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检索条件"主题词=Programming Language"

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Implementation and Application of Pulsed Interleaved Excitation for Dual-Color FCS and RICS

Implementation and Application of Pulsed Interleaved Excitat...

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作者： Jelle Hendrix Don C. Lamb

Pulsed interleaved excitation (PIE) employs pulsed laser sources that are interleaved such that differentially colored fluorophores can be measured or imaged quasi-simultaneously in the absence of spectral crosstalk. PIE improves the robustness and reduces data analysis complexity of many fluorescence techniques, such as fluorescence cross-correlation spectroscopy (FCCS) and raster image cross-correlation spectroscopy (ccRICS), two methods used for quantitative investigation of molecular interactions in vitro and in living cells. However, as PIE is most often used for fluorescence fluctuation spectroscopy and burst analysis experiments and utilizes time-correlated single-photon counting detection and advanced optoelectronics, it has remained a technique that is mostly used by specialized single-molecule research groups. This protocols chapter provides an accessible overview of PIE for anyone considering implementing the method on a homebuilt or commercial microscope. We give details on the instrumentation, data collection and analysis software, on how to properly set up and align a PIE microscope, and finally, on how to perform proper dual-color FCS and RICS experiments. less

关键词： Raster Image Correlation Spectroscopy Fluorescence Cross-correlation Spectroscopy Fluorescence Correlation Spectroscopy (FCS) Confocal Microscopy Fluorescence Fluctuation Spectroscopy FRET Scanning Fluorescence Correlation Spectroscopy Fluorescence Detection Image Analysis Data analysis programming language Lens CLSM FCS Time-correlated single-photon counting FCCS Pulsed interleaved excitation RICS ccRICS

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Interfering Peptides Targeting Protein–Protein Interactions in the Ethylene Plant Hormone Signaling Pathway as Tools to Delay Plant Senescence

Interfering Peptides Targeting Protein–Protein Interactions...

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作者： Alexander Hofmann Alexander Minges Georg Groth

Interfering peptides (iPs) have been recognized as valuable substances to specifically target protein–protein interactions (PPIs) in senescence and disease. Although the concept of iPs has been validated for several PPIs in medical and pharmaceutical research, little attention so far has been paid to the enormous potential iPs that may provide to target and control plant growth and developmental processes or plant environmental responses. However, recent research on PPIs in the ethylene signaling pathway has identified the synthetic peptide NOP-1 derived from the nuclear localization signal of ethylene regulator EIN2 as an efficient inhibitor of typical ethylene responses such as ripening, aging, and senescence. Biophysical and biochemical studies on purified recombinant proteins of the ethylene receptor family from various plant species demonstrate that the synthetic peptide binds in the nM-μM range at the plant target. Here, we describe methods to evaluate and quantify the effect of the NOP-1 peptide on flower senescence as a typical ethylene response in the intact plant system. This approach will help to systematically advance our technological capability to delay plant ethylene responses and to expand shelf-life or vase life of fruits and flowers. less

关键词： Spectroscopy HPLC Python Data analysis programming language Rubus idaeus Protein–protein interactions Interfering peptides Ethylene signaling Plant senescence

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Efficient XML usage within wireless sensor networks 08

Efficient XML usage within wireless sensor networks

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Proceedings of the 4th Annual International Conference on Wireless Internet

作者： Nils Hoeller Christoph Reinke Jana Neumann Sven Groppe Daniel Boeckmann Volker Linnemann Institute of Information Systems Luebeck Germany

ISBN: (纸本)9789639799363

Integrating wireless sensor networks in heterogeneous networks is a complex task. A reason is the absence of a standardized data exchange format that is supported in all participating sub networks. XML has evolved to the de facto standard data exchange format between heterogeneous networks and systems. However, XML usage within sensor networks has not been introduced because of the limited hardware resources. In this paper, we introduce XML template objects making XML usage applicable within sensor networks. This new XML data binding technique provides significant high compression results while still allowing dynamic XML processing and XML navigation. This is a step towards more complex but exchangeable data management in sensor networks and the extension of the service-oriented paradigm to sensor network application engineering.

关键词： database management programming language wireless sensor networks XML

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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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Reverse Engineering Transcriptional Gene Networks

Reverse Engineering Transcriptional Gene Networks

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作者： Vincenzo Belcastro Diego Bernardo

The aim of this chapter is a step-by-step guide on how to infer gene networks from gene expression profiles. The definition of a gene network is given in Subheading 1, where the different types of networks are discussed. The chapter then guides the readers through a data-gathering process in order to build a compendium of gene expression profiles from a public repository. Gene expression profiles are then discretized and a statistical relationship between genes, called mutual information (MI), is computed. Gene pairs with insignificant MI scores are then discarded by applying one of the described pruning steps. The retained relationships are then used to build up a Boolean adjacency matrix used as input for a clustering algorithm to divide the network into modules (or communities). The gene network can then be used as a hypothesis generator for discovering gene function and analyzing gene signatures. Some case studies are presented, and an online web-tool called Netview is described. less

关键词： Microarray Statistical Calculation Electron Microscopy (EM) Immunofluorescence Immunoprecipitation STRING Pathway Or Network Visualization programming language Database Management System Felis catus Mutual information Reverse engineering Gene network

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CD4+ T Cell Epitope Identification from Complex Parasite Antigen Mixtures

CD4+ T Cell Epitope Identification from Complex Parasite Ant...

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作者： Miguel Álvaro-Benito Friederike Ebner Miriam Bertazzon Eliot Morrison

Antigen complexity represents a major challenge for scoring CD4+ T cell immunogenicity, a key hallmark of immunity and with great potential to improve vaccine development. In this chapter, we provide a comprehensive picture of a pipeline that can be applied to virtually any complex antigen to overcome different limitations. Antigens are characterized by Mass Spectrometry to determine the available protein sources and their abundances. A reconstituted in vitro antigen processing system is applied along with bioinformatics tools to prioritize the list of candidates. Finally, the immunogenicity of candidate peptides is validated ex vivo using PBMCs from HLA-typed individuals. This protocol compiles the essential information for executing the whole pipeline while focusing on the candidate epitope prioritizing scheme. less

关键词： Spectroscopy Mass Spectrometry Cell And Tissue Culture Isotope Labeling SDS-PAGE Proteomics Peptide Identification programming language Flow Cytometry DNA Ligation Long-term Culture Co-culture Chromatography FPLC FACS Homo sapiens Antigen presentation MHC II CD4+ T cell reactivity Ascaris spp. parasites Excretory-secretory products (ES) Reconstitution in vitro antigen processing Complex antigen mixtures Anti-human CD40 Anti-human CD28 Anti-biotin Anti-CD3 Anti-HLA-DR

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Inferring cellular and molecular processes in single-cell data with non-negative matrix factorization using Python, R and GenePattern Notebook implementations of CoGAPS

Inferring cellular and molecular processes in single-cell da...

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作者： Jeanette A. Johnson Ashley P. Tsang Jacob T. Mitchell David L. Zhou Julia Bowden Emily Davis-Marcisak Thomas Sherman Ted Liefeld Melanie Loth Loyal A. Goff Jacquelyn W. Zimmerman Ben Kinny-Köster Elizabeth M. Jaffee Pablo Tamayo Jill P. Mesirov Michael Reich Elana J. Fertig Genevieve L. Stein-O’Brien

Non-negative matrix factorization (NMF) is an unsupervised learning method well suited to high-throughput biology. However, inferring biological processes from an NMF result still requires additional post hoc statistics and annotation for interpretation of learned features. Here, we introduce a suite of computational tools that implement NMF and provide methods for accurate and clear biological interpretation and analysis. A generalized discussion of NMF covering its benefits, limitations and open questions is followed by four procedures for the Bayesian NMF algorithm Coordinated Gene Activity across Pattern Subsets (CoGAPS). Each procedure will demonstrate NMF analysis to quantify cell state transitions in a public domain single-cell RNA-sequencing dataset. The first demonstrates PyCoGAPS, our new Python implementation that enhances runtime for large datasets, and the second allows its deployment in Docker. The third procedure steps through the same single-cell NMF analysis using our R CoGAPS interface. The fourth introduces a beginner-friendly CoGAPS platform using GenePattern Notebook, aimed at users with a working conceptual knowledge of data analysis but without a basic proficiency in the R or Python programming language. We also constructed a user-facing website to serve as a central repository for information and instructional materials about CoGAPS and its application programming interfaces. The expected timing to setup the packages and conduct a test run is around 15 min, and an additional 30 min to conduct analyses on a precomputed result. The expected runtime on the user’s desired dataset can vary from hours to days depending on factors such as dataset size or input ***-negative matrix factorization (NMF) is an unsupervised learning method well suited to high-throughput biology. However, inferring biological processes from an NMF result still requires additional post hoc statistics and annotation for interpretation of learned features. Here, we

关键词： Machine Learning Python Statistical Calculation Single-cell RNA-seq Data analysis programming language Seurat Apis Software Computational platforms and environments Bayesian inference

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Manipulating and Basic Analysis of Tabular Metagenomics Datasets Using R

Manipulating and Basic Analysis of Tabular Metagenomics Data...

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作者： Alex Coleman Martin Callaghan

Handling and manipulating tabular datasets is a critical step in every metagenomics analysis pipeline. The R statistical programming language offers a variety of versatile tools for working with tabular data that allow for the development of computationally efficient and reproducible workflows. Here we outline the basics of the R programming language and showcase a number of tools for data manipulation and basic analysis of metagenomics datasets. less

关键词： programming language Data analysis Metagenomics Data handling Reproducible research Data manipulation

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EST Databases and Web Tools for EST Projects

EST Databases and Web Tools for EST Projects

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作者： Yao-Qing Shen Emmet O’Brien Liisa Koski B. Franz Lang Gertraud Burger

This chapter outlines key considerations for constructing and implementing an EST database. Instead of showing the technological details step by step, emphasis is put on the design of an EST database suited to the specific needs of EST projects and how to choose the most suitable tools. Using TBestDB as an example, we illustrate the essential factors to be considered for database construction and the steps for data population and annotation. This process employs technologies such as PostgreSQL, Perl, and PHP to build the database and interface, and tools such as AutoFACT for data processing and annotation. We discuss these in comparison to other available technologies and tools, and explain the reasons for our choices. less

关键词： Statistical Calculation Sequence Annotation Multiple Sequence Alignment Database Management System programming language GenBank Homo sapiens data processing annotation Web interface EST database design data submission

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Metabolite Profiling of Plant Tissues by Liquid Chromatography Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

Metabolite Profiling of Plant Tissues by Liquid Chromatograp...

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作者： Jacob Pollier Alain Goossens

Plants accumulate an overwhelming variety of secondary metabolites that play important roles in defense and interaction of the plant with its environment. To investigate the dynamics of plant secondary metabolism, large-scale untargeted metabolite profiling (metabolomics) is mandatory. Here, we describe a detailed protocol for untargeted metabolite profiling in which methanol extracts of jasmonate-treated plant tissues are analyzed by reversed-phase liquid chromatography coupled to negative-ion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (MS). By means of dedicated integration and alignment software, the relative abundance of thousands of mass peaks, corresponding to hundreds of compounds, is calculated, and mass peaks of which the area is significantly changed by jasmonate treatment are identified. Subsequently, the metabolites corresponding to the significantly changed peaks are tentatively annotated using the accurate mass prediction of the Fourier transform-MS and the generated MS/MS data. Via this method, compounds of medium polarity, such as glucosinolates, alkaloids, phenylpropanoids, flavonoids, polyamines, and saponins, can be analyzed. less

关键词： Metabolomics Liquid Chromatography-mass Spectrometry Liquid Chromatography (LC) Fourier Transform Mass Spectrometry Reversed-phase Liquid Chromatography ESI-FT-ICR Mass Spectrometry Tandem Mass Spectrometry HPLC programming language XCMS FT-MS

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