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.

Prognostic significance of apoptotic cell death in bladder cancer: a tissue microarray study on 179 urothelial carcinomas from cystectomy specimens

To assess the prognostic significance of apoptosis related markers in bladder cancer.

Radiation dose reduction in computer assisted navigation for functional endoscopic sinus surgery--cadaver head experiments and clinical implementation

Computed tomography based navigation for endoscopic sinus surgery is inflationary used despite of major public concern about iatrogenic radiation induced cancer risk. Studies on dose reduction for CAS-CT are almost nonexistent. We validate the use of radiation dose reduced CAS-CT for clinically applied surface registration.

Cross-reactions vs co-sensitization evaluated by in silico motifs and in vitro IgE microarray testing

Using an in silico allergen clustering method, we have recently shown that allergen extracts are highly cross-reactive. Here we used serological data from a multi-array IgE test based on recombinant or highly purified natural allergens to evaluate whether co-reactions are true cross-reactions or co-sensitizations by allergens with the same motifs.

Planetary Gear Modal Vibration Experiments and Correlation against Lumped-Parameter and Finite Element Models

Experimental modal analysis techniques are applied to characterize the planar dynamic behavior of two spur planetary gears. Rotational and translational vibrations of the sun gear, carrier, and planet gears are measured. Experimentally obtained natural frequencies, mode shapes, and dynamic response are compared to the results from lumped-parameter and finite element models. Two qualitatively different classes of mode shapes in distinct frequency ranges are observed in the experiments and confirmed by the lumped-parameter model, which considers the accessory shafts and fixtures in the system to capture all of the natural frequencies and modes. The finite element model estimates the high-frequency modes that have significant tooth mesh deflection without considering the shafts and fixtures. The lumped-parameter and finite element models accurately predict the natural frequencies and modal properties established by experimentation. Rotational, translational, and planet mode types presented in published mathematical studies are confirmed experimentally. The number and types of modes in the low-frequency and high-frequency bands depend on the degrees of freedom in the central members and planet gears, respectively. The accuracy of natural frequency prediction is improved when the planet bearings have differing stiffnesses in the tangential and radial directions, consistent with the bearing load direction. (C) 2012 Elsevier Ltd. All rights reserved.

A Framework for the Automation of Discrete-Event Simulation Experiments

Simulation is an important resource for researchers in diverse fields. However, many researchers have found flaws in the methodology of published simulation studies and have described the state of the simulation community as being in a crisis of credibility. This work describes the project of the Simulation Automation Framework for Experiments (SAFE), which addresses the issues that undermine credibility by automating the workflow in the execution of simulation studies. Automation reduces the number of opportunities for users to introduce error in the scientific process thereby improvingthe credibility of the final results. Automation also eases the job of simulation users and allows them to focus on the design of models and the analysis of results rather than on the complexities of the workflow.

Reporting Experiments in Homeopathic Basic Research—Description of the Checklist Development

The objective of this study was to develop a criteria catalogue serving as a guideline for authors to improve quality of reporting experiments in basic research in homeopathy. A Delphi Process was initiated including three rounds of adjusting and phrasing plus two consensus conferences. European researchers who published experimental work within the last 5 years were involved. A checklist for authors provide a catalogue with 23 criteria. The “Introduction” should focus on underlying hypotheses, the homeopathic principle investigated and state if experiments are exploratory or confirmatory. “Materials and methods” should comprise information on object of investigation, experimental setup, parameters, intervention and statistical methods. A more detailed description on the homeopathic substances, for example, manufacture, dilution method, starting point of dilution is required. A further result of the Delphi process is to raise scientists' awareness of reporting blinding, allocation, replication, quality control and system performance controls. The part “Results” should provide the exact number of treated units per setting which were included in each analysis and state missing samples and drop outs. Results presented in tables and figures are as important as appropriate measures of effect size, uncertainty and probability. “Discussion” in a report should depict more than a general interpretation of results in the context of current evidence but also limitations and an appraisal of aptitude for the chosen experimental model. Authors of homeopathic basic research publications are encouraged to apply our checklist when preparing their manuscripts. Feedback is encouraged on applicability, strength and limitations of the list to enable future revisions.