False alarms in a slit-scan flow system: causes and occurrence rates. Implications and potential solutions.

A slit-scan technique was developed as a basis for an automated prescreening system for gynecologic cytology. A flow system based on this technique was fabricated and tested and results indicated that false alarms (misclassification of objects or events from normal specimens as abnormal) are the greatest remaining obstacle to development of an automated prescreening instrument. A dual view correlation system was fabricated to provide exact image-contour correlation in flow and permit precise determination of causes and occurrence rates of false alarms. This paper presents data from correlation analyses of 23 normal cytologic specimens. Major causes of false alarms and their implications to automated prescreening are discussed. A technique that would eliminate the majority of false alarms in flow is presented.     

A statistical analysis of prescreening alarms in a population of normal and abnormal gynecologic specimens

A multidimensional slit-scan flow system has been developed to serve as an automated prescreening instrument for gynecological cytology. Specimens are classified abnormal based on the number of cells having elevated nuclear fluorescence (alarms). An alarm region in a bivariate histogram of nuclear fluorescence versus nuclear-to-cell-diameter ratio is defined. Alarm region probability arrays are calculated to estimate the probability that an alarm falling in a particular bin of the alarm region is either from a normal or an abnormal specimen. From these arrays, a weighted alarm index is generated. In addition, summary indices are derived that measure how the distribution of alarms in each specimen compares with the average distributions for the normal and abnormal specimen populations. These indices together with current features are evaluated with respect to their utility in specimen classification using a nonparametric classification technique known as recursive partitioning. Resulting classification trees are presented that suggest information in the distribution of alarms in the bivariate histogram. In addition, they validate the features and rules currently used for specimen classification. Recursive partitioning appears to be useful for multivariate classification and is seen as a promising technique for other applications.     

Quantitative cytology of the positive region in flow sorted vaginal smears.

Fifty-one gynecologic specimens were collected from three women's hospitals and mailed in a prefixed status to our laboratory. The specimens were classified into a negative, a suspicious, a postradiation, and a positive group. After single cell dispersion the samples were stained for DNA and protein, analyzed, and sorted in the dual laser equipped Heidelberg flow analyzer sorter (HEIFAS). Particles with elevated DNA values (beyond 3.5 ploidy) and with intermediate protein values were sorted as the positive fraction directly on microscopic slides. After restaining according to Papanicolaou, they were re-evaluated cytologically and identified as tumor cells, dysplastic cells and false alarms. The latter consist of doublets and aggregates of more than two cells, binucleated cells, sperm aggregates and epithelial cells contaminated with bacteria. The different groups showed significant differences regarding the total rate of aggregates to single cells. In general, false alarms were very frequent in the positive region and impeded the statistical classification of the sample. The reduction of false alarms is a prerequisite for prescreening with flow instrumentation.     

A multidimensional slit-scan flow system.

A new slit-scan type flow system is described which provides three (X, Y, and Z) orthogonal one-dimensional projections of cell fluorescence. A photomultiplier tube and two semiconductor array detectors are used to obtain the three slit-scan contours from cells traversing a single fluorescence excitation beam. A high speed, dedicated preprocessor analyzes the three contours in parallel, extracting certain features useful for rejecting cells from which an accurate measurement of nuclear fluorescence cannot be obtain. Contour data is buffered and transferred to a PDP-11/40 computer where nuclear fluorescence is measured and cells are classified. It is anticipated that this new instrument will provide a significant reduction in false alarm rate when applied to prescreening of gynecologic cytology specimens.     

Immunohistochemical Evaluation of Global DNA Methylation: Comparison with in Vitro Radiolabeled Methyl Incorporation Assay

The in vitro radiolabeled methyl incorporation assay, a commonly used technique to evaluate global methylation of DNA, has some disadvantages and limitations. The purpose of the present study was to compare the results of global DNA methylation evaluated by radiolabeled methyl incorporation (CPM/μg of DNA) with immunohistochemical staining of the same tissue sections with a monoclonal antibody developed against 5-methylcytosine (5-mc). We used archival specimens of squamous cell cancer (SCC) of the human lung with a matched uninvolved specimen (n = 18 pairs) and 18 lung specimens from subjects without lung cancer (noncancer specimens) to make this comparison. The immunostaining for 5-mc was reported as a percentage of cells positive for staining as well as a weighted average of the intensity score. The results suggested that both radiolabeled methyl incorporation assay and immunostaining for 5-mc can be used to demonstrate hypomethylation of DNA in SCC tissues compared to matched uninvolved tissues. An advantage of immunostaining, however, is its ability to demonstrate hypomethylation of SCC compared to adjacent bronchial mucosa on the same archival specimen, obviating the need to use sections from both SCC and matched uninvolved tissues. Only by using the immunostaining technique were we able to document a statistically significant difference in DNA methylation between SCC and noncancer tissues. We conclude that the immunostaining technique has advantages over the radiolabeled methyl incorporation assay and may be best suited for evaluation of global DNA methylation when the methylation status of cancer cannot be normalized by methyl incorporation of normal tissues or when the number of samples available for evaluation is small.     

Immunohistochemical Evaluation of Global DNA Methylation: Comparison with in Vitro Radiolabeled Methyl Incorporation Assay

The in vitro radiolabeled methyl incorporation assay, a commonly used technique to evaluate global methylation of DNA, has some disadvantages and limitations. The purpose of the present study was to compare the results of global DNA methylation evaluated by radiolabeled methyl incorporation (CPM/μg of DNA) with immunohistochemical staining of the same tissue sections with a monoclonal antibody developed against 5-methylcytosine (5-mc). We used archival specimens of squamous cell cancer (SCC) of the human lung with a matched uninvolved specimen (n = 18 pairs) and 18 lung specimens from subjects without lung cancer (noncancer specimens) to make this comparison. The immunostaining for 5-mc was reported as a percentage of cells positive for staining as well as a weighted average of the intensity score. The results suggested that both radiolabeled methyl incorporation assay and immunostaining for 5-mc can be used to demonstrate hypomethylation of DNA in SCC tissues compared to matched uninvolved tissues. An advantage of immunostaining, however, is its ability to demonstrate hypomethylation of SCC compared to adjacent bronchial mucosa on the same archival specimen, obviating the need to use sections from both SCC and matched uninvolved tissues. Only by using the immunostaining technique were we able to document a statistically significant difference in DNA methylation between SCC and noncancer tissues. We conclude that the immunostaining technique has advantages over the radiolabeled methyl incorporation assay and may be best suited for evaluation of global DNA methylation when the methylation status of cancer cannot be normalized by methyl incorporation of normal tissues or when the number of samples available for evaluation is small.     

A model for the classification of specimens containing random proportions of abnormal cells

The effect of abnormal cell proportion on the performance of an automated cervical prescreening system is discussed in K.R. Castleman and B.S. White, Cytometry 2:155-18. The model employed assumes fixed proportions of abnormal cells, both in the design stage and in the test stage. In the present paper, an extended model is developed that allows for random variability of this proportion. It is shown, that there is a fundamental, non-zero lower limit to the false-negative specimen error rate, which depends only on the coefficient of variation. This limit may be reached even for moderate values of the coefficient of variation, which implies that a satisfactory prescreening system may not be feasible.     

Multidimensional slit-scan prescreening system: preliminary results of a single blind clinical study

A multidimensional slit-scan flow system was developed to serve as an automated prescreening instrument for gynecological cytology. A 2-year single blind clinical study was carried out to evaluate system performance. Cellular material was collected by scraping the uterine cervix and stained in suspension with acridine orange. Seven hundred and forty specimens (701 patients) including 156 abnormal specimens representing a broad spectrum of abnormality were analyzed. Approximately 50,000 cells were analyzed for each specimen. The system false-positive rate was 17.6% while the false-negative rate was 2.8%. All misclassified abnormals were specimens with cellular changes consistent with a slight dysplasia of nonkeratinizing type. The instrument in its present configuration appeared sensitive to the entire spectrum of abnormality existing in the female genital tract and it classified as abnormal any specimen containing on the order of 0.1% (or greater) abnormal cells.     

Are geometric morphometric analyses replicable? Evaluating landmark measurement error and its impact on extant and fossil Microtus classification

Geometric morphometric analyses are frequently employed to quantify biological shape and shape variation. Despite the popularity of this technique, quantification of measurement error in geometric morphometric datasets and its impact on statistical results is seldom assessed in the literature. Here, we evaluate error on 2D landmark coordinate configurations of the lower first molar of five North American Microtus (vole) species. We acquired data from the same specimens several times to quantify error from four data acquisition sources: specimen presentation, imaging devices, interobserver variation, and intraobserver variation. We then evaluated the impact of those errors on linear discriminant analysis‐based classifications of the five species using recent specimens of known species affinity and fossil specimens of unknown species affinity. Results indicate that data acquisition error can be substantial, sometimes explaining >30% of the total variation among datasets. Comparisons of datasets digitized by different individuals exhibit the greatest discrepancies in landmark precision, and comparison of datasets photographed from different presentation angles yields the greatest discrepancies in species classification results. All error sources impact statistical classification to some extent. For example, no two landmark dataset replicates exhibit the same predicted group memberships of recent or fossil specimens. Our findings emphasize the need to mitigate error as much as possible during geometric morphometric data collection. Though the impact of measurement error on statistical fidelity is likely analysis‐specific, we recommend that all geometric morphometric studies standardize specimen imaging equipment, specimen presentations (if analyses are 2D), and landmark digitizers to reduce error and subsequent analytical misinterpretations.     

CYBEST Model 4. Automated cytologic screening system for uterine cancer utilizing image analysis processing

CYBEST (Cyto-Biologic Electronic Screening System) utilizes image analysis technology for the automated prescreening of cervical cytology specimens. CYBEST Model 3, which includes a television scan system and automatic shading control, achieved our initial goal of rapid specimen processing (no more than three minutes to achieve a final specimen assessment). This paper describes CYBEST Model 4, developed in 1981; with the minicomputer of Model 3 replaced by a microcomputer, Model 4 is considerably smaller, about the size of a business desk. A new parameter, the intranuclear configuration (chromatin pattern), was added to the four parameters used in Model 3. The five parameters now used for the assessment and ranking of cytologic abnormalities are nuclear size, nuclear-cytoplasmic ratio, nuclear optical absorption, nuclear shape and intranuclear configuration. The other features of Model 4 are almost the same as those of Model 3. As an optional function, individual parameter measurement data, assessment of atypicality grade and cell images can be displayed on the CRT monitor by pointing to a cell with a light pen system. After completion of screening of a specimen, the ten cells judged to be most abnormal can be called automatically into the microscope optical field or the CRT monitor (in order ranging from the cell with the highest atypicality rank down) along with their associated data and the system's assessment of the specimen. By connection to a small business computer, all data can be transferred to a floppy disk for later retrieval.     

Comparative analysis of a liquid-based Pap test and concurrent HPV DNA assay of residual samples. A study of 608 cases

OBJECTIVE: To retrospectively study the HPV DNA assay of residual samples from the ThinPrep Pap Test (Cytyc Corporation, Boxborough, Massachusetts, U.S.A.) PreserveCyt (Cytyc) vial as a quality improvement (QI) indicator for management of patients with abnormal cervical cytology. STUDY DESIGN: Six hundred eight residual sample vials of liquid-based Pap-Test specimens were selected for the study based on Pap-test results from October 1998 to March 2001. The specimen vials were forwarded to the reference laboratory (American Medical Laboratories, Chantilly, Virginia, U.S.A.) for HPV DNA assay using the Hybrid Capture System method (Digene Corporation, Gaithersburg, Maryland, U.S.A.). At the time of HPV DNA assay, the residual samples were between 8 days to 10 months old, and each vial contained 4 mL. Of the 608 study cases, 76 were WNL, 115 contained BCC, 172 contained ASCUS, 179 were LSIL and 66 were HSIL. In this study, the 191 WNL and BCC cases were designated as the disease-free control group. The HPV DNA typing results were reported as low-risk, high/intermediate-risk or HPV DNA "not detected" HPV types. The HPV DNA testing results were compared to the Pap-Test diagnoses and statistical analysis performed. RESULTS: The following information reflects the percentage of HPV DNA-positive cases based on the Pap-Test diagnoses: 16.2% in WNL and BCC, 51.1% in ASCUS, 94.4% in LSIL and 98.4% in HSIL. Sensitivity (95.5%), specificity (83.7%), false negative value (4.4%), false positive value (16.2%) and predictive value of a positive (88.3%) and negative (93.5%) Pap-Test were calculated on the basis of HPV DNA testing results for 436 cases that were diagnosed as either SIL or negative (WNL and BCC). ASCUS (172) Pap-Test cases were considered borderline--disease positive and excluded from statistical analysis. CONCLUSION: The HPV DNA assay of residual samples from ThinPrep Pap-Test liquid-based specimens is an objective adjunct to the gynecologic cytology QI protocol and is the gold standard reference test for triaging women with equivocal cytologic diagnoses. The great value of HPV DNA testing is its high sensitivity (95.5%), specificity (83.7%) and negative predictive value (93.5%). HPV DNA testing results can be used as a tool to better determine the need for referrals for colposcopic biopsy, especially for patients with an ASCUS diagnosis. The residual Pap-Test specimens are stable and reproducible for HPV DNA typing. A working flow chart for our gynecologic cytology QI program was produced from the Pap-Test and HPV DNA assay results. This offer presents the added benefit of minimizing the problem of sample variation. The prevalence of HPV infection was 16.2% in this study.     

Rapid identification of human ovarian cancer in second harmonic generation images using radiomics feature analyses and tree‐based pipeline optimization tool

Ovarian cancer is currently one of the most common cancers of the female reproductive organs, and its mortality rate is the highest among all types of gynecologic cancers. Rapid and accurate classification of ovarian cancer plays an important role in the determination of treatment plans and prognoses. Nevertheless, the most commonly used classification method is based on histopathological specimen examination, which is time‐consuming and labor‐intensive. Thus, in this study, we utilize radiomics feature extraction methods and the automated machine learning tree‐based pipeline optimization tool (TOPT) for analysis of 3D, second harmonic generation images of benign, malignant and normal human ovarian tissues, to develop a high‐efficiency computer‐aided diagnostic model. Area under the receiver operating characteristic curve values of 0.98, 0.96 and 0.94 were obtained, respectively, for the classification of the three tissue types. Furthermore, this approach can be readily applied to other related tissues and diseases, and has great potential for improving the efficiency of medical diagnostic processes.     

Deep-seated rectal/anal basaloid carcinoma: useful immunocytochemistry in rare squamous cell carcinoma variants

Objectives:  To report the cytological aspects of ano-rectal basaloid carcinoma (BC) variant in endoscopic ultrasound-guided fine needle aspiration (EUS-FNA) conventional and liquid-based cytology (LBC), in a series of 10 cases of deep-seated squamous cell carcinomas (SCC), and to discuss the diagnostic difficulties in interpreting the morphology and immunocytochemical findings.
Methods:  Ten cases of EUS-FNA smears and LBC specimens of deep-seated pelvic masses were retrospectively collected from January 2001 to November 2006.
Results:  Ten EUS-FNA specimen cases were SCC, eight corresponding to usual SCC and two to BC-variant. Of these two cases, only one was correctly diagnosed by EUS-FNA specimen, whereas in the second case, the initial cytological diagnosis was poorly differentiated adenocarcinoma and the final diagnosis of basaloid carcinoma variant was established on surgical resection. Immunocytochemistry (ICC) using CK7, CK20 and CK34βe12 on FNA specimens confirmed the diagnosis retrospectively.
Conclusion:  The diagnosis of basaloid variant of SCC in a rectal location can be very difficult, both on account of the uncommon location and because of the low specificity of morphological aspects on EUS-FNA smears. The immunocytochemical technique, including a limited spectrum of keratins (CK7, CK20, CK34βe12, and p63) is necessary to avoid this diagnostic pitfall.     

Application of malignancy-associated changes of the cervical epithelium in a hierarchic classification concept

For almost 10 years malignancy-associated changes (MAC) have been consistently found by means of high resolution image analysis of apparently normal uterine cervical cells. This study was performed on Feulgen-stained monolayer specimens from 55 healthy women and 19 patients suffering from various stages of cervical neoplasia. About 200 epithelial cells and 30 trout red blood cells in each case were measured by image cytometry at a spatial resolution of 0.27 micron. The philosophy of classification is based on the hierarchic stepwise definition of 'truly normal' specimens by removal of all suspicious specimens, characterized by the presence of atypical cells or subvisually altered cell populations. The suitability of MAC-sensitive classifiers, in combination with classifiers for the recognition of atypical cells, was demonstrated. The demands of automated prescreening were met by several decision tree procedures (95-100% sensitivity, 85-95% specificity). By focussing on the MAC evidence a new risk group from seemingly healthy women may be defined.     

Progress report of the TUDAB project for automated cancer cell detection.

Two methods for high resolution cell image data acquisition are applied routinely. Cells are either scanned by a computer controlled fast scanning microscope photometer (SMP) or a TV-camera. The software system for digital image analysis was completely revised and implemented on the PR 330 minicomputer. The system contains codes for primary cell data acquisition, segmentation of cells, cell feature extraction and statistical cell analysis. With this system, SMP and TV scanned cell data bases of PAP stained cells in vaginal smears, grouped into several classes, have been built up. Each data base contains 34 primary features and 20 feature combinations for each cell. A linear discriminant analysis is applied routinely for cell classification. The present state of the system and its operation are described, cell features and classification results are shown, and future steps for a prescreening strategy are discussed.     

Statistical approaches for morphological continuous characters: a conceptual model applied to Phytoseiidae (Acari: Mesostigmata)

Marie‐Stephane, T. (2012). Statistical approaches for morphological continuous characters: a conceptual model applied to Phytoseiidae (Acari: Mesostigmata). —Zoologica Scripta, 42, 327–334. Species discrimination is certainly the most current and essential taxonomic task. Despite molecular development, species continue to be delimited using morphological characters. This study provides statistical approaches to assess decision rules, using continuous morphological characters, to determine whether specimens examined belong or not to a same species. As species discrimination is usually based on no overlapping between intraspecific distributions, a general statistical approach has been developed to assess, for a character x, the relation between intraspecific overlapping and (i) the differences between the means of specimen lots corresponding to two species and (ii) the differences between the values borne by two specimens belonging to two species. Then, this conceptual approach was applied to the predatory mite family Phytoseiidae, highlighting that the minimal difference between means of two specimen lots belonging to two species should be of 10.58 μm (for setae <65 μm) and 33.99 μm (for setae >65 μm). When no specimen sets are available but only two specimens compared, the model shows that a difference of 13.24 μm (for setae <65 μm) and 31.74 μm (for setae >65 μm) would be sufficient to conclude that these specimens belong to two species. The presently proposed decision rules are assumed to improve species discrimination and to limit synonymies. Further developments will consist in applying this approach to databases containing species features in order to automatically extract the putative synonyms. Furthermore, such decision rules would also be useful to determine whether a species newly described is really new for science.     

Computer analysis of cervical cells. Automatic feature extraction and classification

A prescreening instrument for cervical smears using computerized image processing and pattern recognition techniques requires that single cells in the specimen can be automatically isolated and analyzed. This paper describes a dual wavelength method for automatic isolation of the cytoplasm and nuclei of cells. Density-oriented, shape-oriented and texture-oriented parameters were calculated and evaluated for more than 600 cells. It is shown that the computer can be taught to distinguish between normal and atypical cells with an accuracy of ca. 97%, while human classification reproducibility is ca. 95%. In addition, an attempt to assign a measure of atypia to individual cells is described.     

LINC01783 accelerated tongue squamous cell carcinoma progression via inhibiting miR-199b-5p

Growing studies illustrated that lncRNAs exert critical roles in development and occurrence of tumours including TSCC. In this research, we indicated that LINC01783 was up-regulated in TSCC cells (SCC1, Cal27, UM1 and SCC4) when compared to NHOK cell. RT-qPCR analysis indicated that LINC01783 was overexpressed in 22 TSCC cases (73.3%, 22/30) compared with no-tumour specimens. LINC01783 level was up-regulated in TSCC specimens when compared to no-tumour specimens. Ectopic expression of LINC01783 promoted TSCC cell cycle and growth and EMT progression in both TSCC cell SCC1 and Cal27. Overexpression of LINC01783 sponged miR-199b-5p in TSCC cell and elevated expression of LINC01783 inhibited miR-199b-5p expression. Moreover, we illustrated that miR-199b-5p was down-regulated in TSCC cells and specimen and LINC01783 level was up-regulated in TSCC specimens when compared to no-tumour specimens. Elevated expression of LINC01783 promoted TSCC cell growth, cycle and EMT progression by sponging miR-199b-5p. These data suggested that LINC01783 functioned as one oncogene and might be one treatment target for TSCC.     

A simplified approach to quasi-linear viscoelastic modeling

The fitting of quasi-linear viscoelastic (QLV) constitutive models to material data often involves somewhat cumbersome numerical convolution. A new approach to treating quasi-linearity in 1-D is described and applied to characterize the behavior of reconstituted collagen. This approach is based on a new principle for including nonlinearity and requires considerably less computation than other comparable models for both model calibration and response prediction, especially for smoothly applied stretching. Additionally, the approach allows relaxation to adapt with the strain history. The modeling approach is demonstrated through tests on pure reconstituted collagen. Sequences of "ramp-and-hold" stretching tests were applied to rectangular collagen specimens. The relaxation force data from the "hold" was used to calibrate a new "adaptive QLV model" and several models from literature, and the force data from the "ramp" was used to check the accuracy of model predictions. Additionally, the ability of the models to predict the force response on a reloading of the specimen was assessed. The "adaptive QLV model" based on this new approach predicts collagen behavior comparably to or better than existing models, with much less computation.