humans, using extreme discordant sib pairs. Here, we examine further the use of extreme concordant sib pairs but consider the effect of parents' phenotypes. Sample sizes necessary to obtain a power of 80% with concordant sib pairs at a significance level of .0001 are given, stratified by parental phenotypes. When there is no residual correlation between sibs, the parental phenotypes have little impact on the sample sizes. When residual correlations between sibs exist, we show, however, that power can be considerably reduced by including extreme sib pairs when the parents also have similarly extreme values. Thus, we recommend the exclusion of such pairs from linkage studies. This recommendation reduces the required sample sizes by 3- to 28-fold. The degree of saving in the required sample sizes varies among different models and allele frequencies. The reduction is most dramatic (a 28-fold reduction) for a rare recessive gene.     

Cell block as an adjunct to conventional Papanicolaou smear for diagnosis of cervical cancer in resource-limited settings

OBJECTIVE: To assess the utility of indigenously prepared cell blocks (CBs) as an adjunct to a conventional smear test in providing a reliable diagnosis of clinically suspicious cervical cancer in resource-limited settings. METHODS: Eighty-six clinically suspicious cervical cancer cases underwent a conventional smear test, CB preparation from residual cellular samples and biopsies at the same sitting. Correlations were performed between these modalities in order to derive the sensitivity and specificity of the CB technique to diagnose cervical cancer. OBSERVATION & RESULTS: Out of 86 clinically suspicious cervical cancers, 72 (83.7%), 70 (81.4%) and 67 (77.9%) cases were diagnosed as malignant on tissue biopsies, CBs and smears respectively. CB-biopsy agreement in the diagnosis of malignancy was feasible in 87.5% of the cases while CB-Pap smear agreement was feasible in 92.5% of the cases. Sensitivity and specificity of CB preparation to diagnose malignancy was 92.5% and 100%, respectively, when the smear was taken as the reference test (excluding the unsatisfactory smears). When biopsy was taken as the gold standard, the sensitivity and specificity of CBs were 87.5% and 100% respectively (excluding the unsatisfactory biopsies). In 8/19 cases where the smear diagnoses were either unsatisfactory or atypical squamous cells/atypical glandular cells, CBs picked up malignant lesions. CONCLUSION: CBs prepared from the residual cellular sample of conventional cervical scrapes augment the sensitivity of the smear test. When used as an adjunct to the smear, CBs aid in providing a reliable diagnosis of cervical cancer in the majority of the clinically suspected cases and thus the biopsy load can be reduced significantly in resource-poor settings.     

A highly sensitive and accurate gene expression analysis by sequencing (“bead-seq”) for a single cell

Analyses of gene expressions in single cells are important for understanding detailed biological phenomena. Here, a highly sensitive and accurate method by sequencing (called “bead-seq”) to obtain a whole gene expression profile for a single cell is proposed. A key feature of the method is to use a complementary DNA (cDNA) library on magnetic beads, which enables adding washing steps to remove residual reagents in a sample preparation process. By adding the washing steps, the next steps can be carried out under the optimal conditions without losing cDNAs. Error sources were carefully evaluated to conclude that the first several steps were the key steps. It is demonstrated that bead-seq is superior to the conventional methods for single-cell gene expression analyses in terms of reproducibility, quantitative accuracy, and biases caused during sample preparation and sequencing processes.     

Sample Size Determination in Comparing Two Population Variances with Paired‐data: Application to Bilirubin Tests

Sample size needed by using paired‐data to compare two population variances is much smaller than that of using usual independent samples. In this paper, we proposed three parametric methods to compare two population variances with paired‐data. After comparing the powers of all three methods, we furnish the tables to indicate the least sample sizes required in various parameter values for the method with the largest power. The bilirubin example is used to illustrate the usefulness of the tables.     

Development and validation of a computerized cytomorphometric method to assess the maturation of vaginal epithelial cells

BACKGROUND: After menopause, declining levels of estrogens may cause vaginal discomfort, or so-called "vaginal atrophy." Evaluation of therapies for vaginal atrophy may be performed using the so-called "maturation index." The maturation index is expressed as the percentage of (para)-basal, intermediate, and superficial epithelial cells in a vaginal smear. Manual assessment of the maturation index is subject to inter- and intraobserver variations. In this study, assessment of the maturation of cells in vaginal smears using automated image analysis was investigated. MATERIALS AND METHODS: Automated assessment, using a commercially available image analysis system, was performed on hematoxylin-eosin-stained cytospin specimens. A training set was constructed by an experienced cytotechnologist, based upon visual classification of stored grey value images. From this, two discriminant functions (DFs) were calculated capable of classifying cells in one of the three types. These cell classifiers were capable of classifying 97% of the cells correctly. Data from automated assessment were compared with those of classical manual counting. Specimens of 13 mature and 6 atrophic vaginal specimens were assessed in duplicate, both manually and by image analysis, using the DFs. RESULTS: No significant interobserver effect was found for image analysis, whereas a significant effect was found for manual counting. Both methods were able to distinguish between matured and atrophic specimens. CONCLUSIONS: It was concluded that for assessment of vaginal maturation, the use of automated image analysis systems is recommended. Besides increased reproducibility, image analysis systems yield additional data describing the size and shape of the cytoplasm and nucleus of cells, which might increase discriminating power.     

The PowerAtlas: a power and sample size atlas for microarray experimental design and research

Background  

Microarrays permit biologists to simultaneously measure the mRNA abundance of thousands of genes. An important issue facing investigators planning microarray experiments is how to estimate the sample size required for good statistical power. What is the projected sample size or number of replicate chips needed to address the multiple hypotheses with acceptable accuracy? Statistical methods exist for calculating power based upon a single hypothesis, using estimates of the variability in data from pilot studies. There is, however, a need for methods to estimate power and/or required sample sizes in situations where multiple hypotheses are being tested, such as in microarray experiments. In addition, investigators frequently do not have pilot data to estimate the sample sizes required for microarray studies.     

Determination of amphetamine and methamphetamine enantiomers by chiral derivatization and gas chromatography–mass spectrometry as a test case for an automated sample preparation system

An automated sample preparation system has been applied to the chiral analysis of amphetamine and methamphetamine using derivatization with trifluoracetyl-L -prolyl chloride (L -TPC) and subsequent separation on a gas chromatography–mass spectrometry (GC-MS) system. Tasks automated were the dilution of standards and the off-line preparation of the diastereoisomer derivatives. Chromatographic performance, sensitivity, and reproducibility of the automated procedure were compared to the equivalent values obtained with two existing assays methods which employ manual derivatiation, either on-column or off-line. Chromatographic performance was unaffected by the derivatization procedure and sensitivity was better for both automated and manual off-line derivatization. Qualitative reproducibility as based on enantiomeric composition was equivalent for all three approaches, while quantitative reproducibility as based on peak areas was best for the automated procedure. Considering the fact that the diastereoisomer derivatives are unstable over time, automated sample preparation with “just-in-time” derivatization can increase the overall precision of the analytical method. The procedures described here are general enough in nature that they could be applied to other chiral or even achiral analytes. © 1994 Wiley-Liss, Inc.     

Similarity indices,sample size and diversity

Summary The effect of sample size and species diversity on a variety of similarity indices is explored. Real values of a similarity index must be evaluated relative to the expected maximum value of that index, which is the value obtained for samples randomly drawn from the same universe, with the diversity and sample sizes of the real samples. It is shown that these expected maxima differ from the theoretical maxima, the values obtained for two identical samples, and that the relationship between expected and theoretical maxima depends on sample size and on species diversity in all cases, without exception. In all cases but one (the Morisita index) the expected maxima depend strongly to fairly strongly on sample size and diversity. For some of the more useful indices empirical equations are given to calculate the expected maximum value of the indices to which the observed values can be related at any combination of sample sizes. It is recommended that the Morisita index be used whenever possible to avoid the complex dealings with effects of sample size and diversity; however, when previous logarithmic transformation of the data is required, which often may be the case, the Morisita-Horn or the Renkonen indices are recommended.     

Fast and accurate preparation fatty acid methyl esters by microwave-assisted derivatization in the yeast Saccharomyces cerevisiae

We present a fast and accurate method for preparation of fatty acid methyl esters (FAMEs) using microwave-assisted derivatization of fatty acids present in yeast samples. The esterification of free/bound fatty acids to FAMEs was completed within 5 min, which is 24 times faster than with conventional heating methods. The developed method was validated in two ways: (1) through comparison with a conventional method (hot plate) and (2) through validation with the standard reference material (SRM) 3275-2 omega-3 and omega-6 fatty acids in fish oil (from the Nation Institute of Standards and Technology, USA). There were no significant differences (P>0.05) in yields of FAMEs with both validations. By performing a simple modification of closed-vessel microwave heating, it was possible to carry out the esterification in Pyrex glass tubes kept inside the closed vessel. Hereby, we are able to increase the number of sample preparations to several hundred samples per day as the time for preparation of reused vessels was eliminated. Pretreated cell disruption steps are not required, since the direct FAME preparation provides equally quantitative results. The new microwave-assisted derivatization method facilitates the preparation of FAMEs directly from yeast cells, but the method is likely to also be applicable for other biological samples.     

Cervex brush versus vaginal–cervical–endocervical (VCE) triple smear techniques in cervical sampling

Cervex brush versus vaginal–cervical–endocervical (VCE) triple smear techniques in cervical sampling
Cervex brush sampling was compared with the conventional triple vaginal–cervical–endocervical (VCE) smear technique. Nine hundred and fifty‐nine Cervex brush smears and 1064 VCE smears were studied. All smears with both methods were technically satisfactory for evaluation. Endocervical cells were found in 90.7% and metaplastic cells in 73.3% of Cervex brush samples and in 92.5% and 64.1% of VCE samples, respectively. There were significantly more metaplastic cells in smears from premenopausal women. Low grade squamous intraepithelial lesion (SIL) was found in three Cervex brush samples and in two VCE samples. High‐grade SIL was found only in one Cervex brush sample. Benign cellular changes were found in 142 Cervex brush samples and in 144 VCE samples. Sampling with the Cervex brush is efficient, simple and fast and gives high quality cervical smears for cytological evaluation.