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Improving Glycoproteomic analysis Workflow by Systematic Evaluation of Glycopeptide Enrichment, Quantification, Mass Spectrometry Approach, and data analysis Strategies

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ANALYTICAL CHEMISTRY 2024年第52期96卷 20481-20490页

作者： Sun, Zhenyu Lih, T. Mamie Woo, Jongmin Jiao, Liyuan Hu, Yingwei Wang, Yuefan Liu, Hongyi Zhang, Hui Johns Hopkins Univ Sch Med Dept Pathol Baltimore MD 21231 USA Johns Hopkins Univ Sch Med Dept Pathol Oncol Urol & Chem & Biomol Engn Baltimore MD 21231 USA

Glycosylation is one of the most prevalent and crucial protein modifications. Quantitative site-specific characterization of glycosylation usually requires sophisticated intact glycopeptide analysis using glycoproteomics. Recent efforts have focused on the interrogation of intact glycopeptide analyses using tandem mass spectrometry. However, a systematic evaluation of the quantitative glycoproteomic workflow is still lacking. This study compared different strategies for glycopeptide enrichment alongside glycopeptide quantitation, as well as mass spectrometry and data analysis strategies, providing a comprehensive assessment of their efficacy. The ZIC-HILIC enrichment method demonstrated superior performance, representing a 26% improvement in identified glycopeptiudes compared to the MAX enrichment method. Quantification using TMT provided high precision and throughput with an average CV of 8%. Through systematic evaluation, this study established that the ZIC-HILIC enrichment method, quantification with TMT, and collision energies of 25, 35, and 45 using tandem mass spectrometry are the optimal workflow for higher-energy collisional dissociation (HCD) fragmentation, significantly enhancing the analysis of intact glycopeptides. Precise energy adjustment is crucial for the identification of certain glycans. Intact glycopeptides were analyzed using different software tools to investigate the identification and quantification of glycopeptides. By applying optimal settings, 5514 unique intact glycopeptides were in luminal and basal patient-derived xenograft (PDX) characterized models, highlighting distinct glycosylation profiles that may influence tumor behavior. This study offers a systematic approach to evaluate glycoproteomic analysis workflow.

关键词： data flow analysis

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data flow analysis on 3D printing for distributed manufacturing information system

Data flow analysis on 3D printing for distributed manufactur...

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4th International Conference on Frontiers of Manufacturing Science and Measuring Technology, ICFMM 2014

作者： Xu, Wen Jin College of Information Science and Technology Qingdao University of Science and Technology Qingdao Shandong China

ISBN: (纸本)9783038351924

3D printing is a new kind technology with great future. As a new processing technology in the intelligent manufacturing, it will change the way of mass production assembly line as the representative of the second industrial revolution. At the same time, distributed production need new data flow strategy and new network for big data. In this article, we introduced the research for the distributed manufacture network and data flow analysis. © (2014) Trans Tech Publications, Switzerland.

关键词： data flow analysis

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Extending data flow coverage with redefinition analysis

Extending data flow coverage with redefinition analysis

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2021 International Conference on Information and Digital Technologies, IDT 2021

作者： Kolchin, Alexander Potiyenko, Stepan Weigert, Thomas V.M. Glushkov Institute of Cybernetics National Academy of Sciences Kyiv Ukraine Updraft Llc PalatineIL United States

data flow-oriented coverage criteria are widely used in software testing. This paper proposes three novel def-use coverage criteria. The main objective of these criteria is to improve the specificity of test goals, to... 详细信息

ISBN: (纸本)9781665436922

关键词： data flow analysis

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data flow analysis in the Presence of Correlated Calls

Data Flow Analysis in the Presence of Correlated Calls

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作者： Rapoport, Marianna University of Waterloo

学位级别：master

This thesis presents a technique to improve the precision of data-flow analyses on object-oriented programs in the presence of correlated calls. We say that two method calls are correlated if they are polymorphic (have multiple targets) and are invoked on the same object. Correlated calls are problematic because they can make existing data-flow analyses consider certain infeasible data-flow paths as valid. This leads to loss in precision of the analysis *** show how infeasible paths can be eliminated for Inter-procedural Finite Distributive Subset (IFDS) problems, a large class of data-flow analysis problems. We show how the precision of IFDS problems can be improved in the presence of correlated calls, by using the Inter-procedural Distributive Environment (IDE) algorithm to eliminate infeasible paths. Using IDE, we eliminate the infeasible paths and obtain a more precise result for the original IFDS *** analysis is implemented in Scala, using the WALA framework for static program analysis on Java bytecode

关键词： data flow analysis programming languages static analysis IDE IFDS correlated calls

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data flow analysis in ROS

Data Flow Analysis in ROS

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ISR/Robotik 2014;41st International Symposium on Robotics

作者： Dariush Forouher Jan Hartmann Erik Maehle Institute of Computer Engineering University of Luebeck

This paper presents an enhancement to the Robot Operating System (ROS), which provides statistics about the data flow between nodes inside the ROS framework. These statistics measurements include message frequency, transportation delay and other metrics on connections between ROS nodes. We enhanced an existing ROS tool, which displays connections between nodes, so that it also displays these measurements. On this basis, we further present a change detection mechanism, using these measurements to detect errors and provide an overall robot health status.

关键词： ROS1 gene data flow Ganglia Connections data flow analysis motor vehicle inspection stations Transport delay Robot

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Towards a type-based abstract semantics for Python

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JOURNAL OF LOGICAL AND ALGEBRAIC METHODS IN PROGRAMMING 2025年 143卷

作者： Nacu, Andrei Alexandru Ioan Cuza Univ Fac Comp Sci 16 Berthelot St Iasi 700483 Romania

Python is a high-level programming language that is strongly, but dynamically typed. In this paper, we propose a type inference framework to compute specifications for Python functions in isolation. To achieve this, we aim to use an abstract-interpretation-based data flow analysis to infer variable types on a subset of Python programs that use built-in types, operators and functions. To evaluate the expressions found in every program point, specifications for the encountered operations functions are required. We propose a method for extracting these specifications from the Typeshed project, which contains a set of annotations for built-in and popular third-party libraries. These specifications will be used then to extend the proposed type inference to large Python programs.

关键词： Python Type inference Type annotations data flow analysis

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Do as You Say: Consistency Detection of data Practice in Program Code and Privacy Policy in Mini-App

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IEEE TRANSACTIONS ON SOFTWARE ENGINEERING 2024年第12期50卷 3225-3248页

作者： Wang, Yin Fan, Ming Liu, Junfeng Tao, Junjie Jin, Wuxia Wang, Haijun Xiong, Qi Liu, Ting Xi An Jiao Tong Univ Key Lab Intelligent Networks & Network Secur Minist Educ Xian 710049 Shaanxi Peoples R China Tencent Big Data Secur Lab Shenzhen 518057 Guangdong Peoples R China

Mini-app is an emerging form of mobile application that combines web technology with native capabilities. Its features, e.g., no need to download and no installation, have made it popular rapidly. However, privacy issues that violate the laws or regulations are breeding in the swiftly expanding mini-app ecosystem. Ensuring consistency between the mini-app's data practices embedded in its program code behavior and privacy policy description is crucial. But no work has systematically investigated the privacy problem of the mini-app before. To achieve this purpose, there are two main challenges. Firstly, the mini-app represents a novel application form, and a deficiency exists in information-sensitive code analysis tools capable of accurately discerning data practices from the code. Secondly, previous studies focusing on consistency have exhibited granularity issues related to data types and consistency patterns. This paper introduces MiniDetector, a novel approach for identifying consistency issues in mini-apps. MiniDetector employs data flow analysis to pinpoint data practices within the program code and utilizes a two-stage prompt engineering process to extract data practices from privacy policies. The results from both analyses are then compared to establish a consistency match. The proposed method undergoes sufficiency evaluations on a dataset comprising 70 mini-apps. Additionally, we conduct a comprehensive analysis of 100,000 mini-apps on the WeChat client in the wild, extracting 3,369 with privacy policies. Astonishingly, only 11 of these meet the consistency requirements, while 3,358 exhibit inconsistencies, resulting in an alarming inconsistency rate of 99.7%.

关键词： Privacy Codes Social networking (online) Message services data privacy Regulation Operating systems Smart phones Prompt engineering Protection Mini-app mini-program privacy consistency compliance detection data flow analysis prompt engineering

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Enhancing Bug-Inducing Commit Identification: A Fine-Grained Semantic analysis Approach

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IEEE TRANSACTIONS ON SOFTWARE ENGINEERING 2024年第11期50卷 3037-3052页

作者： Tang, Lingxiao Ni, Chao Huang, Qiao Bao, Lingfeng Zhejiang Univ State Key Lab Blockchain & Data Secur Hangzhou 310007 Peoples R China Hangzhou High Tech Zone Binjiang Blockchain & Data Hangzhou 310052 Peoples R China Zhejiang Gongshang Univ Sch Comp Sci & Technol Hangzhou 310018 Peoples R China

The SZZ algorithm and its variants have been extensively utilized for identifying bug-inducing commits based on bug-fixing commits. However, these algorithms face challenges when there are no deletion lines in the bug-fixing commit. Previous studies have attempted to address this issue by tracing back all lines in the block that encapsulates the added lines. However, this method is too coarse-grained and suffers from low precision. To address this issue, we propose a novel method in this paper called Sem-SZZ, which is based on fine-grained semantic analysis. Initially, we observe that a significant number of bug-inducing commits can be identified by tracing back the unmodified lines near added lines, resulting in improved precision and F1-score. Building on this observation, we conduct a more fine-grained semantic analysis. We begin by performing program slicing to extract the program part near the added lines. Subsequently, we compare the program's states between the previous version and the current version, focusing on data flow and control flow differences based on the extracted program part. Finally, we extract statements contributing to the bug based on these differences and utilize them to locate bug-inducing commits. We also extend our approach to fit the scenario where the bug-fixing commits contain deleted lines. Experimental results demonstrate that Sem-SZZ outperforms the state-of-the-art methods in identifying bug-inducing commits, regardless of whether the bug-fixing commit contains deleted lines.

关键词： Computer bugs Noise Software algorithms Semantics Reliability Buildings Process control Nickel Linux Chaos SZZ algorithm data flow analysis control flow analysis

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Linear and Non-linear Relational Analyses for Quantum Program Optimization

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PROCEEDINGS OF THE ACM ON PROGRAMMING LANGUAGES-PACMPL 2025年第POPL期9卷 1072-1103页

作者： Amy, Matthew Lunderville, Joseph Simon Fraser Univ Burnaby BC Canada

The phase folding optimization is a circuit optimization used in many quantum compilers as a fast and effective way of reducing the number of high-cost gates in a quantum circuit. However, existing formulations of the optimization rely on an exact, linear algebraic representation of the circuit, restricting the optimization to being performed on straightline quantum circuits or basic blocks in a larger quantum program. We show that the phase folding optimization can be re-cast as an affine relation analysis, which allows the direct application of classical techniques for affine relations to extend phase folding to quantum programs with arbitrarily complicated classical control flow including nested loops and procedure calls. Through the lens of relational analysis, we show that the optimization can be powered-up by substituting other classical relational domains, particularly ones for non-linear relations which are useful in analyzing circuits involving classical arithmetic. To increase the precision of our analysis and infer non-linear relations from gate sets involving only linear operations - such as Clifford+T - we show that the sum-over-paths technique can be used to extract precise symbolic transition relations for straightline circuits. Our experiments show that our methods are able to generate and use non-trivial loop invariants for quantum program optimization, as well as achieve some optimizations of common circuits which were previously attainable only by hand.

关键词： Quantum software compiler optimization data flow analysis relational program analysis invariant generation

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IncIDFA: An Efficient and Generic Algorithm for Incremental Iterative dataflow analysis

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Proceedings of the ACM on Programming Languages 2025年第OOPSLA1期9卷 617-648页

作者： Nougrahiya, Aman Krishna Nandivada, V. IIT Madras India

Iterative dataflow analyses (IDFAs) are important static analyses employed by tools like compilers for enabling program optimizations, comprehension, verification, and more. During compilation of a program, optimizations/transformations can render existing dataflow solutions stale, jeopardizing the optimality and correctness of subsequent compiler passes. Exhaustively recomputing these solutions can be costly. Since most program changes impact only small portions of the flowgraph, several incrementalization approaches have been proposed for various subclasses of IDFAs. However, these approaches face one or more of these limitations: (i) loss of precision compared to exhaustive analysis, (ii) inability to handle arbitrary lattices and dataflow functions, and (iii) lacking fully automated incrementalization of the IDFA. As a result, mainstream compilers lack frameworks for generating precise incremental versions of arbitrary IDFAs, leaving analysis writers to create ad hoc algorithms for incrementalization – an often cumbersome and error-prone task. To tackle these challenges, we introduce IncIDFA, a novel algorithm that delivers precise and efficient incremental variants of any monotone IDFA. IncIDFA utilizes a two-pass approach to maintain precision. Unlike prior works, IncIDFA avoids resetting the dataflow solutions to least informative values when dealing with strongly-connected regions and arbitrary program changes. We formally prove the precision guarantees of IncIDFA for arbitrary dataflow problems and program changes. IncIDFA has been implemented in the IMOP compiler framework for parallel OpenMP C programs. To showcase its generality, we have instantiated IncIDFA to ten specific dataflow analyses, without requiring any additional code for incrementalization. We present an evaluation of IncIDFA on a real-world set of optimization passes, across two different architectures. As compared to exhaustive recomputation, IncIDFA resulted in a speedup of up to 11× (geo

关键词： data flow analysis

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