How effective are mutation testing tools? An empirical analysis of Java mutation testing tools with manual analysis and real faults

Mutation analysis is a well-studied, fault-based testing technique. It requires testers to design tests based on a set of artificial defects. The defects help in performing testing activities by measuring the ratio that is revealed by the candidate tests. Unfortunately, applying mutation to real-world programs requires automated tools due to the vast number of defects involved. In such a case, the effectiveness of the method strongly depends on the peculiarities of the employed tools. Thus, when using automated tools, their implementation inadequacies can lead to inaccurate results. To deal with this issue, we cross-evaluate four mutation testing tools for Java, namely PIT, muJava, Major and the research version of PIT, PITRV, with respect to their fault-detection capabilities. We investigate the strengths of the tools based on: a) a set of real faults and b) manual analysis of the mutants they introduce. We find that there are large differences between the tools’ effectiveness and demonstrate that no tool is able to subsume the others. We also provide results indicating the application cost of the method. Overall, we find that PITRV achieves the best results. In particular, PITRV outperforms the other tools by finding 6% more faults than the other tools combined

NUCKS overexpression in breast cancer

<p>Abstract</p> <p>Background</p> <p>NUCKS (Nuclear, Casein Kinase and Cyclin-dependent Kinase Substrate) is a nuclear, DNA-binding and highly phosphorylated protein. A number of reports show that <it>NUCKS </it>is highly expressed on the level of mRNA in several human cancers, including breast cancer. In this work, NUCKS expression on both RNA and protein levels was studied in breast tissue biopsies consisted of invasive carcinomas, intraductal proliferative lesions, benign epithelial proliferations and fibroadenomas, as well as in primary cultures derived from the above biopsies. Specifically, in order to evaluate the level of NUCKS protein in correlation with the histopathological features of breast disease, immunohistochemistry was employed on paraffin sections of breast biopsies of the above types. In addition, NUCKS expression was studied by means of Reverse Transcription PCR (RT-PCR), real-time PCR (qRT-PCR) and Western immunoblot analyses in the primary cell cultures developed from the same biopsies.</p> <p>Results</p> <p>The immunohistochemical Results showed intense NUCKS staining mostly in grade I and II breast carcinomas compared to normal tissues. Furthermore, NUCKS was moderate expressed in benign epithelial proliferations, such as adenosis and sclerosing adenosis, and highly expressed in intraductal lesions, specifically in ductal carcinomas <it>in situ </it>(DCIS). It is worth noting that all the fibroadenoma tissues examined were negative for NUCKS staining. RT-PCR and qRT-PCR showed an increase of <it>NUCKS </it>expression in cells derived from primary cultures of proliferative lesions and cancerous tissues compared to the ones derived from normal breast tissues and fibroadenomas. This increase was also confirmed by Western immunoblot analysis. Although NUCKS is a cell cycle related protein, its expression does not correlate with Ki67 expression, neither in tissue sections nor in primary cell cultures.</p> <p>Conclusion</p> <p>The results show overexpression of the NUCKS protein in a number of non malignant breast lesions and cancerous tissues. In particular, the NUCKS overexpression in ADH and DCIS indicates a significant role of this protein in neoplastic progression.</p

Altered expression pattern of integrin alphavbeta3 correlates with actin cytoskeleton in primary cultures of human breast cancer

Background: Integrins are transmembrane adhesion receptors that provide the physical link between the actin cytoskeleton and the extracellular matrix. It has been well established that integrins play a major role in various cancer stages, such as tumor growth, progression, invasion and metastasis. In breast cancer, integrin alphavbeta3 has been associated with high malignant potential in cancer cells, signaling the onset of widespread metastasis. Many preclinical breast cancer studies are based on established cell lines, which may not represent the cell behavior and phenotype of the primary tumor of origin, due to undergone genotypic and phenotypic changes. In the present study, short-term primary breast cancer cell cultures were developed. Integrin alphavbeta3 localization was studied in correlation with F-actin cytoskeleton by means of immunofluorescence and immunogold ultrastructural localization. Integrin fluorescence intensities were semi-quantitatively assessed by means of computerized image analysis, while integrin and actin expression was evaluated by Western immunoblotting. Results: In the primary breast cancer epithelial cells integrin alphavbeta3 immunofluorescence was observed in the marginal cytoplasmic area, whereas in the primary normal breast epithelial cells it was observed in the main cell body, i.e. in the ventrally located perinuclear area. In the former, F-actin cytoskeleton appeared well-formed, consisting of numerous and thicker stress fibers, compared to normal epithelial cells. Furthermore, electron microscopy showed increased integrin alphavbeta3 immunogold localization in epithelial breast cancer cells over the area of stress fibers at the basal cell surface. These findings were verified with Western immunoblotting by the higher expression of integrin beta3 subunit and actin in primary breast cancer cells, revealing their reciprocal relation, in response to the higher motility requirements, determined by the malignant potential of the breast cancer cells. Conclusion: A model system of primary breast cancer cell cultures was developed, in an effort to maintain the closest resembling environment to the tumor of origin. Using the above system model as an experimental tool the study of breast tumor cell behavior is possible concerning the adhesion capacity and the migrating potential of these cells, as defined by the integrin alphavbeta3 distribution in correlation with F-actin cytoskeleton

The prognostic role of galectin-3 and endothelial function in patients with heart failure

Background: Heart failure (HF) is nowadays classified as HF with reduced ejection fraction (HFrEF), HF with mildly reduced EF (HFmrEF), and HF with preserved EF (HFpEF). Endothelial dysfunction (assessed by flow-mediated dilatation [FMD]), increased arterial stiffness (assessed by carotid-femoral pulse-wave velocity [PWV]), and galectin-3, a biomarker of myocardial fibrosis, have been linked to major adverse cardiovascular events (MACE) in patients with ischemic HF. Methods: In this study we prospectively enrolled 340 patients with stable ischemic HF. We assessed the brachial artery FMD, carotid-femoral PWV, and galectin-3 levels, and patients were followed up for MACE according to EF group. Results: Interestingly, the FMD values exhibited a stepwise improvement according to left ventricular ejection fraction (LVEF) (HFrEF: 4.74 ± 2.35% vs. HFmrEF: 4.97 ± 2.81% vs. HFpEF: 5.94 ± 3.46%, p = 0.01), which remained significant after the evaluation of possible confounders including age, sex, cardiovascular risk factors, and number of significantly stenosed epicardial coronary arteries (b coefficient: 0.990, 95% confidence interval: 0.166–1.814, p = 0.019). Single-vessel coronary artery disease (CAD) was more frequent in the group of HFpEF (HFrEF: 56% vs. HFmrEF: 64% vs. HFpEF: 73%, p = 0.049). PWV did not display any association with LVEF. Patients who presented MACE exhibited worse FMD values (4.51 ± 2.35% vs. 5.32 ± 2.67%, p = 0.02), and the highest tertile of galectin-3 was linked to more MACEs (36% vs. 5.9%, p = 0.01). Conclusions: Flow-mediated dilatation displayed a linear improvement with LVEF in patients with ischemic HF. Deteriorated values are associated with MACE. Higher levels of galectin-3 might be used for risk stratification of patients with ischemic HF

Cytochemical and biochemical studies of mitochondria in Xenopus laevis oocytes

The differentiation of mitochondria in the previtellogenic oocytes of Xenopus laevis was investigated by means of morphometry, cytochemistry and biochemistry. Morphometrical studies revealed that the number of mitochondria in the previtellogenic oocytes increases enormously. The volume density of these mitochondria was found to remain essentially constant. Changes in the number of cristae in the mitochondria accompanied similar changes of the mean mitochondrial volume. Ultrastructural cytochemistry using 3,3'-diaminobenzidine revealed that cytochrome oxidase activity is exclusively localised on the cristae and intermembrane space of mitochondria. The pattern of staining was always the same and no mitochondria were found unstained. Quantitation of the DAB staining of mitochondria revealed that the amount of stain per unit area in 1 pm sections of the mitochondrial cloud varied, attained a maximum value when 200 pm oocytes were used, and that in late previtellogenic oocytes was significantly reduced. Biochemical assays of succinate dehydrogenase and cytochrome oxidase using mitochondrial fractions obtained from oocytes of various developmental stages suggested that in oocytes from 100 to 300 pm in size a significant decrease in the specific activity of cytochrome oxidase occurs, whereas that of SDH remains essentially constant. However, the low purity of the mitochondrial fractions from oocytes 400-1200 Fm suggests that in these oocytes the specific activities are higher than those estimated, and may actually increase rather than decrease. Previouss workers have found that the amount of mtDNA increases in the previtellogenic oocytes and then is kept at a constant level. In the light of this finding, the results support the view that enrichment of the oocytes in both enzymes is preceded by accumulation of mtDNA. The possible existence of a derepression mechanism, which may trigger the commencement of accumulation of SDH and cytochrome oxidase, is discussed.</p

Design and implementation of a prototype database system for the operational activity schedule of the Hellenic Navy

The Hellenic Navy General Staff has a difficult mission which encompasses tactical, operational, and administrative tasks. The most important operational task for the General Staff is to prepare the Operational Activity Schedule for every ship, subcommand, and command in the Hellenic Navy. In order to more effectively prepare this schedule, an automated database is required. This system would contain all operational activity records for the Hellenic Navy units and other pertinent information. Furthermore, the system would produce ad hoc reports, as well as a variety of other reports designed by the user to support ship maintenance schedule. This thesis designs and implements an automated database system that can be used from the Hellenic Navy General Staff. The methodology followed is the standard systems' development life cycle (SDLC). The requirements for the system are obtained, and the database and application are designed and implemented. Paradox 5.0 for Windows is used for the database management system software. Special issues like training, conversion, and maintenance are taken into consideration. The result of this thesis is a functional application named 'OADS' (Operational Activity Database System) that will fulfill users' requirements, keeps track of the operational activities of the Hellenic Navy units, and help in performing the desired tasks.http://archive.org/details/designndimplemen1094532180NAHellenic Navy author.Approved for public release; distribution is unlimited