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About 10,000 papers for “code modification”

A Proposal of Code Modification Problem for Web Client Programming Using JavaScript

Khaing Hsu Wai, Nobuo Funabiki, Khin Thet Mon et al. · 2021

Programming Learning Assistant System (PLAS) has been developed as a web-based self-learning platform for programming. PLAS offers several types of exercise problems for code reading and code writing skills, namely, grammar-concept understanding problem (GUP), value trace problem (VTP), element fill-in-blank problem (EFP), code completion problem (CCP), and code writing problem (CWP), to support studies at various levels for C, C++, Java, Python, and JavaScript programming and each problem has different targets for the students. JavaScript is commonly used together with HTML and CSS, to introduce dynamic behaviors of web pages in web application systems. Thus, JavaScript should be studied along with them for web client programming. In this paper, we propose a code modification problem (CMP) as a new type in PLAS, to study web client programming using JavaScript. Since a web page is made by using various functions together, reading and understanding sample source codes using them will be an effective way. Actually, students should have a lot of practices in code reading before implementing source codes from scratch. The CMP instance gives a source code using the functions to be studied and the screenshot of the web page generated by it. Then, it requests to modify the code to generate another web page given by the screenshot. The correctness of any answer is checked through string matching with the correct one. For the evaluation, we generated 25 CMP instances and assigned them to 23 students in Okayama University. Their solution results confirm the validity of the proposal.

Cited by 2

Analyzing CLS Vector Variation in CodeBERT with One-Token Source Code Modification

Wakana Hashimoto, Kazuhiro Takeuchi · 2023

This study aims to investigate the properties of CodeBERT, a Large-scale Programming Language Model, when editing source code from its original purpose to another. In programming languages, even small changes in the code can have a significant impact on the functionality and behavior of the program. One-Token changes, which refer to modifying a single character or word within the code, can have a particularly important role in this regard. In this study, we examine the vectors representing the programs that cannot be compiled or do not serve a clear purpose, which often occur during the process of adding features or modifying existing programs, with respect to the semantic distance from which they were edited.

Cited by 0

Code for "A benchmark of computational pipelines for single-cell histone modification data"

Raimundo, Felix, Vert, Jean Philippe, Vallot, Celine · Zenodo (CERN European Organization for Nuclear Research) · 2023

Frozen version of the code used in: "A benchmark of computational pipelines for single-cell histone modification data"<br> <br> For an up to date version refer to https://github.com/google-research/google-research/tree/master/scrna_benchmark For questions on this code, please contact gamaz3ps@gmail.com

Cited by 1Open access

DNA N6-Methyladenine Modification in Plant Genomes—A Glimpse into Emerging Epigenetic Code

Jeyalakshmi Karanthamalai, Aparna Chodon, Shailja Chauhan et al. · Plants · 2020

N<sup>6</sup>-methyladenine (6mA) is a DNA base modification at the 6th nitrogen position; recently, it has been resurfaced as a potential reversible epigenetic mark in eukaryotes. Despite its existence, 6mA was considered to be absent due to its undetectable level. However, with the new advancements in methods, considerable 6mA distribution is identified across the plant genome. Unlike 5-methylcytosine (5mC) in the gene promoter, 6mA does not have a definitive role in repression but is exposed to have divergent regulation in gene expression. Though 6mA information is less known, the available evidences suggest its function in plant development, tissue differentiation, and regulations in gene expression. The current review article emphasizes the research advances in DNA 6mA modifications, identification, available databases, analysis tools and its significance in plant development, cellular functions and future perspectives of research.

Cited by 23Open access

Expanded Genetic Code approaches to introduce post-translational modification into proteins of interest

VITALONI, OTTAVIA · Electronic Theses and Dissertations Repository (University of Pisa) · 2017

In the past few years, the ability to incorporate unnatural amino acids (UAAs) into proteins at defined sites has begun to have a direct impact on the ability of scientists to study biological processes that are difficult or impossible to address by more classical methods. One of the most powerful approaches for incorporating UAAs site-specifically into protein expressed in cells is the genetic code expansion. In this approach, an aminoacyl-tRNA synthetase and a tRNA are used to specifically insert the unnatural amino acid during mRNA translation, in response to an amber stop codon (UAG) placed at a user-defined site in a gene of interest. This has allowed new biological insights into protein conformational changes, protein interactions, elementary processes in signal transduction and, the role of post-translational modifications (PTMs). In this thesis, we employed the orthogonal synthetase/tRNAPylCUA (PylRS/tRNACUAPyl ) pairs from Methanosarcina barkeri (Mb) and M. mazei (Mm), that enables the incorporation of acetyl-Lysine into protein produced in L40 strain of S. cerevisiae. This pairs has emerged as a particularly versatile and orthogonal system for genetic code expansion in E. coli, yeast Saccharomyces cerevisiae and mammalian cells. However, current methods for incorporating UAAs in yeast are based on transient transfection, that lead to very heterogeneous expression, limiting the ability to couple precise perturbation, which may be effected by UAAs mutagenesis, to global proteomic measurements. To overcome this limitation, stable yeast lines, expressing synthetase and tRNA from an integrated locus, will be created for acetyl-Lysine incorporation (“acetylator” yeast). Using this method, several recombinant proteins bearing a post translation modification, in our case acetylation, at a define site can be produced. Lysine acetyla¬tion is a key post-translational modification in regulating chromatin structure and function, resulting of epigenetic phe¬nomena that regulates diverse biological processes, from metabolism to signalling. In this thesis, acetyl-lysine will be inserted into recombinant H3 protein and microtubule associated protein TAU. In the first case, the acetylation of H3 will provide new insights into the role of this PTM in regulating chromatin structure and function; in the second case it would be useful in deciphering the biological and pathological role of different TAU acetylations. To address these questions the newly created acetylator yeast strain will be employ to produce H3 or acetylated TAU proteins that will be used to select intracellular antibodies (intrabodies) that specifically recognize the PTM. This will be done using the Intracellular Antibody Capture (IAC) technology, a yeast two hybrid based technique that allows screening of intrabodies libraries to specific targets (in our case the acetylated H3 or TAU protein). The newly selected intrabodies will then be used as tools to understand/dissect the role of the specific PTM on the whole protein function. Given the growing list of amino acid that can be incorporated using PylRS/tRNAs variants, the natural follow up of this work will be the creation of new stable yeast lines for the introduction of a wide range of other constitutive PTMs, such as phosphorylation or methylation.

Cited by 0

Code for "A benchmark of computational pipelines for single-cell histone modification data"

Raimundo, Felix, Vert, Jean Philippe, Vallot, Celine · Zenodo (CERN European Organization for Nuclear Research) · 2023

Frozen version of the code used in: "A benchmark of computational pipelines for single-cell histone modification data"<br> <br> For an up to date version refer to https://github.com/google-research/google-research/tree/master/scrna_benchmark For questions on this code, please contact gamaz3ps@gmail.com

Cited by 0Open access

m5C modification of mRNA serves a DNA damage code to promote homologous recombination

Hao Chen, Haibo Yang, Xiaolan Zhu et al. · Nature Communications · 2020

Recruitment of DNA repair proteins to DNA damage sites is a critical step for DNA repair. Post-translational modifications of proteins at DNA damage sites serve as DNA damage codes to recruit specific DNA repair factors. Here, we show that mRNA is locally modified by m<sup>5</sup>C at sites of DNA damage. The RNA methyltransferase TRDMT1 is recruited to DNA damage sites to promote m<sup>5</sup>C induction. Loss of TRDMT1 compromises homologous recombination (HR) and increases cellular sensitivity to DNA double-strand breaks (DSBs). In the absence of TRDMT1, RAD51 and RAD52 fail to localize to sites of reactive oxygen species (ROS)-induced DNA damage. In vitro, RAD52 displays an increased affinity for DNA:RNA hybrids containing m<sup>5</sup>C-modified RNA. Loss of TRDMT1 in cancer cells confers sensitivity to PARP inhibitors in vitro and in vivo. These results reveal an unexpected TRDMT1-m<sup>5</sup>C axis that promotes HR, suggesting that post-transcriptional modifications of RNA can also serve as DNA damage codes to regulate DNA repair.

Cited by 168Open access

Modification of the Eta-Invariant Code for Application on a Modular Grid Network

R. G. Hindman · 1983

Abstract : Extensive modifications to the Eta-Invariant code for computation of tubular projectile flowfields are reported. An efficient modular grid network is implemented consisting of a fine mesh near the projectile, a coarse mesh on the interior of the projectile, and a coarse mesh on the exterior region. The conventional implicit factored integration scheme in delta form is modified to allow for block tridiagonal inversion along a line which crosses from one mesh to another. Special intermesh operators are derived for implementation of this idea at the intermesh points and their immediate neighbors. Complex applications topology of various block inversions are discussed in detail.

Cited by 0

Binary solution model for computation of equilibrium compositions. [Modification of NASA CEC code]

C.-C. Hsu, R. H. Land, M. Blander · OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) · 1978

A NASA computer program (CEC) for calculation of complex equilibrium compositions has been modified to take into account the formation of an ideal binary solution from pure condensed species. The thermodynamics of the modification are discussed. Applications are presented.

Cited by 0Open access

Modification of the forms of recourse in the Administrative Procedure Code upon amendment

Lemańska, Joanna · Homo Politicus (Academy of Humanities and Economics in Lodz) · 2017

The article addresses administrative fines as defined under the Administrative Procedure Code after the latest amendment, which went into force on June 1, 2017.By means of the aforementioned amendment, the statute was supplemented with a new section that contains, most of all, general grounds for imposing such fines and using these types of sanctions by administrative bodies.It includes guidelines for the imposition of penalties, as well as rules for waiving penalties and granting relief.It also introduces a provision governing the accrual of interest from late fines and a prescription for imposing and enforcing administrative fines.

Cited by 0Open access

A Software Protection Method based on Time-Sensitive Code and Self-Modification Mechanism

Yuichiro Kanzaki, Akito Monden · 2010

This paper proposes a systematic method for protecting software against malicious reverse engineering attacks. Our method aims to increase the cost of obtaining secret information in a program on the assumption that the adversaries have the ability to perform dynamic analysis as much as static analysis. A program protected by our method contains many time-sensitive codes, which are overwritten with fake (dummy) codes. Each time-sensitive code is modified during execution via self-modification according to the time taken to execute a designated block of the program. If the execution time of the block is within the predetermined range, the time-sensitive code becomes the original one. On the other hand, if the execution time is out of the range, the time-sensitive code becomes the other fake one. In order to obtain the secret information by static analysis, the adversary must find the routines that modify timesensitive codes which are scattered over the program, and must guess the predetermined valid execution time of the target blocks. In order to obtain the secret information by dynamic analysis, the adversary must make the execution reach the restricted points of the program without stopping the execution. As a result, our method helps to construct highly invulnerable software.

Cited by 4

Modification of the Fingerprinting Code Decoding Procedure in the Case of Soft Decision

Alexandra Afanasyeva · 2018

This article proposes a mutual adaptation of the procedure for extracting digital watermark from video sequences and fingerprinting code decoding. Proposed solution includes two interrelated techniques. The first one is a usage of “soft” decision making instead of “hard” decision during watermark extraction. This means that the additional information on extracted bit reliability will be obtained from the hidden channel. The second one is an including of the reliability to decoding procedure. The use of such a solution allows more effective work of fingerprinting codes and achieves zero accusation error rates.

Cited by 0

Development and Modification of Pool Scrubbing Decontamination Factor Evaluation in Severe Accident Code

Weiyi Yao, Marco Pellegrini, Koji Okamoto · 2023

When severe accidents in boiling water reactor and laser cutting in fuel retrieval during nuclear power plant decommissioning release the fission products in the form of aerosols into the containment, which may cause severe accidental damages, the gas mixed with radioactive aerosol particles can be injected into the suppression chamber. Aerosols are retained in the liquid while the gas passing through the pool and this process is called pool scrubbing. The removal effect of the aerosols is represented by decontamination factor (DF) and it is evaluated by severe accident codes such as MELCOR. In MELCOR, SPARC-90 model is used. The hydrodynamics variables such as bubble rise velocity, bubble aspect ratio and bubble diameter are calculated with many assumptions and by empirical formula. The previous comparisons between the calculation results of MELCOR and experimental data show that the physical models used in the MELCOR code have many limitations and need to be modified. In this paper, a code for evaluating the decontamination factor of pool scrubbing was developed. Based on former experimental studies and CFD simulation analysis on the decontamination process of one single bubble, modified bubble hydrodynamic and surface velocity were applied to improve the prediction of DF. The modified simulation results were compared with calculation results with original model and the experimental data. The comparison showed larger discrepancy with new surface velocity model, which indicates that surface velocity model might not be crucial for the underprediction of DF in MELCOR.

Cited by 0