David W. Wall · 1989
Many existing or potential programming tools require the program to be completely recompiled with a special compiler option. This is usually inconvenient for the program developer, and may reduce the usefulness of the tool or the frequency with which the tool is employed. It may also require the maintenance of different versions of standard libraries, each compiled with the appropriate options for a different tool. The difference between modules compiled with and without the special option is often simple and regular. If so, we can effect this difference by modifying the normally-compiled object code at link time, instead of recompiling. This reduces the overhead of using the tool by an order of magnitude, making it much more convenient. i 1. Introduction Recompiling an entire multi-module program from scratch is usually so expensive o that one does it only reluctantly. In spite of this, many useful tools for program ptimization or performance analysis require the recompilation of...
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J.S. Williamson · 2002
A description is given of the Expert Avionics Code Modification (EACM) system, a software environment and a collection of embedded tools which function together to provide a capability for post-development support for avionics software written in the Ada programming language. The EACM system includes four main tools: Connectivity Analyzer (CA), Code Performance Anomaly Detector (CPAD), Shuffler, and Rippler (Side-Effect Analyzer). The purpose of this Ada avionics maintenance/enhancement system is to reduce the amount of resources (i.e. time, cost, and manpower) required to maintain software for processors utilized in avionics applications. Anticipated benefits of the EACM system include increased and easier program understanding, leading to a lower learning curve for new project members; fewer maintenance-generated 'bugs'; and more expedient and less costly enhancements.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
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Samuel L. Myers, Julia C. Elam, Hanna Brown et al. · 1987
OMB No. 0704-0188 ftjbl « reporting burden for th. » cwlecttori of inforiiuiion n «umated to average 1 hour per rewome. including the time for rev.ew.ng imtrucllont. learchmo exitino da » «»re« ga henng and mamta.^ng the data needed, and completing and reve-.ng the collect.«! of informal. Send comments regarding thi * burdenetllmVl««In»&quot;«he??Ü1?S1 JS collection 0 «.nformat.on..ncfud.ng tuggntion « for reducing thn burden, to Wasfwngton Headquarter » Serv.cn. Directorate for infoYmYtlon oiwM ^ and r^rS. i JI?S?i£»
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Emily Brookes, Ana Pombo · Cell Cycle · 2012
Comment on: Brookes E, et al. Cell Stem Cell 2012; 10:157-70.
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Ranieri, Steven · UNM’s Digital Repository (University of New Mexico) · 1991
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G. L. Findley, S. P. McGlynn · International Journal of Quantum Chemistry · 2009
The generalized genetic code [G. L. Findley and S. P. McGlynn, Int. J. Quantum Chem., Quantum Biol. Symp. 6, 313 (1979)] is reviewed from the perspective of recently published empirical evidence which indicates the nonuniversality of the standard genetic code. It is shown how a modified form of universality is retained in the generalized genetic code. In addition, the nature of biological contexts and their relation to the generalized genetic code are discussed.
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Vladimir Itsykson, Denis Timofeyev · 2010
Source code modification is one of the most frequent operations which developers perform in software life cycle. Such operation can be performed in order to add new functionality, fix bugs or bad code style, optimize performance, increase readability, etc. During the modification of existing source code developer needs to find parts of code, which meet to some conditions, and change it according to some rules. Usually developers perform such operations repeatedly by hand using primitive search/replace mechanisms and "copy and paste programming", and that is why manual modification of large-scale software systems is a very error-prone and time-consuming process. Automating source code modifications is one of the possible ways of coping with this problem because it can considerably decrease both the amount of errors and the time needed in the modification process. Automated source code modification technique based on parameterized source code patterns is considered in this article. Intuitive modification description that does not require any knowledge of complex transformation description languages is the main advantage of our technique. We achieve this feature by using a special source code pattern description language which is closely tied with the programming language we're modifying. This allows developers to express the modification at hand as simple "before "/"after" source code patterns very similar to source code. Regexp-like elements are added to the language to increase its expressionalpower. The source code modification is carried out using difference abstract syntax trees. We build a set of transformation operations based on "before"/"after" patterns (using algorithm for change detection in hierarchically structured information) and apply them to those parts of source code that match with the search "before " pattern. After abstract syntax tree transformation is completed we pretty-print them back to source code. A prototype of source code modification system based on this technique has been implemented for the Java programming language. Experimental results show that this technique in some cases can increase the speed of source code modifications by several orders of magnitude, at the same time completely avoiding "copy-and paste " errors. In future we are planning to integrate prototype with existing development environments such as Eclipse and NetBeans.
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Subparagraph (a · 2011
If you need this publication in an alternative format, please call 1-800-525-0127 (voice) or 1-800-833-6388 (TTY relay service).
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Rościsław Krutyhołowa, Karol Zakrzewski, Sebastian Glatt · Current Opinion in Structural Biology · 2019
All types of cellular RNAs are post-transcriptionally modified, constituting the so called 'epitranscriptome'. In particular, tRNAs and their anticodon stem loops represent major modification hotspots. The attachment of small chemical groups at the heart of the ribosomal decoding machinery can directly affect translational rates, reading frame maintenance, co-translational folding dynamics and overall proteome stability. The variety of tRNA modification patterns is driven by the activity of specialized tRNA modifiers and large modification complexes. Notably, the absence or dysfunction of these cellular machines is correlated with several human pathophysiologies. In this review, we aim to highlight the most recent scientific progress and summarize currently available structural information of the most prominent eukaryotic tRNA modifiers.
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lyshc · Zenodo (CERN European Organization for Nuclear Research) · 2021
First release of code for bias modification research
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イズミダ, ソウスケ, ウエダ, ヤスシ, カミヤ, トシヒロ et al. · OUKA (Osaka University Knowledge Archive) (Osaka University) · 2003
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Brett McClintock · Zenodo (CERN European Organization for Nuclear Research) · 2025
install archived packages directly, update CT and Time.name specification for continuous-time models
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Karen Rosier · Repository of the University of Namur · 2006
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Chunyan Jiang, C. N. Davids · OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) · 1995
The general ion-optics code GIOS is a very powerful and useful program for calculating the ion optics of an electromagnetic system. It was used extensively in the design and operation of the Fragment Mass Analyzer (FMA). In the original version of the program a feature is described which allows the initial beam density to be varied with angle, energy, mass, or position. In fact, this feature was never implemented, and only isotropic beam densities are available. In order to make more reliable calculations of reaction yields and FMA transport efficiencies, it is important to be able to use more realistic beam density distributions.
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James L. Van Etten, Yuannan Xia, Dwight E. Burbank et al. · Gene · 1988
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Yoshiki Higo, Yasushi Ueda, Shinji Kusumoto et al. · 2007
Maintaining software systems becomes more difficult as their size and complexity increase. One factor that makes software maintenance more difficult is the presence of code clones. A code clone is defined as a code fragment occurring more than once in identical or similar form into a software system. For example, the presence of code clones is a big factor of overlooking some places that should be modified simultaneously. One technique that helps the number of code clones is refactoring. There are several research efforts that provide support to refactor code clones, but unfortunately some code clones cannot or should not be refactored (ex. stereotyped process, absence of abstraction functionality, performance enhancement). In order to support maintaining the consistency among code clones, we propose a simultaneous modification support method. Given a software system, firstly, a maintainer identifies a code fragment that must be modified. Then, only the code clones between the identified code fragment and the source files of the software system are detected. We developed a simultaneous modification support tool, Libra, and applied it to open source software systems. The results showed that Libra was a good searching tool as much as grep, which is a useful tool of UNIX.
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Lina Herhaus, Ivan Đikić · EMBO Reports · 2015
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Richard Lauman, Benjamin A. García · Molecular Omics · 2020
The discovery and analysis of modifications on proteins and nucleic acids has provided functional information that has rapidly accelerated the field of epigenetics. While protein post-translational modifications (PTMs), especially on histones, have been highlighted as critical components of epigenetics, the post-transcriptional modification of RNA has been a subject of more recently emergent interest. Multiple RNA modifications have been known to be present in tRNA and rRNA since the 1960s, but the exploration of mRNA, small RNA, and inducible tRNA modifications remains nascent. Sequencing-based methods have been essential to the field by creating the first epitranscriptome maps of m<sup>6</sup>A, m<sup>5</sup>C, hm<sup>5</sup>C, pseudouridine, and inosine; however, these methods possess significant limitations. Here, we discuss the past, present, and future of the application of mass spectrometry (MS) to the study of RNA modifications.
Cited by 39Open access
Dong Wook Choi, Cheol Yong Choi · Molecular & Cellular Oncology · 2014
Homeodomain-interacting protein kinase 2 (HIPK2) is a serine/threonine protein kinase that participates in the regulation of diverse cellular activities as a transcriptional cofactor and signal transducer. HIPK2 senses various signaling cues that in turn phosphorylate downstream substrates to coordinate developmental processes, cell cycle regulation, cell proliferation, differentiation, and the DNA damage response. HIPK2 functions are affected by its catalytic activity, stability, and subcellular localization, which in turn are dynamically regulated by diverse post-translational modifications such as polyubiquitination, SUMOylation, phosphorylation, and acetylation. HIPK2 is not modified with small molecules and/or peptides individually or independently, but in a combinatorial manner that is referred to as the "HIPK2 modification code." HIPK2 integrates various signaling cues and senses different doses of DNA damage and ROS stimuli, which are reflected by unique patterns of HIPK2 modification. Hence, the HIPK2 modification code differentially contributes to cellular homeostasis and determination of cell fate depending on cellular context.
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2008
Tools that analyze and enhance large-scale software systems using symbolic reasoning are computationally expensive, and yet processors are cheap. We believe that enabling tools with parallel foundations will lead to qualitatively more useful tools. We have implemented a large-scale industrial-strength program transformation system, the DMS Software Reengineering Toolkit, entirely in PARLANSE, a new parallel language. PARLANSE provides support for irregular fine-grain parallelism with zero-cost exception handling. This paper sketches the motivation for PARLANSE, its parallelism support and how it is used in a number of DMS-based applications, including parallel rewriting and attribute evaluation.
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