bluuebunny/crossref_metadata_2025 huggingface dataset:
Correlation between p53 Status, DNA Ploidy, Proliferation Rate and Nuclear Morphology in Breast Cancer. An Image Cytometric Study
Authors: Friedrich Katrin , Dimmer Volker , Haroske Gunter , Meyer Wolfdietrich , Theissig Franz , Kunze Klaus Dietmar
Published: January 2015

The study was designed to detect differences in the nuclear morphology of tumours and tumour cell populations with different p53 expression in correlation with DNA ploidy and proliferation rate. The paraffin sections from routinely processed samples of 88 breast cancers were immunostained with the monoclonal p53‐antibody DO‐1. After localization and evaluation with a scoring system the sections were destained and stained by the Feulgen method. The nuclei were relocated automatically and measured by means of the image cytometry workstation. Significant differences between the tumours and tumour cell populations with different p53 expression were found in the euploid tumours as well as in the aneuploid tumours and in the breast cancers with a high proliferation rate. The breast cancers with a low immunoreactive score (IRS 1–4) differ from the negative cancers as well as from the cancers with a higher immunoreactive score (IRS 5–12). Evaluating the nuclear populations of the p53 positive cancers, there were differences in the features of the chromatin amount and distribution in the groups of the euploid breast cancers and in cancer with a high proliferation rate. In contrast, the nuclear populations of the aneuploid cancers did not show any differences in their nuclear morphology.

The results showed the different impacts of the p53 expression, DNA ploidy and the proliferation rate on the nuclear morphology in breast cancer.
Groping for Quantitative Digital 3‐D Image Analysis: An Approach to Quantitative Fluorescence In Situ Hybridization in Thick Tissue Sections of Prostate Carcinoma
Authors: Rodenacker Karsten , Aubele Michaela , Hutzler Peter , Umesh Adiga P. S.
Published: January 2015

In molecular pathology numerical chromosome aberrations have been found to be decisive for the prognosis of malignancy in tumours. The existence of such aberrations can be detected by interphase fluorescence in situ hybridization (FISH). The gain or loss of certain base sequences in the desoxyribonucleic acid (DNA) can be estimated by counting the number of FISH signals per cell nucleus. The quantitative evaluation of such events is a necessary condition for a prospective use in diagnostic pathology. To avoid occlusions of signals, the cell nucleus has to be analyzed in three dimensions. Confocal laser scanning microscopy is the means to obtain series of optical thin sections from fluorescence stained or marked material to fulfill the conditions mentioned above.
A graphical user interface (GUI) to a software package for display, inspection, count and (semi‐)automatic analysis of 3‐D images for pathologists is outlined including the underlying methods of 3‐D image interaction and segmentation developed. The preparative methods are briefly described. Main emphasis is given to the methodical questions of computer‐aided analysis of large 3‐D image data sets for pathologists. Several automated analysis steps can be performed for segmentation and succeeding quantification.
However tumour material is in contrast to isolated or cultured cells even for visual inspection, a difficult material. For the present a fully automated digital image analysis of 3‐D data is not in sight. A semi‐automatic segmentation method is thus presented here.
Comparison of Proliferating Cell Nuclear Antigen Expression in Odontogenic Keratocyst and Ameloblastoma: An Immunohistochemical Study
Authors: Takahashi Hiroshi , Fujita Shuichi , Yamabe Shigeru , Moriishi Takeshi , Okabe Haruo , Tajima Yoshifumi , Mizuno Akio
Published: January 2015

Proliferating cell nuclear antigen (PCNA) is a nuclear protein synthesized in the late G1 and S phase of the cell cycle, and immunohistochemical detection of the protein represents a useful marker for the proliferating fraction of cells in tissue specimens. PCNA expression was studied in odontogenic keratocysts (n = 15) and ameloblastomas (n = 46) using an avidin–biotin–peroxidase complex method on routinely processed paraffin sections. The percentage of PCNA‐positive cells determined by point counting was significantly lower in the ameloblastomas (mean 9.4%, standard deviation (SD) 11.0) than in odontogenic keratocysts (mean 29.9%, SD 24.0). In ameloblastomas, the mean percentage of PCNA‐positive cells was lowest in the acanthomatous pattern and highest in plexiform pattern. The mean percentage of PCNA‐positive cells in plexiform pattern was non‐significantly higher than that in follicular pattern. The mean percentage of PCNA‐positive cells in plexiform and follicular patterns was significantly higher than that in cyctic and acanthomatous patterns. The frequency of PCNA‐positive cells was significantly higher in the peripheral cells of follicular and plexiform patterns than in the central cells of both patterns (p < 0.01). Therefore, peripheral cells were regarded as reserve cell of central cells. The mean percentage of PCNA‐positive cells in the epithelial lining of odontogenic keratocyst was not significantly different from those in the peripheral cells of follicular and plexiform patterns of ameloblastoma. In contrast, the odontogenic keratocyst exhibited a mean percentage of PCNA‐positive cells which was statistically higher than that in other histological elements of ameloblastomas. The present study suggests that odontogenic keratocyst is regarded as benign odontogenic tumour.
Multi Parameter Flow Cytometric Assessment of Regenerative Epidermis with Special Reference to the Antiproliferative Effect of Occlusion
Authors: van Rossum M. M. , Mommers J. M. , van de Kerkhof P. C. M. , de Jongh G. J. , van Hooijdonk C. A. E. M. , van Erp P. E. J.
Published: January 2015

Multi parameter flow cytometrical assays permit simultaneous assessment of proliferation, differentiation, and inflammation parameters. In this study, the validation of TO‐PRO‐3 iodide (TP3) compared to propidium iodide (PI) and DE‐K10 compared to RKSE60 were evaluated in tape stripping induced hyperproliferation. No occlusion, Duoderm (intermediate occlusion) and Blenderm (maximal occlusion) were used as a model to evaluate the effect of occlusion on epidermal regeneration. Proliferation in the keratin 10‐negative compartment measured with TP3 proved to be a good approximation of proliferation measured with PI. Other epidermal subpopulations (keratin 10‐dim and ‐bright cells) did not make a relevant contribution to hyperproliferation. DE‐K10 is probable more sensitive than RKSE60 to distinguish populations that differ in degree of differentiation. Occlusion of tape stripped skin resulted in decreased proliferation and increased differentiation. This effect was most pronounced with maximal occlusion. This study showed that occlusion is a therapy, which realises normalisation of hyperproliferative skin disorders.
Immunophenotypic Characterization of Human Bone Marrow Mast Cells. A Flow Cytometric Study of Normal and Pathological Bone Marrow Samples
Authors: Escribano Luis , Orfao Alberto , Villarrubia Jesús , Díaz-Agustín Beatriz , Cerveró Carlos , Rios Agustín , Velasco José L. , Ciudad Juana , Navarro José L. , San Miguel Jesús F.
Published: January 2015

The goal of the present paper was to define the immunophenotype of bone marrow mast cells (BMMC) from healthy controls and patients with hematologic malignancies (HM) based on the use of multiple stainings with monoclonal antibodies analyzed by flow cytometry. Our results show that BMMC from both groups of individuals display a similar but heterogenous immunophenotype. The overall numbers of BMMC are higher in the HM group of individuals (p = 0.08). Three patterns of antigen expression were detected: (1) markers constantly positive in all cases analyzed (CD9, CD29, CD33, CD43, CD44, CD49d, CD49e, CD51, CD71, CD117, and FcεRI), (2) antigens that were constantly negative (CD1a, CD2, CD3, CD5, CD6, CD11a, CD14, CD15, CD16, CD19, CD20, CD21, CD23, CD25, CD30, CD34, CD38, CD41a, CD42b, CD65, CD66b, HLA‐DR, and CD138), and (3) markers that were positive in a variable proportion of cases – CD11b (50%), CD11c (77%), CD13 (40%), CD18 (20%), CD22 (68%), CD35 (27%), CD40 (67%), CD54 (88%) and CD61 (40%). In addition, BMMC from all cases explored were CD45+, and this antigen was expressed at an intensity similar to that of mature granulocytes.

In summary, our results show that BMMC from both healthy controls and HM patients display a relatively heterogenous immunophenotype. Interestingly, we have observed clear differences between the immunophenotype of BMMC and MC from other tissues. This could be due either to the heterogeneity of human MC according to their tissue localization or to the sensitivity of the method used for antigen detection.
p53 Mutations and DNA Ploidy in Colorectal Adenocarcinomas
Authors: Campomenosi Paola , Assereto Paola , Bogliolo Massimo , Fronza Gilberto , Abbondandolo Angelo , Capasso Antonella , Bellomo Patrizia F. , Monaco Roberto , Rapallo Anna , Sciutto Andrea , Orecchia Roberto , Geido Elio , Giaretti Walter
Published: January 2015

The p53 tumour suppressor gene has an important role in the the maintenance of genome stability and its mutational inactivation may be at the origin of aneuploidy in cancer cells. The aim of this study was to determine whether p53 mutations were associated to DNA aneuploidy, as assessed by flow cytometry, in colorectal adenocarcinomas. Analysis of p53 mutations spectrum of the sorted nuclei was done by Denaturing Gradient Gel Electrophoresis (DGGE) and DNA sequencing. Overall, we studied 20 adenocarcinomas, the corresponding control mucosa, and 7 lymph node metastases.

Five tumours (25%) were DNA diploid, while 15 tumours (75%) were composed of DNA aneuploid and diploid subpopulations. DNA diploid control mucosa and adenocarcinomas showed no p53 mutations, while 60% of the tumours with DNA aneuploidy had p53 mutations. Therefore, p53 mutations occurred significantly more often in DNA aneuploid than in DNA diploid tumours (p < 0.04, Fisher’s exact test). Incidences of DNA aneuploidy and p53 mutations in lymph node metastases were 60 and 86%, respectively. In all tumours showing a p53 mutation, the wild‐type allele was not or only bearly visible in DNA aneuploid cells suggesting that, in such cells, aneuploidy is accompanied by complete p53 functional inactivation.

The present observations suggest that p53 mutations may have a role in the origin of aneuploidy at late stages of colorectal carcinogenesis.
Preliminary Characterization of a Monoclonal Antibody (AS‐2) against Cell Cycle Related Proteins
Authors: Nigro Stefano , Rapallo Anna , Di Vinci Angela , Geido Elio , Orecchia Roberto , Giaretti Walter
Published: January 2015

A monoclonal antibody (AS‐2) raised by using isolated nuclei from a human erythroleukemia cell line as immunogen is described.

AS‐2 was of IgM type and recognized proteins present in both isolated cytoplasms and nuclei. The molecular weight of the AS‐2 recognized proteins in the cytoplasm was 200 kDa and 70 and 60 kDa in the nucleus. The relative amount of these proteins were measured simultaneously with DNA content by flow cytometry. We found the highest protein content (or stainability) for both cells and nuclei in late‐G1, S and G2, at approximately the same level, and the lowest content in M and early‐G1. Sorting based on DNA content and AS‐2 associated fluorescence helped identifying the staining pattern of cells and nuclei. Interphase isolated nuclei and cell cytoplasms were characterized by interdispersed staining over the entire surfaces while mitoses showed two dots only. The present preliminary data indicate that the proteins recognized by the AS‐2 monoclonal are cell cycle related and suggest that in mitoses they are associated with the centrosomes.
Cyclin E Expression and Proliferation in Breast Cancer
Authors: Nielsen Niels H. , Arnerlöv Conny , Cajander Stefan , Landberg Göran
Published: January 2015

Cyclin E is a part of the cell cycle machinery and aberrantly expressed in several malignancies including breast cancer. Since cyclin E is cell cycle specifically expressed, we wanted to examine the relation between proliferation and expression of cyclin E with special attention to tumours with overexpression of the protein. Seventy‐four breast tumours were analysed for the expression of cyclin E by immunohistochemistry and Western blotting and related to the growth fraction determined by Ki‐67. Significant correlations were obtained between the growth fraction, the percentage of cyclin E positive cells, the intensity of cyclin E and total amount of cyclin E determined by Western blotting. The majority of the tumours had less cyclin E than Ki‐67 positive cells indicating a conserved cell cycle specific expression of the protein which further was supported by flow cytometric analysis of breast cancer cell lines. The cell cycle specificity of cyclin E was found even in tumours with inactivated retinoblastoma protein (pRB) demonstrating the existence of a pRB independent regulation of cyclin E. A fraction of the tumours had considerably elevated cyclin E levels that were not in relation to the proliferative activity as observed for the other tumours. These tumours were in general highly proliferative and considered to overexpress cyclin E. Patients with tumours of high proliferative activity, high total cyclin E levels or disproportionally elevated cyclin E expressions in relation to proliferation had significantly increased risk of death in breast cancer, whereas the intensity of the immunohistochemical cyclin E staining did not affect the survival.
Relationship between AgNOR Proteins, Ki‐67 Antigen, p53 Immunophenotype and Differentiation Markers in Archival Breast Carcinomas
Authors: Bànkfalvi Àgnes , Schmitz Klaus , Mock Tobias , Kemper Mechthild , Cubick Christiane , Böcker Werner
Published: January 2015

The present study investigated (i) the relationship between standardised morphometric AgNOR parameters (argyrophilic nucleolar organiser region‐associated proteins) and MIB1 growth fraction, and (ii) their correlation with immunohistochemical p53, sex steroid receptor status and histopathological differentiation grade in serial paraffin sections from 39 breast carcinomas. Ten sections were double‐stained for AgNOR/MIB1. AgNOR parameters correlated significantly with MIB1 growth fraction and p53 protein expression. Significant inverse correlation was found between proliferation markers and oestrogen/progesterone receptor status and histopathological grade. AgNOR expression was significantly higher in cycling (MIB1 positive) tumour cells, than in resting (MIB1 negative) ones, however with exceptions. We conclude, that standardised AgNOR parameters correlate with markers of increased malignant potential in breast carcinomas. However, AgNORs seem to reflect proliferation independent cellular and nucleolar activity of tumour cells, as well. We recommend the use of standardised AgNOR analysis for obtaining sound results in routine paraffin sections.
Consensus Report of the Task Force on Standardisation of DNA Flow Cytometry in Clinical Pathology
Authors: Ormerod M. G. , Tribukait B. , Giaretti Walter
Published: January 2015

Guidelines are given to assist the standardisation of DNA flow cytometry in clinical pathology. They have been agreed by a group of twelve scientists from nine European countries.
In situ Apoptotic and Proliferation Index in Laryngeal Squamous Cell Carcinomas
Authors: Hagedorn Hjalmar G. , Tübel Jutta , Wiest Irmgard , Nerlich Andreas G.
Published: January 2015

The rate of cellular growth is mainly influenced by the balance between cell proliferation and cellular decay. Since to our knowledge, no study so far has analysed the rate of proliferation and apoptosis in the normal laryngeal mucosa and in invasive laryngeal carcinomas, we performed a morphological analysis on both parameters in biopsies from 30 patients with laryngeal carcinoma. We applied the TUNEL end labelling technique for the investigation of apoptosis and immunohistochemistry (Ki‐67 antigen) for the determination of the cell proliferation.

In our study we demonstrated that invasive tumour growth of the larynx coincides with an increase of both cellular proliferation and apoptosis. Both parameters, however, affected various tumour areas differently. While there was a preferential expression of the Ki‐67 antigen at the tumour–stroma interface, apoptotic figures could be found randomly distributed in the tumour. This indicates that the replication of tumour cells and tumour cell decay are differently distributed and possibly independently regulated. Since we observed a particularly strong increase of cell proliferation at the tumour–stroma interface which outnumbered the corresponding rate of apoptosis by far, the enhanced cell proliferation at the tumour border seems to be a main factor for tumour growth.

A statistical evaluation revealed significant correlation between the apoptotic index and the degree of tumour cell differentiation, indicating that a high rate of apoptosis coincides with a high level of tumour cell differentiation.

There was, however, no statistically significant correlation between prognostic clinical parameters and the rate of apoptosis or that of proliferation.
The Statistical Properties of Host Load
Authors: Dinda Peter A.
Published: January 2015

Understanding how host load changes over time is instrumental in predicting the execution time of tasks or jobs, such as in dynamic load balancing and distributed soft real‐time systems. To improve this understanding, we collected week‐long, 1 Hz resolution traces of the Digital Unix 5 second exponential load average on over 35 different machines including production and research cluster machines, compute servers, and desktop workstations. Separate sets of traces were collected at two different times of the year. The traces capture all of the dynamic load information available to user‐level programs on these machines. We present a detailed statistical analysis of these traces here, including summary statistics, distributions, and time series analysis results. Two significant new results are that load is self‐similar and that it displays epochal behavior. All of the traces exhibit a high degree of self‐similarity with Hurst parameters ranging from 0.73 to 0.99, strongly biased toward the top of that range. The traces also display epochal behavior in that the local frequency content of the load signal remains quite stable for long periods of time (150–450 s mean) and changes abruptly at epoch boundaries. Despite these complex behaviors, we have found that relatively simple linear models are sufficient for short‐range host load prediction.
Comparison of Different Double Immunostaining Protocols for Paraffin Embedded Liver Tissue
Authors: Schütz Alexander , Tannapfel Andrea , Wittekind Christian
Published: January 2015

Most of the double immunostaining protocols that have been introduced so far have been developed for application on fresh frozen material or based on different species antibodies. In liver tissue, general problems of double immunostaining techniques are further complicated by tissue‐specific difficulties, such as necrosis or high intracellular protein content. To assess a reliable double immunostaining protocol for archived, paraffin embedded liver tissue, different protocols based on the use of same species primary antibodies were evaluated in terms of sensitivity, specificity and non‐specific background staining in pathological liver specimens. We compared peroxidase–anti‐peroxidase, alkaline phosphatase–anti‐alkaline phosphatase (PAP/APAP), labelled‐avidin–biotin (LAB/LAB) and digoxigenin–anti‐digoxigenin (dig–a‐dig/PAP) techniques using different cytokeratin antibodies and an antibody against PCNA. Comparison of the double immunostaining techniques revealed a high sensitivity and specificity in all procedures. Sections, which were stained employing PAP/APAP‐technique, displayed a higher background staining compared to sections which were treated with the LAB/LAB or dig–a‐dig/PAP protocol. In contrast to the dig–a‐dig/PAP protocol, the LAB/LAB technique provides a better time/cost relationship. Therefore, we would like to recommend a modified LAB/LAB protocol for simultaneous detection of different antigens in archived liver tissue.
Primary Unit for Statistical Analysis in Morphometry: Patient or Cell?
Authors: Tsybrovskyy Oleksiy , Berghold Andrea
Published: January 2015

In a series of 16 oxyphilic follicular neoplasms of the thyroid (8 adenomas and 8 carcinomas), three different approaches for the analysis of morphometric data were evaluated. It was shown that the statistical design of morphometric studies is by nature nested due to subsampling of cells within each patient. Therefore, the most appropriate analysis would be to account for this hierarchical structure. However, related statistical methods are not at present well established, especially as far as classification rules are concerned. Therefore, the nested design is converted into the simple factorial one by considering only one kind of statistical unit – either patients or cells. The results of the study presented indicate that ignoring the patient as unit of analysis leads to a substantial error in statistical output, regardless of the particular procedure applied. Moreover, the size of the error can be neither diminished nor controlled. Choosing patients as primary units assures accurate results and also has an advantage of gaining some additional information by calculating several distributional estimates in each patient. However, this approach often requires a reduction of dimensions and, furthermore, is not encouraged in certain fields of quantitative cytology. Advantages and disadvantages of all approaches have been summarized and practical recommendations for their use have been worked out.
Ha‐ras Oncogene Effect on DNA Content and Chromatin Supraorganization in benzo[a]pyrene‐Transformed Human Breast Epithelial Cells
Authors: Mello Maria Luiza S. , de Campos Vidal Benedicto , Russo Jose
Published: January 2015

When transfected to benzo[a]pyrene (BP)‐transformed MCF‐10F human breast epithelial cells (BP1 cell line) the c‐Ha‐ras oncogene has proven to enhance the neoplastic changes initiated by exposure to BP, giving rise to an aggressive tumorigenic cell line, BP1‐Tras. We have previously demonstrated by image analysis that BP affects the DNA content and the chromatin supraorganization of MCF‐10F cells. Here Feulgen‐stained BP1‐Tras cells were studied by image analysis in order to evaluate possible additional changes in DNA content and chromatin texture induced by insertion of the ras oncogene. A high variability in DNA content also including polyploidy or near‐polyploidy, and an increase in the packing states of the chromatin which became still condensed in BP1 cells were found in BP1‐Tras cells. The results differed from those reported for the BP1‐E1 cell line which is also an aggressive tumorigenic cell line, but was attained through progressive passages of BP‐transformed cells. It was demonstrated that different patterns of changes in DNA content and chromatin organization may be involved in equally aggressive tumorigenic BP‐transformed cell lines originated from the same cell line by different mechanisms.
Immunocytochemistry and DNA‐image Cytometry in Diagnostic Effusion Cytology. II. Diagnostic Accuracy in Equivocal Smears
Authors: Motherby Helma , Friedrichs Nicolaus , Kube Mary , Nadjari Bahram , Knops Kristiane , Donner Andreas , Baschiera Betty , Dalquen Peter , Böcking Alfred
Published: January 2015

To determine sensitivity and specificity of different antibodies for the immunocytochemical detection of malignant cells in diagnostically equivocal effusions in comparison with those achieved by DNA‐image cytometry. 65 cytologically doubtful effusions of the serous cavities were stained with twelve antibodies. Furthermore, DNA‐image cytometry was performed. Data were correlated with patient follow‐up. Sensitivity of cellular staining of Ber‐EP4 for the identification of malignant cells was 77.8%, specificity of absent staining for benign cells was 100%. Positive predictive value for the identification of malignant cells was 100%, negative value 65.5%. Sensitivity of DNA‐aneuploidy for the identification of malignancy was 82.9%, specificity of DNA‐non‐aneuploidy for benignity 94.7%. The positive predictive value of DNA‐aneuploidy for the occurrence of malignant cells was 96.7%. Negative predictive value of DNA‐non‐aneuploidy was 72.0%. Combining immunocytochemistry applying Ber‐EP4 only and DNA‐cytometry in equivocal effusions resulted in a sensitivity of 88.9% for the identification of malignant cells associated with a 95.0% specificity. Positive predictive value was 97.7%, the negative one 79.2%.
Heterogeneity in Breast Cancer and the Problem of Relevance of Findings
Authors: Aubele M. , Werner M.
Published: January 2015

Many attempts are made to identify critical genetic events responsible for the development and progression of breast cancer. There is increasing evidence that breast cancer is a heterogeneous disease, both, phenotypically as well as with respect to its molecular biologically. It is, therefore, extremely difficult to establish a diagnostically and prognostically relevant tumourigenesis model. Emerging new techniques such as microarrays, will provide us with a wealth of additional data over the next years. The precise sampling of tumour material in clearly defined histopathological lesions will be a prerequisite for the assignment of specific genetic alterations to defined stages of breast disease.
Comparison of Different Telepathology Solutions for Primary Frozen Section Diagnostic
Authors: Hufnagl P. , Bayer G. , Oberbarnscheidt P. , Wehrstedt K. , Guski H. , Hauptmann S. , Dietel M.
Published: January 2015

In a retrospective study on a set of 125 cases we compared the following three telepathology solutions for primary frozen section diagnosis: ATM‐TP (connection via ATM), TPS 1.0 (connection via LAN) and TELEMIC (connection via Internet), which represent different concepts of telepathological procedures.

A set of 125 routine frozen sections (breast) was selected from the Charité cases of the year 1999. Four experienced pathologists diagnosed retrospectively all of these cases.

Using the ATM‐TP and TPS systems and 53 of them with the TELEMIC system. Using the ATM‐TP we recorded no false positive (0%), 4 false negative (3.2%) and 4 deferred (3.2%) cases. Using the TPS we recorded no false positive (0%), 4 false negative (3.2%) and 4 deferred (3.2%) cases. Using the TELEMIC we recorded in 53 cases no false positive (0%), no false negative (0%) and 16 deferred (30.2%) cases.

The average time of 2.2 minutes per case using ATM‐TP is also short enough for routine frozen section diagnostic. This is also true for the TPS system with 7.2 minutes per case.
Restriction Enzyme Analysis of DNA Methylation in “Condensed” Chromatin of Ha‐Ras‐Transformed NIH 3T3 Cells
Authors: Mello Maria Luiza S. , Chambers Ann F. , Vidal Benedicto C. , Planding Wolfgang , Schenck Ulrich
Published: January 2015

Increased amounts of chromatin condensation (i.e., localized areas of high DNA density, or chromatin higher order packing state) have been described in NIH 3T3 cells transformed with the Ha‐ras oncogene. The structural basis for this oncogene‐mediated alteration in nuclear organization is unknown. Since DNA methylation is likely to be involved in regulating the nucleosomal level of DNA packaging, we studied the role of DNA methylation in higher‐order chromatin organization induced by Ha‐ras. CpG‐methylated DNA content was estimated in “condensed” chromatin of Ha‐ras‐transformed NIH 3T3 cell lines which differ in ras expression and ras‐induced metastatic ability but present approximately the same values of “condensed” chromatin areas. The question posed was that if DNA methylation were involved with the chromatin higher‐order organization induced by Ha‐ras in these cell lines, the methylated DNA density in the “condensed” chromatin would also be the same. The DNA evaluation was performed by video image analysis in Feulgen‐stained cells previously subjected to treatment with Msp I and Hpa II restriction enzymes, which distinguish between methylated and non‐methylated DNA. The amount of methylated CpG sequences not digested by Hpa II in “condensed” chromatin regions was found to vary in the studied ras‐transformed cell lines. DNA CpG methylation status is thus suggested not to be involved with the higher order chromatin condensation induced by ras transformation in the mentioned NIH 3T3 cell lines.
P3T+: A Performance Estimator for Distributed and Parallel Programs
Authors: Fahringer T. , Požgaj A.
Published: January 2015

Developing distributed and parallel programs on today′s multiprocessor architectures is still a challenging task. Particular distressing is the lack of effective performance tools that support the programmer in evaluating changes in code, problem and machine sizes, and target architectures. In this paper we introduce P3T+ which is a performance estimator for mostly regular HPF (High Performance Fortran) programs but partially covers also message passing programs (MPI). P3T+ is unique by modeling programs, compiler code transformations, and parallel and distributed architectures. It computes at compile‐time a variety of performance parameters including work distribution, number of transfers, amount of data transferred, transfer times, computation times, and number of cache misses. Several novel technologies are employed to compute these parameters: loop iteration spaces, array access patterns, and data distributions are modeled by employing highly effective symbolic analysis. Communication is estimated by simulating the behavior of a communication library used by the underlying compiler. Computation times are predicted through pre‐measured kernels on every target architecture of interest. We carefully model most critical architecture specific factors such as cache lines sizes, number of cache lines available, startup times, message transfer time per byte, etc. P3T+ has been implemented and is closely integrated with the Vienna High Performance Compiler (VFC) to support programmers develop parallel and distributed applications. Experimental results for realistic kernel codes taken from real‐world applications are presented to demonstrate both accuracy and usefulness of P3T+.
The AppLeS Parameter Sweep Template: User‐Level Middleware for the Grid
Authors: Casanova Henri , Obertelli Graziano , Berman Francine , Wolski Richard
Published: January 2015

The Computational Grid is a promising platform for the efficient execution of parameter sweep applications over large parameter spaces. To achieve performance on the Grid, such applications must be scheduled so that shared data files are strategically placed to maximize re‐use, and so that the application execution can adapt to the deliverable performance potential of target heterogeneous, distributed and shared resources. Parameter sweep applications are an important class of applications and would greatly benefit from the development of Grid middleware that embeds a scheduler for performance and targets Grid resources transparently. In this paper we describe a user‐level Grid middleware project, the AppLeS Parameter Sweep Template (APST), that uses application‐level scheduling techniques [1] and various Grid technologies to allow the efficient deployment of parameter sweep applications over the Grid. We discuss several possible scheduling algorithms and detail our software design. We then describe our current implementation of APST using systems like Globus [2], NetSolve [3] and the Network Weather Service [4], and present experimental results.
Coordinate Free Programming of Computational Fluid Dynamics Problems
Authors: Grant Philip W. , Haveraaen Magne , Webster Michael F.
Published: January 2015

It has long been acknowledged that the development of scientific applications is in need of better software engineering practices. Here we contrast the difference between conventional software development of CFD codes with a method based on coordinate free mathematics. The former approach leads to programs where different aspects, such as the discretisation technique and the coordinate systems, can get entangled with the solver algorithm. The latter approach yields programs that segregate these concerns into fully independent software modules. Such considerations are important for the construction of numerical codes for practical problems. The two approaches are illustrated on the coating problem: the simulation of coating a wire with a polymer.
Scalable Algorithms for Adaptive Statistical Designs
Authors: Oehmke Robert , Hardwick Janis , Stout Quentin F.
Published: January 2015

We present a scalable, high‐performance solution to multidimensional recurrences that arise in adaptive statistical designs. Adaptive designs are an important class of learning algorithms for a stochastic environment, and we focus on the problem of optimally assigning patients to treatments in clinical trials. While adaptive designs have significant ethical and cost advantages, they are rarely utilized because of the complexity of optimizing and analyzing them. Computational challenges include massive memory requirements, few calculations per memory access, and multiply‐nested loops with dynamic indices. We analyze the effects of various parallelization options, and while standard approaches do not work well, with effort an efficient, highly scalable program can be developed. This allows us to solve problems thousands of times more complex than those solved previously, which helps make adaptive designs practical. Further, our work applies to many other problems involving neighbor recurrences, such as generalized string matching.
Legal Aspects of Telepathology
Authors: Dierks Christian
Published: January 2015

In some legal surroundings telepathology is considered a breach of registrational barriers. The recommendation of the G 8 states in Europe for required legislation in telemedicine suggests to recognise that the localization of the remote health care professional defines the site not only of licensure but also of liability. This approach must be considered helpful, since it can solve many problems brought about by the doubtful results of private international law and conventions like the European Union (EU) and Lugano Convention. Under today′s conditions in private international law it must be considered essential to agree upon a choice of law and stipulate a court of jurisdiction when doing telepathology. However, the opposing aims of insuring the patients claims and avoiding jurisdictions that exceed the local expectations of the medical professional must be reconciled. Data protection and data security are other crucial topics that require attention. Generally speaking, the principles of minimum data exchange, anonymity, pseudonymity and cryptography must be established as a basis for all telepathology procedures. Only when personal data is needed, its use can be legitimated. Written consent of the patient is advised. To guarantee a cross‐border security level the regulations of the EU‐Data Protection Directive need to be transformed into national law. In practise, cross‐border dataflow shall only take place where the security level can be maintained even within the other country. Finally, reimbursement questions must be answered to establish a sound economical basis for telepathology. The spatial distance between the participants may yield the question, whether the service has been rendered to an extent necessary and sufficient for reimbursement. If reimbursement takes place on a cross‐border or cross‐regional level, severe disturbances of the health systems can occur. Regulation schemes or treaties need therefore to be developed to avoid such disturbances and encompass mutual standards of care as well as methods to balance reimbursement.
Programmed Cell Death, Proliferating Cell Nuclear Antigen and p53 Expression in Mouse Colon Mucosa during Diet‐Induced Tumorigenesis
Authors: Risio Mauro , Sarotto Ivana , Rossini Francesco Paolo , Newmark Harold , Yang Kan , Lipkin Martin
Published: January 2015

Western‐style diets (WDs) trigger and sustain the early phases of tumorigenesis in mouse colon, and when continued throughout the life span lead to the development of dysplastic crypts. In order to evaluate the roles both of cell proliferation and programmed cell death (PCD) in WD‐induced tumorigenesis, immunohistochemical detection of proliferating nuclear antigen (PCNA), in situ end labeling (TUNEL) of DNA breaks, and p53 protein were carried out in mouse colonic mucosa during prolonged feeding of two WDs. PCNA Labeling Index of colonic crypts was significantly higher in WD‐treated animals than in controls only at the beginning of the nutritional study, the gap rapidly bridged by increased cell proliferation spontaneously occurring in the colonic mucosa during aging. A transient early homeostatic activation of PCD at the base of the crypt also was observed in WD groups. No changes in PCD were seen in the upper third of the crypt or in surface epithelium throughout the study, indicating that PCD in that colonic crypt segment produces a constant flux of cell loss, uninfluenced by homeostatic fluctuations. A major finding was an irreversible, progressive, age‐related decline of PCD at the crypt base in both control and treated animals that occurred during the second half of the rodents  life span. p53 protein was not immunohistochemically detected, suggesting that neither overexpression of wild‐type nor mutated forms of the protein are involved in the above mentioned changes.
Teleeducation and Telepathology for Open and Distance Education
Authors: Szymas Janusz
Published: January 2015

Our experience in creating and using telepathology system and multimedia database for education is described. This program packet currently works in the Department of Pathology of University Medical School in Poznan. It is used for self‐education, tests, services and for the examinations in pathology, i.e., for dental students and for medical students in terms of self‐education and individual examination services. The system is implemented on microcomputers compatible with IBM PC and works in the network system Netware 5.1. Some modules are available through the Internet. The program packet described here accomplishes the TELEMIC system for telepathology, ASSISTANT, which is the administrator for the databases, and EXAMINATOR, which is the executive program. The realization of multi‐user module allows students to work on several working areas, on random be chosen different sets of problems contemporary. The possibility to work in the exercise mode will image files and questions is an attractive way for self‐education. The standard format of the notation files enables to elaborate the results by commercial statistic packets in order to estimate the scale of answers and to find correlation between the obtained results. The method of multi‐criterion grading excludes unlimited mutual compensation of the criteria, differentiates the importance of particular courses and introduces the quality criteria. The packet is part of the integrated management information system of the department of pathology. Applications for other telepathological systems are presented.
Portable Library of Migratable Sockets
Authors: Bubak Marian , Żbik Dariusz , Albada Dick van , Iskra Kamil , Sloot Peter
Published: January 2015

Efficient load balancing is essential for parallel distributed computing. Many parallel computing environments use TCP or UDP through the socket interface as a communication mechanism. This paper presents the design and development of a prototype implementation of a network interface that can preserve communication between processes during process migration. This new communication library is a substitution for the well‐known socket interface. It is implemented in user — space; it is portable, and no modifications of user applications are required. TCP/IP is applied for internal communication, which guarantees relatively high performance and portability.
Automatic Registration and Error Detection of Multiple Slices Using Landmarks
Authors: Frimmel Hans , Egevad Lars , Busch Christer , Bengtsson Ewert
Published: January 2015

Objectives. When analysing the 3D structure of tissue, serial sectioning and staining of the resulting slices is sometimes the preferred option. This leads to severe registration problems. In this paper, a method for automatic registration and error detection of slices using landmark needles has been developed. A cost function takes some parameters from the current state of the problem to be solved as input and gives a quality of the current solution as output. The cost function used in this paper, is based on a model of the slices and the landmark needles. The method has been used to register slices of prostates in order to create 3D computer models. Manual registration of the same prostates has been undertaken and compared with the results from the algorithm. Methods. Prostates from sixteen men who underwent radical prostatectomy were formalin fixed with landmark needles, sliced and the slices were computer reconstructed. The cost function takes rotation and translation for each prostate slice, as well as slope and offset for each landmark needle as input. The current quality of fit of the model, using the input parameters given, is returned. The function takes the built‐in instability of the model into account. The method uses a standard algorithm to optimize the prostate slice positions. To verify the result, s standard method in statistics was used. Results. The methods were evaluated for 16 prostates. When testing blindly, a physician could not determine whether the registration shown to him were created by the automated method described in this paper, or manually by an expert, except in one out of 16 cases. Visual inspection and analysis of the outlier confirmed that the input data had been deformed. The automatic detection of erroneous slices marked a few slices, including the outlier, as suspicious. Conclusions. The model based registration performs better than traditional simple slice‐wise registration. In the case of prostate slice registration, other aspects, such as the physical slicing method used, may be more important to the final result than the selection of registration method to use.
Development of Mixed Mode MPI / OpenMP Applications
Authors: Smith Lorna , Bull Mark
Published: January 2015

MPI / OpenMP mixed mode codes could potentially offer the most effective parallelisation strategy for an SMP cluster, as well as allowing the different characteristics of both paradigms to be exploited to give the best performance on a single SMP. This paper discusses the implementation, development and performance of mixed mode MPI / OpenMP applications. The results demonstrate that this style of programming will not always be the most effective mechanism on SMP systems and cannot be regarded as the ideal programming model for all codes. In some situations, however, significant benefit may be obtained from a mixed mode implementation. For example, benefit may be obtained if the parallel (MPI) code suffers from: poor scaling with MPI processes due to load imbalance or too fine a grain problem size, memory limitations due to the use of a replicated data strategy, or a restriction on the number of MPI processes combinations. In addition, if the system has a poorly optimised or limited scaling MPI implementation then a mixed mode code may increase the code performance.
Effect of Osmolarity and Presence of Serum on the Efficiency of Cell Transfection Using Immunoporation
Authors: Tzavelas C. , Smith P. , Horefti E. , Rickwood D.
Published: January 2015

Immunoporation is a novel method of cell transfection based upon the use of a new type of beads, Immunofect beads, that can be targeted to make holes in different types of cells depending on the type of bead used. It is known that the efficiency of transfection of cells by some techniques can be affected by the presence of serum and another important factor that appears to affect transfection efficiency and cell viability is the osmolarity of the transfection medium. This report presents studies on the effects of serum and varying osmolarity on the efficiency of transfection using immunoporation. The results clearly indicate that in hypertonic media the presence of serum decreases the efficiency of transfection. In the case of osmolarity, increasing the osmolarity of the immunoporation medium increases the efficiency of transfection but above about 650 mOsm this increasing efficiency is offset by the much lower viability of the cells.
DNA Ploidy and S‐Phase Fraction in Carcinoma of the Gallbladder Related to Histopathology, Number of Gallstones and Survival 1
Authors: Gustafsson Ulf , Einarsson Curt , Eriksson Lennart C. , Gadaleanu Virgil , Sahlin Staffan , Tribukait Bernhard
Published: January 2015

Gallstones are a risk factor for the development of gallbladder cancer. We studied DNA ploidy and cell cycle composition by flow cytometry in archival specimens from 52 gall bladder carcinomas in relation to histopathological grade, tumour stage, gallstone number and survival. 69% of the gallbladder carcinomas showed aneuploidy. All tumours with single stones (N=11) were aneuploid while only 61% of tumours with multiple stones (N=41) were aneuploid (p=0.002). DNA aneuploidy was related to increase in T‐category (p=0.01), grade (p=0.02), and nuclear pleomorphism (p=0.0005). The distribution of DNA ploidy shifted from tetraploid in low stage towards triploid positions in high stage tumours (p=0.02) combined with higher S‐phase values in triploid tumours (p=0.05). S‐phase fraction increased during development from normal tissue to dysplasia, cancer in situ and cancer in diploid cases (p=0.0002), and further at the change from diploid to aneuploid (p=0.004). At a median cancer specific survival time of four months patients with diploid tumours had a better survival than those with aneuploid tumours (p=0.02). In multivariate analysis of the tumour characteristic, only T‐category and tumour grade were independent prognostic factors. The shift from diploid to aneuploid and the further shift of ploidy within aneuploid tumours are in agreement with the concept of a clonal development of gallbladder cancer. These changes are combined with a stepwise increase in the fraction of S‐phase cells. Low frequency of symptoms in single stone patients may be the reason for detection of malignancy at a late stage of tumour development.
Fibroblast Growth Factor Receptor 3 (FGFR3)–Analyses of the S249C Mutation and Protein Expression in Primary Cervical Carcinomas
Authors: Dai Haiyan , Holm Ruth , Kristensen Gunnar B. , Abeler Vera M. , Børresen‐Dale Anne‐Lise , Helland Åslaug
Published: January 2015

Fibroblast growth factor receptor 3 (FGFR3) seems to play an inhibitory role in bone development, as activating mutations in the gene underlie disorders such as achondroplasia and thanatophoric dysplasia. Findings from multiple myeloma (MM) indicate that FGFR3 also can act as an oncogene, and mutation of codon 249 in the fibroblast growth factor receptor 3 (FGFR3) gene was recently detected in 3/12 primary cervical carcinomas. We have analysed 91 cervical carcinomas for this specific S249C mutation using amplification created restriction site methodology (ACRS), and detected no mutations. Immunohistochemistry was performed on 73 of the tumours. Reduced protein staining was seen in 43 (58.8%) samples. Six of the tumours (8.2%) revealed increased protein staining compared with normal cervical tissue. These patients had a better prognosis than those with reduced or normal levels, although not statistically significant. This report weakens the hypothesis of FGFR3 as an oncogene of importance in cervical carcinomas.