Extraction of Transcript Diversity from Scientific Literature

Transcript diversity generated by alternative splicing and associated mechanisms contributes heavily to the functional complexity of biological systems. The numerous examples of the mechanisms and functional implications of these events are scattered throughout the scientific literature. Thus, it is crucial to have a tool that can automatically extract the relevant facts and collect them in a knowledge base that can aid the interpretation of data from high-throughput methods. We have developed and applied a composite text-mining method for extracting information on transcript diversity from the entire MEDLINE database in order to create a database of genes with alternative transcripts. It contains information on tissue specificity, number of isoforms, causative mechanisms, functional implications, and experimental methods used for detection. We have mined this resource to identify 959 instances of tissue-specific splicing. Our results in combination with those from EST-based methods suggest that alternative splicing is the preferred mechanism for generating transcript diversity in the nervous system. We provide new annotations for 1,860 genes with the potential for generating transcript diversity. We assign the MeSH term “alternative splicing” to 1,536 additional abstracts in the MEDLINE database and suggest new MeSH terms for other events. We have successfully extracted information about transcript diversity and semiautomatically generated a database, LSAT, that can provide a quantitative understanding of the mechanisms behind tissue-specific gene expression. LSAT (Literature Support for Alternative Transcripts) is publicly available at http://www.bork.embl.de/LSAT/

Attaining Doppler Precision of 10 cm s^(-1) with a Lock-in Amplified Spectrometer

We explore the radial velocity performance benefits of coupling starlight to a fast-scanning interferometer and a fast-readout spectrometer with zero readout noise. By rapidly scanning an interferometer, we can decouple wavelength calibration errors from precise radial velocity measurements, exploiting the advantages of lock-in amplification. In a Bayesian framework, we investigate the correlation between wavelength calibration errors and resulting radial velocity errors. We construct an end-to-end simulation of this approach to address the feasibility of achieving 10 cm s^(-1) radial velocity precision on a typical Sun-like star using existing, 5 m-class telescopes. We find that such a precision can be reached in a single night, opening up possibilities for ground-based detections of Earth-Sun analog systems

Stability and Instability of Relativistic Electrons in Classical Electro magnetic Fields

The stability of matter composed of electrons and static nuclei is investigated for a relativistic dynamics for the electrons given by a suitably projected Dirac operator and with Coulomb interactions. In addition there is an arbitrary classical magnetic field of finite energy. Despite the previously known facts that ordinary nonrelativistic matter with magnetic fields, or relativistic matter without magnetic fields is already unstable when the fine structure constant, is too large it is noteworthy that the combination of the two is still stable provided the projection onto the positive energy states of the Dirac operator, which defines the electron, is chosen properly. A good choice is to include the magnetic field in the definition. A bad choice, which always leads to instability, is the usual one in which the positive energy states are defined by the free Dirac operator. Both assertions are proved here.Comment: LaTeX fil

Ten Simple Rules for Getting Help from Online Scientific Communities

The increasing complexity of research requires scientists to work at the intersection of multiple fields and to face problems for which their formal education has not prepared them. For example, biologists with no or little background in programming are now often using complex scripts to handle the results from their experiments; vice versa, programmers wishing to enter the world of bioinformatics must know about biochemistry, genetics, and other fields. In this context, communication tools such as mailing lists, web forums, and online communities acquire increasing importance. These tools permit scientists to quickly contact people skilled in a specialized field. A question posed properly to the right online scientific community can help in solving difficult problems, often faster than screening literature or writing to publication authors. The growth of active online scientific communities, such as those listed in Table S1, demonstrates how these tools are becoming an important source of support for an increasing number of researchers. Nevertheless, making proper use of these resources is not easy. Adhering to the social norms of World Wide Web communication—loosely termed “netiquette”—is both important and non-trivial. In this article, we take inspiration from our experience on Internet-shared scientific knowledge, and from similar documents such as “Asking the Questions the Smart Way” and “Getting Answers”, to provide guidelines and suggestions on how to use online communities to solve scientific problems

Charge Fluctuations on Membrane Surfaces in Water

We generalize the predictions for attractions between over-all neutral surfaces induced by charge fluctuations/correlations to non-uniform systems that include dielectric discontinuities, as is the case for mixed charged lipid membranes in an aqueous solution. We show that the induced interactions depend in a non-trivial way on the dielectric constants of membrane and water and show different scaling with distance depending on these properties. The generality of the calculations also allows us to predict under which dielectric conditions the interaction will change sign and become repulsive

The Common Oceanographer: Crowdsourcing the Collection of Oceanographic Data

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Koinonia

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Performance of Monolayer Graphene Nanomechanical Resonators with Electrical Readout

The enormous stiffness and low density of graphene make it an ideal material for nanoelectromechanical (NEMS) applications. We demonstrate fabrication and electrical readout of monolayer graphene resonators, and test their response to changes in mass and temperature. The devices show resonances in the MHz range. The strong dependence of the resonant frequency on applied gate voltage can be fit to a membrane model, which yields the mass density and built-in strain. Upon removal and addition of mass, we observe changes in both the density and the strain, indicating that adsorbates impart tension to the graphene. Upon cooling, the frequency increases; the shift rate can be used to measure the unusual negative thermal expansion coefficient of graphene. The quality factor increases with decreasing temperature, reaching ~10,000 at 5 K. By establishing many of the basic attributes of monolayer graphene resonators, these studies lay the groundwork for applications, including high-sensitivity mass detectors