recently,building robot has become the current trend for the teaching and learning the subject of science in elementary and secondary *** objective of this paper is to propose a teaching approach for programming langu...
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(纸本)9781424463671
recently,building robot has become the current trend for the teaching and learning the subject of science in elementary and secondary *** objective of this paper is to propose a teaching approach for programming language by the application of weblog on robot *** is hoped that such an approach may make learning more enjoyable as well as effective and may further motivate students in future experiments.A study of teaching computer program in high school with VPL-based tool to construct robots was *** formed in team to build robots and write program to perform the specified *** result shows that students have achieved good results in terms of learning motivation.
Deep sequencing has many possible applications; one of them is the identification and quantification of RNA editing sites. The most common type of RNA editing is adenosine to inosine (A-to-I) editing. A prerequisite f...
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Deep sequencing has many possible applications; one of them is the identification and quantification of RNA editing sites. The most common type of RNA editing is adenosine to inosine (A-to-I) editing. A prerequisite for this editing process is a double-stranded RNA (dsRNA) structure. Such dsRNAs are formed as part of the microRNA (miRNA) maturation process, and it is therefore expected that miRNAs are affected by A-to-I editing. Indeed, tens of editing sites were found in miRNAs, some of which change the miRNA binding specificity. Here, we describe a protocol for the identification of RNA editing sites in mature miRNAs using deep sequencing data. less
We present SCENIC, a computational method for simultaneous gene regulatory network reconstruction and cell-state identification from single-cell RNA-seq data (http://*** ). On a compendium of single-cel...
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We present SCENIC, a computational method for simultaneous gene regulatory network reconstruction and cell-state identification from single-cell RNA-seq data (http://*** ). On a compendium of single-cell data from tumors and brain, we demonstrate that cis-regulatory analysis can be exploited to guide the identification of transcription factors and cell states. SCENIC provides critical biological insights into the mechanisms driving cellular heterogeneity. less
Protein post-translational modifications (PTMs) are essential elements of cellular communication. Their variations in abundance can affect cellular pathways, leading to cellular disorders and diseases. A widely used m...
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Protein post-translational modifications (PTMs) are essential elements of cellular communication. Their variations in abundance can affect cellular pathways, leading to cellular disorders and diseases. A widely used method for revealing PTM-mediated regulatory networks is their label-free quantitation (LFQ) by high-resolution mass spectrometry. The raw data resulting from such experiments are generally interpreted using specific software, such as MaxQuant, MassChroQ, or Proline for instance. They provide data matrices containing quantified intensities for each modified peptide identified. Statistical analyses are then necessary (1) to ensure that the quantified data are of good enough quality and sufficiently reproducible, (2) to highlight the modified peptides that are differentially abundant between the biological conditions under study. The objective of this chapter is therefore to provide a complete data analysis pipeline for analyzing the quantified values of modified peptides in presence of two or more biological conditions using the R software. We illustrate our pipeline starting from MaxQuant outputs dealing with the analysis of A549-ACE2 cells infected by SARS-CoV-2 at different time stamps, freely available on PRIDE (PXD020019). less
This chapter overviews the quality control (QC) issues for SNP-based genotyping methods used in genome-wide association studies. The main metrics for evaluating the quality of the genotypes are discussed followed by a...
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This chapter overviews the quality control (QC) issues for SNP-based genotyping methods used in genome-wide association studies. The main metrics for evaluating the quality of the genotypes are discussed followed by a worked out example of QC pipeline starting with raw data and finishing with a fully filtered dataset ready for downstream analysis. The emphasis is on automation of data storage, filtering, and manipulation to ensure data integrity throughput the process and on how to extract a global summary from these high dimensional datasets to allow better-informed downstream analytical decisions. All examples will be run using the R statistical programming language followed by a practical example using a fully automated QC pipeline for the Illumina platform. less
Dynamic clamp is a technique that combines computer modeling with experimental electrophysiology and is used to examine how specific ion channels modulate a variety of single-cell activities, by artificially emulating...
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Dynamic clamp is a technique that combines computer modeling with experimental electrophysiology and is used to examine how specific ion channels modulate a variety of single-cell activities, by artificially emulating the response properties of specific ionic conductances during an electrophysiological recording. This is accomplished by continuously and instantaneously varying the current that is injected into a recorded neuron as a function of a computer-generated conductance and of the difference between its apparent reversal potential and the actual fluctuations of the membrane potential of the recorded cell. Dynamic clamp is often used to model voltage-independent, voltage-dependent, and synaptic ion currents and is very useful to study how cortical neurons compute and integrate diverse synaptic currents or sequences of synaptic inputs into specific spike-train outputs. Cortical networks are composed of highly heterogeneous cell types, and it is often difficult to dissect individual aspects of signal propagation between neurons and how they contribute to shape network activities underlying several cortical functions. Here, we describe some implementations of the dynamic clamp technique useful to studying the contribution of different elements of cortical circuits to the generation of single cell spike outputs. less
High-resolution multiphoton imaging of live cells has become an invaluable method to study protein dynamics in highly compartmentalized subcellular environments. Here we describe procedures that we recently developed ...
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High-resolution multiphoton imaging of live cells has become an invaluable method to study protein dynamics in highly compartmentalized subcellular environments. Here we describe procedures that we recently developed to quantify rhodopsin mobility within and between retinal rod photoreceptor light signaling microcompartments, the disc membrane lobules, using multiphoton fluorescence relaxation after photoconversion. less
In recent years R has become de facto statistical programming language of choice for statisticians and it is also arguably the most widely used generic environment for analysis of high-throughput genomic data. In this...
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In recent years R has become de facto statistical programming language of choice for statisticians and it is also arguably the most widely used generic environment for analysis of high-throughput genomic data. In this chapter we discuss some approaches to improve performance of R when working with large SNP datasets. less
There are a number of options available to researchers who wish to collect and analyze viral metagenomes (viromes) from environmental samples. Here we describe a laboratory procedure for generation of viromes from fre...
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There are a number of options available to researchers who wish to collect and analyze viral metagenomes (viromes) from environmental samples. Here we describe a laboratory procedure for generation of viromes from freshwater samples, specifically targeting dsDNA bacteriophages. We also discuss methods for bioinformatic analysis of the resulting data. less
This chapter is intended to introduce the fundamental principles of the heat map, the most widely used medium to present high-throughput data, to scientists unaccustomed to analyzing large data sets. Its scope include...
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This chapter is intended to introduce the fundamental principles of the heat map, the most widely used medium to present high-throughput data, to scientists unaccustomed to analyzing large data sets. Its scope includes describing the general features of heat maps, how their components are designed, the meaning of parameters such as “distance method” and “linkage method,” and the influence of manipulations such as row-scaling and logarithmic transformations on data interpretation and presentation. This chapter may serve as a guide to understanding the use of heat maps in published analyses or to aid in their design, allowing efficient interpretations of high-throughput experiments, exploration of hypotheses, or clear communications of findings. less
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