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Concept: Internet Archive

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BACKGROUND: The Tea Party, which gained prominence in the USA in 2009, advocates limited government and low taxes. Tea Party organisations, particularly Americans for Prosperity and FreedomWorks, oppose smoke-free laws and tobacco taxes. METHODS: We used the Legacy Tobacco Documents Library, the Wayback Machine, Google, LexisNexis, the Center for Media and Democracy and the Center for Responsive Politics (opensecrets.org) to examine the tobacco companies' connections to the Tea Party. RESULTS: Starting in the 1980s, tobacco companies worked to create the appearance of broad opposition to tobacco control policies by attempting to create a grassroots smokers' rights movement. Simultaneously, they funded and worked through third-party groups, such as Citizens for a Sound Economy, the predecessor of AFP and FreedomWorks, to accomplish their economic and political agenda. There has been continuity of some key players, strategies and messages from these groups to Tea Party organisations. As of 2012, the Tea Party was beginning to spread internationally. CONCLUSIONS: Rather than being a purely grassroots movement that spontaneously developed in 2009, the Tea Party has developed over time, in part through decades of work by the tobacco industry and other corporate interests. It is important for tobacco control advocates in the USA and internationally, to anticipate and counter Tea Party opposition to tobacco control policies and ensure that policymakers, the media and the public understand the longstanding connection between the tobacco industry, the Tea Party and its associated organisations.

Concepts: United States, Tobacco, Tobacco industry, Democracy, Legacy Tobacco Documents Library, Internet Archive, Wayback Machine, Citizens for a Sound Economy

6

Scientific Data Analysis Resources (SDARs) such as bioinformatics programs, web servers and databases are integral to modern science, but previous studies have shown that the Uniform Resource Locators (URLs) linking to them decay in a time-dependent manner, with ∼27% decayed to date. Because SDARs are overrepresented among science’s most cited papers over the past 20 years, loss of widely used SDARs could be particularly disruptive to scientific research. We identified URLs in MEDLINE abstracts and used crowdsourcing to identify which reported the creation of SDARs. We used the Internet Archive’s Wayback Machine to approximate ‘death dates’ and calculate citations/year over each SDAR’s lifespan. At first glance, decayed SDARs did not significantly differ from available SDARs in their average citations per year over their lifespan or journal impact factor (JIF). But the most cited SDARs were 94% likely to be relocated to another URL versus only 34% of uncited ones. Taking relocation into account, we find that citations are the strongest predictors of current online availability after time since publication, and JIF modestly predictive. This suggests that URL decay is a general, persistent phenomenon affecting all URLs, but the most useful/recognized SDARs are more likely to persist.

Concepts: Scientific method, Prediction, Science, World Wide Web, Impact factor, Internet, Uniform Resource Locator, Internet Archive

5

With the migration of the written record from paper to digital format, archivists and historians must urgently consider how web content should be conserved, retrieved and analysed. The British Library has recently acquired a large number of UK domain websites, captured 1996-2010, which is colloquially termed the Dark Domain Archive while technical issues surrounding user access are resolved. This article reports the results of an invited pilot project that explores methodological issues surrounding use of this archive. It asks how the relationship between UK public health and local government was represented on the web, drawing on the ‘declinist’ historiography to frame its questions. It points up some difficulties in developing an aggregate picture of web content due to duplication of sites. It also highlights their potential for thematic and discourse analysis, using both text and image, illustrated through an argument about the contradictory rationale for public health policy under New Labour.

Concepts: Health economics, Medicine, United Kingdom, World Wide Web, Website, Internet, Internet Archive, Web archiving

2

The PRoteomics IDEntifications (PRIDE) database is one of the world-leading data repositories of mass spectrometry (MS)-based proteomics data. Since the beginning of 2014, PRIDE Archive (http://www.ebi.ac.uk/pride/archive/) is the new PRIDE archival system, replacing the original PRIDE database. Here we summarize the developments in PRIDE resources and related tools since the previous update manuscript in the Database Issue in 2013. PRIDE Archive constitutes a complete redevelopment of the original PRIDE, comprising a new storage backend, data submission system and web interface, among other components. PRIDE Archive supports the most-widely used PSI (Proteomics Standards Initiative) data standard formats (mzML and mzIdentML) and implements the data requirements and guidelines of the ProteomeXchange Consortium. The wide adoption of ProteomeXchange within the community has triggered an unprecedented increase in the number of submitted data sets (around 150 data sets per month). We outline some statistics on the current PRIDE Archive data contents. We also report on the status of the PRIDE related stand-alone tools: PRIDE Inspector, PRIDE Converter 2 and the ProteomeXchange submission tool. Finally, we will give a brief update on the resources under development ‘PRIDE Cluster’ and ‘PRIDE Proteomes’, which provide a complementary view and quality-scored information of the peptide and protein identification data available in PRIDE Archive.

Concepts: Protein, Mass spectrometry, Peptide, Proteome, Identification, Archive, Internet Archive, Proteomics Standards Initiative

1

Discoverability of sequence data in primary data archives is proportional to the richness of contextual information associated with the data. Here, we describe an exercise in the improvement of contextual information surrounding sample records associated with metagenomics sequence reads available in the European Nucleotide Archive. We outline the annotation process and summarize findings of this effort aimed at increasing usability of publicly available environmental data. Furthermore, we emphasize the benefits of such an exercise and detail its costs. We conclude that such a third party annotation approach is expensive and has value as an element of curation, but should form only part of a more sustainable submitter-driven approach.Database URL: http://www.ebi.ac.uk/ena.

Concepts: Costs, Cost, The Europeans, Archive, Primary source, Primary election, Internet Archive

0

This article argues that the online archive and exhibit “U.S. Homophile Internationalism” effectively contributes to the democratizing effects that digital archives and online initiatives are having on the practice of history. “U.S. Homophile Internationalism” is an online archive of over 800 digitized articles, letters, advertisements, and other materials from the U.S. homophile press that reference six non-U.S. regions of the world. It also provides visitors with introductory regional essays, annotated bibliographies, and an interactive map feature. This essay weaves “U.S. Homophile Internationalism” into the debates in community-run LGBTQ archives regarding the digitization of archival materials and the possibilities presented by digital public history. In doing so, it outlines the structure and content of “U.S. Homophile Internationalism,” highlighting how it increases the public accessibility of primary sources, encourages historical research on regions of the world that have not been adequately represented in LGBTQ history writing, and creates interactive components to support public engagements with the website.

Concepts: Geographic information system, Digitizing, History, Archive, Digital, Primary source, Internet Archive

0

Mold deterioration of historical documents in archives and libraries is a frequent and complex phenomenon that may have important economic and cultural consequences. In addition, exposure to toxic fungal metabolites might produce health problems. In this work, samples of broths of fungal species isolated from the documentary material and from indoor environmental samples of the Archive of Bogotá have been analyzed to investigate the presence of mycotoxins. High resolution mass spectrometry made possible to search for a large number of mycotoxins, even without reference standards available at the laboratory. For this purpose, a screening strategy based on ultra-high pressure liquid chromatography coupled to quadrupole-time of flight mass spectrometry (UHPLC-QTOF MS) under MS(E) mode was applied. A customized home-made database containing elemental composition for around 600 mycotoxins was compiled. The presence of the (de)protonated molecule measured at its accurate mass was evaluated in the samples. When a peak was detected, collision induced dissociation fragments and characteristic isotopic ions were also evaluated and used for tentative identification, based on structure compatibility and comparison with literature data (if existing). Up to 44 mycotoxins were tentatively identified by UHPLC-QTOF MS. 34 of these tentative compounds were confirmed by subsequent analysis using a targeted LC-MS/MS method, supporting the strong potential of QTOF MS for identification/elucidation purposes. The presence of mycotoxins in these samples might help to reinforce safety measures for researchers and staff who work on reception, restoration and conservation of archival material, not only at the Archive of Bogotá but worldwide.

Concepts: Mass spectrometry, Fungus, Mycotoxin, Chromatography, Analytical chemistry, Penicillium, Archive, Internet Archive

0

The timely and accurate identification of adverse drug reactions (ADRs) following drug approval is a persistent and serious public health challenge. Aggregated data drawn from anonymized logs of Web searchers has been shown to be a useful source of evidence for detecting ADRs. However, prior studies have been based on the analysis of established ADRs, the existence of which may already be known publically. Awareness of these ADRs can inject existing knowledge about the known ADRs into online content and online behavior, and thus raise questions about the ability of the behavioral log-based methods to detect new ADRs. In contrast to previous studies, we investigate the use of search logs for the early detection of known ADRs. We use a large set of recently labeled ADRs and negative controls to evaluate the ability of search logs to accurately detect ADRs in advance of their publication. We leverage the Internet Archive to estimate when evidence of an ADR first appeared in the public domain and adjust the index date in a backdated analysis. Our results demonstrate how search logs can be used to detect new ADRs, the central challenge in pharmacovigilance.

Concepts: Pharmacology, Adverse drug reaction, Knowledge, Behavior, Public, Plato, Log, Internet Archive

0

In 1864, Anton von Tröltsch in Würzburg, Hermann Schwartze in Halle/Saale, and Adam Politzer in Vienna founded the Archiv für Ohrenheilkunde (Archive of Otology), the ancestor of the European Archives of Oto-Rhino-Laryngology and Head and Neck. It was the world’s first journal solely devoted to otology, and thus to otorhinolaryngology. The aim of this study was to analyse the structure of this journal and its contents during the first 50 years of its publication, until it definitively became an otorhinolaryngological journal in 1915. A total of 2,271 articles were registered during this time. They were classified according to content topic, article type, and the number of figures and graphs that they contained. Almost three-quarters of the articles were related to purely otological topics, as implied by the journal’s title. Until the turn of the twentieth century, the majority of the articles were original papers or case reports. The number of original papers declined over the decades in favour of case reports. One-third of each volume usually consisted of a vast variety of items, such as congress announcements, conference proceedings, and book reviews. The journal also maintained a wide variety of scientific and current social and political subjects. Otological reviews and conference proceedings were key landmarks of the journal. All of these various papers provided an overview of the historical organisation and development of otology between 1864 and 1914. At that time, the Archiv für Ohrenheilkunde was a leading national and international journal.

Concepts: Head and neck anatomy, Academic publishing, Otology, Archive, Otolaryngology, Implied volatility, Academic conference, Internet Archive

0

Web-based technologies have been increasingly used in Picture Archive and Communication Systems (PACS), in services related to storage, distribution and visualization of medical images. Nowadays, many healthcare institutions are outsourcing their repositories to the Cloud. However, managing communications between multiple geo-distributed locations is still challenging due to the complexity of dealing with huge volumes of data and bandwidth requirements. Moreover, standard methodologies still do not take full advantage of outsourced archives, namely because their integration with other in-house solutions is troublesome. In order to improve the performance of distributed medical imaging networks, a smart routing mechanism was developed. This includes an innovative cache system based on splitting and dynamic management of DICOM objects. The proposed solution was successfully deployed in a regional PACS archive. The results obtained proved that it is better than conventional approaches, as it reduces remote access latency and also the required cache storage space.

Concepts: Medicine, Medical imaging, Management, IMAGE, Archive, Requirement, Cache, Internet Archive