Applications of the ACGT Master Ontology on Cancer

In this paper we present applications of the ACGT Master Ontology (MO) which is a new terminology resource for a transnational network providing data exchange in oncology, emphasizing the integration of both clinical and molecular data. The development of a new ontology was necessary due to problems with existing biomedical ontologies in oncology. The ACGT MO is a test case for the application of best practices in ontology development. This paper provides an overview of the application of the ontology within the ACGT project thus far

Generalized Swiss-cheese cosmologies: Mass scales

We generalize the Swiss-cheese cosmologies so as to include nonzero linear momenta of the associated boundary surfaces. The evolution of mass scales in these generalized cosmologies is studied for a variety of models for the background without having to specify any details within the local inhomogeneities. We find that the final effective gravitational mass and size of the evolving inhomogeneities depends on their linear momenta but these properties are essentially unaffected by the details of the background model.Comment: 10 pages, 14 figures, 1 table, revtex4, Published form (with minor corrections

Detailed Analysis of Nearby Bulgelike Dwarf Stars III. Alpha and Heavy-element abundances

The present sample of nearby bulgelike dwarf stars has kinematics and metallicities characteristic of a probable inner disk or bulge origin. Ages derived by using isochrones give 10-11 Gyr for these stars and metallicities are in the range -0.80< [Fe/H]< +0.40. We calculate stellar parameters from spectroscopic data, and chemical abundances of Mg, Si, Ca, Ti, La, Ba, Y, Zr and Eu are derived by using spectrum synthesis. We found that [alpha-elements/Fe] show different patterns depending on the element. Si, Ca and Ti-to-iron ratios decline smoothly for increasing metallicities, and follow essentially the disk pattern. O and Mg, products of massive supernovae, and also the r-process element Eu, are overabundant relative to disk stars, showing a steeper decline for metallicities [Fe/H] > -0.3 dex. [s-elements/Fe] roughly track the solar values with no apparent trend with metallicity for [Fe/H] < 0, showing subsolar values for the metal rich stars. Both kinematical and chemical properties of the bulgelike stars indicate a distinct identity of this population when compared to disk stars.Comment: 21 pages, 9 figures, to appear in Ap

Bioinformatics advances in saliva diagnostics

There is a need recognized by the National Institute of Dental & Craniofacial Research and the National Cancer Institute to advance basic, translational and clinical saliva research. The goal of the Salivaomics Knowledge Base (SKB) is to create a data management system and web resource constructed to support human salivaomics research. To maximize the utility of the SKB for retrieval, integration and analysis of data, we have developed the Saliva Ontology and SDxMart. This article reviews the informatics advances in saliva diagnostics made possible by the Saliva Ontology and SDxMart

Long term survivors with metastatic pancreatic adenocarcinoma treated with gemcitabine: a retrospective analysis

<p>Abstract</p> <p>Background</p> <p>Metastatic pancreatic adenocarcinoma has a short median overall survival (OS) of 5–6 months. However, a subgroup of patients survives more than 1 year. We analyzed the survival outcomes of this subgroup and evaluated clinical and pathological factors that might affect survival durations.</p> <p>Methods</p> <p>We identified 20 patients with metastatic or recurrent pancreatic adenocarcinoma who received single-agent gemcitabine and had an OS longer than 1 year. Baseline data available after the diagnosis of metastatic or recurrent disease was categorized as: 1) <it>clinical/demographic data </it>(age, gender, ECOG PS, number and location of metastatic sites); 2) <it>Laboratory data </it>(Hematocrit, hemoglobin, glucose, LDH, renal and liver function and CA19-9); 3) <it>Pathologic data </it>(margins, nodal status and grade); 4) <it>Outcomes data </it>(OS, Time to Treatment Failure (TTF), and 2 year-OS). The lowest CA19-9 levels during treatment with gemcitabine were also recorded. We performed a univariate analysis with OS as the outcome variable.</p> <p>Results</p> <p>Baseline logarithm of CA19-9 and total bilirubin had a significant impact on OS (HR = 1.32 and 1.31, respectively). Median OS and TTF on gemcitabine were 26.9 (95% CI = 18 to 32) and 11.5 (95% CI = 9.0 to 14.3) months, respectively. Two-year OS was 56.4%, with 7 patients alive at the time of analysis.</p> <p>Conclusion</p> <p>A subgroup of patients with metastatic pancreatic cancer has prolonged survival after treatment with gemcitabine. Only bilirubin and CA 19-9 levels were predictive of longer survival in this population. Further analysis of potential prognostic and predictive markers of response to treatment and survival are needed.</p

Local and global behaviour of nonlinear equations with natural growth terms

This paper concerns a study of the pointwise behaviour of positive solutions to certain quasi-linear elliptic equations with natural growth terms, under minimal regularity assumptions on the underlying coefficients. Our primary results consist of optimal pointwise estimates for positive solutions of such equations in terms of two local Wolff's potentials.Comment: In memory of Professor Nigel Kalto

Evolution of the Velocity Ellipsoids in the Thin Disk of the Galaxy and the Radial Migration of Stars

Data from the revised Geneva--Copenhagen catalog are used to study the influence of radial migration of stars on the age dependences of parameters of the velocity ellipsoids for nearby stars in the thin disk of the Galaxy, assuming that the mean radii of the stellar orbits remain constant. It is demonstrated that precisely the radial migration of stars, together with the negative metallicity gradient in the thin disk,are responsible for the observed negative correlation between the metallicities and angular momenta of nearby stars, while the angular momenta of stars that were born at the same Galactocentric distances do not depend on either age or metallicity. (abridged)Comment: Astronomy Reports, Vol. 86 No. 9, P.1117-1126 (2009

Generalized Swiss-Cheese Cosmologies II: Spherical Dust

The generalized Swiss - cheese model, consisting of a Lema\^itre - Tolman (inhomogeneous dust) region matched, by way of a comoving boundary surface, onto a Robertson-Walker background of homogeneous dust, has become a standard construction in modern cosmology. Here we ask if this construction can be made more realistic by introducing some evolution of the boundary surface. The answer we find is no. To maintain a boundary surface using the Darmois - Israel junction conditions, as opposed to the introduction of a surface layer, the boundary must remain exactly comoving. The options are to drop the assumption of dust or allow the development of surface layers. Either option fundamentally changes the original construction.Comment: 5 pages revtex 4.1 Final form to appear in Phys. Rev.

Requirements for the formal representation of pathophysiology mechanisms by clinicians

Knowledge of multiscale mechanisms in pathophysiology is the bedrock of clinical practice. If quantitative methods, predicting patient-specific behaviour of these pathophysiology mechanisms, are to be brought to bear on clinical decision-making, the Human Physiome community and Clinical community must share a common computational blueprint for pathophysiology mechanisms. A number of obstacles stand in the way of this sharing—not least the technical and operational challenges that must be overcome to ensure that (i) the explicit biological meanings of the Physiome's quantitative methods to represent mechanisms are open to articulation, verification and study by clinicians, and that (ii) clinicians are given the tools and training to explicitly express disease manifestations in direct contribution to modelling. To this end, the Physiome and Clinical communities must co-develop a common computational toolkit, based on this blueprint, to bridge the representation of knowledge of pathophysiology mechanisms (a) that is implicitly depicted in electronic health records and the literature, with (b) that found in mathematical models explicitly describing mechanisms. In particular, this paper makes use of a step-wise description of a specific disease mechanism as a means to elicit the requirements of representing pathophysiological meaning explicitly. The computational blueprint developed from these requirements addresses the Clinical community goals to (i) organize and manage healthcare resources in terms of relevant disease-related knowledge of mechanisms and (ii) train the next generation of physicians in the application of quantitative methods relevant to their research and practice