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About 10,000 papers for “code modification”

A tRNA modification pattern that facilitates interpretation of the genetic code

Isao Masuda, Ya‐Ming Hou · Frontiers in Microbiology · 2024

Interpretation of the genetic code from triplets of nucleotides to amino acids is fundamental to life. This interpretation is achieved by cellular tRNAs, each reading a triplet codon through its complementary anticodon (positions 34-36) while delivering the amino acid charged to its 3'-end. This amino acid is then incorporated into the growing polypeptide chain during protein synthesis on the ribosome. The quality and versatility of the interpretation is ensured not only by the codon-anticodon pairing, but also by the post-transcriptional modifications at positions 34 and 37 of each tRNA, corresponding to the wobble nucleotide at the first position of the anticodon and the nucleotide on the 3'-side of the anticodon, respectively. How each codon is read by the matching anticodon, and which modifications are required, cannot be readily predicted from the codon-anticodon pairing alone. Here we provide an easily accessible modification pattern that is integrated into the genetic code table. We focus on the Gram-negative bacterium <i>Escherichia coli</i> as a model, which is one of the few organisms whose entire set of tRNA modifications and modification genes is identified and mapped. This work provides an important reference tool that will facilitate research in protein synthesis, which is at the core of the cellular life.

Cited by 6Open access

Modification of Neutron Kinetic Code for Plate Type Fuel Nuclear Reactor

Salah Ud‐Din Khan, Salah Ud‐Din Khan, Shahab Ud‐Din Khan et al. · Science and Technology of Nuclear Installations · 2013

The research is conducted on the modification of neutron kinetic code for the plate type fuel nuclear reactor. REMARK is a neutron kinetic code that works only for the cylindrical type fuel nuclear reactor. In this research, our main emphasis is on the modification of this code in order to be applicable for the plate type fuel nuclear reactor. For this purpose, detailed mathematical studies have been performed and are subjected to write the program in Fortran language. Since REMARK code is written in Fortran language, so we have developed the program in Fortran and then inserted it into the source library of the code. The main emphasis is on the modification of subroutine in the source library of the code for hexagonal fuel assemblies with plate type fuel elements in it. The number of steps involved in the modification of the code has been included in the paper. The verification studies were performed by considering the small modular reactor with hexagonal assemblies and plate type fuel in it to find out the power distribution of the reactor core. The purpose of the research is to make the code work for the hexagonal fuel assemblies with plate type fuel element.

Cited by 2Open access

NaturalEdit: Code Modification through Direct Interaction with Adaptive Natural Language Representation

Ningzhi Tang, David Meininger, Gelei Xu et al. · ArXiv.org · 2025

Code modification requires developers to comprehend code, plan changes, articulate intentions, and validate outcomes, making it a cognitively demanding process. Generated natural language code summaries aid comprehension but remain static and limited in supporting the full workflow. We present NaturalEdit, a system that makes code summaries interactive and adaptive representations directly linked to source code. Grounded in the Cognitive Dimensions of Notations, NaturalEdit implements a paradigm of code modification through interaction with natural language representations through three key features: (1) adaptive multi-faceted representation of code summaries with flexible Abstraction Gradient; (2) interactive mapping mechanisms between summaries and codes, ensuring a tight Closeness of Mapping; and (3) intent-driven, bidirectional synchronization that reduces Viscosity in editing and validation. A technical evaluation confirms the performance of NaturalEdit, and a user study with 12 developers shows that it enhances comprehension, intent articulation, and validation, giving developers greater confidence and control.

Cited by 0Open access

A central role for ubiquitination within a circadian clock protein modification code

Katarina Stojkovic, Simon S. Wing, Nicolas Cermakian · Frontiers in Molecular Neuroscience · 2014

Circadian rhythms, endogenous cycles of about 24 h in physiology, are generated by a master clock located in the suprachiasmatic nucleus of the hypothalamus and other clocks located in the brain and peripheral tissues. Circadian disruption is known to increase the incidence of various illnesses, such as mental disorders, metabolic syndrome, and cancer. At the molecular level, periodicity is established by a set of clock genes via autoregulatory translation-transcription feedback loops. This clock mechanism is regulated by post-translational modifications such as phosphorylation and ubiquitination, which set the pace of the clock. Ubiquitination in particular has been found to regulate the stability of core clock components but also other clock protein functions. Mutation of genes encoding ubiquitin ligases can cause either elongation or shortening of the endogenous circadian period. Recent research has also started to uncover roles for deubiquitination in the molecular clockwork. Here, we review the role of the ubiquitin pathway in regulating the circadian clock and we propose that ubiquitination is a key element in a clock protein modification code that orchestrates clock mechanisms and circadian behavior over the daily cycle.

Cited by 106Open access

Model for nucleosome modification circuits, using a code with two histone modifications.

Kim Sneppen (16768), Ian B. Dodd (271363) · Figshare · 2015

&lt;p&gt;(A) A simple modification scheme previously shown to be capable of giving heritable bistability &lt;a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002643#pcbi.1002643-Micheelsen1" target="_blank"&gt;[24]&lt;/a&gt;, &lt;a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002643#pcbi.1002643-Dodd2" target="_blank"&gt;[25]&lt;/a&gt; in which one residue per nucleosome is either unmodified (0) or modified (1), generating two nucleosome types, each associated with a distinct epigenetic regulatory state (E1 or E2). The grey box indicates the nucleosome type (R) that is added after DNA replication, which causes roughly half of the nucleosomes in the system to be converted to the R type. Interconversion reactions (red arrows) may occur at a rate that is unaffected by nearby nucleosomes (dashed red arrows) or are stimulated by enzymes recruited by other nucleosomes (green arrows). The green double-tailed arrow indicates direct cooperativity due to recruitment by two nucleosomes. (B) A three nucleosome-type scheme also shown to give heritable bistability &lt;a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002643#pcbi.1002643-Dodd1" target="_blank"&gt;[11]&lt;/a&gt;, &lt;a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002643#pcbi.1002643-Sneppen1" target="_blank"&gt;[21]&lt;/a&gt;, in which a single residue per nucleosome can exist in three modification states (e.g. H3K9ac, H3K9 and H3K9me). (C) Extended scheme analyzed here in which each nucleosome can be modified (1) or not (0) at two different histone positions, making a total of 4 nucleosome types (00, 10, 01, 11; e.g. H3K4K9, H3K4meK9, H3K4K9me, H3K4meK9me). [Note that our model effectively only considers the modification combinations for each half-nucleosome (one copy of each histone protein), whereas two binary modifications on each half nucleosome give 10 different full-nucleosome types (00/00, 00/01, 00/10, 00/11, 01/01, 01/10, 01/11, 10/10, 10/11, 11/11)]. Enzymatic transitions between types are by addition or removal of one modification. Each of the patterns of recruitment-reaction connections are defined by a specific circuit code that lists the recruiting nucleosome (0, 1, 2, 3) for each of the eight reactions; non-recruited ‘noise’ transitions are denoted ‘x’. We term the specific circuit shown in (C) the “classical” motif due to its similarity with the previously studied three nucleosome-type motif shown in (B). (D) Time course displaying strong bistability for the circuit in (C), showing the numbers of E1 and E2 nucleosomes in a 30 nucleosome system (with noise level ).&lt;/p&gt;

Cited by 0Open access

MODIFICATION OF THE NDOSEQ CODE IN THE LIGHT OF ICRP-60 RECOMMENDATIONS

Asma Ashfaq, Mati Ullah, Mati Ullah · The Nucleus · 2020

After the availability of additional data, the International Commission on Radiological Protection (ICRP) revised the Quality Factors for neutrons and instead has recommended radiation weighting factors (WR) in their Report No. ICRP-60. These recommendations have serious consequences for many operational neutron dosimetry services. The ICRP-60 recommendations include the reduction in dose limits from 50 mSv to 20 mSv per year, change in the quality factors and the dose estimation in some circumstances down to a few mSv per year. The overall effect of the ICRP-60 recommendations is to reduce the detection threshold in order to account for the reduction in the effective equivalent dose. We have studied the impact of ICRP-60 recommendations on the response of CR-39 based fast neutron dosimeter and have modified the computer code NDOSEQ in the light of ICRP 60 recommendations. The NDOSEQ Code simulates the dose equivalent response of the electrochemically etched CR-39 detector to fast neutron in the energy range of 70 keV to 20 MeV for up to five hydrogenous front radiators.

Cited by 0Open access

Exploring Direct Instruction and Summary-Mediated Prompting in LLM-Assisted Code Modification

Ningzhi Tang, Emory Smith, Yu Huang et al. · 2025

This paper presents a study of using large language models (LLMs) in modifying existing code. While LLMs for generating code have been widely studied, their role in code modification remains less understood. Although “prompting” serves as the primary interface for developers to communicate intents to LLMs, constructing effective prompts for code modification introduces challenges different from generation. Prior work suggests that natural language summaries may help scaffold this process, yet such approaches have been validated primarily in narrow domains like SQL rewriting. This study investigates two prompting strategies for LLM-assisted code modification: Direct Instruction Prompting, where developers describe changes explicitly in free-form language, and SummaryMediated Prompting, where changes are made by editing the generated summaries of the code. We conducted an exploratory study with 15 developers who completed modification tasks using both techniques across multiple scenarios. Our findings suggest that developers followed an iterative workflow: understanding the code, localizing the edit, and validating outputs through execution or semantic reasoning. Each prompting strategy presented tradeoffs: direct instruction prompting was more flexible and easier to specify, while summary-mediated prompting supported comprehension, prompt scaffolding, and control. Developers’ choice of strategy was shaped by task goals and context, including urgency, maintainability, learning intent, and code familiarity. These findings highlight the need for more usable prompt interactions, including adjustable summary granularity, reliable summarycode traceability, and consistency in generated summaries.

Cited by 0

Modification V to the computer code, STRETCH, for predicting coated- particle behavior

K. H. Valentine · OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) · 1975

Several modifications have been made to the stress analysis code, STRETCH, in an attempt to improve agreement between the calculated and observed behavior of pyrocarbon-coated fuel particles during irradiation in a reactor environment.Specific areas of the code that have been modified are the neutron-induced densification model and the neutron-induced creep calculation.,Also, the capability for modeling surface temperature variations has been added.HFIR Target experiments HT-12 through HT-15 have been simulated with the modified code, and the neutron-fluence vs particle-failure predictions compare favorably with the experimental results.Listings of the modified FORTRAN IV main source program and additional FORTRAN IV functions are provided along with instructions far supplying the additional input data.

Cited by 0Open access

An Experiment on the Effects of Modularity on Code Modification and Understanding

Ewan Tempero, Kelly Blincoe, Danielle Lottridge · 2023

Good modularity is seen as an important goal in software design. Achieving this goal is claimed to improve, among other things, the understandability and modifiability of a design. Yet, when teaching software design, we see that students limit the amount of modularity that they introduce into their code and cannot see the benefit of further modularity. This could be because they do not understand the benefits, but it could also be that these benefits are limited for inexperienced developers. In order to teach the benefits of modularity we need to understand what, if any, benefits exist for students. We conducted a controlled experiment where 40 students performed a modification task on two different designs, one with higher modularity than the other. Students were better able to successfully complete the task with the design with higher modularity. However, we found a trend where understanding was lower for the high modularity design. These results suggest modularity is beneficial to students, and that understanding of modularity needs to be better supported when teaching software design.

Cited by 1

A posttranslational modification code for CFTR maturation is altered in cystic fibrosis

Sandra Pankow, Casimir Bamberger, John R. Yates · Science Signaling · 2019

The multistep process regulating the maturation of membrane proteins in the endoplasmic reticulum (ER) and the secretory pathway is disrupted in many protein misfolding disorders. Mutations in the ion channel CFTR that impair its folding and subsequent localization to the plasma membrane cause cystic fibrosis (CF), an inherited and eventually lethal disease that impairs the function of multiple organs, mostly the lungs. Here, we found that proper maturation of CFTR is dependent on cross-talk between phosphorylation and methylation events in the regulatory insertion (RI) element of the protein. Manipulating these posttranslational modifications (PTMs) prevented the maturation of wild-type CFTR and instead induced its degradation by ER quality control systems. Deletion of Phe<sup>508</sup> (ΔF508), the most prevalent mutation in CF, and other mutations in CFTR that impair its trafficking, such as N1303K, also led to quantitative and qualitative PTM changes that prevented the maturation of misfolded CFTR. Further analysis revealed that a wild-type CFTR-like PTM pattern and function was restored in ΔF508 CFTR when cells were cultured at 28°C but only in the presence of the kinase CK2α. Furthermore, the ability to replicate this PTM pattern predicted the efficacy of treatments in restoring ΔF508 CFTR activity. Accordingly, evaluation of patient information revealed that point mutations of several of the modification sites are associated with clinical CF. These findings identify a minimal quantitative and qualitative PTM code for CFTR maturation that distinguishes correctly folded from misfolded CFTR.

Cited by 43

Neutralizing SQL Injection Attack Using Server Side Code Modification in Web Applications

Asish Kumar Dalai, Sanjay Kumar Jena · Security and Communication Networks · 2017

Reports on web application security risks show that SQL injection is the top most vulnerability. The journey of static to dynamic web pages leads to the use of database in web applications. Due to the lack of secure coding techniques, SQL injection vulnerability prevails in a large set of web applications. A successful SQL injection attack imposes a serious threat to the database, web application, and the entire web server. In this article, the authors have proposed a novel method for prevention of SQL injection attack. The classification of SQL injection attacks has been done based on the methods used to exploit this vulnerability. The proposed method proves to be efficient in the context of its ability to prevent all types of SQL injection attacks. Some popular SQL injection attack tools and web application security datasets have been used to validate the model. The results obtained are promising with a high accuracy rate for detection of SQL injection attack.

Cited by 22Open access

Exploring Direct Instruction and Summary-Mediated Prompting in LLM-Assisted Code Modification

Ningzhi Tang, Earl Smith, Yu Huang et al. · ArXiv.org · 2025

This paper presents a study of using large language models (LLMs) in modifying existing code. While LLMs for generating code have been widely studied, their role in code modification remains less understood. Although "prompting" serves as the primary interface for developers to communicate intents to LLMs, constructing effective prompts for code modification introduces challenges different from generation. Prior work suggests that natural language summaries may help scaffold this process, yet such approaches have been validated primarily in narrow domains like SQL rewriting. This study investigates two prompting strategies for LLM-assisted code modification: Direct Instruction Prompting, where developers describe changes explicitly in free-form language, and Summary-Mediated Prompting, where changes are made by editing the generated summaries of the code. We conducted an exploratory study with 15 developers who completed modification tasks using both techniques across multiple scenarios. Our findings suggest that developers followed an iterative workflow: understanding the code, localizing the edit, and validating outputs through execution or semantic reasoning. Each prompting strategy presented trade-offs: direct instruction prompting was more flexible and easier to specify, while summary-mediated prompting supported comprehension, prompt scaffolding, and control. Developers' choice of strategy was shaped by task goals and context, including urgency, maintainability, learning intent, and code familiarity. These findings highlight the need for more usable prompt interactions, including adjustable summary granularity, reliable summary-code traceability, and consistency in generated summaries.

Cited by 0Open access

NeuroSync: Intent-Aware Code-Based Problem Solving via Direct LLM Understanding Modification

Zhang, Wenshuo, Shen, Leixian, Xu, Shuchang et al. · arXiv (Cornell University) · 2025

Conversational LLMs have been widely adopted by domain users with limited programming experience to solve domain problems. However, these users often face misalignment between their intent and generated code, resulting in frustration and rounds of clarification. This work first investigates the cause of this misalignment, which dues to bidirectional ambiguity: both user intents and coding tasks are inherently nonlinear, yet must be expressed and interpreted through linear prompts and code sequences. To address this, we propose direct intent-task matching, a new human-LLM interaction paradigm that externalizes and enables direct manipulation of the LLM understanding, i.e., the coding tasks and their relationships inferred by the LLM prior to code generation. As a proof-of-concept, this paradigm is then implemented in NeuroSync, which employs a knowledge distillation pipeline to extract LLM understanding, user intents, and their mappings, and enhances the alignment by allowing users to intuitively inspect and edit them via visualizations. We evaluate the algorithmic components of NeuroSync via technical experiments, and assess its overall usability and effectiveness via a user study (N=12). The results show that it enhances intent-task alignment, lowers cognitive effort, and improves coding efficiency.

Cited by 0Open access

Novation and modification of the obligation: article 1203 of the Civil code

Castellanos Cámara, Sandra · Communities in ADDI (University of the Basque Country) · 2019

[ES] El artículo 1203 del Código civil español es invocado como el principal soporte de aquella tesis, predominante en doctrina y jurisprudencia, que atribuye a la novación una eficacia distinta de la típicamente extintiva, al reconocerse junto a ella la existencia de una novación modificativa. Este trabajo tiene por objeto el replanteamiento de dicha conclusión a través de un detenido análisis de la letra de la norma y de los supuestos que engloba.

Cited by 0Open access

Neutralizing SQL Injection Attack on Web Application Using Server Side Code Modification

O. Sarjiyus, M. B. El-Yakub · International Journal of Scientific Research in Computer Science Engineering and Information Technology · 2019

SQL Injection attacks pose a very serious security threat to Web applications and web servers. They allow attackers to obtain unrestricted access to the databases underlying the applications and to the potentially sensitive and important information these databases contain. This research, “Neutralizing SQL Injection attack on web application using server side code modification” proposes a method for boosting web security by detecting SQL Injection attacks on web applications by modification on the server code so as to minimize vulnerability and mitigate fraudulent and malicious activities. This method has been implemented on a simple website with a database to register users with an admin that has control privileges. The server used is a local server and the server code was written with PHP as the back end. The front end was designed using MySQL. PHP server side scripting language was used to modify codes. ‘PDO prepare’ a tool to prepare parameters to be executed. The proposed method proved to be efficient in the context of its ability to prevent all types of SQL injection attacks. Acunetix was used to test the vulnerability of the code, and the code was implemented on a simple website with a simple database. Some popular SQL injection attack tools and web application security datasets have been used to validate the model. Unlike most approaches, the proposed method is quite simple to implement yet highly effective. The results obtained are promising with a high accuracy rate for detection of SQL injection attack.

Cited by 3Open access