Mining frequent bug-fix code changes

Detecting bugs as early as possible plays an important role in ensuring software quality before shipping. We argue that mining previous bug fixes can produce good knowledge about why bugs happen and how they are fixed. In this paper, we mine the change history of 717 open source projects to extract bug-fix patterns. We also manually inspect many of the bugs we found to get insights into the contexts and reasons behind those bugs. For instance, we found out that missing null checks and missing initializations are very recurrent and we believe that they can be automatically detected and fixed.

Mining tissue microarray data to uncover combinations of biomarker expression patterns that improve intermediate staging and grading of clear cell renal cell cancer

PURPOSE: Tumor stage and nuclear grade are the most important prognostic parameters of clear cell renal cell carcinoma (ccRCC). The progression risk of ccRCC remains difficult to predict particularly for tumors with organ-confined stage and intermediate differentiation grade. Elucidating molecular pathways deregulated in ccRCC may point to novel prognostic parameters that facilitate planning of therapeutic approaches. EXPERIMENTAL DESIGN: Using tissue microarrays, expression patterns of 15 different proteins were evaluated in over 800 ccRCC patients to analyze pathways reported to be physiologically controlled by the tumor suppressors von Hippel-Lindau protein and phosphatase and tensin homologue (PTEN). Tumor staging and grading were improved by performing variable selection using Cox regression and a recursive bootstrap elimination scheme. RESULTS: Patients with pT2 and pT3 tumors that were p27 and CAIX positive had a better outcome than those with all remaining marker combinations. A prolonged survival among patients with intermediate grade (grade 2) correlated with both nuclear p27 and cytoplasmic PTEN expression, as well as with inactive, nonphosphorylated ribosomal protein S6. By applying graphical log-linear modeling for over 700 ccRCC for which the molecular parameters were available, only a weak conditional dependence existed between the expression of p27, PTEN, CAIX, and p-S6, suggesting that the dysregulation of several independent pathways are crucial for tumor progression. CONCLUSIONS: The use of recursive bootstrap elimination, as well as graphical log-linear modeling for comprehensive tissue microarray (TMA) data analysis allows the unraveling of complex molecular contexts and may improve predictive evaluations for patients with advanced renal cancer.

A history of frequent dental care reduces the risk of tooth loss but not periodontitis in older subjects

OBJECTIVES: Information on the significance of dental care in older adults is limited. We hypothesized that regular dental visits has an effect on the number of remaining teeth and periodontal conditions in older subjects. MATERIALS AND METHODS: 1020 randomly selected individuals age 60 - 96 from the Swedish National Study on Aging and Care Blekinge received a comprehensive oral health examination. RESULTS: Dentate women and men had, on average 18.4 teeth (SD +7.6,) and 18.9 teeth (SD + 7.5) respectively (NS). In the youngest group (60 and 66 years old) with less than one dental visit per year, 37% had >20 teeth, compared with 73% among those with at least annual visits. Among the old-old, comparable figures were 1.8 % and 37% respectively. Across age groups, bleeding on probing was 23 %.When adjusting for age, and number of teeth GLM univariate analysis failed to demonstrate an effect of dental visit frequency on alveolar bone loss (p = 0.18), the number of periapical lesions (p = 0.65), or the number of endodontically treated teeth ( p = 0.41). Frequent dental visitors had more teeth than infrequent visitors (p = 0.001). CONCLUSIONS: Tooth loss and alveolar bone loss severity increase with age. Individuals with regular dental visits retained more teeth but the frequency of dental visits had no impact on plaque deposits, gingival inflammation, or alveolar bone levels.

Her2 amplification is significantly more frequent in lymph node metastases from urothelial bladder cancer than in the primary tumours

Her2, an alias for the protein of v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian), might be an attractive therapeutic target in metastasising bladder cancer. Genotype and phenotype of primary tumours and their metastases may differ.

Comparative trends in hospitalizations for osteoporotic fractures and other frequent diseases between 2000 and 2008

In Switzerland, the number, incidence, and cost of acute hospitalizations for major osteoporotic fractures (MOF) and major cardiovascular events (MCE) increased in both women and men between 2000 and 2008, although the mean length of stay (LOS) was significantly reduced. Similar trend patterns were observed for hip fractures and strokes (decrease) and nonhip fractures and acute myocardial infarctions (increase).

Intrathyroid adenomas in primary hyperparathyroidism: are they frequent enough to guide surgical strategy?

Ectopic parathyroid adenoma, including intrathyroid adenoma, is a common cause of failed parathyroid operations. The aim of this study was to evaluate the operative strategy/outcome in patients with primary hyperparathyroidism (pHPT), with special regard to intrathyroid adenomas.

Genome sequence of Desulfosporosinus sp. OT, an acidophilic sulfate-reducing bacterium from copper mining waste in Norilsk, Northern Siberia

We have sequenced the genome of Desulfosporosinus sp. OT, a Gram-positive, acidophilic sulfate-reducing Firmicute isolated from copper tailing sediment in the Norilsk mining-smelting area in Northern Siberia, Russia. This represents the first sequenced genome of a Desulfosporosinus species. The genome has a size of 5.7 Mb and encodes 6,222 putative proteins.

Dental injuries in pediatric patients with facial fractures are frequent and severe

This study was carried out to identify the occurrence, type, location, and severity of dental injuries (DIs), as well as predictors for DIs, in pediatric patients with facial fractures.

Uranium mining industry views on ICRP statement on radon

In 2009, the International Commission on Radiological Protection issued a statement on radon which stated that the dose conversion factor for radon progeny would likely double, and the calculation of risk from radon should move to a dosimetric approach, rather than the longstanding epidemiological approach. Through the World Nuclear Association, whose members represent over 90% of the world's uranium production, industry has been examining this issue with a goal of offering expertise and knowledge to assist with the practical implementation of these evolutionary changes to evaluating the risk from radon progeny. Industry supports the continuing use of the most current epidemiological data as a basis for risk calculation, but believes that further examination of these results is needed to better understand the level of conservatism in the potential epidemiological-based risk models. With regard to adoption of the dosimetric approach, industry believes that further work is needed before this is a practical option. In particular, this work should include a clear demonstration of the validation of the dosimetric model which includes how smoking is handled, the establishment of a practical measurement protocol, and the collection of relevant data for modern workplaces. Industry is actively working to address the latter two items.

Alteration of host cell phenotype by Theileria annulata and Theileria parva: mining for manipulators in the parasite genomes

The apicomplexan parasites Theileria annulata and Theileria parva cause severe lymphoproliferative disorders in cattle. Disease pathogenesis is linked to the ability of the parasite to transform the infected host cell (leukocyte) and induce uncontrolled proliferation. It is known that transformation involves parasite dependent perturbation of leukocyte signal transduction pathways that regulate apoptosis, division and gene expression, and there is evidence for the translocation of Theileria DNA binding proteins to the host cell nucleus. However, the parasite factors responsible for the inhibition of host cell apoptosis, or induction of host cell proliferation are unknown. The recent derivation of the complete genome sequence for both T. annulata and T. parva has provided a wealth of information that can be searched to identify molecules with the potential to subvert host cell regulatory pathways. This review summarizes current knowledge of the mechanisms used by Theileria parasites to transform the host cell, and highlights recent work that has mined the Theileria genomes to identify candidate manipulators of host cell phenotype.