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.

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.

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.

TA-RE: An Exchange Language for Mining Software Repositories

Software repositories have been getting a lot of attention from researchers in recent years. In order to analyze software repositories, it is necessary to first extract raw data from the version control and problem tracking systems. This poses two challenges: (1) extraction requires a non-trivial effort, and (2) the results depend on the heuristics used during extraction. These challenges burden researchers that are new to the community and make it difficult to benchmark software repository mining since it is almost impossible to reproduce experiments done by another team. In this paper we present the TA-RE corpus. TA-RE collects extracted data from software repositories in order to build a collection of projects that will simplify extraction process. Additionally the collection can be used for benchmarking. As the first step we propose an exchange language capable of making sharing and reusing data as simple as possible.

Clinical field trial examining an implant with a sand-blasted, acid-etched surface

BACKGROUND: Conventionally, endosseous dental implants have required 3 to 6 months of uninterrupted healing based on observations for dental implants that were characterized by a relatively smooth machined surface. Many studies have since demonstrated that implants with a roughened surface resulted in greater bone apposition, earlier bone contact, and a stronger bond between the implant and the bone, suggesting that implants with roughened surfaces could be loaded earlier than 3 to 6 months. Formal clinical studies confirmed that implants with rough surfaces can have abutments placed and be loaded occlusally as early as 6 weeks postplacement. The purpose of this prospective, human clinical investigation was to evaluate a large number of implants with a specific rough surface (sand-blasted acid-etched [SLA]) placed in everyday practice under routine private-practice conditions. METHODS: A prospective, multicenter, human clinical observational study was initiated with the goal of recruiting a minimum of 500 patients and 800 implants. The implants were to be placed and restored in predominantly private-practice settings around the world. Ninety-two practitioners in 16 countries agreed to participate, and 86 followed the study design. Patients had to be in good health, have sufficient bone to encase the implant, and agree to return for recall appointments. Exclusion criteria included heavy smoking (>10 cigarettes a day) and bone augmentation procedures at the implant site. All implants were two-piece (an abutment was to be placed after 6 weeks of healing) and were characterized by the presence of a transmucosal polished collar. Each implant had an SLA surface. All implants were positioned using a non-submerged (single-stage) surgical technique. Survival and success rates were calculated by life-table analyses. RESULTS: A total of 706 patients were enrolled and 1,406 implants were placed. In the final analyses, 590 patients with 990 implants (70.4% of those enrolled) met all inclusion criteria, including placement of an abutment and provisional restoration within 63 days of surgical placement. The majority of implants were 10 and 12 mm long (78.7%) and were placed in type II and III bone (87%). Seventy-three percent of the implants were placed in the mandible, and 27% were placed in the maxilla. The cumulative survival rate was 99.56% at 3 years and 99.26% at 5 years. The overall success rate was 99.12% at 3 years and 97.38% after 5 years. CONCLUSIONS: Under private-practice conditions, implants with an SLA surface could be placed and restored predictably within 6 to 8 weeks. Data from this prospective, multicenter, human observational study reinforced the results of more formal clinical studies and demonstrated that implants with the SLA surface can be restored in patients in approximately half of the time of conventional healing periods.