bluuebunny/crossref_metadata_2025 huggingface dataset:
Critical Evaluation of Techniques to Detect and Measure Cell Death – Study in a Model of UV Radiation of the Leukaemic Cell Line HL60
Authors: Leite Marina , Quinta‐Costa Margarida , Leite Pedro Simas , Guimarães José Eduardo
Published: January 2015

The reliability of eight distinct methods (Giemsa staining, trypan blue exclusion, acridine orange/ethidium bromide (AO/EB) double staining for fluorescence microscopy and flow cytometry, propidium iodide (PI) staining, annexin V assay, TUNEL assay and DNA ladder) for detection and quantification of cell death (apoptosis and necrosis) was evaluated and compared. Each of these methods detects different morphological or biochemical features of these two processes. The comparative analysis of the 8 techniques revealed that AO/EB (read in fluorescence microscopy) provides a reliable method to measure cells in different compartments (or pathways) of cell death though it is very time consuming. PI staining and TUNEL assay were also sensitive in detecting very early signs of apoptosis, but do not allow precise quantification of apoptotic cells. These three methods were concordant in relation to induction of apoptosis and necrosis in HL60 cells with the various UV irradiation time periods tested. Both AO/EB (read by flow cytometry) and annexin V‐FITC/PI failed to detect the same number of early apoptotic cells as the other three methods. Trypan blue is valueless for this purpose. Giemsa and DNA ladder might be useful as confirmatory tests in some situations.
Impulse: Memory System Support for Scientific Applications
Authors: Carter John B. , Hsieh Wilson C. , Stoller Leigh B. , Swanson Mark , Zhang Lixin , McKee Sally A.
Published: January 2015

Impulse is a new memory system architecture that adds two important features to a traditional memory controller. First, Impulse supports application‐specific optimizations through configurable physical address remapping. By remapping physical addresses, applications control how their data is accessed and cached, improving their cache and bus utilization. Second, Impulse supports prefetching at the memory controller, which can hide much of the latency of DRAM accesses. Because it requires no modification to processor, cache, or bus designs, Impulse can be adopted in conventional systems. In this paper we describe the design of the Impulse architecture, and show how an Impulse memory system can improve the performance of memory‐bound scientific applications. For instance, Impulse decreases the running time of the NAS conjugate gradient benchmark by 67%. We expect that Impulse will also benefit regularly strided, memory‐bound applications of commercial importance, such as database and multimedia programs.
Compiler Optimization to Improve Data Locality for Processor Multithreading
Authors: Sinharoy Balaram
Published: January 2015

Over the last decade processor speed has increased dramatically, whereas the speed of the memory subsystem improved at a modest rate. Due to the increase in the cache miss latency (in terms of the processor cycle), processors stall on cache misses for a significant portion of its execution time. Multithreaded processors has been proposed in the literature to reduce the processor stall time due to cache misses. Although multithreading improves processor utilization, it may also increase cache miss rates, because in a multithreaded processor multiple threads share the same cache, which effectively reduces the cache size available to each individual thread. Increased processor utilization and the increase in the cache miss rate demands higher memory bandwidth. A novel compiler optimization method has been presented in this paper that improves data locality for each of the threads and enhances data sharing among the threads. The method is based on loop transformation theory and optimizes both spatial and temporal data locality. The created threads exhibit high level of intra‐thread and inter‐thread data locality which effectively reduces both the data cache miss rates and the total execution time of numerically intensive computation running on a multithreaded processor.
Flow Cytometric Immunophenotyping of Mature Lymphatic Neoplasias Using Knowledge Guided Cluster Analysis
Authors: Barlage Stefan , Rothe Gregor , Knuechel Ruth , Schmitz Gerd
Published: January 2015

Flow cytometry is widely used for the immunological characterization of hematopoietic malignancies. Discrimination of normal and malignant cellular immunophenotypes is the most critical step in data analysis, especially if multi‐color analysis is performed on highly heterogenous cell suspensions. We therefore investigated, whether adaptive, simultaneous multiparameter gating allowed automated, operator independent analysis of data obtained from the immunophenotyping of blood or bone marrow samples with regard to the presence of non‐Hodgkin lymphoma cells. The identification of physiological and malignant cells was achieved by predefining population boundaries, based on the expectations of the population’s location in two‐dimensional dot plots. The prospective application of these predefined region boundaries in 52 blood and bone marrow samples enabled identification of lymphoma cells with regard to their presence and immunophenotype, based on the correlation of markers as defined in multiple tubes. Our data confirm that highly standardized data analysis methods can reduce the variability of analysis and support the expert in establishing a rapid classification of the sample.
Human Breast Carcinomal Tissues Display Distinctive FTIR Spectra: Implication for the Histological Characterization of Carcinomas
Authors: Gao Tiyu , Feng Jun , Ci Yunxiang
Published: January 2015

Fourier transform infrared spectroscopic study of human breast normal and carcinomal tissues has been carried out. Some distinctive spectral differences which are mainly due to nucleic acids and proteins are observed between normal and carcinomal tissues. This method of analysis results in nearly 100% diagnostic accuracy of carcinomal tissues from normal tissues. The spectral patterns of well‐differentiated carcinomal tissues exhibit marked heterogeneity, however that of poorly differentiated carcinomas demonstrate significant similarity. Apocrine, tubular, intraductal and mucinous carcinomas and invasive infiltrating ductal carcinomal tissues can be discriminated based on their characteristic spectra. The spectral differences confirm the possibility of using FTIR as an accurate and rapid technique to distinguish between normal and malignant breast tissues and classify breast carcinomas in different subtypes.
Deformable Models for Segmentation of CLSM Tissue Images and Its Application in FISH Signal Analysis
Authors: Umesh Adiga P. S. , Chaudhuri B. B.
Published: January 2015

In this paper we present an application of deformable models for the segmentation of volumetric tissue images. The three‐dimensional images are obtained using confocal microscope. The segmented images have been used for the quantitative analysis of the Fluorescence In Situ Hybridization (FISH) signals. An ellipsoidal surface initialized around the cell of interest acts as a deformable model. The deformable model surface voxels are subjected to various internal and external forces derived from underlying image features as well as externally imposed constraints. The deformable model converges to the optimum cell shape when the vector sum of all the forces acting on the model is zero. The result of segmentation is used to confirm the cell membership of the FISH signals and to reject all the signals that lie outside the cell nuclei. Three‐dimensional region isolation and labeling technique is used to label and count the FISH signals per cell nucleus. A simple study on the effect of different segmentation methods over a quantitative analysis of FISH signals is also presented.
Evaluation of Heterogeneity of DNA Ploidy in Early Gastric Cancers
Authors: Osterheld M. C. , Laurini R. , Saraga E. , Bosman F. T.
Published: January 2015

DNA ploidy has been shown to be a predictive parameter for prognosis in various solid tumours. The prognostic value of DNA‐ploidy in gastric cancers is still a matter of controversy. A possible explanation for the discrepant results reported in the literature could be sampling error in tumours with multiple stemlines differing in DNA‐ploidy. In order to determine whether or not such heterogeneity exists in early gastric carcinoma, we have performed DNA cytophotometry on multiple samples of a group of 17 early gastric carcinomas, of which 8 were pure intramucosal and 9 were infiltrating into the submucosa. We found an aneuploid DNA‐stemline in 8 (47%) early gastric cancers, more often in tumours invading into the submucosa (5/9) than in purely mucosal tumours (3/8). Multiple DNA‐stemlines were found more frequently in submucosally infiltrating tumours (4/5). These results confirm the presence of DNA‐aneuploid early gastric carcinoma which are frequently heterogeneous and suggest that heterogeneity occurs more frequently in tumours invading the submucosa. This heterogeneity is best detected by analysing multiple samples of tumours for DNA‐ploidy.
Inverse Relationship Between Leydig Cell Density and Metastatic Potential of Prostatic Adenocarcinoma
Authors: Wang W. John , Yeh Y. Albert , Stout Paul , Fan Kang
Published: January 2015

Purpose: Evaluate the relationship between metastatic potential of prostatic adenocarcinoma (PC) and testicular Leydig cell density. Materials and methods: Tissue samples from 111 men, age 52–85, with PC and bilateral orchiectomy were evaluated for Leydig cell density. The patients were divided into two groups: Group A were patients with metastasis (n=36) and Group B were patients without metastasis (n=75). Leydig cell density was determined by direct manual microscopic cell count on the tissue sections. The means of cell counts by four pathologists, expressed as cell/0.78 mm2 were used for analysis. The normally distributed data were analyzed by two‐tail Student’s t‐test. Thirty‐eight age‐compatible autopsy cases who died of unrelated causes served as normal controls. Results: The mean of Leydig cell count in group A patients was 14.43 (14.43 ± 1.19 SE). Mean of Group B was 47.05 (47.05 ± 4.05 SE) whereas normal controls displayed a mean of 48.66 (48.66 ± 2.94 SE). Group A was significantly different from control (p<0.00001). Group A and Group B were also significant different (p<0.001) whereas control was not significantly different from Group B (p>0.75). Conclusions: Patients with metastatic adenocarcinoma of prostate, as a group, have a significantly lower Leydig cell density than patients without metastasis or patients without PC in compatible age groups. The hormonal relationship between this observation is however unknown. One possible explanation is that PC subpopulation with metastatic potential may require different level of endogenous androgen or are androgen‐independent.
Immunocytochemistry and DNA‐Image Cytometry in Diagnostic Effusion Cytology I. Prevalence of Markers in Tumour Cell Positive and Negative Smears
Authors: Motherby Helma , Kube Mary , Friedrichs Nikolaus , Nadjari Bahram , Knops Kristiane , Donner Andreas , Baschiera Betty , Dalquen Peter , Böcking Alfred
Published: January 2015

To determine the prevalence of immunocytochemical positivities for a panel of antibodies in benign and malignant cells in effusions with known follow‐up in order to use these as diagnostic markers. Besides their ability to identify malignant epithelial cells their contribution to the differential diagnosis between carcinomatoses and mesotheliomas was investigated. 101 tumour cell positive and 53 negative effusions were stained with 12 different antibodies. Results were scored semiquantitatively per cell type. Furthermore, DNA‐image cytometry was performed. While prevalence of Ber‐EP4 positivity was 95.4% in metastatic carcinoma cells, it was 0% in those from mesotheliomas. No cell type reacted with this marker in benign effusions (0%). Ber‐EP4 correctly differentiated between metastatic carcinoma and mesothelioma in 98.0%. Prevalence of DNA‐aneuploidy was 95.4% in metastatic carcinomas, 57.1% in mesotheliomas and 0% in reactive effusions. Combining immunocytochemistry (Ber‐EP4 positivity) and DNA‐image cytometry (aneuploidy) results in a 100% detection of metastatic carcinomatoses and 57.1% of mesotheliomas. Both markers furthermore allowed a correct differentiation of these entities in 98%.
Origin of Microcells in the Human Sarcoma Cell Line HT‐1080
Authors: Buiķis Indulis , Harju Līga , Freivalds Tālivaldis
Published: January 2015

The aim of this study was to investigate the development of microcells in the human sarcoma cell line HT‐1080 after interference with thiophosphamidum. We found that damaged interphase macrocells located at the projection of the nucleolus may form one or several microcells. The micronuclei of the microcells intensively incorporate the thymidine analogue 5‐bromo‐2′‐deoxyuridine and strongly express argyrophilic nucleolar organiser region proteins. At an early phase of the development, the micronuclei contain fragmented DNA, but in subsequent phases, the micronuclei accumulate polymeric DNA, simultaneously with an increase in their size. After desintegration of the damaged macrocell, the microcells appear in the intercellular space. The microcells can enter mitosis and they strongly express the lung resistance protein. Electron microscopic observations suggest that coiled bodies are involved in the development of the microcells. Since the observed path of microcell formation differs from apoptotic cell fragmentation into apoptotic bodies, we propose a new term for this microcell development: sporosis. We suggest that self‐renewal of the tumour stem cells is likely based on sporosis.
The Cost of being Object‐Oriented: A Preliminary Study
Authors: Budimlić Zoran , Kennedy Ken , Piper Jeff
Published: January 2015

Since the introduction of the Java programming language, there has been widespread interest in the use Java for the high performance scientific computing. One major impediment to such use is the performance penalty paid relative to Fortran. To support our research on overcoming this penalty through compiler technology, we have developed a benchmark suite, called OwlPack, which is based on the popular LINPACK library. Although there are existing implementations of LINPACK in Java, most of these are produced by direct translation from Fortran. As such they do not reflect the style of programming that a good object‐oriented programmer would use in Java. Our goal is to investigate how to make object‐oriented scientific programming practical. Therefore we developed two object‐oriented versions of LINPACK in Java, a true polymorphic version and a “Lite” version designed for higher performance. We used these libraries to perform a detailed performance analysis using several leading Java compilers and virtual machines, comparing the performance of the object‐oriented versions of the benchmark with a version produced by direct translation from Fortran. Although Java implementations have been made great strides, they still fall short on programs that use the full power of Java’s object‐oriented features. Our ultimate goal is to drive research on compiler technology that will reward, rather than penalize good object‐oriented programming practice.
Quantitative Immunohistochemical Analyses of the Expression of E‐Cadherin, Thrombomodulin, CD44H and CD44v6 in Primary Tumours of pharynx/larynx Squamous Cell Carcinoma and their Lymph Node Metastases
Authors: Gaspar Rocío Hernández , de los Toyos Juan R. , Marcos César Álvarez , Riera José Ramón , Sampedro Andrés
Published: January 2015

The quantitative expression of E‐cadherin, thrombomodulin, CD44H and CD44v6 in 32 specimens of primary tumours of pharynx/larynx squamous cell carcinoma and their lymph node metastases was studied by immunohistochemistry. With the aim of obtaining comparative and objective data, image acquisition conditions were kept unaltered for all the measurements and the immunostaining intensity was quantified by applying an image processing system. On the one hand, correlations were only observed between CD44H and CD44v6, both in primary tumours and metastases, and between E‐cadherin and TM in metastases. On the other hand, statistical analyses of paired data did not show significant differences in the expression of these markers between the two tumour sites. In agreement with previous reports, E‐cadherin expression was rather low or negative in primary tumours and metastases of the three poorly differentiated specimens we studied, as well as that of TM, but otherwise some of these samples showed intermediate immunostaining levels of CD44H/CD44v6. It may be concluded from the present study that the quantitative expression of these adhesion molecules in well established lymph node metastases of pharynx/larynx squamous cell carcinoma is essentially unaltered in relation to their primary sites.
Menhir: An Environment for High Performance Matlab
Authors: Chauveau Stéphane , Bodin François
Published: January 2015

In this paper we present Menhir a compiler for generating sequential or parallel code from the Matlab language. The compiler has been designed in the context of using Matlab as a specification language. One of the major features of Menhir is its retargetability to generate parallel and sequential C or Fortran code. We present the compilation process and the target system description for Menhir. Preliminary performances are given and compared with MCC, the MathWorks Matlab compiler.
CRAUL: Compiler and Run‐Time Integration for Adaptation under Load
Authors: Ioannidis Sotiris , Rencuzogullari Umit , Stets Robert , Dwarkadas Sandhya
Published: January 2015

Clusters of workstations provide a cost‐effective, high performance parallel computing environment. These environments, however, are often shared by multiple users, or may consist of heterogeneous machines. As a result, parallel applications executing in these environments must operate despite unequal computational resources. For maximum performance, applications should automatically adapt execution to maximize use of the available resources. Ideally, this adaptation should be transparent to the application programmer. In this paper, we present CRAUL (Compiler and Run‐Time Integration for Adaptation Under Load), a system that dynamically balances computational load in a parallel application. Our target run‐time is software‐based distributed shared memory (SDSM). SDSM is a good target for parallelizing compilers since it reduces compile‐time complexity by providing data caching and other support for dynamic load balancing. CRAUL combines compile‐time support to identify data access patterns with a run‐time system that uses the access information to intelligently distribute the parallel workload in loop‐based programs. The distribution is chosen according to the relative power of the processors and so as to minimize SDSM overhead and maximize locality. We have evaluated the resulting load distribution in the presence of different types of load – computational, computational and memory intensive, and network load. CRAUL performs within 5–23% of ideal in the presence of load, and is able to improve on naive compiler‐based work distribution that does not take locality into account even in the absence of load.
Irregular Computations in Fortran – Expression and Implementation Strategies
Authors: Prins Jan F. , Chatterjee Siddhartha , Simons Martin
Published: January 2015

Modern dialects of Fortran enjoy wide use and good support on high‐performance computers as performance‐oriented programming languages. By providing the ability to express nested data parallelism, modern Fortran dialects enable irregular computations to be incorporated into existing applications with minimal rewriting and without sacrificing performance within the regular portions of the application. Since performance of nested data‐parallel computation is unpredictable and often poor using current compilers, we investigate threading and flattening, two source‐to‐source transformation techniques that can improve performance and performance stability. For experimental validation of these techniques, we explore nested data‐parallel implementations of the sparse matrix‐vector product and the Barnes–Hut n‐body algorithm by hand‐coding thread‐based (using OpenMP directives) and flattening‐based versions of these algorithms and evaluating their performance on an SGI Origin 2000 and an NEC SX‐4, two shared‐memory machines.
Diagnosis and Prognosis of Neuroendocrine Tumours of the Lung by Means of High Resolution Image Analysis
Authors: Jütting Uta , Gais Peter , Rodenacker Karsten , Böhm Joachim , Koch Susanne , Präuer Heinz W. , Höfler Heinz
Published: January 2015

Neuroendocrine tumours (NET) of the lung are divided in subtypes with different malignant potential. The first is the benign or low‐grade malignant tumours, well‐differentiated, called typical carcinoids (TC) and the second is the high‐grade malignant tumours, poorly differentiated of small (SCLC) or large cell type (LCLC). Between these tumour types lies the well‐differentiated carcinoma with a lower grade of malignancy (WDNEC). In clinical routine it is very important with regard to prognosis to distinguish patients with low malignant potential from those with higher ones. In this study 32 cases of SCLC, 13 of WDNEC and 14 of TC with a follow‐up time up to 7 years were collected. Sections 4 μm thick from paraffin embedded tissue were Feulgen stained. By means of high resolution image analysis 100 nuclei per case were randomly gathered to extract morphometric, densitometric and textural quantitative features. To investigate the ploidy status of the tumour the corrected DNA distribution was calculated. Stepwise linear discriminant analysis to differentiate the classes and Cox regression analysis for the survival time analysis were applied. Using chromatin textural and morphometric features in two two‐class discriminations, 11 of the 14 TC cases and 8 of the 13 WDNEC cases were correctly classified and 11/13 WDNEC cases and 28/32 SCLC cases, respectively. The WDNEC cases are more similar in chromatin structure to TC than to SCLC. For the survival analysis, only chromatin features were selected to differentiate patients with better and worse prognosis independent of staging and tumour type.
Quantification of Eosinophilic Granule Protein Deposition in Biopsies of Inflammatory Skin Diseases by Automated Image Analysis of Highly Sensitive Immunostaining
Authors: Kiehl Peter , Falkenberg Katrin , Vogelbruch Markus , Kapp Alexander
Published: January 2015

Eosinophilic granulocytes are major effector cells in inflammation. Extracellular deposition of toxic eosinophilic granule proteins (EGPs), but not the presence of intact eosinophils, is crucial for their functional effect in situ. As even recent morphometric approaches to quantify the involvement of eosinophils in inflammation have been only based on cell counting, we developed a new method for the cell‐independent quantification of EGPs by image analysis of immunostaining. Highly sensitive, automated immunohistochemistry was done on paraffin sections of inflammatory skin diseases with 4 different primary antibodies against EGPs. Image analysis of immunostaining was performed by colour translation, linear combination and automated thresholding. Using strictly standardized protocols, the assay was proven to be specific and accurate concerning segmentation in 8916 fields of 520 sections, well reproducible in repeated measurements and reliable over 16 weeks observation time. The method may be valuable for the cell‐independent segmentation of immunostaining in other applications as well.
Automatic Migration from PARMACS to MPI in Parallel Fortran Applications
Authors: Hempel Rolf , Zimmermann Falk
Published: January 2015

The PARMACS message passing interface has been in widespread use by application projects, especially in Europe. With the new MPI standard for message passing, many projects face the problem of replacing PARMACS with MPI. An automatic translation tool has been developed which replaces all PARMACS 6.0 calls in an application program with their corresponding MPI calls. In this paper we describe the mapping of the PARMACS programming model onto MPI. We then present some implementation details of the converter tool.
Influence of Sampling Practices on the Appearance of DNA Image Histograms of Prostate Cells in FNAB Samples
Authors: Buhmeida Abdelbaset , Kuopio Teijo , Collan Yrjö
Published: January 2015

Twenty‐one fine needle aspiration biopsies (FNAB) of the prostate, diagnostically classified as definitely malignant, were studied. The Papanicolaou or H&E stained samples were destained and then stained for DNA with the Feulgen reaction. DNA cytometry was applied after different sampling rules. The histograms varied according to the sampling rule applied. Because free cells between cell groups were easier to measure than cells in the cell groups, two sampling rules were tested in all samples: (i) cells in the cell groups were measured, and (ii) free cells between cell groups were measured. Abnormal histograms were more common after the sampling rule based on free cells, suggesting that abnormal patterns are best revealed through the free cells in these samples. The conclusions were independent of the applied histogram interpretation method.
Automatic Choice of Scheduling Heuristics for Parallel/Distributed Computing
Authors: Ferner Clayton S. , Babb Robert G.
Published: January 2015

Task mapping and scheduling are two very difficult problems that must be addressed when a sequential program is transformed into a parallel program. Since these problems are NP‐hard, compiler writers have opted to concentrate their efforts on optimizations that produce immediate gains in performance. As a result, current parallelizing compilers either use very simple methods to deal with task scheduling or they simply ignore it altogether. Unfortunately, the programmer does not have this luxury. The burden of repartitioning or rescheduling, should the compiler produce inefficient parallel code, lies entirely with the programmer. We were able to create an algorithm (called a metaheuristic), which automatically chooses a scheduling heuristic for each input program. The metaheuristic produces better schedules in general than the heuristics upon which it is based. This technique was tested on a suite of real scientific programs written in SISAL and simulated on four different network configurations. Averaged over all of the test cases, the metaheuristic out‐performed all eight underlying scheduling algorithms; beating the best one by 2%, 12%, 13%, and 3% on the four separate network configurations. It is able to do this, not always by picking the best heuristic, but rather by avoiding the heuristics when they would produce very poor schedules. For example, while the metaheuristic only picked the best algorithm about 50% of the time for the 100 Gbps Ethernet, its worst decision was only 49% away from optimal. In contrast, the best of the eight scheduling algorithms was optimal 30% of the time, but its worst decision was 844% away from optimal.
Textural Analysis of Nuclear Mitotic Apparatus Antigen (NuMA) Spatial Distribution in Interphase Nuclei from Human Drug‐Resistant CEM Lymphoblasts
Authors: Rafki‐Beljebbar Naima , Liautaud‐Roger Françoise , Ploton Dominique , Dufer Jean
Published: January 2015

In tumour cell lines, the resistance of cancer cells to a variety of structurally unrelated chemotherapeutic drugs is termed multidrug‐resistance or MDR. We reported previously that MDR leukemic cells displayed nuclear texture changes, as assessed by image cytometry. The nature of these changes remained uncertain but they could be associated with alterations of the nuclear matrix which could serve an important role in DNA organization and chromatin structure. Therefore, we have compared the textural features observed in G0/G1 nuclei from human leukemic CEM cells and their MDR variant CEM‐VLB, after staining of either DNA by Feulgen method or nuclear matrix by immunodetection of NuMA antigen on DNase treated samples. Chromatin or NuMA distributions within the nucleus were evaluated by image cytometry. Changes in textural parameters indicate that modifications of NuMA distribution observed in MDR cells are parallel to those observed at the whole chromatin level (i.e., a more decondensed and coarse texture with increase of Energy and Long‐run sections and decrease of Contrast and Short‐run sections). Moreover, Optical Densities measurements indicate that MDR cells seem to contain less NuMA, a datum confirmed by immunoblotting of nuclear proteins. In conclusion, chromatin changes observed by image cytometry in drug‐resistant human leukemic CEM cells appear associated with modifications of the nuclear matrix structure.
The Use of Fractal Features from the Periphery of Cell Nuclei as a Classification Tool
Authors: Nielsen Birgitte , Albregtsen Fritz , Danielsen Håvard E.
Published: January 2015

A polygonization‐based method is used to estimate the fractal dimension and several new scalar lacunarity features from digitized transmission electron micrographs (TEM) of mouse liver cell nuclei. The fractal features have been estimated in different segments of 1D curves obtained by scanning the 2D cell nuclei in a spiral‐like fashion called “peel‐off scanning”. This is a venue to separate estimates of fractal features in the center and periphery of a cell nucleus. Our aim was to see if a small set of fractal features could discriminate between samples from normal liver, hyperplastic nodules and hepatocellular carcinomas. The Bhattacharyya distance was used to evaluate the features. Bayesian classification with pooled covariance matrix and equal prior probabilities was used as the rule for classification. Several single fractal features estimated from the periphery of the cell nuclei discriminated samples from the hyperplastic nodules and hepatocellular carcinomas from normal ones. The outer 25–30% of the cell nuclei contained important texture information about the differences between the classes. The polygonization‐based method was also used as an analysis tool to relate the differences between the classes to differences in the chromatin structure.
Telediagnosis of Transbronchial Fine Needle Aspirations – A Feasibility Study
Authors: Kayser K. , Kayser G. , Becker H. D. , Herth F.
Published: January 2015

Aim: To analyze the diagnostic accuracy of telediagnostic procedures for transbronchial fine needle aspirations. Material and Methods: A double blind study was performed on cytological slides of 54 randomly selected cases with transbronchial fine needle aspirations. The slides were digitized using a Leica digital camera DC100 mounted on a microscope Leica Laborlux S, and analyzed by an experienced pathologist without knowing the definite diagnosis or any additional clinical data. The diagnoses stated by analyzing the digital images were compared to the final conventional diagnoses. In addition, the duration of the digital diagnosis, used magnifications, and difficulties for correct sampling were documented. Results: The “digital” diagnoses of the 54 cases were all in general agreement with the definite diagnoses. No wrong positive or wrong negative case in respect to malignant/non‐malignant (31/23) or to small cell/non‐small cell (9/22) occurred. The performance of a digital diagnosis lasted for 115 s at average (15–260 s), and is significantly longer compared to that of conventional fine needle aspiration judgement (20 s). The screening magnification was commonly set to ×2.5, that for definite diagnostic analysis ×40. Benign diseases (2 tuberculosis and 3 sarcoidosis cases) were correctly classified. Conclusions: Telepathology systems can probably be used for fine needle aspiration analysis without major diagnostic errors. Their use can improve the endoscopic sampling and avoid second anesthesia when missing the lesion of request during the first examination.
Diagnostic Errors in Interactive Telepathology
Authors: Stauch G. , Schweppe K. W. , Kayser K.
Published: January 2015

Telepathology (TP) as a service in pathology at a distance is now widely used. It is integrated in the daily workflow of numerous pathologists. Meanwhile, in Germany 15 departments of pathology are using the telepathology technique for frozen section service; however, a common recognised quality standard in diagnostic accuracy is still missing. In a first step, the working group Aurich uses a TP system for frozen section service in order to analyse the frequency and sources of errors in TP frozen section diagnoses for evaluating the quality of frozen section slides, the important components of image quality and their influences an diagnostic accuracy. The authors point to the necessity of an optimal training program for all participants in this service in order to reduce the risk of diagnostic errors. In addition, there is need for optimal cooperation of all partners involved in TP service.
Digital Imaging Analysis for the Study of Endotoxin‐Induced Mitochondrial Ultrastructure Injury
Authors: Joshi Mandar S. , Crouser Elliott D. , Julian Mark W. , Schanbacher Brandon L. , Bauer John Anthony
Published: January 2015

Primary defects in mitochondrial function have been implicated in over 100 diverse diseases. In situ, mitochondria possess unique and well‐defined morphology in normal healthy cells, but diseases linked to defective mitochondrial function are characterized by the presence of morphologically abnormal and swollen mitochondria with distorted cristae. In situ study of mitochondrial morphology is established as an indicator of mitochondrial health but thus far assessments have been via subjective evaluations by trained observers using discontinuous scoring systems. Here we investigated the value of digital imaging analysis to provide for unbiased, reproducible, and convenient evaluations of mitochondrial ultrastructure. Electron photomicrographs of ileal mucosal mitochondria were investigated using a scoring system previously described by us, and also analyzed digitally by using six digital parameters which define size, shape, and electron density characteristics of over 700 individual mitochondria. Statistically significant changes in mitochondrial morphology were detected in LPS treated animals relative to vehicle control using both the subjective scoring system and digital imaging parameters (p < 0:05). However, the imaging approach provided convenient and high throughput capabilities and was easily automated to remove investigator influences. These results illustrate significant changes in ileal mucosal mitochondrial ultrastructure during sepsis and demonstrate the value of digital imaging technology for routine assessments in this setting.
Chromosomal Composition of Aneuploid Clones with Different DNA Contents in Head and Neck Squamous Cell Carcinomas as Determined by Combined Flow Cytometry and Fluorescence In Situ Hybridization
Authors: Hemmer Joerg , Hauser Carmen
Published: January 2015

Studies with DNA flow cytometry (FCM) have shown that DNA contents of aneuploid tumour clones vary in a wide range. The aim of this study was to analyse whether homologous chromosomal changes exist despite the individual differences that may be of general relevance for the development of gross aneuploidy in squamous cell carcinomas of the head and neck. Fluorescence in situ hybridization (FISH) with 13 centromere‐specific DNA probes was applied to 3 diploid and 11 aneuploid tumours with DNA indices ranging between 0.8 and 2.2. Disomic and monosomic cell populations were prevalent findings in DNA‐diploid tumours. Polysomies were common in aneuploid tumours. Different degrees of aneusomy for identical chromosomes were recurrent features in aneuploid tumours. FISH signal heterogeneity was identified for all chromosomes. The mean number of aneusomic cell populations identified for DNA‐aneuploid tumours ranged between 1.6 for chromosome 17 and 3.1 for chromosome 3. Inconsistencies between FISH and FCM data may indicate that centromere‐specific DNA probes identify gains and losses of marker DNA due to complex karyotypic rearrangements rather than absolute changes in chromosome numbers. Overall, there was no evidence of the critical involvement of particular chromosomes in the development of different DNA contents.
Spontaneous Apoptosis, Oxidative Status and Immunophenotype Markers in Blood Lymphocytes of AIDS Patients
Authors: Losa Gabriele A. , Graber Riccardo
Published: January 2015

Peripheral blood mononuclear cells (PBMC) from 251 HIV‐positive drug abusers of known clinical stage and from 40 healthy donors were tested for conventional immunologic markers (CD3, CD4, CD8, CD19, CD14, CD16/CD56, CD45 and HLA‐DR). Additional cell parameters and the occurrence of spontaneous apoptosis (programmed cell death) were investigated on freshly isolated PBMC by flow cytometric measurement of either annexin‐V bound to plasma membrane phosphatidylserine or propidium iodide uptake. The activity of γ‐glutamyltransferase (γ‐GT), an ectoenzyme contributing to the synthesis of the intracellular antioxidant glutathione (GSH) and involved in early apoptosis, was also determined in these cells. Immunocompetent T‐cell counts were lower in HIV+ patients, with the exception of CD8+ and HLA‐DR+ lymphocytes. The external binding of annexin‐V was significantly higher in HIV+ PBMC and occurred in both CD8+ and CD4+ T‐lymphocyte subsets. The activity of γ‐GT, was significantly lower in the PBMC from HIV+ patients, indicating that the redox status of PBMC may be affected in HIV+ individuals. Finally, the most dominant features characterising patients receiving antiretroviral therapy were greater long‐term stability in the distribution of various cell parameters excepted the level of apoptosis.
Polypeptide Expression in Prostate Hyperplasia and Prostate Adenocarcinoma
Authors: Alaiya Ayodele , Roblick Uwe , Egevad Lars , Carlsson Adelaide , Franzén Bo , Volz Daniela , Huwendiek Sören , Linder Stig , Auer Gert
Published: January 2015

Cells were collected from prostate hyperplasias (n=6) and prostate carcinomas (n=6) and subjected to two‐dimensional gel electrophoresis (2‐DE). The resulting polypeptide patterns were analysed with the PDQUEST computer software. Malignant tumors showed significant increases in the level of expression of proliferating cell nuclear antigen (PCNA), calreticulin, HSP 90 and pHSP 60, oncoprotein 18(v), elongation factor 2, glutathione‐S‐transferase π (GST‐π), superoxide dismutase and triose phosphate isomerase. In addition, decreases in the levels of tropomyosin‐1 and 2 and cytokeratin 18 were observed in prostate carcinomas compared to prostate hyperplasias. This pattern of alterations is similar to that observed in other carcinomas in our previous studies. All malignant tumors showed simultaneous alterations in 5 or more of 9 markers studied, whereas only one case of benign hyperplasia showed alterations in 5 markers. The EST‐data base for prostate tumors available from NCI (CGAP) was searched for the expression of the mRNAs corresponding to proteins identified in our gels. Large differences in the relative expression of mRNAs and proteins were observed. Our data show alterations in the pattern of polypeptide expression in prostate carcinomas which are similar to those observed in other carcinomas.
Morphological Evidence for a Subpopulation Selection Effect by Estrogen and Antiestrogen Treatments in the Heterogeneous MCF‐7 Cell Line
Authors: Palmari Jacqueline , Wallet France , Berard Julien , Berthois Yolande , Martin Pierre Marie , Dussert Christophe
Published: January 2015

Recently, we developed a method to quantitatively study tumour cell heterogeneity in terms of both nuclear size and estrogen receptor (ER) content by image cytometry. The method, previously used to analyse the proliferation of the breast cancer cell line MCF‐7, was applied here to analyse the growth of this cell line under estradiol (E2), hydroxytamoxifen (OH‐TAM), and both E2 and OH‐TAM treatments. The method extracts characteristic parameters of single nuclei and features that measure the global and local organisation of the cells in their growing phase. Modifications of the heterogeneity of the cell line are emphasised through phenotypic changes and modifications of the spatial organisation of the cells. The hormone (E2) generates a very fast growth of cells with small nuclei that became ER negative in the long term. The antihormone (OH‐TAM) produces a gradual selection of ER negative or poorly positive cells with large nuclei. These modifications are reversed when E2 and OH‐TAM are simultaneously used. Moreover, estradiol induces a permissive context of proliferation, whereas hydroxytamoxifen acts only on some subpopulations. The combination of cell count, cytomorphology, and cell organisation revealed the magnitude of the potential of structuration of hormones or antihormones on in vitro growing cells.
New Algorithms Based on the Voronoi Diagram Applied in a Pilot Study on Normal Mucosa and Carcinomas
Authors: Sudbø J. , Marcelpoil R. , Reith A.
Published: January 2015

An adequate reproducibility in the description of tissue architecture is still a challenge to diagnostic pathology, sometimes with unfortunate prognostic implications. To assess a possible diagnostic and prognostic value of quantitiative tissue architecture analysis, structural features based on the Voronoi Diagram (VD) and its subgraphs were developed and tested.

A series of 27 structural features were developed and tested in a pilot study of 30 cases of prostate cancer, 10 cases of cervical carcinomas, 8 cases of tongue cancer and 8 cases of normal oral mucosa. Grey level images were acquired from hematoxyline‐eosine (HE) stained sections by a charge coupled device (CCD) camera mounted on a microscope connected to a personal computer (PC) with an image array processor. From the grey level images obtained, cell nuclei were automatically segmented and the geometrical centres of cell nuclei were computed. The resulting 2‐dimensional (2D) swarm of pointlike seeds distributed in a flat plane was the basis for construction of the VD and its subgraphs. From the polygons, triangulations and arborizations thus obtained, 27 structural features were computed as numerical values. Comparison of groups (normal vs. cancerous oral mucosa, cervical and prostate carcinomas with good and poor prognosis) with regard to distribution in the values of the structural features was performed with Student′s t‐test.

We demonstrate that some of the structural features developed are able to distinguish structurally between normal and cancerous oral mucosa (P=0.001), and between good and poor outcome groups in prostatic (P=0.001) and cervical carcinomas (P=0.001).

We present results confirming previous findings that graph theory based algorithms are useful tools for describing tis‐ sue architecture (e.g., normal versus malignant). The present study also indicates that these methods have a potential for prognostication in malignant epithelial lesions.
Config: A Case Study in Combining Software Engineering Techniques
Authors: Maley David , Spence Ivor
Published: January 2015

Config is a software component of the Graphical R‐Matrix Atomic Collision Environment. Its development is documented as a case study combining several software engineering techniques: formal specification, generic programming, object‐oriented programming, and design by contract. It is specified in VDM++; and implemented in C++, a language which is becoming more than a curiosity amongst the scientific programming community. C++supports object orientation, a powerful architectural paradigm in designing the structure of software systems, and genericity, an orthogonal dimension to the inheritance hierarchies facilitated by object oriented languages. Support in C++ for design by contract can be added in library form. The combination of techniques make a substantial contribution to the overall software quality.
Caveats: Numerical Requirements in Graph Theory Based Quantitation of Tissue Architecture
Authors: Sudbø J. , Marcelpoil R. , Reith A.
Published: January 2015

Graph theory based methods represent one approach to an objective and reproducible structural analysis of tissue architecture. By these methods, neighborhood relations between a number of objects (e.g., cells) are explored and inherent to these methods are therefore certain requirements as to the number of objects to be included in the analysis. However, the question of how many objects are required to achieve reproducible values in repeated computations of proposed structural features, has previously not been adressed specifically.

After digitising HE stained slides and storing them as grey level images, cell nuclei were segmented and their geometrical centre of gravity were computed, serving as the basis for construction of the Voronoi diagram (VD) and its subgraphs. Variations in repeated computations of structural features derived from these graphs were related to the number of cell nuclei included in the analysis.

We demonstrate a large variation in the values of the structural features from one computation to another in one and the same section when only a limited number of cells (100–500) are included in the analysis. This variation decreased with increasing number of cells analyzed. The exact number of cells required to achieve reproducible values differ significantly between tissues, but not between separate cases of similar lesions. There are no significant differences between normal and malignantly changed tissues in oral mucosa with respect to how many cells must be included.

For graph theory based analysis of tissue architecture, care must be taken to include an adequate number of objects; for some of the structural features we have tested, more than 3000 cells.
Specific Changes of Chromatin Structure in Nuclei of Normal Epithelium Adjacent to Laryngeal Squamous Cell Carcinoma
Authors: Dreyer Thomas , Knoblauch Iris , Garner David , Doudkine Alexei , MacAulay Calum , Palcic Branko , Popella Christian
Published: January 2015

The aim of this study was to confirm the existence of specific nuclear texture feature alterations of histologically normal epithelial borders nearby invasive laryngeal cancer (NC).

Paraffin sections of NC and of chronic inflammations unrelated to cancer (CI) were analysed for nuclear texture and for integrated optical density (IOD‐index) and were compared to normal epithelium of patients without evidence of cancer (NE). Several discriminant functions based on nuclear texture features were trained to separate different subgroups.

As the most important result, specific nuclear texture feature shifts were only found in NC with high‐density lymphocytic stroma infiltrate (NC+). Classification of nuclei of NE versus NC+ was correct in 70%. The same classifier was correct in only 58% when nuclei of NE were classified versus CI. We also found lower values of IOD‐Index within the NC+ group when compared to NE (p < 0:001).
Case Study on Algebraic Software Methodologies for Scientific Computing
Authors: Haveraaen Magne
Published: January 2015

The use of domain specific languages and appropriate software architectures are currently seen as the way to enhance reusability and improve software productivity. Here we outline a use of algebraic software methodologies and advanced program constructors to improve the abstraction level of software for scientific computing. This leads us to the language of coordinate free numerics as an alternative to the traditional coordinate dependent array notation. This provides the backdrop for the three accompanying papers: Coordinate Free Programming of Computational Fluid Dynamics Problems, centered around an example of using coordinate free numerics, Machine and Collection Abstractions for User-Implemented Data-Parallel Programming, exploiting the higher abstraction level when parallelising code, and An Algebraic Programming Style for Numerical Software and its Optimization, looking at high‐level transformations enabled by the domain specific programming style.