Using the Gene Ontology to Annotate Biomedical Journal Articles

We are creating a gold-standard corpus of manually annotated full-text biomedical journal articles toward natural-language-processing applications. Central to this is our use of entire ontologies of the Open Biomedical Ontologies initiative as well as other terminologies as term sources, in contrast to most other such annotation projects, which have used small, ad hoc schemas. In addition to the standard difficulties in such annotation projects, each of the terminologies we have used has idiosyncrasies and ambiguities that present further challenges to consistent, high-quality annotation of these articles. In this paper we present and discuss the most salient of these with regard to the Gene Ontology that we have encountered and addressed in our annotation guidelines and training. The utility of these guidelines can be seen in the high and still-increasing interannotator-agreement statistics that we continually monitor.
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Effects of RANKL-Targeted Therapy in Immunity and Cancer.

The role of the receptor activator of nuclear factor-κB ligand (RANKL)/RANK system is well characterized within bone, where RANKL/RANK signaling mediates osteoclastogenesis and bone resorption. However, this system has also been shown to influence biologic processes beyond the skeletal system, including in the immune system and in cancer. RANKL/RANK signaling is important in lymph-node development, lymphocyte differentiation, dendritic cell survival, T-cell activation, and tolerance induction. The RANKL/RANK axis may also have direct, osteoclast-independent effects on tumor cells. Indeed, activity of the RANKL/RANK pathway in cancer cells has been correlated with tumor progression and advanced disease. Denosumab, a fully human monoclonal antibody against RANKL, inhibits osteoclastogenesis and is widely used not just for the treatment of osteoporosis, but for the prevention of skeletal-related events from bone metastases in solid malignancies such as breast and prostate cancer. The potential effects of denosumab on the immune system have been largely ignored. Nevertheless, with the emergence of immunotherapies for cancer, denosumab may impact the effectiveness of these therapies, especially if they are given in combination. In this article, we review the role of RANKL/RANK in bone, immunity, and cancer. Examining the potential effects of routine treatment with denosumab beyond the bone represents an important area of investigation

Squarks in Tevatron Dilepton Events ?

We consider unusual events in the CDF and D0 dilepton+jets sample with very high ET(lepton) and ET(missing). It is possible, but very unlikely, that these events originate from top quark pair production; however, they have characteristics that are better accounted for by decays of supersymmetric quarks with mass in the region of 300 GeV.Comment: 5 pages, 2 postscript (eps) figures, uses sprocl.sty (included

RGtk2: A Graphical User Interface Toolkit for R

Graphical user interfaces (GUIs) are growing in popularity as a complement or alternative to the traditional command line interfaces to R. RGtk2 is an R package for creating GUIs in R. The package provides programmatic access to GTK+ 2.0, an open-source GUI toolkit written in C. To construct a GUI, the R programmer calls RGtk2 functions that map to functions in the underlying GTK+ library. This paper introduces the basic concepts underlying GTK+ and explains how to use RGtk2 to construct GUIs from R. The tutorial is based on simple and pratical programming examples. We also provide more complex examples illustrating the advanced features of the package. The design of the RGtk2 API and the low-level interface from R to GTK+ are discussed at length. We compare RGtk2 to alternative GUI toolkits for R.

trackr: A Framework for Enhancing Discoverability and Reproducibility of Data Visualizations and Other Artifacts in R

Research is an incremental, iterative process, with new results relying and building upon previous ones. Scientists need to find, retrieve, understand, and verify results in order to confidently extend them, even when the results are their own. We present the trackr framework for organizing, automatically annotating, discovering, and retrieving results. We identify sources of automatically extractable metadata for computational results, and we define an extensible system for organizing, annotating, and searching for results based on these and other metadata. We present an open-source implementation of these concepts for plots, computational artifacts, and woven dynamic reports generated in the R statistical computing language

Hub flexibility effects on propfan vibration

The significance of hub flexibility in the nonlinear static and dynamic analyses of advanced turboprop blades is assessed. The chosen blade is the 0.175 scale model of the GE-A7-B4 unducted fan blade. A procedure for coupling the effective hub stiffness matrix to an MSC/NASTRAN finite element model is defined and verified. A series of nonlinear static and dynamic analyses are conducted on the blade for both rigid and flexible hug configurations. Results indicate that hub flexibility is significant in the nonlinear static and dynamic analyses of the GE-A7-B4. In order to insure accuracy in analyses of other blades, hub flexibility should always be considered