Cryo-Electron Microscopy Training at the Wadsworth Center

2000 ◽  
Vol 6 (S2) ◽  
pp. 278-279
Author(s):  
Robert A. Grassucci ◽  
Joachim Frank
Keyword(s):  
Electron Microscopy ◽  
Web Page ◽  
Web Browser ◽  
Novice User ◽  
Cryo Electron Microscopy ◽  
Set Up ◽  
Page Figure ◽  
The Web

Training of students, postdocs and scientists in the techniques and instrumentation of Cryo-electron microscopy has many challenges. This is especially the case at the Wadsworth center where there are a variety of techniques as well as instruments to choose from, each of them having certain nuances that need to be recognized before they can be fully taken advantage of. There are also users with many levels of experience that need to be trained to use the equipment and techniques effectively. For this reason we have chosen to incorporate many of the protocols which are used into an internal web page. The web browser is a very effective tool for conveying detailed information on a variety of levels.A novice user is asked to go through the EM training web page (Figure 1) and then select the Philips EM420 use link to get a feel for the steps that will be involved to set up and operate the microscope.

scholarly journals Practical Experience with Hole-Free Phase Plates for Cryo Electron Microscopy

2016 ◽  
Vol 22 (6) ◽  
pp. 1316-1328 ◽  
Author(s):  
Michael Marko ◽  
Chyongere Hsieh ◽  
Eric Leith ◽  
David Mastronarde ◽  
Sohei Motoki
Keyword(s):  
Electron Microscopy ◽  
High Resolution ◽  
Practical Experience ◽  
Phase Plate ◽  
Native State ◽  
Automated Data Collection ◽  
Cryo Electron Microscopy ◽  
Transmission Electron ◽  
Phase Plates ◽  
Set Up

AbstractPhase plate (PP) imaging has proven to be valuable in transmission cryo electron microscopy of unstained, native-state biological specimens. Many PP types have been described, however until the recent implementation of the “hole-free” phase plate (HFPP), imaging has been challenging. We found the HFPP to be simple to construct and to set up in the transmission electron microscopy, but care in implementing automated data collection is needed. Performance may be variable, both initially and over time, thus it is important to monitor and evaluate image quality by observing the power spectrum. We found that while some HFPPs gave transfer to high resolution without CTF oscillation, most reached high resolution when operated with modest defocus.

Extensions of Web Browsers useful to Knowledge Workers

2012 ◽  
pp. 239-273
Author(s):  
Sarah Vert
Keyword(s):  
Knowledge Workers ◽  
Knowledge Worker ◽  
Working Environment ◽  
The Internet ◽  
Web Browsers ◽  
Web Page ◽  
Web Browser ◽  
Internet Explorer ◽  
The One ◽  
The Web

This chapter focuses on the Internet working environment of Knowledge Workers through the customization of the Web browser on their computer. Given that a Web browser is designed to be used by anyone browsing the Internet, its initial configuration must meet generic needs such as reading a Web page, searching for information, and bookmarking. In the absence of a universal solution that meets the specific needs of each user, browser developers offer additional programs known as extensions, or add-ons. Among the various browsers that can be modified with add-ons, Mozilla’s Firefox is perhaps the one that first springs to mind; indeed, Mozilla has built the Firefox brand around these extensions. Using this example, and also considering the browsers Google Chrome, Internet Explorer, Opera and Safari, the author will attempt to demonstrate the potential of Web browsers in terms of the resources they can offer when they are customizable and available within the working environment of a Knowledge Worker.

scholarly journals igv.js: an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV)

2020 ◽  
Author(s):  
James T. Robinson ◽  
Helga Thorvaldsdóttir ◽  
Douglass Turner ◽  
Jill P. Mesirov
Keyword(s):  
Single Line ◽  
Integrative Genomics ◽  
Web Page ◽  
Web Browser ◽  
The Web

Abstractigv.js is an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV). It can be easily dropped into any web page with a single line of code and has no external dependencies. The viewer runs completely in the web browser, with no backend server and no data pre-processing required.

scholarly journals Live analysis and reconstruction of single-particle cryo-electron microscopy data with CryoFLARE

2019 ◽  
Author(s):  
Andreas D. Schenk ◽  
Simone Cavadini ◽  
Nicolas H. Thomä ◽  
Christel Genoud
Keyword(s):  
Electron Microscopy ◽  
Data Collection ◽  
Single Particle ◽  
Integrated Reporting ◽  
Seamless Integration ◽  
High Resolution Data ◽  
User Input ◽  
Cryo Electron Microscopy ◽  
New Processing ◽  
Set Up

AbstractEfficient, reproducible and accountable single-particle cryo-electron microscopy structure determination is tedious and often impeded by lack of a standardized procedure for data analysis and processing. To address this issue, we have developed the FMI Live Analysis and Reconstruction Engine (CryoFLARE). CryoFLARE is a modular open-source platform offering easy integration of new processing algorithms developed by the cryo-EM community. It provides a user-friendly interface that allows fast setup of standardized workflows, serving the need of pharmaceutical industry and academia alike who need to optimize throughput of their microscope. To consistently document how data is processed, CryoFLARE contains an integrated reporting facility to create reports.Live analysis and processing parallel to data acquisition are used to monitor and optimize data quality. Problems at the level of the sample preparation (heterogeneity, ice thickness, sparse particles, areas selected for acquisition, etc.) or misalignments of the microscope optics can quickly be detected and rectified before data collection is continued. Interfacing with automated data collection software for retrieval of acquisition metadata reduces user input needed for analysis, and with it minimizes potential sources of errors and workflow inconsistencies. Local and remote export support in Relion-compatible job and data format allows seamless integration into the refinement process. The support for non-linear workflows and fine-grained scheduling for mixed workflows with separate CPU and GPU based calculation steps ensures optimal use of processing hardware. CryoFLARE’s flexibility allows it to be used for all types of image acquisitions, ranging from sample screening to high-resolution data collection, and offers a new alternative for setting up image processing workflows. It can be used without modifications of the hardware/software delivered by the microscope supplier. As it is running on a server in parallel to the hardware used for acquisition, it can easily be set up for remote display connections and fast control of the acquisition status.

scholarly journals Phish-Shelter

2022 ◽  
Vol 15 (1) ◽  
pp. 1-23
Author(s):  
Rizwan Ur Rahman ◽  
Lokesh Yadav ◽  
Deepak Singh Tomar
Keyword(s):  
Credit Card ◽  
Third Party ◽  
Supervised Machine Learning ◽  
Detection Accuracy ◽  
Web Page ◽  
Web Browser ◽  
Feature Sets ◽  
Confidential Data ◽  
Degree Of Similarity ◽  
The Web

Phishing attack is a deceitful attempt to steal the confidential data such as credit card information, and account passwords. In this paper, Phish-Shelter, a novel anti-phishing browser is developed, which analyzes the URL and the content of phishing page. Phish-Shelter is based on combined supervised machine learning model.Phish-Shelter browser uses two novel feature set, which are used to determine the web page identity. The proposed feature sets include eight features to evaluate the obfuscation-based rule, and eight features to identify search engine. Further, we have taken eleven features which are used to discover contents, and blacklist based rule. Phish-Shelter exploited matching identity features, which determines the degree of similarity of a URL with the blacklisted URLs. Proposed features are independent from third-party services such as web browser history or search engines result. The experimental results indicate that, there is a significant improvement in detection accuracy using proposed features over traditional features.

scholarly journals WebMonitoring software system: Finite state machines for monitoring the web

2013 ◽  
Vol 10 (1) ◽  
pp. 1-23
Author(s):  
Vesna Pajic ◽  
Dusko Vitas ◽  
Gordana Pavlovic-Lazetic ◽  
Milos Pajic
Keyword(s):  
Information Search ◽  
Search Engines ◽  
Finite State Machines ◽  
Software System ◽  
State Machines ◽  
Web Page ◽  
Finite State ◽  
Set Up ◽  
The Moment ◽  
The Web

This paper presents a software system called WebMonitoring. The system is designed for solving certain problems in the process of information search on the web. The first problem is improving entering of queries at search engines and enabling more complex searches than keyword-based ones. The second problem is providing access to web page content that is inaccessible by common search engines due to search engine?s crawling limitations or time difference between the moment a web page is set up on the Internet and the moment the crawler finds it. The architecture of the WebMonitoring system relies upon finite state machines and the concept of monitoring the web. We present the system?s architecture and usage. Some modules were originally developed for the purpose of the WebMonitoring system, and some rely on UNITEX, linguistically oriented software system. We hereby evaluate the WebMonitoring system and give directions for further development.

scholarly journals Enrich Awareness of Users to Detect Phishing Websites

2019 ◽  
Vol 8 (6S3) ◽  
pp. 648-650
Keyword(s):  
Social Engineering ◽  
Identity Theft ◽  
Web Pages ◽  
Web Page ◽  
Web Browser ◽  
Data Set ◽  
Training And Education ◽  
Precautionary Measures ◽  
And Training ◽  
The Web

Phishing attack is used for identity theft with the help of social engineering and some sophisticated attacks. To attract the user by clicking a URL and is trapped to a phishing Web page. Security for user’s credentials is one of most important factor for organizations nowadays. It can be achieved through several ways like education and training. Through training and education the level of awareness will be increased also it helps to mitigate phishing. Approach with several steps is introduced in this paper, where a user must take a look or take these precautionary measures if the user is browsing any Web browser. We found it possible to detect Phishing Web pages without anti Phishing solutions. This approach contains several steps to examine whether the Web page is a real Web page or a fake Webpage. All these steps will check the phishing features exist in that Web page or not. For evaluation of our approach we analyzed the data set of Phish Tank, this data set is full of Phishing Web Pages. The purpose of evaluation is to check the features discussed in our approach to aware the user. From the following result it is resulted that the user can detect without using any Anti Phishing solution just by taking some steps to check the Web page for certain features.

Scanning Probe Microscopy: Internet Resource Development and Integration into Undergraduate Curriculum

1997 ◽  
Vol 3 (S2) ◽  
pp. 1279-1280
Author(s):  
R.J. Kline ◽  
D.N. Leonard ◽  
A.D. Batchelor ◽  
P.E. Russell
Keyword(s):  
Scanning Probe Microscopy ◽  
Materials Science ◽  
Undergraduate Curriculum ◽  
Scanning Probe ◽  
The Internet ◽  
Internet Resource ◽  
Web Page ◽  
Probe Microscopy ◽  
Set Up ◽  
The Web

The Internet has become a very valuable educational resource. It allows a person to be able to reach a very large, diverse audience across the world with ease. With NSF Combined Research-Curriculum Development (CRCD) funding, we have begun to use the Internet as an educational and technical resource for people wanting to learn about Scanning Probe Microscopy (SPM). We have set up a web page with informative information for people of all levels of SPM knowledge. We are actively combining SPM research and education into the materials science and engineering undergraduate curriculum. We also use the web page as a way to publish our findings to help other universities integrate SPM into their curriculums.The URL is: http://spm.aif.ncsu.eduThe web page is divided into seven main components. Each component has a specific intended audience and purpose. We have designed some components for people who have never heard of SPM and others for people who run SPM labs.

New challenges to image processing posed by cryo-Electron microscopy of single particles

1991 ◽  
Vol 49 ◽  
pp. 422-423
Author(s):  
Joachim Frank
Keyword(s):  
Electron Microscopy ◽  
Phase Contrast ◽  
Particle Orientation ◽  
Single Particles ◽  
Contrast Transfer Function ◽  
Virtual Absence ◽  
Cryo Electron Microscopy ◽  
Spatial Frequencies ◽  
New Challenges ◽  
Particle Images

Compared with images of negatively stained single particle specimens, those obtained by cryo-electron microscopy have the following new features: (a) higher “signal” variability due to a higher variability of particle orientation; (b) reduced signal/noise ratio (S/N); (c) virtual absence of low-spatial-frequency information related to elastic scattering, due to the properties of the phase contrast transfer function (PCTF); and (d) reduced resolution due to the efforts of the microscopist to boost the PCTF at low spatial frequencies, in his attempt to obtain recognizable particle images.

Enhanced information from biological materials through technological improvements in cryo-electron microscopy

1992 ◽  
Vol 50 (1) ◽  
pp. 788-789
Author(s):  
Marc J.C. de Jong ◽  
Wim M. Busing ◽  
Max T. Otten
Keyword(s):  
Electron Microscopy ◽  
Electron Beam ◽  
Biological Materials ◽  
Electron Crystallography ◽  
Cryo Electron Microscopy ◽  
Transmission Electron ◽  
The Many ◽  
Technological Improvements ◽  
Beam Damage

Biological materials damage rapidly in the electron beam, limiting the amount of information that can be obtained in the transmission electron microscope. The discovery that observation at cryo temperatures strongly reduces beam damage (in addition to making it unnecessaiy to use chemical fixatives, dehydration agents and stains, which introduce artefacts) has given an important step forward to preserving the ‘live’ situation and makes it possible to study the relation between function, chemical composition and morphology.Among the many cryo-applications, the most challenging is perhaps the determination of the atomic structure. Henderson and co-workers were able to determine the structure of the purple membrane by electron crystallography, providing an understanding of the membrane's working as a proton pump. As far as understood at present, the main stumbling block in achieving high resolution appears to be a random movement of atoms or molecules in the specimen within a fraction of a second after exposure to the electron beam, which destroys the highest-resolution detail sought.

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