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Researchers from academia and the corporate-sector rely on scholarly digital libraries to access articles. Attackers take advantage of innocent users who consider the articles' files safe and thus open PDF-files with little concern. In addition, researchers consider scholarly libraries a reliable, trusted, and untainted corpus of papers. For these reasons, scholarly digital libraries are an attractive-target and inadvertently support the proliferation of cyber-attacks launched via malicious PDF-files. In this study, we present related vulnerabilities and malware distribution approaches that exploit the vulnerabilities of scholarly digital libraries. We evaluated over two-million scholarly papers in the CiteSeerX library and found the library to be contaminated with a surprisingly large number (0.3-2%) of malicious PDF documents (over 55% were crawled from the IPs of US-universities). We developed a two layered detection framework aimed at enhancing the detection of malicious PDF documents, Sec-Lib, which offers a security solution for large digital libraries. Sec-Lib includes a deterministic layer for detecting known malware, and a machine learning based layer for detecting unknown malware. Our evaluation showed that scholarly digital libraries can detect 96.9% of malware with Sec-Lib, while minimizing the number of PDF-files requiring labeling, and thus reducing the manual inspection efforts of security-experts by 98%.

This article describes several features in the MAFFT online service for multiple sequence alignment (MSA). As a result of recent advances in sequencing technologies, huge numbers of biological sequences are available and the need for MSAs with large numbers of sequences is increasing. To extract biologically relevant information from such data, sophistication of algorithms is necessary but not sufficient. Intuitive and interactive tools for experimental biologists to semiautomatically handle large data are becoming important. We are working on development of MAFFT toward these two directions. Here, we explain (i) the Web interface for recently developed options for large data and (ii) interactive usage to refine sequence data sets and MSAs.

Investing in documenting your bioinformatics software well can increase its impact and save your time. To maximize the effectiveness of your documentation, we suggest following a few guidelines we propose here. We recommend providing multiple avenues for users to use your research software, including a navigable HTML interface with a quick start, useful help messages with detailed explanation and thorough examples for each feature of your software. By following these guidelines, you can assure that your hard work maximally benefits yourself and others.

This paper reports on a study evaluating the value of a documentary as a key medium to communicate design research. We present information from the evaluation of a second screen application using video as well as a scientific paper, in order to assess how the efficacy and usefulness of using such a documentary for science communication is perceived when compared to a scientific paper. Techniques of a method called Design Documentary, developed to inspire design research teams through video, combined with science journalism were the basis of the production. Twelve researchers and students were shown the documentary and asked to read the paper in counter-balanced order. Our qualitative results show that the documentary as a complementary means of communication can bring benefits to research communication, since it delivers information the paper cannot provide. However, the fact the video is not suited for peer review might restrict its place when compared to the paper. On the overall, participants thought both formats are valuable and are complementary. ispartof: pages:747-754 ispartof: Procedia Computer Science vol:100 pages:747-754 ispartof: CENTERIS location:PORTUGAL, Porto 2016 status: published

BACKGROUND: The objectives of the study were to develop web-based Spanish and Catalan versions of the EQ-5D-Y, and to compare scores and psychometric properties with the paper version. METHODS: Web-based and paper versions of EQ-5D-Y were included in a cross-sectional study in Palafolls (Barcelona), Spain and administered to students (n = 923) aged 8 to 18 years from 2 primary and 1 secondary school and their parents. All students completed both the web-based and paper versions during school time with an interval of at least 2 h between administrations. The order of administration was randomized. Participants completed EQ-5D-Y, a measure of mental health status (the Strengths and Difficulties Questionnaire), and sociodemographic variables using a self-administered questionnaire. Parents questionnaire included parental level of education and presence of chronic conditions in children. Missing values, and floor and ceiling effects were compared between versions. Mean score differences were computed for the visual analogue scale (VAS). Percentage of agreement, kappa index (k) and intraclass correlation coefficient (ICC) were computed to analyze the level of agreement between web-based and paper versions on EQ-5D-Y dimensions and VAS. Known groups validity was analyzed and compared between the two formats. RESULTS: Participation rate was 77 % (n = 715). Both formats of EQ-5D-Y showed low percentages of missing values (n = 2, and 4 to 9 for web and paper versions respectively), and a high ceiling effect by dimension (range from 79 % to 96 %). Percent agreement for EQ-5D-Y dimensions on the web and paper versions was acceptable (range 89 % to 97 %), and k ranged from 0.55 (0.48-0.61, usual activities dimension) to 0.75 (0.68-0.82, mobility dimension). Mean score difference on the VAS was 0.07, and the ICC for VAS scores on the two formats was 0.84 (0.82-0.86). Both formats showed acceptable ability to discriminate according to self-perceived health, reporting chronic conditions, and mental health status. CONCLUSIONS: The digital EQ-5D-Y showed almost identical VAS scores and acceptable levels of agreement on dimensions. Both formats demonstrated acceptable levels of construct validity. Availability of the Spanish and Catalan web-version will facilitate its use in HRQOL assessment and in economic evaluation. The study was financed by the Spanish Ministry of Health, contract N° PI12/01296.

Many medical journals, publishing in national languages, meet serious financial problems and difficulties when they attempt to become indexed in the international indices. Obviously, this not only affects the scientific quality of non-indexed medical journals (NIMJs) but also affects the awareness of the scientific community of topics with apparently local but potentially broader scientific significance. This is a reality for over 100 Greek medical journals, none of which has a life longer than 30 years or more than 2000 subscribers. Among them, the 'Archives of Hellenic Medicine' (AHM) is published and sponsored by the Athens Medical Society (the oldest medical society in Greece founded in 1835). This peer-reviewed Journal is being published for 13 years, bimonthly, in Greek. Attempting to overcome the above mentioned problems and to be involved in the process of discovering the most effective way of scientific 'skywriting', 2 years ago, the AHM entered full-text in the Web and it was decided that up to 500% of its volume should be covered by English-language papers. As a result, the AHM are now included in the main Web lists of medical journals and their home page is linked in many academic pages having approximately 500 hits/month. Furthermore, 45 retrievals of AHM's English-language papers or English abstracts of Greek-language articles were reported by e-mail response from abroad. Considered apart from the paper-publishing, the expenses of the digital publishing of the AHM are about half of those of paper-publishing, as they were before the appearance of the Journal in the Web. Up to now, about 40% of the Journal's digital publishing cost is covered by advertisements included in its pages and by a modification of its paper-publishing policy. It is concluded that the international scientific community is not indifferent for information published in NIMJs. Medical national minorities working abroad express special interest for this type of information. The Web makes the NIMJs accessible to these potential readers, who would never have the chance to acquire them in their printed form.

Background: Survey response rates have been declining over the past decade. The more widespread use of the Internet and Web-based technologies among potential health survey participants suggests that Web-based questionnaires may be an alternative to paper questionnaires in future epidemiological studies. Objective: To compare response rates in a population of parents by using 4 different modes of data collection for a questionnaire survey of which 1 involved a nonmonetary incentive. Methods: A random sample of 3148 parents of Danish children aged 2-17 years were invited to participate in the Danish part of the NordChild 2011 survey on their children’s health and welfare. NordChild was conducted in 1984 and 1996 in collaboration with Finland, Iceland, Norway, and Sweden using mailed paper questionnaires only. In 2011, all countries used conventional paper versions only except Denmark where the parents were randomized into 4 groups: (1) 789 received a paper questionnaire only (paper), (2) 786 received the paper questionnaire and a log-in code to the Web-based questionnaire (paper/Web), (3) 787 received a log-in code to the Web-based questionnaire (Web), and (4) 786 received log-in details to the Web-based questionnaire and were given an incentive consisting of a chance to win a tablet computer (Web/tablet). In connection with the first reminder, the nonresponders in the paper, paper/Web, and Web groups were also present with the opportunity to win a tablet computer as a means of motivation. Descriptive analysis was performed using chi-square tests. Odds ratios were used to estimate differences in response rates between the 4 modes. Results: In 2011, 1704 of 3148 (54.13%) respondents answered the Danish questionnaire. The highest response rate was with the paper mode (n=443, 56.2%). The other groups had similar response rates: paper/Web (n=422, 53.7%), Web (n=420, 53.4%), and Web/tablet (n=419, 53.3%) modes. Compared to the paper mode, the odds for response rate in the paper/Web decreased by 9% (OR 0.91, 95% CI 0.74-1.10) and by 11% (OR 0.89, 95% CI 0.73-1.09) in the Web and Web/tablet modes. The total number of responders for NordChild declined from 10,291 of 15,339 (67.09%) in 1984 and 10,667 of 15,254 (69.93%) in 1996 to 7805 of 15,945 (48.95%) in 2011 with similar declines in all 5 Nordic countries. Conclusions: Web-based questionnaires could replace traditional paper questionnaires with minor effects on response rates and lower costs. The increasing effect on the response rate on participants replying for a nonmonetary incentive could only be estimated within the 2 Web-based questionnaire modes before the first reminder. Alternative platforms to reach higher participation rates in population surveys should reflect the development of electronic devices and the ways in which the population primarily accesses the Internet. [J Med Internet Res 2013;15(8):e173]

Structural computing represents a form of hypertext, in which structure is foregrounded in the analysis, design and implementation of systems. Until now, the vast majority of structural computing work has focused on the implementation of frameworks. The applications implemented in these environments are often reimplementations of existing hypertext applications, intended to show the utility of the provided environments in terms of implementation, interoperability, or other metrics. Often, spatial hypertext applications are reimplemented, since they are seen as particularly good tests of structural computing infrastructures. This is because the demonds they pose are quite different from many other types of hypertext applications. However, structural computing researchers have failed to reanalyse and redesign these applications in a structurally-aware way. There are substantial improvements that result from rethinking such applications from a structure-first perspective. In this paper, we present such a reanalysis, and describe its implications for spatial hypertext within structural computing environments.

To the Editor: I wish to report yet one more use for the ubiquitous Post-it, this time as an aid in cardiac physical diagnosis. The adhesive on Post-it notes consists of tiny spheres that are stick...