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1.
AMIA Jt Summits Transl Sci Proc ; 2014: 96-101, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-25717408

RESUMO

The tranSMART knowledge management and high-content analysis platform is a flexible software framework featuring novel research capabilities. It enables analysis of integrated data for the purposes of hypothesis generation, hypothesis validation, and cohort discovery in translational research. tranSMART bridges the prolific world of basic science and clinical practice data at the point of care by merging multiple types of data from disparate sources into a common environment. The application supports data harmonization and integration with analytical pipelines. The application code was released into the open source community in January 2012, with 32 instances in operation. tranSMART's extensible data model and corresponding data integration processes, rapid data analysis features, and open source nature make it an indispensable tool in translational or clinical research.

2.
Phys Rev Lett ; 110(14): 148303, 2013 Apr 05.
Artigo em Inglês | MEDLINE | ID: mdl-25167045

RESUMO

Using experiments and simulations, we investigate the clusters that form when colloidal spheres stick irreversibly to--or "park" on--smaller spheres. We use either oppositely charged particles or particles labeled with complementary DNA sequences, and we vary the ratio α of large to small sphere radii. Once bound, the large spheres cannot rearrange, and thus the clusters do not form dense or symmetric packings. Nevertheless, this stochastic aggregation process yields a remarkably narrow distribution of clusters with nearly 90% tetrahedra at α = 2.45. The high yield of tetrahedra, which reaches 100% in simulations at α = 2.41, arises not simply because of packing constraints, but also because of the existence of a long-time lower bound that we call the "minimum parking" number. We derive this lower bound from solutions to the classic mathematical problem of spherical covering, and we show that there is a critical size ratio α(c) = (1 + sqrt[2]) ≈ 2.41, close to the observed point of maximum yield, where the lower bound equals the upper bound set by packing constraints. The emergence of a critical value in a random aggregation process offers a robust method to assemble uniform clusters for a variety of applications, including metamaterials.


Assuntos
Coloides/química , DNA/química , Modelos Químicos , Simulação por Computador , Eletricidade Estática
3.
J Proteome Res ; 7(4): 1490-9, 2008 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-18311903

RESUMO

There is strong preclinical evidence that cancer, including breast cancer, undergoes immune surveillance. This continual monitoring, by both the innate and the adaptive immune systems, recognizes changes in protein expression, mutation, folding, glycosylation, and degradation. Local immune responses to tumor antigens are amplified in draining lymph nodes, and then enter the systemic circulation. The antibody response to tumor antigens, such as p53 protein, are robust, stable, and easily detected in serum; may exist in greater concentrations than their cognate antigens; and are potential highly specific biomarkers for cancer. However, antibodies have limited sensitivities as single analytes, and differences in protein purification and assay characteristics have limited their clinical application. For example, p53 autoantibodies in the sera are highly specific for cancer patients, but are only detected in the sera of 10-20% of patients with breast cancer. Detection of p53 autoantibodies is dependent on tumor burden, p53 mutation, rapidly decreases with effective therapy, but is relatively independent of breast cancer subtype. Although antibodies to hundreds of other tumor antigens have been identified in the sera of breast cancer patients, very little is known about the specificity and clinical impact of the antibody immune repertoire to breast cancer. Recent advances in proteomic technologies have the potential for rapid identification of immune response signatures for breast cancer diagnosis and monitoring. We have adapted programmable protein microarrays for the specific detection of autoantibodies in breast cancer. Here, we present the first demonstration of the application of programmable protein microarray ELISAs for the rapid identification of breast cancer autoantibodies.


Assuntos
Antígenos de Neoplasias/imunologia , Autoanticorpos/sangue , Neoplasias da Mama/imunologia , Análise Serial de Proteínas/métodos , Autoanticorpos/análise , Biomarcadores/sangue , Neoplasias da Mama/sangue , Neoplasias da Mama/diagnóstico , Ensaio de Imunoadsorção Enzimática , Epitopos de Linfócito B/imunologia , Antígenos Nucleares do Vírus Epstein-Barr/imunologia , Feminino , Humanos , Proteínas Inibidoras de Apoptose , Proteínas Associadas aos Microtúbulos/imunologia , Proteínas de Neoplasias/imunologia , Neoplasias Ovarianas/sangue , Neoplasias Ovarianas/imunologia , Survivina , Proteína Supressora de Tumor p53/imunologia
4.
J Am Chem Soc ; 126(4): 1262-5, 2004 Feb 04.
Artigo em Inglês | MEDLINE | ID: mdl-14746499

RESUMO

We have recently proposed and demonstrated an approach that enables the acquisition of multidimensional nuclear magnetic resonance (NMR) spectra within a single scan. A promising application opened up by this new accelerated form of data acquisition concerns the possibility of monitoring in real time the chemical nature of analytes subject to a continuous flow. The present paper illustrates such potential, with the real-time acquisition of a series of 2D 1H NMR spectra arising from a mixture of compounds subject to a continuous liquid chromatography (LC) separation. This real-time 2D NMR identification of chemicals eluted minutes apart under usual LC-NMR conditions differs from the way in which LC-2D NMR has hitherto been carried out, which relies on stopped-flow modes of operations whereby fractions are first collected and then subject to individual, aliquot-by-aliquot analyses. The real-time LC-2D NMR experiment hereby introduced can be implemented in a straightforward manner using modern commercial LC-NMR hardware, thus opening up immediate possibilities in high-throughput characterizations of complex molecules.


Assuntos
Cromatografia Líquida/métodos , Imageamento por Ressonância Magnética/métodos , Cromatografia Líquida/instrumentação , Imageamento por Ressonância Magnética/instrumentação
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