Scientific Knowledge Object Patterns

Web technology is revolutionizing the way diverse scientific knowledge is produced and disseminated. In the past few years, a handful of discourse representation models have been proposed for the externalization of the rhetoric and argumentation captured within scientific publications. However, there hasn’t been a unified interoperable pattern that is commonly used in practice by publishers and individual users yet. In this paper, we introduce the Scientific Knowledge Object Patterns (SKO Patterns) towards a general scientific discourse representation model, especially for managing knowledge in emerging social web and semantic web. © ACM, 2011. This is the author's version of the work. It is posted here by permission of ACM for your personal use. Not for redistribution. The definitive version is going to be published in "Proceedings of 15th European Conference on Pattern Languages of Programs", (2011) http://portal.acm.org/event.cfm?id=RE197&CFID=8795862&CFTOKEN=1476113

BlackWatch:increasing attack awareness within web applications

Web applications are relied upon by many for the services they provide. It is essential that applications implement appropriate security measures to prevent security incidents. Currently, web applications focus resources towards the preventative side of security. Whilst prevention is an essential part of the security process, developers must also implement a level of attack awareness into their web applications. Being able to detect when an attack is occurring provides applications with the ability to execute responses against malicious users in an attempt to slow down or deter their attacks. This research seeks to improve web application security by identifying malicious behaviour from within the context of web applications using our tool BlackWatch. The tool is a Python-based application which analyses suspicious events occurring within client web applications, with the objective of identifying malicious patterns of behaviour. This approach avoids issues typically encountered with traditional web application firewalls. Based on the results from a preliminary study, BlackWatch was effective at detecting attacks from both authenticated, and unauthenticated users. Furthermore, user tests with developers indicated BlackWatch was user friendly, and was easy to integrate into existing applications. Future work seeks to develop the BlackWatch solution further for public release

Optimizing Computation of Recovery Plans for BPEL Applications

Web service applications are distributed processes that are composed of dynamically bounded services. In our previous work [15], we have described a framework for performing runtime monitoring of web service against behavioural correctness properties (described using property patterns and converted into finite state automata). These specify forbidden behavior (safety properties) and desired behavior (bounded liveness properties). Finite execution traces of web services described in BPEL are checked for conformance at runtime. When violations are discovered, our framework automatically proposes and ranks recovery plans which users can then select for execution. Such plans for safety violations essentially involve "going back" - compensating the executed actions until an alternative behaviour of the application is possible. For bounded liveness violations, recovery plans include both "going back" and "re-planning" - guiding the application towards a desired behaviour. Our experience, reported in [16], identified a drawback in this approach: we compute too many plans due to (a) overapproximating the number of program points where an alternative behaviour is possible and (b) generating recovery plans for bounded liveness properties which can potentially violate safety properties. In this paper, we describe improvements to our framework that remedy these problems and describe their effectiveness on a case study.Comment: In Proceedings TAV-WEB 2010, arXiv:1009.330

Why ownership pluralism still matters in a multi-platform world

This chapter examines the effects of changing technology on landscapes of media provision and consumption and considers whether the greater choice made possible by digital technology and changing patterns of consumption obviate the need for special interventions to restrict media ownership for the sake of pluralism. News Corporation's bid for BSkyB in 2011 clearly exemplified how, not least in times of technological change, patterns of ownership are shaped by economic and strategic factors. Digitisation has encouraged greater cross-sectoral convergence providing an extra spur towards strategies of diversification and multi-platform expansion in the media industry. Even so, and despite the transition to a more web-connected era, as this chapter argues there remain good grounds for concerns about the power wielded by dominant media organisations in relation to production and circulation of news, ideas and cultural and political values within contemporary societies

Astrophysicists and physicists as creators of ArXiv-based commenting resources for their research communities. An initial survey

This paper conveys the outcomes of what results to be the first, though initial, overview of commenting platforms and related 2.0 resources born within and for the astrophysical community (from 2004 to 2016). Experiences were added, mainly in the physics domain, for a total of 22 major items, including four epijournals, and four supplementary resources, thus casting some light onto an unexpected richness and consonance of endeavours. These experiences rest almost entirely on the contents of the database ArXiv, which adds to its merits that of potentially setting the grounds for web 2.0 resources, and research behaviours, to be explored. Most of the experiences retrieved are UK and US based, but the resulting picture is international, as various European countries, China and Australia have been actively involved. Final remarks about creation patterns and outcome of these resources are outlined. The results integrate the previous studies according to which the web 2.0 is presently of limited use for communication in astrophysics and vouch for a role of researchers in the shaping of their own professional communication tools that is greater than expected. Collaterally, some aspects of ArXiv s recent pathway towards partial inclusion of web 2.0 features are touched upon. Further investigation is hoped for.Comment: Journal article 16 page

Spatio-temporal patterns of multi-trophic biodiversity and food-web characteristics uncovered across a river catchment using environmental DNA

Accurate characterisation of ecological communities with respect to their biodiversity and food-web structure is essential for conservation. However, combined empirical study of biodiversity and multi-trophic food webs at a large spatial and temporal resolution has been prohibited by the lack of appropriate access to such data from natural systems. Here, we assessed biodiversity and food-web characteristics across a 700 km$^{2}$ riverine network over seasons using environmental DNA. We found contrasting biodiversity patterns between major taxonomic groups. Local richness showed statistically significant, season-dependent increases and decreases towards downstream location within the catchment for fish and bacteria, respectively. Meanwhile, invertebrate richness remained spatially unchanged but varied across seasons. The structure of local food webs, such as link density and nestedness, also varied across space and time. However, these patterns did not necessarily mirror those observed for biodiversity and functional feeding characteristics. Our results suggest that biodiversity patterns and food-web dynamics are not directly scalable to each other even at the same spatial and temporal scales. In order to conserve species diversity as well as the functional trophic integrity of communities, patterns of biodiversity and food-web characteristics must thus be jointly studied

If you build it, will they come? How researchers perceive and use web 2.0

Over the past 15 years, the web has transformed the way we seek and use information. In the last 5 years in particular a set of innovative techniques – collectively termed ‘web 2.0’ – have enabled people to become producers as well as consumers of information. It has been suggested that these relatively easy-to-use tools, and the behaviours which underpin their use, have enormous potential for scholarly researchers, enabling them to communicate their research and its findings more rapidly, broadly and effectively than ever before. This report is based on a study commissioned by the Research Information Network to investigate whether such aspirations are being realised. It seeks to improve our currently limited understanding of whether, and if so how, researchers are making use of various web 2.0 tools in the course of their work, the factors that encourage or inhibit adoption, and researchers’ attitudes towards web 2.0 and other forms of communication. Context: How researchers communicate their work and their findings varies in different subjects or disciplines, and in different institutional settings. Such differences have a strong influence on how researchers approach the adoption – or not – of new information and communications technologies. It is also important to stress that ‘web 2.0’ encompasses a wide range of interactions between technologies and social practices which allow web users to generate, repurpose and share content with each other. We focus in this study on a range of generic tools – wikis, blogs and some social networking systems – as well as those designed specifically by and for people within the scholarly community. Method: Our study was designed not only to capture current attitudes and patterns of adoption but also to identify researchers’ needs and aspirations, and problems that they encounter. We began with an online survey, which collected information about researchers’ information gathering and dissemination habits and their attitudes towards web 2.0. This was followed by in-depth, semi-structured interviews with a stratified sample of survey respondents to explore in more depth their experience of web 2.0, including perceived barriers as well as drivers to adoption. Finally, we undertook five case studies of web 2.0 services to investigate their development and adoption across different communities and business models. Key findings: Our study indicates that a majority of researchers are making at least occasional use of one or more web 2.0 tools or services for purposes related to their research: for communicating their work; for developing and sustaining networks and collaborations; or for finding out about what others are doing. But frequent or intensive use is rare, and some researchers regard blogs, wikis and other novel forms of communication as a waste of time or even dangerous. In deciding if they will make web 2.0 tools and services part of their everyday practice, the key questions for researchers are the benefits they may secure from doing so, and how it fits with their use of established services. Researchers who use web 2.0 tools and services do not see them as comparable to or substitutes for other channels and means of communication, but as having their own distinctive role for specific purposes and at particular stages of research. And frequent use of one kind of tool does not imply frequent use of others as well

Risk factors for COPD exacerbations in inhaled medication users: the COPDGene study biannual longitudinal follow-up prospective cohort.

BackgroundDespite inhaled medications that decrease exacerbation risk, some COPD patients experience frequent exacerbations. We determined prospective risk factors for exacerbations among subjects in the COPDGene Study taking inhaled medications.Methods2113 COPD subjects were categorized into four medication use patterns: triple therapy with tiotropium (TIO) plus long-acting beta-agonist/inhaled-corticosteroid (ICS ± LABA), tiotropium alone, ICS ± LABA, and short-acting bronchodilators. Self-reported exacerbations were recorded in telephone and web-based longitudinal follow-up surveys. Associations with exacerbations were determined within each medication group using four separate logistic regression models. A head-to-head analysis compared exacerbation risk among subjects using tiotropium vs. ICS ± LABA.ResultsIn separate logistic regression models, the presence of gastroesophageal reflux, female gender, and higher scores on the St. George's Respiratory Questionnaire were significant predictors of exacerbator status within multiple medication groups (reflux: OR 1.62-2.75; female gender: OR 1.53 - OR 1.90; SGRQ: OR 1.02-1.03). Subjects taking either ICS ± LABA or tiotropium had similar baseline characteristics, allowing comparison between these two groups. In the head-to-head comparison, tiotropium users showed a trend towards lower rates of exacerbations (OR = 0.69 [95 % CI 0.45, 1.06], p = 0.09) compared with ICS ± LABA users, especially in subjects without comorbid asthma (OR = 0.56 [95% CI 0.31, 1.00], p = 0.05).ConclusionsEach common COPD medication usage group showed unique risk factor patterns associated with increased risk of exacerbations, which may help clinicians identify subjects at risk. Compared to similar subjects using ICS ± LABA, those taking tiotropium showed a trend towards reduced exacerbation risk, especially in subjects without asthma.Trial registrationClinicalTrials.gov NCT00608764, first received 1/28/2008

Towards Query Logs for Privacy Studies: On Deriving Search Queries from Questions

Translating verbose information needs into crisp search queries is a phenomenon that is ubiquitous but hardly understood. Insights into this process could be valuable in several applications, including synthesizing large privacy-friendly query logs from public Web sources which are readily available to the academic research community. In this work, we take a step towards understanding query formulation by tapping into the rich potential of community question answering (CQA) forums. Specifically, we sample natural language (NL) questions spanning diverse themes from the Stack Exchange platform, and conduct a large-scale conversion experiment where crowdworkers submit search queries they would use when looking for equivalent information. We provide a careful analysis of this data, accounting for possible sources of bias during conversion, along with insights into user-specific linguistic patterns and search behaviors. We release a dataset of 7,000 question-query pairs from this study to facilitate further research on query understanding.Comment: ECIR 2020 Short Pape