2,755 research outputs found
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
Koinonia
Best Practice FeaturesLife on Life Learning: Steps Towards Authentic Mentoring, Brian Jensen
The Heart of the Honor Code: I am My Brother\u27s Keeper, Emily J. Darnell
Spotlight FeaturesOld People are Whole Persons, Too: Why Understanding Heritage is a Foundational Component of College Student Development, Philip Byers
Ministry and Learning in Residence Life, Josh Arnold
Shepherding in an Age of Edupunks, Drew Moser
The Gap in the Curtain: Seeing Pieces of a Residential Community\u27s Future, David Johnstone
InterviewsA Conversation with Juana Bordas, conducted by Rob Pepper
Looking Into the Future: Two Educators\u27 Perspectives on Christian Higher Education, by Kim Stave and Ken Heffner (edited by Kirstin Vander Giessen-Reitsma)
Book ReviewsThe Unlikely Disciple (by Kevin Roose), reviewed by Christopher Bohle
ReflectionsSeven Greek Words that Mean the World to Me, Bob Crow
FeaturesThe President\u27s Corner
Editor\u27s Deskhttps://pillars.taylor.edu/acsd_koinonia/1013/thumbnail.jp
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
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