Photosynthesis and the Web: 2008

The World Wide Web has become an important resource for public awareness and for educating the world’s population, including its political leaders, students, researchers, teachers, and ordinary citizens seeking information. Relevant information on photosynthesis-related web sites is grouped into several categories: (1) group sites, (2) sites by subject, (3) individual researcher’s sites, (4) sites for educators and students, and (5) other useful sites.     

A list of personal perspectives with selected quotations,along with lists of tributes,historical notes,Nobel and Kettering awards related to photosynthesis

The history of photosynthesis research can be found in original papers and books. However, a special history is available from the prefatory chapters and the personal perspectives of various researchers who published them in several journals over the last 40 years. We have compiled a list of such perspectives published since 1964. Selection is not easy, especially of authors who were not directly engaged in photosynthesis research; some are included for their special insights related to central issues in the study of photosynthesis. Our journal, Photosynthesis Research, contains other valuable historic data in the occasional tributes, obituaries and historical notes, that have been published. Lists of these items are included. This article ends by listing the Nobel prizes related to photosynthesis and the Kettering Awards for Excellence in Photosynthesis Research. Wherever possible, a web page address is provided. The web page addresses have been taken from the article `Photosynthesis and the Web: 2001' by Larry Orr and Govindjee, available at http://www.life.uiuc.edu/govindjee/photoweb and at http://photoscience.la.asu.edu/photosyn/ photoweb/default.html. ‘When I find a bit of leisure I trifle with my papers. This is one of the lesser frailities. – Horace, Satires I, IV. This revised version was published online in June 2006 with corrections to the Cover Date.     

404 not found: the stability and persistence of URLs published in MEDLINE

MOTIVATION: The advent of the World Wide Web has enabled unprecedented supplementation of traditional journal publications, allowing access to resources, such as video, sound, software, databases, datasets too large to publish, and even supplementary information and discussion. However, unlike traditional publications, continued availability of these online resources is not guaranteed. An automated survey was conducted to quantify the growth in Uniform Resource Locators (URLs) published to date in MEDLINE abstracts, their current availability and distribution by journal. RESULTS: Of 1630 unique URLs identified, formatting and/or spelling errors were detected within 201 (12%) of them as published. After corrections were made, a survey revealed that approximately 63% of these URLs were consistently available, and another 19% were available intermittently. The rate of failure was far worse for anonymous login to FTP sites, with only 12 of 33 sites (36%) responding. This survey also shows that journals vary disproportionately in the number of web citations published, suggesting policy implementation among a few could have a profound impact overall. Out of the 306 journals with a URL published in an abstract, Bioinformatics published the most (12% of total). AVAILABILITY: URL database and program available by request.     

The Atlas of Chinese World Wide Web Ecosystem Shaped by the Collective Attention Flows

The web can be regarded as an ecosystem of digital resources connected and shaped by collective successive behaviors of users. Knowing how people allocate limited attention on different resources is of great importance. To answer this, we embed the most popular Chinese web sites into a high dimensional Euclidean space based on the open flow network model of a large number of Chinese users’ collective attention flows, which both considers the connection topology of hyperlinks between the sites and the collective behaviors of the users. With these tools, we rank the web sites and compare their centralities based on flow distances with other metrics. We also study the patterns of attention flow allocation, and find that a large number of web sites concentrate on the central area of the embedding space, and only a small fraction of web sites disperse in the periphery. The entire embedding space can be separated into 3 regions(core, interim, and periphery). The sites in the core (1%) occupy a majority of the attention flows (40%), and the sites (34%) in the interim attract 40%, whereas other sites (65%) only take 20% flows. What’s more, we clustered the web sites into 4 groups according to their positions in the space, and found that similar web sites in contents and topics are grouped together. In short, by incorporating the open flow network model, we can clearly see how collective attention allocates and flows on different web sites, and how web sites connected each other.     

SeWeR: a customizable and integrated dynamic HTML interface to bioinformatics services

SUMMARY: Sequence analysis using Web Resources (SeWeR) is an integrated, Dynamic HTML (DHTML) interface to commonly used bioinformatics services available on the World Wide Web. It is highly customizable, extendable, platform neutral, completely server-independent and can be hosted as a web page as well as being used as stand-alone software running within a web browser.     

LSMAC vs. LSNAT: Scalable cluster‐based Web servers

Server scalability is more important than ever in today's client/server dominated network environments. Recently, researchers have begun to consider cluster-based computers using commodity hardware as an alternative to expensive specialized hardware for building scalable Web servers. In this paper, we present performance results comparing two cluster-based Web servers based on different server architectures: OSI layer two dispatching (LSMAC) and OSI layer three dispatching (LSNAT). Both cluster-based server systems were implemented as application-space programs running on commodity hardware in contrast to other, similar, solutions which require specialized hardware/software. We point out the advantages and disadvantages of both systems. We also identify when servers should be clustered and when clustering will not improve performance. This revised version was published online in July 2006 with corrections to the Cover Date.     

Idraparinux or Idrabiotaparinux for Long-Term Venous Thromboembolism Treatment: A Systematic Review and Meta-Analysis of Randomized Controlled Trials

Background

Venous thromboembolism (VTE) is a prevalent disease with potential serious consequences. Idraparinux and idrabiotaparinux are two kinds of long-acting pentasaccharides. Evidence has shown that idraparinux and idrabiotaparinux are effective anticoagulants. However, up to now, there is no consensus on whether they are better than other anticoagulation methods for long-term VTE treatment.

Objective

To evaluate the effect of idraparinux or idrabiotaparinux versus other anticoagulation methods for long-term VTE treatment.

Methods

We searched Cochrane Central Register of Controlled Trials, PubMed, Embase, Web of science, clinical trial registry web sites (clinical trials,WHO clinical trial registry), Googlescholar, PubMed related articles and companies'' web sites electronically up to Dec 30^th, 2012 and manually searched the reference lists and conference proceedings. Only randomized controlled trial (RCT) involving adult patients comparing idraparinux and/or idrabiotaparinux versus other anticoagulation methods for long-term VTE treatment was included. Two reviewers evaluated the studies and extracted data independently. Pooled risk ratios (RRs) were calculated as outcome measures and Revman 5.2 software was used to analyze data. Our primary efficacy and safety outcomes were the recurrent VTE and major bleeding rates.

Results

We included four RCTs and involved 8584 participants on idraparinux or idrabiotaparinux versus standard warfarin for VTE treatment from 9364 references. We did not perform meta-analysis on the VTE rate because of the significant heterogeneity. We used the fixed effect model to analyze the safety outcomes and demonstrated that idraparinux or idrabiotaparinux decreased major bleeding rate significantly (RR 0.73, 95% CI 0.54 to 0.98, P = 0.04) but had a trend to increase the all cause mortality (RR 1.26, 95% CI 1.00 to 1.57, P = 0.05) compared with warfarin.

Conclusions

Until now there is not sufficient evidence to clarify whether idraparinux or idrabiotaparinux is as effective and safe as the standard warfarin treatment for VTE treatment.     

MIIB: A Metric to Identify Top Influential Bloggers in a Community

Social networking has revolutionized the use of conventional web and has converted World Wide Web into the social web as users can generate their own content. This change has been possible due to social web platforms like forums, wikis, and blogs. Blogs are more commonly being used as a form of virtual communication to express an opinion about an event, product or experience and can reach a large audience. Users can influence others to buy a product, have certain political or social views, etc. Therefore, identifying the most influential bloggers has become very significant as this can help us in the fields of commerce, advertisement and product knowledge searching. Existing approaches consider some basic features, but lack to consider some other features like the importance of the blog on which the post has been created. This paper presents a new metric, MIIB (Metric for Identification of Influential Bloggers), based on various features of bloggers’ productivity and popularity. Productivity refers to bloggers’ blogging activity and popularity measures bloggers’ influence in the blogging community. The novel module of BlogRank depicts the importance of blog sites where bloggers create their posts. The MIIB has been evaluated against the standard model and existing metrics for finding the influential bloggers using dataset from the real-world blogosphere. The obtained results confirm that the MIIB is able to find the most influential bloggers in a more effective manner.     

PhishTackle—a web services architecture for anti-phishing

Phishing is web based criminal activity of making innocent online users to reveal sensitive information into fake web sites. Such fake web sites lead to fraudulent charges against individuals and corporations. Phishers have a lot of methods to design and host phished web pages, so in reality there cannot be a single solution that can help us combat phishing. As technology advances, the phishing techniques being used are also getting advanced and hence it demands the anti-phishing techniques also to be upgraded and the new techniques are to be included along with the existing methods. But most of the anti-phishing techniques today do not satisfy these criteria. In this paper, we propose service oriented three-layer architecture model for detecting and identifying phishing web sites as it overcomes the shortcomings of existing anti-phishing solutions. This model enables us to separate the user interface layer from the anti-phishing components layer. This is done through web service middleware layer, which provides us with the freedom of building our own anti-phishing components layer in an efficient and flexible way, independent of other layers. Anti-phishing components layer provides a set of reusable components to convert webpage into feature vectors using finest heuristic methods and external repositories of information. The feature vectors act as an input to trained support vector machine classifier to generate phishing label which determines whether a webpage is legitimate or a phishing page. This when experimented, displayed the significance and importance of three-layered architecture model along with combination of heuristics in detection of phishing webpage. This results in high accuracy of 99 % with less than 1 % of false positive rate.     

Mouse-human comparative map resources on the Web

Comparative maps have been a valuable resource for extrapolating biological information among organisms. The relationship between mouse and human maps provides a framework for integrating information from each species and thereby increasing the utility of all available data such as gene location, structure and function. This review describes the various public resources, both databases and web sites, containing genome-wide mouse-human comparative map information available through the World-Wide Web. We will focus on the use and applicability of these resources in their current form and consider future potential directions.     

Photosynthesis Web resources

Online access to the Internet and the World Wide Web has become important for public awareness and for educating the world’s population, including its political leaders, students, researchers, teachers, and ordinary citizens seeking information. After a brief Introduction, relevant information found on photosynthesis-related Web sites and other online locations is presented under five categories: (a) group sites, (b) sites by subject, (c) individual researcher’s sites, (d) sites for educators and students, and (e) other useful sites.     

Photosynthesis online

Online access to the Internet and the World Wide Web have become important for public awareness and for educating the world’s population, including its political leaders, students, researchers, teachers, and ordinary citizens seeking information. Relevant information on photosynthesis-related Web sites and other online locations is grouped into several categories: (1) group sites, (2) sites by subject, (3) individual researcher’s sites, (4) sites for educators and students, and (5) other useful sites.     

Securing web services with biometrics

Web services are evolving and gaining wide acceptance as a standard for distributed computing. Organisations are starting to rely on them to conduct their core business, thereby enabling access to a huge amount of sensitive personal, medical and financial information that they hold, as well as information held on behalf of their customers, such as governments. Clearly, security for such web services is critical. Biometrics can play an important role in web services in a number of ways, providing improved levels of security and convenience for end-users. Emerging XML-based standards for carrying biometric information and exploiting cryptographic techniques may act as an enabler for biometrics.There has been considerable excitement in the world of information technology about web services. Indeed, they are seen as the next major revolution hitting the internet, enabling applications and organisations to interact with one another more directly and efficiently. However, security for web services is seen as a major challenge to be overcome before widespread deployment is possible. At the same time, biometric technologies continue to advance, with growing impetus behind the establishment of common standards for distributed biometric systems. This article explores web services and biometrics and examines the potential for the technologies to be of mutual benefit to each other.     

Presentation Accuracy of the Web Revisited: Animation Methods in the HTML5 Era

Using the Web to run behavioural and social experiments quickly and efficiently has become increasingly popular in recent years, but there is some controversy about the suitability of using the Web for these objectives. Several studies have analysed the accuracy and precision of different web technologies in order to determine their limitations. This paper updates the extant evidence about presentation accuracy and precision of the Web and extends the study of the accuracy and precision in the presentation of multimedia stimuli to HTML5-based solutions, which were previously untested. The accuracy and precision in the presentation of visual content in classic web technologies is acceptable for use in online experiments, although some results suggest that these technologies should be used with caution in certain circumstances. Declarative animations based on CSS are the best alternative when animation intervals are above 50 milliseconds. The performance of procedural web technologies based on the HTML5 standard is similar to that of previous web technologies. These technologies are being progressively adopted by the scientific community and have promising futures, which makes their use advisable to utilizing more obsolete technologies.     

Web Queries as a Source for Syndromic Surveillance

In the field of syndromic surveillance, various sources are exploited for outbreak detection, monitoring and prediction. This paper describes a study on queries submitted to a medical web site, with influenza as a case study. The hypothesis of the work was that queries on influenza and influenza-like illness would provide a basis for the estimation of the timing of the peak and the intensity of the yearly influenza outbreaks that would be as good as the existing laboratory and sentinel surveillance. We calculated the occurrence of various queries related to influenza from search logs submitted to a Swedish medical web site for two influenza seasons. These figures were subsequently used to generate two models, one to estimate the number of laboratory verified influenza cases and one to estimate the proportion of patients with influenza-like illness reported by selected General Practitioners in Sweden. We applied an approach designed for highly correlated data, partial least squares regression. In our work, we found that certain web queries on influenza follow the same pattern as that obtained by the two other surveillance systems for influenza epidemics, and that they have equal power for the estimation of the influenza burden in society. Web queries give a unique access to ill individuals who are not (yet) seeking care. This paper shows the potential of web queries as an accurate, cheap and labour extensive source for syndromic surveillance.     

Conspecific and Heterospecific Attraction: A Mechanism of Web-site Selection Leading to Aggregation Formation by Web-building Spiders

This study investigated whether conspecific and/or heterospecific attraction to silk is a mechanism of web-site selection leading to aggregation formation by two species of web-building spiders, Hypochilus thorelli Marx (Araneae: Hypochilidae) and Achaearanea tepidariorum (C.L. Koch) (Araneac: Theridiidae). We determined that the spatial distribution of these two spiders was clumped and that H. thorelli had a greater tendency to aggregate than did A. tepidariorum. To determine the mechanism responsible for this spatial pattern, we conducted three field experiments. We examined web-site selection by H. thorelli in three contexts: no spiders or webs present (cue removed), vacant webs present, and occupied webs present. In the case where no webs were present, there was no tendency for spiders to choose previously occupied sites as web sites. When vacant webs were present, spiders chose to occupy the vacant webs. When occupied webs were present, spiders either invaded webs and evicted the owners, or settled adjacent to and attached their webs to those of residents. Various microhabitat variables (height, angle, temperature, humidity, and substrate character of the rock surface) of randomly selected unoccupied sites and the web sites chosen by spiders were compared. There were no detectable differences between web sites and unoccupied sites with respect to any of the variables measured. This leads us to conclude that web-site choice by immigrating spiders was based on the presence of silk rather than other features of the site.