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作者： Anne-Claire Jacomin Ioannis P. Nezis

Oogenesis is a fundamental biological process for the transmission of genetic information to the next generations. Drosophila has proven to be a valuable model for elucidating the molecular and cellular mechanisms involved in this developmental process. It has been shown that autophagy participates in the maturation of the egg chamber. Here we provide a protocol for monitoring and quantification of the autophagic process in the Drosophila germline cells using the fluorescent reporters mCherry-DmAtg8a and GFP-mCherry-DmAtg8a. less

关键词： Dissection Fiji Microscopy ImageJ Statistical Calculation programming language Pull-down Assay GraphPad Prism Drosophila Drosophila melanogaster Saccharomyces cerevisiae Lens Autophagy Germline cells GAL4/UAS system mCherry-DmAtg8a GFP-mCherry-DmAtg8a

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Studying the Early Stages of Protein Aggregation Using Replica Exchange Molecular Dynamics Simulations

Studying the Early Stages of Protein Aggregation Using Repli...

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作者： Joan-Emma Shea Zachary A. Levine

The simulation of protein aggregation poses several computational challenges due to the disparate time and lengths scales that are involved. This chapter focuses on the use of atomistically detailed simulations to probe the initial steps of aggregation, with an emphasis on the Tau peptide as a model system, run under a replica exchange molecular dynamics protocol. less

关键词： Molecular Dynamics Simulation Protein Folding Analysis Statistical Calculation programming language Protein aggregation Intrinsically disordered proteins Protein folding Alzheimer’s disease Tau protein Amyloid fibrils

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The Study of Plagiarism Detection for Object-Oriented programming language

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2nd International Conference on Computational Collective Intelligence: Technologies and Applications

作者： Kuo, Jong-Yih Wang, Wei-Ting Natl Taipei Univ Technol Dept Comp Sci & Informat Engn Taipei Taiwan

ISBN: (纸本)9783642166952

The purpose of this thesis is to study the plagiarism detection method aiming at C++ programs. We proposed the corresponding preventive measures by summarizing the common types of plagiarism attack through observation and statistical analysis. Using text analysis, structure analysis, and variable analysis would prevent misjudgment. Finally, we implemented the CPD(C++ Plagiarism Detection) system and compare it with other existing systems, and the experimental result shows us that our system can detect more kinds of plagiarism attacks than other existing systems.

关键词： programming language Plagiarism

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Understanding language Profile of Open Source Software using Association Rule Mining

Understanding Language Profile of Open Source Software using...

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Future Technologies Conference

作者： Munish Saini Kuljit Kaur Chahal Dept. of Computer Science Guru Nanak Dev University

ISBN: (纸本)9781509041725

The development of open source software has gained popularity. Most of the software projects use diverse sets of programming languages for development. In this work, the Knowledge Discovery in Data (KDD) approach to analyze the data of 30,518 open source projects hosted on SourceForge. The process of knowledge discovery is explored by using the association rule mining algorithm to find the programming languages, which are often used together in combination for the development of software project. The group-matrix based visualization technique is further implied to visualize the generated associated group of languages. The generated knowledge base and visualization of associated languages provide current and future developers with insight knowledge of multiple set of programming languages which are used together frequently for the development of open source software projects.

关键词： Open source software programming language Association rule mining Knowledge discovery in data (KDD) Group-matrix based visualization

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False Discovery Rate Estimation in Proteomics

False Discovery Rate Estimation in Proteomics

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作者： Suruchi Aggarwal Amit Kumar Yadav

With the advancement in proteomics separation techniques and improvements in mass analyzers, the data generated in a mass-spectrometry based proteomics experiment is rising exponentially. Such voluminous datasets necessitate automated computational tools for high-throughput data analysis and appropriate statistical control. The data is searched using one or more of the several popular database search algorithms. The matches assigned by these tools can have false positives and statistical validation of these false matches is necessary before making any biological interpretations. Without such procedures, the biological inferences do not hold true and may be outright misleading. There is a considerable overlap between true and false positives. To control the false positives amongst a set of accepted matches, there is a need for some statistical estimate that can reflect the amount of false positives present in the data processed. False discovery rate (FDR) is the metric for global confidence assessment of a large-scale proteomics dataset. This chapter covers the basics of FDR, its application in proteomics, and methods to estimate FDR. less

关键词： Shotgun Proteomics Proteomics Database Search Genomics Data analysis programming language False discovery rate Posterior error probability Target-decoy Peptide spectrum matches Statistical validation

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Development of intelligent control system for X-ray streak camera in diagnostic instrument manipulator

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NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION A-ACCELERATORS SPECTROMETERS DETECTORS AND ASSOCIATED EQUIPMENT 2015年 799卷 124-131页

作者： Pei, Chengquan Wu, Shengli Tian, Jinshou Liu, Zhen Fang, Yuman Gao, Guilong Liang, Lingliang Wen, Wenlong Xi An Jiao Tong Univ Minist Educ Key Lab Phys Elect & Devices Xian 710049 Peoples R China Chinese Acad Sci Xian Inst Opt & Precis Mech Xian 710119 Peoples R China Univ Chinese Acad Sci Beijing 100039 Peoples R China

An intelligent control system for an X ray streak camera in a diagnostic instrument manipulator (DIM) is proposed and implemented, which can control time delay, electric focusing, image gain adjustment, switch of sweep voltage, acquiring environment parameters etc. The system consists of 16 A/D converters and 16 D/A converters, a 32-channel general purpose input/output (GPIO) and two sensors. An isolated DC/DC converter with multi-outputs and a single mode filer were adopted to reduce the interference generated by the common ground among the A/D, D/A and I/O. The software was designed using graphical programming language and can remotely access the corresponding instrument from a website. The entire intelligent control system can acquire the desirable data at a speed of 30 Mb/s and store 11 for later analysis. The intelligent. system was implemented on a streak camera in a DIM and it shows a temporal resolution of 11.25 ps, spatial distortion of less than 10% and dynamic range of 279:1. The intelligent control system has been successfully used in a streak camera to verify the synchronization of multi-channel laser on the Confinement Fusion (C) 2015 Elsevier B.V. All rights reserved.

关键词： Intelligent control system Streak camera Diagnostic instrument manipulator Isolated power programming language

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IgE Epitope Mapping Using Peptide Microarray Immunoassay

IgE Epitope Mapping Using Peptide Microarray Immunoassay

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作者： Gustavo Gimenez Sara Benedé Jing Lin

IgE epitope mapping of food allergens contributes to a better understanding of the pathogenesis of food allergy and may become an additional tool for food allergy diagnosis/prognosis. Microarray platforms which allow for simultaneous screening of a large number of peptides corresponding to the sequences of food allergens are ideally suited for large-scale IgE epitope mapping. Here we describe the method of performing a reliable and sensitive peptide microarray immunoassay, which was developed in our lab and results in the identification of candidate IgE epitope biomarkers useful in determining allergic disease severity and prognosis, as well as in the prediction of treatment outcomes. A gastric digestion model that can be applied to prescreen peptides and reduce costs in the peptide microarray is also described in this chapter. less

关键词： Epitope Mapping Peptide Microarray Immunoassay Immunolabeling Data analysis Microarray programming language GraphPad Prism IgE Food allergy Gastric digestion Anti-biotin Anti-human IgE

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Syntax and Semantics of Coding in Python

Syntax and Semantics of Coding in Python

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作者： Jeremy Meulemans Tonya Ward Dan Knights

Python is a dynamically typed programming language providing a unique blend of power, simplicity and expressiveness that has quickly established itself as a major player in technical fields. The language is built around a very natural syntax, making it an ideal language for both beginners to programming and scientists looking for rapid research implementation. Usage cases from simple file formatting to determining the impact of oil degradation in obtained metagenomic sequence data are facilitated by features of the language. For example, the study of oil breakdown by bacterial communities is likely to involve handling very high-dimensional data, including both the metabolites present in oil and the hundreds of bacterial species often present in environmental communities. The ease of incorporating existing Python modeling packages and the solid frameworks provided by python for scientific computing make this an ideal language for analyzing these types of data. less

关键词： Python programming language Introduction Coding language Problem solving

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Atomistic Molecular Dynamics Simulations of DNA Minicircle Topoisomers: A Practical Guide to Setup, Performance, and Analysis

Atomistic Molecular Dynamics Simulations of DNA Minicircle T...

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作者： Thana Sutthibutpong Agnes Noy Sarah Harris

While DNA supercoiling is ubiquitous in vivo, the structure of supercoiled DNA is more challenging to study experimentally than simple linear sequences because the DNA must have a closed topology in order to sustain superhelical stress. DNA minicircles, which are closed circular double-stranded DNA sequences typically containing between 60 and 500 base pairs, have proven to be useful biochemical tools for the study of supercoiled DNA mechanics. We present detailed protocols for constructing models of DNA minicircles in silico, for performing atomistic molecular dynamics (MD) simulations of supercoiled minicircle DNA, and for analyzing the results of the calculations. These simulations are computationally challenging due to the large system sizes. However, improvements in parallel computing software and hardware promise access to improve conformational sampling and simulation timescales. Given the concurrent improvements in the resolution of experimental techniques such as atomic force microscopy (AFM) and cryo-electron microscopy, the study of DNA minicircles will provide a more complete understanding of both the structure and the mechanics of supercoiled DNA. less

关键词： Molecular Dynamics Simulation Atomic Force Microscopy (AFM) Cryo-EM NMR Gel Electrophoresis Cryo-electron Tomography Python Data analysis programming language DNA supercoiling

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The Challenges and the Opportunities of Teaching the Introductory Computer programming Course: Case Study 5

The Challenges and the Opportunities of Teaching the Introdu...

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5th International Conference on e-Learning (econf)

作者： Hegazi, Mohamed Osman Alhawarat, Mohammad Prince Sattam Bin Abdulaziz Univ Coll Comp Engn & Sci Dept Comp Sci Alkharj Saudi Arabia

ISBN: (纸本)9781467394314

Teaching practical courses has always constituted burdens on colleges offering non-technical degrees. One of these courses is computer programming, especially in degrees like computer science, information systems and software engineering. In such programs, students are expected to take between 2-5 computer programming courses. Success ratio in the first course is usually low. Why is it low and how this ratio can be increased is discussed in this paper. This is carried out in the context of an introductory computer programming course at the college of computer engineering and sciences (CCES) at Prince Sattam Bin Abdulaziz University in Kingdom of Saudi Arabia. This study also relies on the teaching experience of the authors in different countries including -for around ten years: UK, USA, Sudan, Jordan and Kingdom of Saudi Arabia. To figure out problems and solutions for teaching introductory computer programming course, then interviews with selected instructors who teach such course at the college are conducted. Also, a questionnaire has been designed and distributed to students. The results of the analysis for both the interviews and the questionnaire have been used along with the results of similar studies to recommend solutions of problems occur in such course. As questionnaire shows, most students think that giving the whole course in the lab will be much better and also they prefer not to work alone. These and other recommendations presented in this study are especially appropriate for similar institutions in the Middle-East and Gulf area.

关键词： Teaching programming language Practical Course Computer programming Course

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