scholarly journals Selection of a novel class of RNA–RNA interaction motifs based on the ligase ribozyme with defined modular architecture

2008 ◽  
Vol 36 (11) ◽  
pp. 3600-3607 ◽  
Author(s):  
Shoji P. Ohuchi ◽  
Yoshiya Ikawa ◽  
Yoshikazu Nakamura
2020 ◽  
Vol 21 (11) ◽  
pp. 3852
Author(s):  
Martin Raden ◽  
Fabio Gutmann ◽  
Michael Uhl ◽  
Rolf Backofen

In silico RNA-RNA interaction prediction is widely applied to identify putative interaction partners and to assess interaction details in base pair resolution. To verify specific interactions, in vitro evidence can be obtained via compensatory mutation experiments. Unfortunately, the selection of compensatory mutations is non-trivial and typically based on subjective ad hoc decisions. To support the decision process, we introduce our COmPensatOry MUtation Selector CopomuS. CopomuS evaluates the effects of mutations on RNA-RNA interaction formation using a set of objective criteria, and outputs a reliable ranking of compensatory mutation candidates. For RNA-RNA interaction assessment, the state-of-the-art IntaRNA prediction tool is applied. We investigate characteristics of successfully verified RNA-RNA interactions from the literature, which guided the design of CopomuS. Finally, we evaluate its performance based on experimentally validated compensatory mutations of prokaryotic sRNAs and their target mRNAs. CopomuS predictions highly agree with known results, making it a valuable tool to support the design of verification experiments for RNA-RNA interactions. It is part of the IntaRNA package and available as stand-alone webserver for ad hoc application.


Author(s):  
Chetan Kapoor ◽  
Nathan Pettus ◽  
Rich Hooper ◽  
Delbert Tesar

Abstract Mechanical systems for manufacturing in the past have represented monolithic, dedicated machines which remain expensive and inflexible relative to product changes due to market demands. It is the goal of the Robotics Research Group at the University of Texas at Austin (UTRRG) to develop a complete generalized modular architecture for intelligent machines (robots). This paper discusses the various issues involved in the design and selection of system controller hardware, servo controller hardware, real-time software, operating systems, and the software design methodologies. These constructs are required for the realization of a revolutionary, advanced intelligent flexible manufacturing system which offers the same success potential as that of a personal computer.


2019 ◽  
Vol 42 ◽  
Author(s):  
Gian Domenico Iannetti ◽  
Giorgio Vallortigara

Abstract Some of the foundations of Heyes’ radical reasoning seem to be based on a fractional selection of available evidence. Using an ethological perspective, we argue against Heyes’ rapid dismissal of innate cognitive instincts. Heyes’ use of fMRI studies of literacy to claim that culture assembles pieces of mental technology seems an example of incorrect reverse inferences and overlap theories pervasive in cognitive neuroscience.


1975 ◽  
Vol 26 ◽  
pp. 395-407
Author(s):  
S. Henriksen

The first question to be answered, in seeking coordinate systems for geodynamics, is: what is geodynamics? The answer is, of course, that geodynamics is that part of geophysics which is concerned with movements of the Earth, as opposed to geostatics which is the physics of the stationary Earth. But as far as we know, there is no stationary Earth – epur sic monere. So geodynamics is actually coextensive with geophysics, and coordinate systems suitable for the one should be suitable for the other. At the present time, there are not many coordinate systems, if any, that can be identified with a static Earth. Certainly the only coordinate of aeronomic (atmospheric) interest is the height, and this is usually either as geodynamic height or as pressure. In oceanology, the most important coordinate is depth, and this, like heights in the atmosphere, is expressed as metric depth from mean sea level, as geodynamic depth, or as pressure. Only for the earth do we find “static” systems in use, ana even here there is real question as to whether the systems are dynamic or static. So it would seem that our answer to the question, of what kind, of coordinate systems are we seeking, must be that we are looking for the same systems as are used in geophysics, and these systems are dynamic in nature already – that is, their definition involvestime.


1978 ◽  
Vol 48 ◽  
pp. 515-521
Author(s):  
W. Nicholson

SummaryA routine has been developed for the processing of the 5820 plates of the survey. The plates are measured on the automatic measuring machine, GALAXY, and the measures are subsequently processed by computer, to edit and then refer them to the SAO catalogue. A start has been made on measuring the plates, but the final selection of stars to be made is still a matter for discussion.


Author(s):  
P.J. Killingworth ◽  
M. Warren

Ultimate resolution in the scanning electron microscope is determined not only by the diameter of the incident electron beam, but by interaction of that beam with the specimen material. Generally, while minimum beam diameter diminishes with increasing voltage, due to the reduced effect of aberration component and magnetic interference, the excited volume within the sample increases with electron energy. Thus, for any given material and imaging signal, there is an optimum volt age to achieve best resolution.In the case of organic materials, which are in general of low density and electric ally non-conducting; and may in addition be susceptible to radiation and heat damage, the selection of correct operating parameters is extremely critical and is achiev ed by interative adjustment.


Author(s):  
P. M. Lowrie ◽  
W. S. Tyler

The importance of examining stained 1 to 2μ plastic sections by light microscopy has long been recognized, both for increased definition of many histologic features and for selection of specimen samples to be used in ultrastructural studies. Selection of specimens with specific orien ation relative to anatomical structures becomes of critical importance in ultrastructural investigations of organs such as the lung. The uantity of blocks necessary to locate special areas of interest by random sampling is large, however, and the method is lacking in precision. Several methods have been described for selection of specific areas for electron microscopy using light microscopic evaluation of paraffin, epoxy-infiltrated, or epoxy-embedded large blocks from which thick sections were cut. Selected areas from these thick sections were subsequently removed and re-embedded or attached to blank precasted blocks and resectioned for transmission electron microscopy (TEM).


Author(s):  
K.-H. Herrmann ◽  
D. Krahl ◽  
H.-P Rust

The high detection quantum efficiency (DQE) is the main requirement for an imagerecording system used in electron microscopy of radiation-sensitive specimens. An electronic TV system of the type shown in Fig. 1 fulfills these conditions and can be used for either analog or digital image storage and processing [1], Several sources of noise may reduce the DQE, and therefore a careful selection of various elements is imperative.The noise of target and of video amplifier can be neglected when the converter stages produce sufficient target electrons per incident primary electron. The required gain depends on the type of the tube and also on the type of the signal processing chosen. For EBS tubes, for example, it exceeds 10. The ideal case, in which all impinging electrons create uniform charge peaks at the target, is not obtainable for several reasons, and these will be discussed as they relate to a system with a scintillator, fiber-optic and photo-cathode combination as the first stage.


Author(s):  
L.E. Murr ◽  
A.B. Draper

The industrial characterization of the machinability of metals and alloys has always been a very arbitrarily defined property, subject to the selection of various reference or test materials; and the adoption of rather naive and misleading interpretations and standards. However, it seems reasonable to assume that with the present state of knowledge of materials properties, and the current theories of solid state physics, more basic guidelines for machinability characterization might be established on the basis of the residual machined microstructures. This approach was originally pursued by Draper; and our presentation here will simply reflect an exposition and extension of this research.The technique consists initially in the production of machined chips of a desired test material on a horizontal milling machine with the workpiece (specimen) mounted on a rotary table vice. A single cut of a specified depth is taken from the workpiece (0.25 in. wide) each at a new tool location.


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