bluuebunny/crossref_metadata_2025 huggingface dataset:
Silica Induces Changes in Cytosolic Free Calcium, Cytosolic pH, and Plasma Membrane Potential in Bovine Alveolar Macrophages
Authors: Tárnok Attila , Schlüter Thomas , Berg Ingeborg , Gercken Günther
Published: January 2015

The mineral‐dust induced activation of pulmonary phagocytes is thought to be involved in the induction of severe lung diseases. The activation of bovine alveolar macrophages (BAM) by silica was investigated by flow cytometry. Short‐term incubation (10 min) of BAM with silica gel and quartz dust particles induced increases in the cytosolic free calcium concentration ([Ca2+]i), decreases in intracellular pH (pHi), and increases in plasma membrane potential (PMP). The extent of these changes was concentration dependent, related to the type of dust and was due to Ca2+ influx from the extracellular medium. An increase in [Ca2+]i was inhibited, when extracellular Ca2+ was removed. Furthermore the calcium signal was quenched by Mn2+ and diminished by the calcium channel blocker verapamil. The protein kinase C specific inhibitor bisindolylmaleimide II (GF 109203 X) did not inhibit the silica‐induced [Ca2+]i rise. In contrast, silica‐induced cytosolic acidification and depolarization were inhibited by GF 109203 X but not by removal of extracellular calcium. Addition of TiO2 particles or heavy metal‐containing dusts had no effect on any of the three parameters. Our data suggest the existence of silica‐activated transmembrane ion exchange mechanisms in BAM, which might be involved in the specific cytotoxicity of silica by Ca2+‐dependent and independent pathways.
Towards Architecture‐Adaptable Parallel Programming
Authors: Kumaran Santhosh , Quinn Michael J.
Published: January 2015

Parallel processing is facing a software crisis. The primary reasons for this crisis are the short life span and small installation base of parallel architectures. In this article, we propose a solution to this problem in the form of an architecture‐adaptable programming environment. Our method is different from high‐level procedural programming languages in two ways: (1) our system automatically selects the appropriate parallel algorithm to solve the given problem efficiently on the specified architecture; (2) by using a divide‐and‐conquer template as the basic mechanism for achieving parallelism, we considerably simplify the implementation of the system on a new platform. There is a trade‐off, however: the loss of generality. From a pragmatic point of view, this is not a major liability since our strategy will be useful in building domain‐specific problem solving environments and application‐oriented compilers, which can be easily and effectively ported to diverse architectures. We give preliminary results from a case study in which our method is used to adapt the parallel implementations of the conjugate gradient algorithm on a multiprocessor, a multicomputer, and a workstation network.
Morphological Heterogeneity of p53 Positive and p53 Negative Nuclei in Breast Cancers Stratified by Clinicopathological Variables
Authors: Friedrich Katrin , Dimmer Volker , Haroske Gunter , Meyer Wolfdietrich , Theissig Franz , Thieme Berit , Kunze Klaus Dietmar
Published: January 2015

The study was aimed to detect differences in nuclear morphology between nuclear populations as well as between tumours with different p53 expression in breast cancers with different clinicopathological features, which also reflect the stage of tumour progression. The p53 immunohistochemistry was performed on paraffin sections from 88 tumour samples. After the cells had been localised by means of an image cytometry workstation and their immunostaining had been categorised visually, the sections were destained and stained by the Feulgen protocol. The nuclei were relocated and measured cytometrically by the workstation.

There were significant differences in the nuclear features between tumours as well as between nuclear populations with different p53 expression in the most subgroups. The variability of nuclear shape in tumour groups, classified by the tumour size or the lymph node status, increase with the p53 immunoreactive score, whereas in tumours grouped by the Bloom–Richardson grade features of the chromatin distribution were different between the p53 staining categories.

The nuclear subpopulations showed differences in the amount and distribution of chromatin in most subgroups.

The results demonstrate the relationship between the nuclear morphology and the p53 expression in different stages of breast cancers. The p53 status is an important factor of the biological behaviour but not the only one.
Opening the Black Box: the Relationship between Neural Networks and Linear Discriminant Functions
Authors: Kemp Roger A. , MacAulay Calum , Palcic Branko
Published: January 2015

Over the last ten years feed‐forward neural networks have become a popular tool for statistical decision making. During this time, they have been applied in many fields, including cytological classification. Neural networks are often treated as a black box, whose inner workings are concealed from the researcher. This is unfortunate, since the inner workings of a neural network can be understood in a manner similar to that of a linear discriminant function, which is the standard tool that researchers use for decision making.

This paper discusses feed‐forward neural networks and some methods to improve their performance for classification problems. Their relationship to discriminant functions will be examined for a simple two‐dimensional classification problem.
Lymphoid Infiltrates in B Cell Non Hodgkin’s Lymphoma: Comparing Nuclear Characteristics between Lymph Node and Bone Marrow; and Evaluating Diagnostic Features of Bone Marrow Infiltrates in Paraffin Embedded Tissues
Authors: Deverell Mark H. , Best Elizabeth , Salisbury Jonathan R.
Published: January 2015

Distinguishing non Hodgkin’s lymphoma from benign lymphoid aggregates in bone marrow is well recognised to be difficult. Our objective was to evaluate nuclear morphology, and to perform morphometry on benign and neoplastic lymphoid infiltrates, to establish if objective criteria were of value in the diagnosis of neoplasia. By comparing neoplastic infiltrates in bone marrow with infiltrates in lymph nodes, the validity of grading non Hodgkin’s lymphoma on the basis of bone marrow histology alone was assessed. 82 cases of B cell non Hodgkin’s lymphoma (44 low grade and 38 high grade), known to have both lymph node and bone marrow involvement at the time of presentation, were compared with bone marrow trephines containing reactive lymphoid infiltrates.

The results suggest that in paraffin embedded tissue from bone marrow trephines, nuclear morphology, nuclear area and the nuclear contour index cannot, in most cases, be used to distinguish reactive from neoplastic lymphoid infiltrates although mean nuclear area supports a diagnosis of a neoplastic infiltrate if it can be shown that the nuclei are larger than would be expected in reactive infiltrates. Such differences are subtle and often not appreciable without the use of quantitative techniques. The frequent occurrence of discordant infiltrates in high grade lymphomas means grading of lymphoma on the basis of bone marrow appearances is often unrealistic.
Parameters Derived from Integrated Nuclear Fluorescence, Syntactic Structure Analysis, and Vascularization in Human Lung Carcinomas
Authors: Kayser Klaus , Richter Barbara , Stryciak Richard , Gabius Hans‐Joachim
Published: January 2015

Combined measurements of integrated nuclear fluorescence (INF) and vascularization were performed on surgical specimens of human lung carcinomas. Histological slides of formalin‐fixed, paraffin‐embedded tissue samples were treated with Texas Red‐labeled antibody to factor VIII and the fluorochrome DAPI. The resulting images were analyzed with an epi‐illumination fluorescence microscope and two different filter blocks. The first image displayed the vessels, and the second the DAPI‐stained nuclei of surrounding cells. The extent of vascularization was assessed by calculating the volume fraction (Vv), the surface fraction (Sv), the area, and the minimum diameter of the vessels. The INF was measured in tumour cells and lymphocytes, and was grouped according to the distance from the nearest vascular boundary into the intervals of 0–20, 21–40, 41–60, 61–80, and >80 μ. The numerical densities (Nv) as well as the percentages of S‐phase‐related tumour cell fraction (SPRF) and of tumour cells with an INF > 5C were computed. A minimum of 50 vessels and 300 tumour cells were examined. The material included 100 cases with primary lung carcinoma (39 epidermoid carcinomas, 39 adenocarcinomas, 13 large cell carcinomas, three small cell anaplastic carcinomas, and 6 carcinoid tumours). On the average, the volume density of the stroma amounts to 16.7%, and that of the vessels (Vv) to 12.8%. The minimum diameter of the intratumoral vessels is 13 μ and the measured circumference 138 μ. The numerical densities of tumour cells (lymphocytes) decrease with increasing distance from the vascular boundary from 6.3 (1.7) to 1.0 (0.1). A reduction is also seen in the percentage of the SPRF from 10.7 to 8.1%. The percentage of tumour cells with an INF > 5C, however, is positively correlated to the distance from the vascular surfaces from 34.2 to 38.2%. The measurements reveal that tumour cells are densely positioned and have an increased proportion of proliferation in the populations close to perivascular spaces, whereas chromosome abnormalities are seen more frequently, when tumour cells are located at a distance >20 μ from the vascular surfaces.
Kemari: A Portable High Performance Fortran System for Distributed Memory Parallel Processors
Authors: Kamachi T. , MÜller A. , RÜhl R. , Seo Y. , Suehiro K. , Tamura M.
Published: January 2015

We have developed a compilation system which extends High Performance Fortran (HPF) in various aspects. We support the parallelization of well‐structured problems with loop distribution and alignment directives similar to HPF′s data distribution directives. Such directives give both additional control to the user and simplify the compilation process. For the support of unstructured problems, we provide directives for dynamic data distribution through user‐defined mappings. The compiler also allows integration of message‐passing interface (MPI) primitives. The system is part of a complete programming environment which also comprises a parallel debugger and a performance monitor and analyzer. After an overview of the compiler, we describe the language extensions and related compilation mechanisms in detail. Performance measurements demonstrate the compiler′s applicability to a variety of application classes.
DDT: A Research Tool for Automatic Data Distribution in High Performance Fortran
Authors: AyguadÉ Eduard , Garcia Jordi , GironÈs MercÉ , Grande M. Luz , Labarta JesÚs
Published: January 2015

This article describes the main features and implementation of our automatic data distribution research tool. The tool (DDT) accepts programs written in Fortran 77 and generates High Performance Fortran (HPF) directives to map arrays onto the memories of the processors and parallelize loops, and executable statements to remap these arrays. DDT works by identifying a set of computational phases (procedures and loops). The algorithm builds a search space of candidate solutions for these phases which is explored looking for the combination that minimizes the overall cost; this cost includes data movement cost and computation cost. The movement cost reflects the cost of accessing remote data during the execution of a phase and the remapping costs that have to be paid in order to execute the phase with the selected mapping. The computation cost includes the cost of executing a phase in parallel according to the selected mapping and the owner computes rule. The tool supports interprocedural analysis and uses control flow information to identify how phases are sequenced during the execution of the application.
Proteasome (Prosome) Subunit Variations during the Differentiation of Myeloid U937 Cells
Authors: Henry Laurent , Baz Ahsene , Château Marie-Thérèse , Caravano René , Scherrer Klaus , Bureau Jean Paul
Published: January 2015

20S proteasomes (prosomes/multicatalytic proteinase) are protein particles built of 28 subunits in variable composition. We studied the changes in proteasome subunit composition during the differentiation of U937 cells induced by phorbol‐myristate‐acetate or retinoic acid plus 1,25‐dihydroxy‐cholecalciferol by western blot, flow cytometry and immuno‐fluorescence. p25K (C3), p27K (IOTA) and p30/33K (C2) subunits were detected in both the nucleus and cytoplasm of undifferentiated cells. Flow cytometry demonstrated a biphasic decrease in proteasome subunits detection during differentiation induced by RA+VD. PMA caused an early transient decrease in these subunits followed by a return to their control level, except for p30/33K, which remained low. Immuno‐fluorescence also showed differences in the cytolocalization of the subunits, with a particular decrease in antigen labeling in the nucleus of RA+VD‐induced cells, and a scattering in the cytoplasm and a reorganization in the nucleus of PMA‐induced cells. Small amounts of proteasomal proteins were seen on the outer membrane of non‐induced cells; these membrane proteins disappeared when treated with RA+VD, whereas some increased on PMA‐induced cells. The differential changes in the distribution and type of proteasomes in RA+VD and PMA‐induced cells indicate that, possibly, 20S proteasomes may play a role in relation to the mechanisms of differentiation and the inducer used.
Run‐Time and Compiler Support for Programming in Adaptive Parallel Environments
Authors: Edjlali Guy , Guyagrawal Gagan , Sussman Alan , Humphries Jim , Saltz Joel
Published: January 2015

For better utilization of computing resources, it is important to consider parallel programming environments in which the number of available processors varies at run‐time. In this article, we discuss run‐time support for data‐parallel programming in such an adaptive environment. Executing programs in an adaptive environment requires redistributing data when the number of processors changes, and also requires determining new loop bounds and communication patterns for the new set of processors. We have developed a run‐time library to provide this support. We discuss how the run‐time library can be used by compilers of high‐performance Fortran (HPF)‐like languages to generate code for an adaptive environment. We present performance results for a Navier‐Stokes solver and a multigrid template run on a network of workstations and an IBM SP‐2. Our experiments show that if the number of processors is not varied frequently, the cost of data redistribution is not significant compared to the time required for the actual computation. Overall, our work establishes the feasibility of compiling HPF for a network of nondedicated workstations, which are likely to be an important resource for parallel programming in the future.
Dynamic Changes in Quantitative Features of Human Gastric Lesions
Authors: Enchev Ventzeslav , Rigaut Jean Paul
Published: January 2015

Quantitative DNA, morphometric cellular and nuclear variables were evaluated in surgical biopsies from patients with various gastric lesions: chronic gastritis, chronic ulcers, adenomatous polyps (gastric adenomas), primary carcinomas and their corresponding lymph‐node metastases. Paraffin‐embedded tissue sections were studied by static cytophotometry (plug method), karyometry (measurements with a graduated eyepiece micrometer of the major and minor axes of the elliptic nuclear profiles, and calculation of profile areas), and measurements of cellular profiles (largest and smallest caliper diameters). Tissue lymphocytes from the same slide were used as diploid controls for the DNA evaluations.

An increase of both cellular and nuclear dimensions and DNA content was noted in all pathological tissues, as compared to normal mucosa; the highest values are found in primary gastric carcinomas. A progressive pattern increase of cellular and nuclear dimensions and of DNA content was observed through normal to cancerous tissues, chronic gastritis, chronic ulcers and adenomatous polyps (adenomas). Lymph‐node metastases, in our study, had smaller nuclear (cellular) dimensions than primary cancers.
Assessing Slide Coverage by Cytoscreeners during the Primary Screening of Cervical Smears, Using the AxioHOMEⓇ Microscope System
Authors: Baker Robert W. , Brugal Gerard , Coleman Dulcie V.
Published: January 2015

We have used the HOME Microscope system to examine the screening patterns of cytotechnologists who undertake the primary screening of cervical smears, in order to measure accuracy of screening against screening time, slide coverage, and mean screening rate. Twelve cytotechnologists engaged routinely on cervical screening volunteered for this study. They were asked to perform primary screening of 10 test slides under normal laboratory conditions in the normal way. Slide coverage and screening time were recorded on the HOME system. Slide maps were prepared and the results analysed.

The exercise demonstrated that all primary screeners fail at some point to scan the whole of the slide during primary screening. The maps produced by the HOME system clearly demonstrated that 5 different types of error can occur that lead to incomplete coverage of the slide. Mean slide coverage was 84%, and some individuals averaged only 66% coverage. The results show that there is a major problem in the education of some individual cytotechnologists in slide coverage. This could be rectified by the incorporation of a HOME system into every training centre, and the establishment of a protocol for assessment of slide coverage in competence examinations. Furthermore, the exercise has shown that even those individuals who normally attain a good standard of slide coverage would be able to improve slide coverage given access to the daily use of a HOME Microscope, or a system with equivalent screening/reviewing functionality.
Various Statistical Methods in Use for Evaluating Human Malignant Gastric Specimens
Authors: Enchev Ventzeslav , Vukov Mircho
Published: January 2015

This paper presents the use of certain statistical methods (comparison of means – independent samples t‐test, multiple linear regression analysis, multiple logistic regression analysis, analysis of clusters, etc.) included in the SPSS Statistical Package used to classify the patients quantitatively evaluated after a subtotal resection of their stomachs. The group consisted of 40 patients subdivided into two groups: primary neoplasia of the stomach (20 patients), and corresponding lymphogenic deposits in the abdominal perigastric lymph nodes (20 patients). Paraffin‐embedded tissue sections (thickness 4–5µm) prepared as consecutive hematoxylin‐eosin‐stained slides were morphometrically measured by a rotation of a graduated eyepiece‐micrometer; thus, we obtained the minor and major axes’ lengths of the elliptic nuclear profiles and the minor and major caliper diameters of the corresponding cellular profiles. These four variables were used to determine the dynamic changes in quantitative features of human gastric lesions when passing from normal histological structures, through hyperplastic processes (chronic gastritis), gastric precancer (ulcers and polyps with or without malignancy) till the development of primary carcinomas and their corresponding lymphogeneous metastases. Besides the increased cytomorphometrical measures, we also noted an opportunity to classify the patients according to these data as well as to add to the knowledge of our consultation system for clinical aid and use, recently published in the literature.
DNA Aneuploidy by Flow Cytometry Is an Independent Prognostic Factor in Gastric Cancer
Authors: Abad Mar , Ciudad Juana , Rincon Manuel R. , Silva Isabel , Paz-Bouza José I. , Lopez Antonio , Alonso Alberto G. , Bullon Agustin , Orfao Alberto
Published: January 2015

In the present study the prognostic value of both DNA ploidy and the proliferative activity of tomour cells were studied in a series of 76 consecutive patients suffering from gastric tumours. DNA ploidy and the proliferative index (as measured by the percentage of S‐phase cells) were determined by flow cytometry using fresh tumour specimens.

The presence of DNA aneuploid clones by flow cytometry was detected in 62% of the cases (mean DNA index of 1.63 ± 0.46; range 1.08–2.92), the mean proportion of S‐phase cells being of 18.4 ± 11.5%. In comparison with diploid cases, aneuploid tumours showed a higher proliferative activity (cases with more than 15% S‐phase cells: 18.4% versus 6.1%, p = 0.0001) as well as a higher incidence of node involvement (95% versus 68%, p = 0.001). By contrast, no significant differences were detected with respect to sex, age, histologic grade and type, clinical stage, tumour size and the incidence of extranodal involvement.

Upon grouping the patients according to the proportion of S‐phase cells no significant differences were observed for the clinical and biological parameters explored except for an association between a high percentage of S‐phase cells and the presence of DNA aneuploidy (40% versus 96%, p = 0.0001). Regarding survival the presence of DNA aneuploidy was significantly associated with poor outcome as compared to the diploid cases (median of 15 versus 26 months, p = 0.005). By contrast, the proportion of S‐phase cells did not predict patients’s outcome.

Multivariate analysis of prognostic factors showed that the presence of DNA aneuploidy (p = 0.003) together with the histologic type (p = 0.03) and the existence of extranodal metastases (p = 0.05) were the best combination of prognostic factors for survival prediction.
Detection of c‐erbB‐2 mRNAs Using Dig‐Labelled Oligonucleotide Probe with in situ Hybridisation in Human Breast Carcinoma: Comparison with Immunohistochemical Results
Authors: Öztürk Melek , Bolkent Sema , Yilmazer Selma , Kaner Gültekin , Ünal Hilal
Published: January 2015

Amplification and overexpression of the c‐erbB‐2 oncogene are of prognostic significance in human breast cancer. Overexpression of c‐erbB‐2 is the result of gene amplification. However, increased transcript levels of c‐erbB‐2 are also detected in the absence of gene amplification. In this study for the detection of the overexpression mRNA in situ hybridisation (ISH) and immunohistochemistry (IHC) were used. Our aim was to develop the suitable mRNA ISH protocol for formalin‐fixed paraffin‐embedded material and to compare the localisation of transcripts and protein products in 20 primary breast carcinomas. Sections were immunostained with monoclonal c‐erbB‐2 antibody. In ISH method digoxigenin‐labelled oligoprobe was used for the detection of c‐erbB‐2 mRNAs. We determined optimal condition for the ISH procedure (e.g., probe concentration, digestion, post washing). c‐erbB‐2 protein overproduction was detected in 11/20 cases with IHC. The mRNA signals were observed in malignant cell cytoplasm in 6/20 cases by ISH. ISH positive signals were found in only one case without detected overexpression of the protein. There were cell to cell variations in the hybridisation signals even within individual tumours. The ISH and IHC positive signals for c‐erbB‐2 was observed mostly in infiltrating ductal carcinomas that belong to aggressive lesions.
Automatic Quantification of Immunohistochemically Stained Cell Nuclei Based on Standard Reference Cells
Authors: Ranefall Petter , Wester Kenneth , Andersson Ann-Catrin , Busch Christer , Bengtsson Ewert
Published: January 2015

A fully automatic method for quantification of images of immunohistochemically stained cell nuclei by computing area proportions, is presented. Agarose embedded cultured fibroblasts were fixed, paraffin embedded and sectioned at 4 µm. They were then stained together with 4 µm sections of the test specimen obtained from bladder cancer material.

A colour based classifier is automatically computed from the control cells. The method was tested on formalin fixed paraffin embedded tissue section material, stained with monoclonal antibodies against the Ki67 antigen and cyclin A protein. Ki67 staining results in a detailed nuclear texture with pronounced nucleoli and cyclin A staining is obtained in a more homogeneously distributed pattern.

However, different staining patterns did not seem to influence labelling index quantification, and the sensitivity to variations in light conditions and choice of areas within the control population was low. Thus, the technique represents a robust and reproducible quantification method.

In tests measuring proportions of stained area an average standard deviation of about 1.5% for the same field was achieved when classified with classifiers created from different control samples.
Automatic Cell Segmentation in Cyto‐ and Histometry Using Dominant Contour Feature Points
Authors: Pal U. , Rodenacker Karsten , Chaudhuri B. B.
Published: January 2015

Automatic cell segmentation has various application potentials in cytometry and histometry. In this paper, an automatic cluster (touching) cell segmentation approach using the dominant contour feature points has been presented. Dominant feature points are the locations of indentation on the contour of the cluster. First, dominant feature points on the contour of the cluster are detected by distance profile. Next, using shape features of the cells, these feature points are selected for segmentation. We compared the results of the proposed method with manual segmentation and observed that the method has an overall accuracy about to 82%.
Genetic Heterogeneity of Benign Thyroid Lesions
Authors: Ferrer-Roca O. , Pérez-Gómez J. A. , Cigudosa J. C. , Gómez E. , Estévez M.
Published: January 2015

The present series includes 75 thyroid lesions (38 goiters, 30 adenomas, 3 follicullo‐papillary encapsulated carcinomas and 4 normal thyroid) that were studied by static and flow cytometry. Four cases were also analyzed by in situ hybridization (centromeric probes for chromosomes 1 and 17) and 10 cases by G‐banding cytogenetics. Results demonstrate a polymorphysm and genetic instability in the thyroid tissue that may be related to the spontaneous polyploidization of their cells. The most consistent finding in cytometry was the presence of two clones associated with clinical or histological hyperactivity (46% versus 23% in non‐functioning cases; X2 distribution with a p < 0.05).

Chromosomal anomalies were detected in two out of 10 cases: 46, XX, t(5,19) in 87% of cells of a diffuse hyperplastic goiter and 49, XX, +7, +17, +22 in 19% of cells of thyroiditis case. Finally, the in situ hybridization technique showed hidden trisomies of clonal origin in all of the cases studied.

Evaluation of clonal trisomies by the in situ hybridization technique using the confidence interval of a binomial distribution is discussed.
Histopathologic and Flow‐Cytometric Analysis of Neoplastic and Benign “background” Tissue in Breast Carcinoma Resections
Authors: Visscher Daniel W. , Gingrich Debra S. , Leon-Armin Carmen , Tabaczka Pamela , Crissman John D.
Published: January 2015

Two‐color, multiparametric synthesis phase fraction (SPF) analysis of cytokeratin‐labeled epithelial cells was flow cytometrically performed on both benign (SPFb) and malignant tissue samples (if available, SPFt) from 132 mastectomy/lumpectomy specimens. These data were then correlated with clinicopathologic features, including (1) tumor differentiation, (2) the proportion of tumor comprised of duct carcinoma‐in situ (DCIS), and (3) the histology of accompanying benign breast tissue, classified by predominant microscopic pattern as intact, normal terminal duct lobular units (NTDLU, 34% of cases), atrophic (AT, 33% of cases), proliferative fibrocystic (PFC, 26% of cases), and non‐proliferative fibrocystic (NPFC, 7% of cases). SPFt was inversely correlated with extent of DCIS (DCIS =0 – 20% tumor volume – 12.7% mean SPFt, vs. DCIS >20% tumor volume – 6.4% mean SPFt, p = 0.001). SPFt also correlated with the histology of background benign breast tissue (NTDLU – 14.8% mean SPFt vs. AT – 6.9% mean SPFt vs. PFC – 12.7% mean SPFt, p = 0.05) but it did not correlate with patient age or SPFb (overall mean =0.73%). SPFb was correlated with patient age (>56 yr – 0.59% mean SPFb vs. < yr – 0.84% mean SPFb, p = 0.02), with background histology (NTDLU – 1.1% mean SPFb vs. AT – 0.43% mean SPFb vs. PFC – 0.70% mean SPFb, p < 0.02) and with the grade of the neoplasm (well/moderate – 0.58% mean vs. poorly differentiated – 0.85% mean, p = 0.04). Patients having a background of PFC were significantly older than patients with a background of NTDLU (45.2 yr vs. 60.2 yr, p = 0.01).

We conclude: (1) breast carcinomas arising from a background of more actively cycling pre‐involutional or proliferative fibrocystic epithelium have a greater proliferative fraction than tumors arising from atrophic epithelium, implying that the differentiation status of target cells may impact the effect(s) of tumorigenic events; (2) PFC may represent delayed, abnormal or interrupted involution rather than a hyperproliferative state relative to NTDLU, suggesting that it facilitates neoplasia by extending the period of exposure to promoter agents such as endogenous hormones, and (3) lower SPFt in breast neoplasia with more abundant “residual” DCIS may reflect a lengthier pre‐invasive disease interval due to intrinsically less aggressive phenotype.
The Chromatin Pattern of Cell Nuclei Is of Prognostic Value for Renal Cell Carcinomas
Authors: François Christine , Remmelink Myriam , Petein Michel , van Velthoven Roland , Danguy André , Wespes Eric , Salmon Isabelle , Kiss Robert , Decaestecker Christine
Published: January 2015

Using a series of 105 renal cell carcinomas (RCCs) we investigated whether features quantitatively describing the appearance of Feulgen‐stained nuclei and, more particularly, of their chromatin (on the basis of computer‐assisted microscopy) can contribute any significant prognostic information. Thirty morphonuclear and 8 nuclear DNA content‐related variables were thus generated. The actual prognostic values of this set of cytometric variables was compared (by means of discriminant statistical analysis) to conventional diagnostic and/or prognostic markers including histopathological grades, tumour invasion levels and the presence or absence of metastases. We obtained complete clinical follow‐ups for 49 of the 105 RCC patients under study, making it possible to define a subset of patients with a bad prognosis (i.e., who died in the 12 months following nephrectomy) and a subset of patients with a good prognosis (i.e., who survived at least 24 months following nephrectomy). An original method of data analysis related to artificial intelligence (decision tree induction) enabled a strong prognostic model to be set up. In the case of 10 new patients, this model identified all the dead patients as having a bad survival status, with a total of 8 correct predictions. Another prognostic model similarly generated enabled the correct predictions to be confirmed.
Automatic Quantification of Microvessels Using Unsupervised Image Analysis
Authors: Ranefall Petter , Wester Kenneth , Busch Christer , Malmström Per-Uno , Bengtsson Ewert
Published: January 2015

An automatic method for quantification of images of microvessels by computing area proportions and number of objects is presented. The objects are segmented from the background using dynamic thresholding of the average component size histogram.

To be able to count the objects, fragmented objects are connected, all objects are filled, and touching objects are separated using a watershed segmentation algorithm.

The method is fully automatic and robust with respect to illumination and focus settings.

A test set consisting of images grabbed with different focus and illumination for each field of view, was used to test the method, and the proposed method showed less variation than the intraoperator variation using manual threshold.

Further, the method showed good correlation to manual object counting (r = 0.80) on an other test set.
Synovial sarcoma. Evaluation of Prognosis with Emphasis on the Study of DNA Ploidy and Proliferation (PCNA and Ki‐67) Markers
Authors: M. Lopes José , Hannisdal Einar , Bjerkehagen Bodil , Bruland Øyvind S. , Danielsen Håvard E. , Pettersend Erik O. , Sobrinho-Simões Manuel , Nesland Jahn M.
Published: January 2015

Controversy still exists regarding the validity of parameters commonly used in the evaluation of prognosis of patients with synovial sarcoma (SS). Forty‐nine cases of previously untreated primary SS (23 females and 26 males, ranging in age from 7 to 81, with 31 tumors located in the lower extremity, 8 at the upper extremity and 10 at the trunchus), without regional lymph‐node or distant metastases were studied. We investigated the relationship between (flow and image) DNA cytometry, proliferation activity, clinicopathologic parameters, and relapse‐free and overall survival of the patients. The prognostic value of gender, age, duration of symptoms, location, compartmentalization, size, adequacy of surgical margins, residual tumor, adjuvant therapy, histologic subtype, extent of necrosis, glandular differentiation, calcification, and extent of hemangiopericytic areas, mitotic rate, amount of mast cells, blood vessel invasion, histologic (UICC and NCI) grades, DNA ploidy, percentage of cells in S and S+G2 phases, PCNA and Ki‐67 labeling indices (LI), and TNM (UICC) stage of the tumors, were evaluated by univariate and multivariate (Cox hazard model) analyses. Short duration of symptoms (<12 months), biphasic SS, scarcity of mast cells (<10/10 HPF), high mitotic rate (≥10/10 HPF), high histologic grade (grade 3), high PCNA‐LI (≥20%), high Ki‐67‐LI (≥10%), DNA aneuploidy, and advanced TNM stage (stage III) were features associated with significantly shorter relapse‐free and overall 5‐year survival rates in the univariate analyses. Scarcity of mast cells, high mitotic rate, or high PCNA‐LI were significant predictors of poor survival, in addition to TNM stage in the multivariate analyses. The amount of mast cells was inversely correlated with mitotic rate and PCNA‐LI. Scarcity of mast cells, high mitotic rate, or high PCNA‐LI are factors associated with poor prognosis, in addition to advanced TNM stage in patients with localized SS
A Technique for Section Thickness Evaluation for Microphotometry and Image Analysis of Sectioned Nuclei
Authors: Cabrini R. L. , Folco A. , Orrea S. , Savino M. T. , Schwint A. M. , Itoiz M. E.
Published: January 2015

The exact knowledge of the section thickness is a requisite for making the necessary corrections on DNA measurements in tissue sections. Several methods have been proposed to evaluate section thickness, each of them with advantages and disadvantages depending on the type of specimen and equipment available. We herein report another method based on preparation of standard material whose optical density varies as a function of its thickness and is sectioned and measured alongside the tissue specimen. The standards consist of celloidin cylinders stained with the PAS reaction and embedded in paraffin. For prior characterization of the cylinders, sections of different thickness were obtained and mounted. The optical density of each section was measured by direct microphotometry or image analysis. The actual thickness of each section was evaluated following re‐embedding of piled groups of sections in a paraffin block and transversal sectioning. The thickness was then measured with a micrometric eye‐piece. Optical density and actual thickness of each section were plotted on a normogram curve. Once a given tissue is sectioned alongside with the reference cylinder, the actual thickness is determined by its optical density on the normogram curve.
Automatic Quantification of Immunohistochemically Stained Cell Nuclei Using Unsupervised Image Analysis
Authors: Ranefall Petter , Wester Kenneth , Bengtsson Ewert
Published: January 2015

A method for quantification of images of immunohistochemically stained cell nuclei by computing area proportions is presented. The image is transformed by a principal component transform. The resulting first component image is used to segment the objects from the background using dynamic thresholding of the P2/A‐histogram, where P2/A is a global roundness measure. Then the image is transformed into principal component hue, defined as the angle around the first principal component. This image is used to segment positive and negative objects. The method is fully automatic and the principal component approach makes it robust with respect to illumination and focus settings. An independent test set consisting of images grabbed with different focus and illumination for each field of view was used to test the method, and the proposed method showed less variation than the intraoperator variation using supervised Maximum Likelihood classification.
Evaluation of Residual Cellularity and Proliferation on Preoperatively Treated Breast Cancer: A Comparison between Image Analysis and Light Microscopy Analysis
Authors: Corletto Valentina , Verderio Paolo , Giardini Roberto , Cipriani Sonia , Di Palma Silvana , Rilke Franco
Published: January 2015

Histopathology has been suggested as a reliable method for tumour reduction evaluation of preoperatively treated breast cancer. Immunocytochemistry can be used to enhance the visibility of residual tumour cellularity and in the evaluation of its proliferative activity. We compared Image Analysis (IA) with Light Microscopy Analysis (LMA) on sections of breast carcinomas treated with preoperative chemo‐ or chemo/radiotherapy in the evaluation of the Neoplastic Cell Density (NCD) (69 cases) and the Proliferation Index (PI) (35 cases). NCD was expressed as the immunoreactive area to cytokeratin over the total original neoplastic area and PI was expressed as the number of immunostained tumoural nuclei with MIB1 MoAb over the total of tumoural nuclei. The intraobserver agreement and that between IA and LMA for both indices were estimated by the common (Kw) and the jackknife weighted kappa statistic (w). The extent of agreement of each considered category was also assessed by means of the category‐specific kappa statistics (Kcs). The intraobserver agreement within LMA for NCD and PI and that between IA and LMA for PI were both satisfactory. Upon evaluation of the NCD, the agreement between IA and LMA showed unsatisfactory results, especially when the ratio between the residual tumour cells and the background was critical.
DNA‐Cytometry of Progressive and Regressive Cervical Intraepithelial Neoplasia
Authors: Hanselaar Antonius G. J. M. , Poulin Neal , Pahlplatz Martin M. M. , Garner David , MacAulay Calum , Matisic Jasenka , LeRiche Jean , Palcic Branko
Published: January 2015

A retrospective analysis was performed on archival cervical smears from a group of 56 women with cervical intraepithelial neoplasia (CIN), who had received follow‐up by cytology only. Automated image cytometry of Feulgen‐stained DNA was used to determine the differences between progressive and regressive lesions. The first group of 30 smears was from women who had developed cancer after initial smears with dysplastic changes (progressive group). The second group of 26 smears with dysplastic changes had shown regression to normal (regressive group). The goal of the study was to determine if differences in cytometric features existed between the progressive and regressive groups. CIN categories I, II and III were represented in both groups, and measurements were pooled across diagnostic categories. Images of up to 700 intermediate cells were obtained from each slide, and cells were scanned exhaustively for the detection of diagnostic cells. Discriminant function analysis was performed for both intermediate and diagnostic cells. The most significant differences between the groups were found for diagnostic cells, with a cell classification accuracy of 82%. Intermediate cells could be classified with 60% accuracy. Cytometric features which afforded the best discrimination were characteristic of the chromatin organization in diagnostic cells (nuclear texture). Slide classification was performed by thresholding the number of cells which exhibited progression associated changes (PAC) in chromatin configuration, with an accuracy of 93 and 73% for diagnostic and intermediate cells, respectively. These results indicate that regardless of the extent of nuclear atypia as reflected in the CIN category, features of chromatin organization can potentially be used to predict the malignant or progressive potential of CIN lesions.
A Morphometric Analysis of Nucleoli in Cultured Carcinoma Cells of the Human Thyroid
Authors: Andersen Lars , Kayser Lars , Keiding Niels , Thomsen Jens
Published: January 2015

Cells from 7 patients operated on for thyroid cancer were investigated. Samples of cells from the carcinoma and from the normal thyroid tissue were cultured with and without TSH stimulation. For light microscopy, serial sections of cells were cut and the size of nucleoli was measured and the number of nucleoli per cell counted. At the electron microscopic level the number and the volume of the fibrillar centres (FC) were estimated taking the Swiss cheese effect into account. The areal densities of FC, the fibrillar and granular component in nucleoli were determined by point counting. The results indicate that the malignant transformation has no influence on the size of the FC, but the observed numbers as well as the total area of FC are larger in cancer cells than in the normal thyroid epithelial cells. The nucleolar density of the fibrillar component is larger and that of the granular component is smaller in thyroid carcinoma cells than in non‐malignant thyroid epithelial cells (p = 0.0001). Thus simple morphometry at the electron microscopic level might be helpful to discriminate between thyroid epithelial cells and thyroid carcinoma cells in culture.
Cellular Automaton Simulation of Tumour Growth – Equivocal Relationships between Simulation Parameters and Morphologic Pattern Features
Authors: Smolle Josef
Published: January 2015

Objective: To develop an interpretation procedure which estimates simulation parameters (tumour cell motility, tumour cell adhesion, autocrine and paracrine growth control, stroma destruction) of simulated patterns solely based on morphometric features of the morphologic pattern.

Methods: A cellular automaton computer simulation program was developed which produces morphologic patterns by growth of a seed of tumour cells. At the beginning of each simulation run certain simulation parameters are assigned to the tumour cells. After the run has been completed, the resulting pattern is evaluated by a set of morphometric features. Simulation parameters and resulting morphometric features of 27,800 simulations were stored in a database and were used for the evaluation of potential relationships.

Results: Correlation analysis showed highly significant correlations between morphometric features on the one hand and the preset simulation parameters (tumour cell motility, tumour cell adhesion, autocrine and paracrine growth control, stroma destruction) on the other. Correlation coefficients, however, varied from 0.72 to 0.99. When only one simulation parameter varied while all others were kept constant, morphometric features yielded a highly reliable estimate of the particular simulation parameter. When variability was extended to 4 simulation parameters, morphometric features were less effective in estimating the setting of the parameters. Though in all patterns tested several possible simulation parameter constellations could be ruled out, morphometric features were usually compatible with more than one set of simulation parameters thus preventing a straightforward interpretation.

Conclusions: Though simulation parameters significantly and reproducibly influence the resulting morphologic pattern as characterized by morphometric features, estimates of the simulation parameters based on morphometric features yield equivocal results.
Cell Proliferation Activity and Prognostic Index in Squamous Cell Lung Carcinoma
Authors: Alvarez-Riesgo José Antonio , Sampedro Andrés , Hernández Radhamés , Folgueras María Victoria , Salas-Bustamante Ana , Cueto Antonio
Published: January 2015

Flow Cytometry (FC) has been incorporated into cancer research in relation to its prognostic value together with histological parameters and TNM stages. We have studied by means of FC the cell cycle of 132 samples from male patients with Squamous Cell Lung Carcinoma (SQCLC). All of the patients received curative surgery and the clinical follow‐up was 60 months. The clinical and cytometric parameters were evaluated in order to predict the patients’ outcome. The presence of tumoural recurrence and the tumoural stage showed statistical significance associated with survival. The multivariant analysis reveals radiotherapy (p = 0.004) as protective variable and the high S‐phase fraction (SPF) (p = 0.001) and stage IIIA (p = 0.012) as risk factors. The SPF appears as an independent prognostic factor for overall survival time. We can build a prognostic index representative of different prognostic groups, which allows us to improve the individual monitoring of these patients.
On the Automatic Parallelization of Sparse and Irregular Fortran Programs
Authors: Lin Yuan , Padua David
Published: January 2015

Automatic parallelization is usually believed to be less effective at exploiting implicit parallelism in sparse/irregular programs than in their dense/regular counterparts. However, not much is really known because there have been few research reports on this topic. In this work, we have studied the possibility of using an automatic parallelizing compiler to detect the parallelism in sparse/irregular programs. The study with a collection of sparse/irregular programs led us to some common loop patterns. Based on these patterns new techniques were derived that produced good speedups when manually applied to our benchmark codes. More importantly, these parallelization methods can be implemented in a parallelizing compiler and can be applied automatically.
Improved Sensitivity in Comparative Genomic Hybridization Analysis of DNA Heteroploid Cell Mixtures after Pre‐Enrichment of Subpopulations by Fluorescence Activated Cell Sorting
Authors: Larsen Jacob , Kirchhoff Maria , Rose Hanne , Gerdes Tommy , Maahr Jan , Lundsteen Claes , Larsen Jørgen K.
Published: January 2015

Cytogenetic analysis of solid tumors with comparative genomic hybridization (CGH) is hampered by the dilution of DNA from individual tumor subpopulations with DNA from other cells. We investigated to what extent this dilution effect can be alleviated using fluorescence activated cell sorting (flow sorting) of experimental DNA heteroploid cell mixtures prior to CGH. From mixtures of normal lymphocytes with triploid K‐562 cells the individual components were sorted according to stemline DNA content and processed by CGH in comparison with pure K‐562 samples and the original mixtures. Compared with 30 autosome copy number imbalances found in pure K‐562 samples, a mixture with 32% K‐562 cells showed 16 imbalancies, and none were detected in mixtures with 13% or 5% K‐562 cells. In contrast, 29, 22 and 23 imbalances were detected in K‐562 nuclei sorted from the 32%, 13% and 5% mixtures, respectively. This indicate that CGH analysis of flow sorted DNA aneuploid subpopulations enables a specific cytogenetic analysis of the individual subclones in a DNA heteroploid cell population.