Separation of oxidatively damaged DNA Nucleobases and Nucleosides on Packed and Monolith C18 Columns by HPLC-UV-EC

This study involves the incorporation of a commercially available Phenomenex Onyx C18 monolith column into the separation and detection of oxidative DNA damage. It includes thorough investigation of monolith performance and a comparison of the performance of monolith columns with a commercially available packed Restek reverse phase Ultra C18 column for the separation of DNA bases and nucleosides. The performance of the monolith was examined using efficiency, resolution, plate height, asymmetry and retention times, and in each case showed improved or at least comparable results in the separation of a mix of DNA bases and nucleosides. A 90% reduction, from just under 40 min. to just under 4 min., was obtained in the elution time of this separation. To the best of our knowledge, this is the first report of a fast monolith column separation successfully coupled to both a UV-vis and EC detector, which is especially useful for analysis of oxidative DNA damage. The determination of 8-oxoG and 8-OH-dG, oxidation products of guanine and 2’-deoxyguanosine, respectively, may be compromised by their ease of oxidation and therefore the fast separation, selective and sensitive detection, with no artifactual oxidation, detailed in this report, is ideal

Nickel(II)-catalysed oxidative guanine and DNA damage beyond 8-oxoguanine

Oxidative DNA damage is one of the most important and most studied mechanisms of disease. It has been associated with a range of terminal diseases such as cancer, heart disease, hepatitis, and HIV, as well as with a variety of everyday ailments. There are various mechanisms by which this type of DNA damage can be initiated, through radiation and chemical oxidation, among others; however, these mechanisms have yet to be fully elucidated. A HPLC-UV-EC study of the oxidation of DNA mediated by nickel(II) obtained results that show an erratic, almost oscillatory formation of 8-oxoguanine (8-oxoG) from free guanine and from guanine in DNA. Sporadic 8-oxoG concentrations were also observed when 8-oxoG alone was subjected to these conditions. A HPLC-MS/MS study showed the formation of oxidised-guanidinohydantoin (oxGH) from free guanine at pH 11, and the formation of guanidinohydantoin (GH) from DNA at pH 5.5

WARCreate: Create Wayback-Consumable WARC Files From Any Webpage

The Internet Archive\u27s Wayback Machine is the most common way that typical users interact with web archives. The Internet Archive uses the Heritrix web crawler to transform pages on the publicly available web into Web ARChive (WARC) files, which can then be accessed using the Wayback Machine. Because Heritrix can only access the publicly available web, many personal pages (e.g. password-protected pages, social media pages) cannot be easily archived into the standard WARC format. We have created a Google Chrome extension, WARCreate, that allows a user to create a WARC file from any webpage. Using this tool, content that might have been otherwise lost in time can be archived in a standard format by any user. This tool provides a way for casual users to easily create archives of personal online content. This is one of the first steps in resolving issues of long term storage, maintenance, and access of personal digital assets that have emotional, intellectual, and historical value to individuals

Impact of URI Canonicalization on Memento Count

Quantifying the captures of a URI over time is useful for researchers to identify the extent to which a Web page has been archived. Memento TimeMaps provide a format to list mementos (URI-Ms) for captures along with brief metadata, like Memento-Datetime, for each URI-M. However, when some URI-Ms are dereferenced, they simply provide a redirect to a different URI-M (instead of a unique representation at the datetime), often also present in the TimeMap. This infers that confidently obtaining an accurate count quantifying the number of non-forwarding captures for a URI-R is not possible using a TimeMap alone and that the magnitude of a TimeMap is not equivalent to the number of representations it identifies. In this work we discuss this particular phenomena in depth. We also perform a breakdown of the dynamics of counting mementos for a particular URI-R (google.com) and quantify the prevalence of the various canonicalization patterns that exacerbate attempts at counting using only a TimeMap. For google.com we found that 84.9% of the URI-Ms result in an HTTP redirect when dereferenced. We expand on and apply this metric to TimeMaps for seven other URI-Rs of large Web sites and thirteen academic institutions. Using a ratio metric DI for the number of URI-Ms without redirects to those requiring a redirect when dereferenced, five of the eight large web sites' and two of the thirteen academic institutions' TimeMaps had a ratio of ratio less than one, indicating that more than half of the URI-Ms in these TimeMaps result in redirects when dereferenced.Comment: 43 pages, 8 figure

WARCreate - Create Wayback-Consumable WARC Files From Any Webpage

[First Slide] What is WARCreate? Google Chrome extension Creates WARC files Enables preservation by users from their browser First steps in bringing Institutional Archiving facilities to the P

WARCreate and WAIL: WARC, Wayback, and Heritrix Made Easy

[First slide] The Problem Institutional Tools, Personal Archivists ON YOUR MACHINE -Complex to Operate -Require Infrastructure DELEGATED TO INSTITUTIONS -$$$ -Lose original perspective Locale content tailoring (DC vs. San Francisco) Observation Medium (PC web browser vs. Crawler

Client-Assisted Memento Aggregation Using The Prefer Header

[First paragraph] Preservation of the Web ensures that future generations have a picture of how the web was. Web archives like Internet Archive\u27s Wayback Machine, WebCite, and archive.is allow individuals to submit URIs to be archived, but the captures they preserve then reside at the archives. Traversing these captures in time as preserved by multiple archive sources (using Memento [8]) provides a more comprehensive picture of the past Web than relying on a single archive. Some content on the Web, such as content behind authentication, may be unsuitable or inaccessible for preservation by these organizations. Furthermore, this content may be inappropriate for the organizations to preserve due to reasons of privacy or exposure of personally identifiable information [4]. However, preserving this content would ensure an even-more comprehensive picture of the web and may be useful for future historians who wish to analyze content beyond the capability or suitability of archives created to preserve the public Web

Avoiding Zombies in Archival Replay Using ServiceWorker

[First paragraph] A Composite Memento is an archived representation of a web page with all the page requisites such as images and stylesheets. All embedded resources have their own URIs, hence, they are archived independently. For a meaningful archival replay, it is important to load all the page requisites from the archive within the temporal neighborhood of the base HTML page. To achieve this goal, archival replay systems try to rewrite all the resource references to appropriate archived versions before serving HTML, CSS, or JS. However, an effective server-side URL rewriting is difficult when URLs are generated dynamically using JavaScript. A failure of correct URL rewriting might yield an invalid/unintended URI or resolve to a live resource. Such live resources, leaking into a composite memento, are called zombies

A Survey of Archival Replay Banners

We surveyed various archival systems to compare and contrast different techniques used to implement an archival replay banner. We found that inline plain HTML injection is the most common approach, but prone to style conflicts. Iframe-based banners are also very common and while they do not have style conflicts, they suffer from screen real estate wastage and limited design choices. Custom Elements-based banners are promising, but due to being a new web standard, these are not yet widely deployed