2,003 research outputs found

    Tools and collaborative environments for bioinformatics research

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    Advanced research requires intensive interaction among a multitude of actors, often possessing different expertise and usually working at a distance from each other. The field of collaborative research aims to establish suitable models and technologies to properly support these interactions. In this article, we first present the reasons for an interest of Bioinformatics in this context by also suggesting some research domains that could benefit from collaborative research. We then review the principles and some of the most relevant applications of social networking, with a special attention to networks supporting scientific collaboration, by also highlighting some critical issues, such as identification of users and standardization of formats. We then introduce some systems for collaborative document creation, including wiki systems and tools for ontology development, and review some of the most interesting biological wikis. We also review the principles of Collaborative Development Environments for software and show some examples in Bioinformatics. Finally, we present the principles and some examples of Learning Management Systems. In conclusion, we try to devise some of the goals to be achieved in the short term for the exploitation of these technologies

    The quadruplex r(CGG)n destabilizing cationic porphyrin TMPyP4 cooperates with hnRNPs to increase the translation efficiency of fragile X premutation mRNA

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    The 5′ untranslated region of the FMR1 gene which normally includes 4–55 d(CGG) repeats expands to > 55–200 repeats in carriers of fragile X syndrome premutation. Although the levels of premutation FMR1 mRNA in carrier cells are 5–10-fold higher than normal, the amount of the product FMR protein is unchanged or reduced. We demonstrated previously that premutation r(CGG)n tracts formed quadruplex structures that impeded translation and lowered the efficiency of protein synthesis. Normal translation could be restored in vivo by the quadruplex r(CGG)n destabilizing action of CBF-A and hnRNP A2 proteins. Here we report that the quadruplex-interacting cationic porphyrin TMPyP4 by itself and in cooperation with CBF-A or hnRNP A2 also unfolded quadruplex r(CGG)n and increased the efficiency of translation of 5′-(CGG)99 containing reporter firefly (FL) mRNA. TMPyP4 destabilized in vitro a (CGG)33 intramolecular quadruplex structure and enhanced the translation of 5′-(CGG)99-FL mRNA in a rabbit reticulocyte lysate and in HEK293 cells. The efficiency of translation of (CGG)99-FL mRNA was additively increased in cells exposed to TMPyP4 together with CBF-A. Whereas low doses of TMPyP4, CBF-A or hnRNP A2 by themselves did not affect the in vivo utilization of (CGG)99-FL mRNA, introduction of TMPyP4 together with either protein synergistically augmented its translation efficiency

    Intelligent chilled mirror humidity sensor

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    A new, intelligent, chilled mirror humidity instrument has been designed for use on buoys and ships. The design goal is to make high quality dew point temperature measurements for a period of up to one year from an unattended platform, while consuming as little power as possible. Nominal system accuracy is 0.3°C, and a measure of data quality is provided to indicate possible drift in calibration. Energy consumption is typically 800 Joules per measurement; standby power consumption is 0.05 watts. Control of the instrument is managed by an onboard central processing unit which is programmable in BASIC, and communication to an external data logger is provided through an RS232 compatible interface. This report describes the preliminary sensor tests that led to this new design and provides the complete technical description required for fabrication.Funding was provided by the Office of Naval Research under contract Number N00014-84-C-0134, and the National Science Foundation through grant Number OCE87- 09614

    Diffractive Guiding of Waves by a Periodic Array of Slits

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    We show that in order to guide waves, it is sufficient to periodically truncate their edges. The modes supported by this type of wave guide propagate freely between the slits, and the propagation pattern repeats itself. We experimentally demonstrate this general wave phenomenon for two types of waves: (i) plasmonic waves propagating on a metal-air interface that are periodically blocked by nanometric metallic walls, and (ii) surface gravity water waves whose evolution is recorded, the packet is truncated, and generated again to show repeated patterns. This guiding concept is applicable for a wide variety of waves.Comment: 5 pages, 4 figure
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