Automatic document classification of biological literature

Background: Document classification is a wide-spread problem with many applications, from organizing search engine snippets to spam filtering. We previously described Textpresso, a text-mining system for biological literature, which marks up full text according to a shallow ontology that includes terms of biological interest. This project investigates document classification in the context of biological literature, making use of the Textpresso markup of a corpus of Caenorhabditis elegans literature. Results: We present a two-step text categorization algorithm to classify a corpus of C. elegans papers. Our classification method first uses a support vector machine-trained classifier, followed by a novel, phrase-based clustering algorithm. This clustering step autonomously creates cluster labels that are descriptive and understandable by humans. This clustering engine performed better on a standard test-set (Reuters 21578) compared to previously published results (F-value of 0.55 vs. 0.49), while producing cluster descriptions that appear more useful. A web interface allows researchers to quickly navigate through the hierarchy and look for documents that belong to a specific concept. Conclusions: We have demonstrated a simple method to classify biological documents that embodies an improvement over current methods. While the classification results are currently optimized for Caenorhabditis elegans papers by human-created rules, the classification engine can be adapted to different types of documents. We have demonstrated this by presenting a web interface that allows researchers to quickly navigate through the hierarchy and look for documents that belong to a specific concept

Simulation of Micro-Electronic FlowFET Systems

A microelectronic fluidic system has been investigated by modeling and 3D simulation of fluid flow controlled by an applied gate voltage. The simulations have helped to characterize a novel FlowFET (a fluidic Field Effect Transistor) device under fault-free conditions. The FlowFET operates by applying a voltage field from a gate electrode in the insulated side wall of a microchannel to modulate the ␣-potential at the shear plane [1]. The change in ␣-potential can be used to control both the magnitude and direction of the electroosmotic flow in the microchannel

Two-Dimensional Hydrodynamics of Pre-Core Collapse: Oxygen Shell Burning

By direct hydrodynamic simulation, using the Piecewise Parabolic Method (PPM) code PROMETHEUS, we study the properties of a convective oxygen burning shell in a SN 1987A progenitor star prior to collapse. The convection is too heterogeneous and dynamic to be well approximated by one-dimensional diffusion-like algorithms which have previously been used for this epoch. Qualitatively new phenomena are seen. The simulations are two-dimensional, with good resolution in radius and angle, and use a large (90-degree) slice centered at the equator. The microphysics and the initial model were carefully treated. Many of the qualitative features of previous multi-dimensional simulations of convection are seen, including large kinetic and acoustic energy fluxes, which are not accounted for by mixing length theory. Small but significant amounts of carbon-12 are mixed non-uniformly into the oxygen burning convection zone, resulting in hot spots of nuclear energy production which are more than an order of magnitude more energetic than the oxygen flame itself. Density perturbations (up to 8%) occur at the `edges' of the convective zone and are the result of gravity waves generated by interaction of penetrating flows into the stable region. Perturbations of temperature and electron fraction at the base of the convective zone are of sufficient magnitude to create angular inhomogeneities in explosive nucleosynthesis products, and need to be included in quantitative estimates of yields. Combined with the plume-like velocity structure arising from convection, the perturbations will contribute to the mixing of nickel-56 throughout supernovae envelopes. Runs of different resolution, and angular extent, were performed to test the robustness of theseComment: For mpeg movies of these simulations, see http://www.astrophysics.arizona.edu/movies.html Submitted to the Astrophysical Journa

Two-photon ionization of Helium studied with the multiconfigurational time-dependent Hartree-Fock method

The multiconfigurational time-dependent Hartree-Fock method (MCTDHF) is applied for simulations of the two-photon ionization of Helium. We present results for the single- and double ionization from the groundstate for photon energies in the non-sequential regime, and compare them to direct solutions of the Schr\"odinger equation using the time-dependent (full) Configuration Interaction method (TDCI). We find that the single-ionization is accurately reproduced by MCTDHF, whereas the double ionization results correctly capture the main trends of TDCI

Automated Hovering in Health Care — Watching Over the 5000 Hours

The dominant form of health care financing in the United States supports a reactive, visit-based model in which patients are seen when they become ill, typically during hospitalizations and at outpatient visits. That care model falls short not just because it is expensive and often fails to proactively improve health, but also because so much of health is explained by individual behaviors,1 most of which occur outside health care encounters. Indeed, even patients with chronic illness might spend only a few hours a year with a doctor or nurse, but they spend 5000 waking hours each year engaged in everything else — including deciding whether to take prescribed medications or follow other medical advice, deciding what to eat and drink and whether to smoke, and making other choices about activities that can profoundly affect their health