Combined morphometrical and syntactic structure analysis as tools for histomorphological insight into human lung carcinoma growth

Histological sections of formalin-fixed, paraffin-embedded tissue comprising 60 surgical specimens of human lung carcinoma were Feulgen stained. The histomorphological images were transferred to an automated image analysing system (VISIAC) and analysed as follows. The geometrical centers of tumor cell nuclei were defined as vertices, and the minimum spanning tree (MST) was calculated based on the two-dimensional distance between the vertices. Segmentation of the images was performed semiautomatically by interactive definition of nuclei of interest and automated detection of nuclear boundaries. Several morphometric features of tumor cell nuclei were measured including size, DNA-content (extinction), and form factor, and were set in relation to parameters of the MST. The following results were obtained: DNA-content and tumor cell nucleus size ('center cell') of different microscopic tumor growth patterns are related to the number of nearest neighboring cells. No relation was found in the neighboring (surrounding) cells. The different cell types of lung carcinoma, i.e., the different microscopic tumor textures expressed the relation of center cell features to the parameters of MST. A high amount of DNA content in branching points of the MST for epidermoid carcinoma may be interpreted as carcinoma growing in epidermoid textures tend to proliferate from tumor cell nuclei related to at least one neighboring cell. The opposite was found for large cell anaplastic carcinoma (no perceptible microscopic textures of the tumors) which showed the highest DNA content in tumor cell nuclei but which was not related to any neighboring cells. This technique allows analysis of growth centers and microenvironment conditions in human lung cancer in relation to tumor texture at the light microscopy level.     

Cytomorphology of subependymal giant cell astrocytoma.

The cytomorphology of three subependymal giant cell astrocytomas (SEGA) is described. The tumors occurred in the left lateral ventricle of three males with tuberous sclerosis. The often-polarized spindle and epithelioid tumor cells possessed dense eosinophilic cytoplasm, eccentric nuclei and visible, occasionally prominent nucleoli. In addition, they displayed thick or hairlike processes and had a distinct tendency to form cohesive clusters as well as pseudorosettes. Occasional binucleate and multinucleate cells, as well as "strap" cells and nuclear cytoplasmic inclusions, were further features of this unique tumor. In cytologic terms the principal differential diagnostic considerations include gemistocytic astrocytoma, giant cell glioblastoma and ependymoma. Since, in isolation, SEGA may represent a "forme fruste" of tuberous sclerosis and since patients with tuberous sclerosis may have brain tumors other than SEGA, it is of diagnostic importance to recognize the cytomorphologic features of this essentially benign brain tumor.     

Cell chirality regulates coherent angular motion on small circular substrates

Collective cell migration occurs in a wide range of physiological and pathological processes, such as wound healing and tumor metastasis. Experiments showed that many types of cells confined in circular islands can perform coherent angular rotation, yet the underlying mechanisms remain unclear. Here we propose a biomechanical model, including the membrane, microtubules, and nucleus, to study the spatiotemporal evolutions of small cell clusters in confined space. We show that cells can spontaneously transfer from “radial pattern” to “chiral pattern” due to fluctuations. For a pair of cells with identical chiral orientation, the cluster rotates in the opposite direction of the chiral orientation, and the fluctuations can reverse the cluster’s rotational direction. Interestingly, during the persistent rotation, each cell rotates around its own centroid while it is revolving around the island center and shows a constant side to the island center, as tidal locking in astronomy. Furthermore, for a few more cells, coherent angular rotation also appears, and the emergence of a central cell can accelerate the cluster rotation. These findings shed light on collective cell migration in life processes and help to understand the spatiotemporal dynamics of active matter.     

Ortholog clustering on a multipartite graph

We present a method for automatically extracting groups of orthologous genes from a large set of genomes by a new clustering algorithm on a weighted multipartite graph. The method assigns a score to an arbitrary subset of genes from multiple genomes to assess the orthologous relationships between genes in the subset. This score is computed using sequence similarities between the member genes and the phylogenetic relationship between the corresponding genomes. An ortholog cluster is found as the subset with the highest score, so ortholog clustering is formulated as a combinatorial optimization problem. The algorithm for finding an ortholog cluster runs in time O(|E| + |V| log |V|), where V and E are the sets of vertices and edges, respectively, in the graph. However, if we discretize the similarity scores into a constant number of bins, the runtime improves to O(|E| + |V|). The proposed method was applied to seven complete eukaryote genomes on which the manually curated database of eukaryotic ortholog clusters, KOG, is constructed. A comparison of our results with the manually curated ortholog clusters shows that our clusters are well correlated with the existing clusters     

Fine needle aspiration cytologic findings of breast mucinous neoplasms: differential diagnosis between mucocelelike tumor and mucinous carcinoma

OBJECTIVE: To report the cytologic findings of mucocelelike tumor and mucinous carcinoma. STUDY DESIGN: All mucinous neoplasms diagnosed by fine needle aspiration and confirmed by histologic examination were reviewed to detect the cytologic findings helpful for the differentiation. The cytologic findings were correlated with the histologic findings. RESULTS: Cytologically, mucinous carcinomas were highly cellular and showed many single epithelial cells and variably formed epithelial cell clusters in abundant extracellular mucin. Malignant cells exhibited round, atypical nuclei; granular chromatin; and small nucleoli. Mucocele like tumor showed low cellularity with scanty, monolayered, small sheets of epithelial cells and abundant, extracellular mucin. Myoepithelial cells were present within the epithelial cell sheets. Tumor cells were usually small, with uniform, round nuclei; fine chromatin; and absence of nucleoli. CONCLUSION: Cytologic findings of mucocelelike tumor and mucinous carcinoma were different in cellularity, shape of cell clusters and nuclear features, although mucocelelike tumors having a carcinoma component were similar to mucinous carcinoma. Awareness of the cytologic findings of breast mucinous neoplasms is important to make a specific diagnosis.     

Clathrin coats at 21 A resolution: a cellular assembly designed to recycle multiple membrane receptors.

We present a map at 21 A resolution of clathrin assembled into cages with the endocytic adaptor complex, AP-2. The map was obtained by cryo-electron microscopy and single-particle reconstruction. It reveals details of the packing of entire clathrin molecules as they interact to form a cage with two nested polyhedral layers. The proximal domains of each triskelion leg depart from a cage vertex in a skewed orientation, forming a slightly twisted bundle with three other leg domains. Thus, each triskelion contributes to two connecting edges of the polyhedral cage. The clathrin heavy chains continue inwards under the vertices with local 3-fold symmetry, the terminal domains contributing to 'hook-like' features which form an intermediate network making possible contacts with the surface presented by the inner adaptor shell. A node of density projecting inwards from the vertex may correspond to the C-termini of clathrin heavy chains which form a protrusion on free triskelions at the vertex. The inter-subunit interactions visible in this map provide a structural basis for considering the assembly of clathrin coats on a membrane and show the contacts which will need to be disrupted during disassembly.     

Centrosomes and cancer.

The centrosome functions as the major microtubule organizing center (MTOC) of the cell and as such it determines the number, polarity, and organization of interphase and mitotic microtubules. Cytoplasmic organization, cell polarity and the equal partition of chromosomes into daughter cells at the time of cell division are all dependent on the normal function of the centrosome and on its orderly duplication, once and only once, in each cell cycle. Malignant tumor cells show characteristic defects in cell and tissue architecture and in chromosome number that can be attributed to inappropriate centrosome behavior during tumor progression. In this review, we will summarize recent observations linking centrosome defects to disruption of normal cell and tissue organization and to chromosomal instability found in malignant tumors.     

Fine needle aspiration cytology of basal cell adenoma of the salivary gland

OBJECTIVE: To formulate cytologic features for differential diagnosis of basal cell adenoma (BCA). STUDY DESIGN: The usefulness of 5 items for a cytologically definitive diagnosis of BCA was examined. The 5 items in 8 BCA and 22 non-BCA cases (adenoid cystic carcinoma [ADCC], basal cell adenocarcinoma, myoepithelioma, pleomorphic adenoma and polymorphous low-grade adenocarcinoma) that displayed mimicking cytology were examined cytologically. RESULTS: The useful items were < 5.1 microm in mean of epithelial nuclear short diameter; mild atypia on definitive diagnosis; stromal cell cluster combining smooth margin surrounding the epithelial cell cluster or containing the epithelial cell cluster; epithelial clusters surrounded by or adhered to a thick, hyalinized smooth margin without stromal cluster; and closely fastened, tight clusters with denser cytoplasm than ADCC, but an indistinct border, with oval nuclei and no hyaline cells. CONCLUSION: Five items are useful criteria for BCA.     

A new fast algorithm for solving the minimum spanning tree problem based on DNA molecules computation

The minimum spanning tree (MST) problem is to find minimum edge connected subsets containing all the vertex of a given undirected graph. It is a vitally important NP-complete problem in graph theory and applied mathematics, having numerous real life applications. Moreover in previous studies, DNA molecular operations usually were used to solve NP-complete head-to-tail path search problems, rarely for NP-hard problems with multi-lateral path solutions result, such as the minimum spanning tree problem. In this paper, we present a new fast DNA algorithm for solving the MST problem using DNA molecular operations. For an undirected graph with n vertex and m edges, we reasonably design flexible length DNA strands representing the vertex and edges, take appropriate steps and get the solutions of the MST problem in proper length range and O(3m + n) time complexity. We extend the application of DNA molecular operations and simultaneity simplify the complexity of the computation. Results of computer simulative experiments show that the proposed method updates some of the best known values with very short time and that the proposed method provides a better performance with solution accuracy over existing algorithms.     

Cytologic features of pilocytic astrocytoma in cerebrospinal fluid specimens

OBJECTIVE: To illustrate the cytomorphologic features of pilocytic astrocytoma (PA) in cerebrospinal fluid (CSF) samples. STUDY DESIGN: A search of records from 1965 to 2001 was performed to identify all patients with a diagnosis of PA in whom CSF samples were examined. Slides from CSF samples originally reported as atypical, suspicious or positive were reviewed and the cytomorphologic features assessed. RESULTS: Two hundred ninety-three patients with a diagnosis of PA were identified. Of these, 44 had a total of 65 cytologic preparations of CSF. In 34 patients (77.2%) the CSF cytology was negative, in 5 (11.4%) either atypical or suspicious, and in 5 (11.4%) positive for neoplastic cells. The tumors in the 5 positive cases arose in the cerebellar hemispheres (2), cerebellar vermis (1), thalamus (1) and tectum with extension into the fourth ventricle (1). All positive samples were hypercellular, with an average of 5 cell clusters per case (range, 3-11). The clusters were composed of cohesive epithelioid cells with a mean of 8 cells per cluster. In addition, some cases had scattered, isolated, single cells. These single neoplastic cells had prominent, hairlike cytoplasmic processes. The cells in clusters appeared epithelioid, with oval nuclei, mild nuclear pleomorphism, finely or slightly coarsely granular chromatin and cobweblike cytoplasm. CONCLUSION: The cytomorphologic features of PAs recapitulate their histologic characteristics. The tumor cells are recognizable in CSF samples and readily distinguishable from histiocytes and ependymal cells.     

Contextual analysis complements single-cell analysis in the diagnosis of breast cancer in fine needle aspirates

Image analysis techniques were used to characterize individual nuclei of cells and entire clusters of cells in hematoxylin-and-eosin-stained smears of fine needle aspirates of the breast to determine the ability of these techniques to distinguish benign from malignant cases. Analysis of the individual nuclear features showed significant differences in nuclear area, shape (bending energy), texture and integrated darkness between benign and malignant samples. Analysis of the clusters demonstrated that the benign clusters were fewer in number, more cellular (average gray level) and larger than malignant clusters. A statistical classifier was constructed to test the discriminatory accuracy for benign and malignant cases. Good discrimination was found for both the individual nuclei and the clusters when analyzed separately, although a few cases were misclassified by each type of analysis. When combined, the two classifiers achieved a completely accurate classification. This suggests the complementary nature of high-resolution single-cell analysis and the more global cluster analysis techniques.     

Subset clustering of binary sequences, with an application to genomic abnormality data

This article develops a model-based approach to clustering multivariate binary data, in which the attributes that distinguish a cluster from the rest of the population may depend on the cluster being considered. The clustering approach is based on a multivariate Dirichlet process mixture model, which allows for the estimation of the number of clusters, the cluster memberships, and the cluster-specific parameters in a unified way. Such a clustering approach has applications in the analysis of genomic abnormality data, in which the development of different types of tumors may depend on the presence of certain abnormalities at subsets of locations along the genome. Additionally, such a mixture model provides a nonparametric estimation scheme for dependent sequences of binary data.     

Classification and three-dimensional reconstruction of unevenly distributed or symmetry mismatched features of icosahedral particles

Methods for the three-dimensional reconstruction of icosahedral particles, such as spherical viruses, from electron micrographs are well established. These methods take advantage of the 60-fold symmetry of the icosahedral group. Several features within these particles, however, may deviate from icosahedral symmetry. Examples include viral genomes, symmetry mismatched vertex proteins, unique DNA packaging vertices, flexible proteins, and proteins that are present at less than 100% occupancy. Such asymmetrically distributed features are smeared in the final density map when icosahedral symmetry is applied. Here, we describe a novel approach to classifying, analysing, and obtaining three-dimensional reconstructions of such features. The approach uses the orientation information derived from the icosahedral orientation search to facilitate multivariate statistical analysis and to limit the orientational degrees of freedom for reconstruction. We demonstrate the application of this approach to images of Kelp fly Virus. In this case, each virion may have two different types of fivefold vertex. We use our approach to produce independent reconstructions of the two types of vertex.     

Identification of a high-risk subgroup in cytology-positive stage IIIA endometrial cancer

OBJECTIVE: To identify a high-risk subgroup among patients with cytology-positive stage IIIA endometrial cancer. STUDY DESIGN: Fifty-four stage IIIA endometrial cancer patients who were positive only on peritoneal cytology were divided into two groups based on the cytologic pattern of their peritoneal smears. In group A, malignant cell clusters had well-defined edges, while the tumor cell clusters had scalloped edges in group B. The prognostic significance of these findings was investigated. RESULTS: The five-year disease-free survival rate was 97.5% in group A (n=40) versus 50% in group B (n = 14). Multivariate analysis confirmed that the cytologic pattern had an independent influence on survival. CONCLUSION: Positive peritoneal cytology composed of malignant cell clusters with well-defined edges has no impact on survival. Only endometrial cancer patients who show tumor cell clusters with scalloped edges in peritoneal smears are worth considering for upstaging.     

The orientation of iron-sulfur clusters and a spin-coupled ubiquinone pair in the mitochondrial membrane.

Oriented multilayers made from beef heart and yeast mitochondria and submitochondrial particles were studied using electron paramagnetic resonance. EPR signals from membrane-bound iron-sulfur clusters and from a spin-coupled ubiquinone pair are highly orientation dependent, implying that these redox centers are fixed in the membrane at definite angles relative to the membrane plane. Typically the iron-iron axis (gz) of the binuclear iron-sulfur clusters is in the membrane plane. This finding is discussed in terms of the protein structure. The tetranuclear iron-sulfur clusters can have their gz axis either perpendicular or parallel to the membrane plane, but intermediate orientation was not observed.     

Automated quantitative analysis of epithelial cell scatter

Epithelial cell scatter is a well-known in vitro model for the study of epithelial-mesenchymal transition (EMT). Scatter recapitulates many of the events that occur during EMT, including the dissociation of multicellular structures and increased cell motility. Because it has been implicated in tumor invasion and metastasis, much effort has been made to identify the molecular signals that regulate EMT. To better understand the quantitative contributions of these signals, we have developed metrics that quantitatively describe multiple aspects of cell scatter. One metric (cluster size) quantifies the disruption of intercellular adhesions while a second metric (nearest-neighbor distance) quantifies cell dispersion. We demonstrate that these metrics delineate the effects of individual cues and detect synergies between them. Specifically, we find epidermal growth factor (EGF), cholera toxin (CT) and insulin to synergistically reduce cluster sizes and increase nearest-neighbor distances. To facilitate the rapid measurement of our metrics from live-cell images, we have also developed automated techniques to identify cell nuclei and cell clusters in fluorescence images. Taken together, these studies provide broadly applicable quantitative image analysis techniques and insight into the control of epithelial cell scatter, both of which will contribute to the understanding of EMT and metastasis.Key words: cell scatter, EMT, automated image analysis     

Three-dimensional image processing for morphometric analysis of epithelium sections.

The reproducible classification of poorly differentiated abnormal epithelium specimens is still a diagnostic problem. The computer-aided method described here improves the differentiation between benign and malignant epithelium specimens. Hematoxylin and eosin-stained sections of normal squamous epithelium, dysplasia, carcinoma in situ, and carcinoma were scanned in a TV microscope system and analyzed by means of image processing methods on a DEC 5000/200 workstation. From the 15-20 microns thick histological sections, 3-5 focus positions in steps of 1-4 microns were scanned. The segmentation of the cell nuclei was performed automatically by color analysis and geometric operations. For each nucleus the best focus level was selected and at this level the center of the cell was calculated. Graph theoretical methods were applied to analyze the morphometry of the epithelium specimens. The minimal spanning tree was computed in the three-dimensional (3D) space of the sections with the selected centers of the nuclei as vertices. The best feature found for discrimination of the specimens is the average length of all edges in a tree. In the two-dimensional (2D) analysis we had to accept an error probability of about 20% in differentiation of dysplasia and carcinoma. In contrast to this we differentiated normal squamous epithelium, dysplasia, and carcinoma with a correct classification rate of 100% in the 3D analysis.     

The linear clusters of oogonial cells in the development of telotrophic ovarioles in polyphageColeoptera

Summary During the premetamorphic development of coleopteran telotrophic ovaries the culsters of sister oogonial cells, in which the differentiation of nurse cells and oocytes occurs, are arranged in linear chains. This results from a series of mitoses with the consistent orientation of the spindle parallel to the long axis of the ovariole. As a result of incomplete cytokinesis, the oogonial cells in each sibling cluster are linked to each other by intercellular bridges occupied by fusomes. As a rule, at each cluster division the basal cell (i.e. the oocyte progenitor) starts to divide first. From this cell a wave of mitoses spreads toward the anterior end of the cluster, resulting in a mitotic gradient. It is suggested that the failure of the fusomes in adjacent cells to fuse into one continuous fusome (i.e. polyfusome) allows the spindles to orientate with their long axes parallel to the long axis of the sibling cluster. This would explain why the oogonial divisions in coleopteran telotrophic ovaries generate linear chains of cells rather than the cyst-like arrangement which is typical for polytrophic sibling clusters. Dividing sibling clusters within ovarioles are arranged in bundles. The presence of intercellular bridges between sibling clusters seems to be the underlying cause of this nonrandom distribution of the mitotically active clusters. The transverse bridges have been found to occur between the basal cells as well as between the cells located more anteriorly in adjacent sibling clusters. The transverse bridges are filled with typical fusomes, which in more anterior parts of sibling clusters may fuse with the fusomes of adjacent sister oogonial cells into polyfusomes. The transverse bridges between the basal cells are incorporated in the oocytes. The pattern of sibling cluster formation described in this paper apparently occurs widespread in polyphagous Coleoptera, since it has been found in three relatively distantly related families.     

Fine needle aspiration cytology of epithelial-myoepithelial carcinoma of salivary glands. A report of three cases.

BACKGROUND: Epithelial-myoepithelial carcinoma is a rare, low grade malignant tumor of the salivary glands. Histologically, it has a biphasic cellular composition and exhibits a high degree of differentiation. The fine needle aspiration cytology of this rare tumor is rarely described in the literature. CASES: We report the fine needle aspiration cytology of three epithelial-myoepithelial carcinomas, arising in the right parotid, left parotid and minor salivary gland of the hard palate. Cytology showed a biphasic population consisting of cells of ductal epithelial and myoepithelial origin arranged in small clusters and sheets. The myoepithelial cells had small, uniform nuclei; ample, clear cytoplasm and distinct cell borders, while the ductal epithelial cells had larger, mildly pleomorphic nuclei and scanty cytoplasm. These ductal cells tended to form tubules among background sheets of clear myoepithelial cells. This feature, if present, was an important diagnostic clue. Hyaline material surrounding cell clusters and focal adenoid cystic carcinoma-like areas with orangeophilic globules were also not uncommon. CONCLUSION: While the cytologic appearance of epithelial-myoepithelial carcinoma may closely mimic that of other salivary gland tumors, such as adenoid cystic carcinoma, pleomorphic adenoma and basal cell adenoma, certain peculiar cytologic features may allow a distinction to be made on fine needle aspiration biopsy.