BSDD-2.0: Biomolecules Segment Display Device - An updated web accessible computing resource

The existing internet computing resource, Biomolecules Segment Display Device (BSDD), has been updated with several additional useful features. An advanced option is provided to superpose the structural motifs obtained from a search on the Protein Data Bank (PDB) in order to see if the three-dimensional structures adopted by identical or similar sequence motifs are the same. Furthermore, the options to display structural aspects like inter- and intra-molecular interactions, ion-pairs, disulphide bonds, etc. have been provided.The updated resource is interfaced with an up-to-date copy of the public domain PDB as well as 25 and 90% non-redundant protein structures. Further, users can upload the three-dimensional atomic coordinates (PDB format) from the client machine. A free molecular graphics program, JMol, is interfaced with it to display the three-dimensional structures.

AQUAMAN: a web-based decision support system for irrigation scheduling in peanuts

Peanut (Arachis hypogaea L.) is an economically important legume crop in irrigated production areas of northern Australia. Although the potential pod yield of the crop in these areas is about 8 t ha(-1), most growers generally obtain around 5 t ha(-1), partly due to poor irrigation management. Better information and tools that are easy to use, accurate, and cost-effective are therefore needed to help local peanut growers improve irrigation management. This paper introduces a new web-based decision support system called AQUAMAN that was developed to assist Australian peanut growers schedule irrigations. It simulates the timing and depth of future irrigations by combining procedures from the food and agriculture organization (FAO) guidelines for irrigation scheduling (FAO-56) with those of the agricultural production systems simulator (APSIM) modeling framework. Here, we present a description of AQUAMAN and results of a series of activities (i.e., extension activities, case studies, and a survey) that were conducted to assess its level of acceptance among Australian peanut growers, obtain feedback for future improvements, and evaluate its performance. Application of the tool for scheduling irrigations of commercial peanut farms since its release in 2004-2005 has shown good acceptance by local peanuts growers and potential for significantly improving yield. Limited comparison with the farmer practice of matching the pan evaporation demand during rain-free periods in 2006-2007 and 2008-2009 suggested that AQUAMAN enabled irrigation water savings of up to 50% and the realization of enhanced water and irrigation use efficiencies.

Fish mediate high food web connectivity in the lower reaches of a tropical floodplain river

High levels of hydrological connectivity during seasonal flooding provide significant opportunities for movements of fish between rivers and their floodplains, estuaries and the sea, possibly mediating food web subsidies among habitats. To determine the degree of utilisation of food sources from different habitats in a tropical river with a short floodplain inundation duration (similar to 2 months), stable isotope ratios in fishes and their available food were measured from three habitats (inundated floodplain, dry season freshwater, coastal marine) in the lower reaches of the Mitchell River, Queensland (Australia). Floodplain food sources constituted the majority of the diet of large-bodied fishes (barramundi Lates calcarifer, catfish Neoarius graeffei) captured on the floodplain in the wet season and for gonadal tissues of a common herbivorous fish (gizzard shad Nematalosa come), the latter suggesting that critical reproductive phases are fuelled by floodplain production. Floodplain food sources also subsidised barramundi from the recreational fishery in adjacent coastal and estuarine areas, and the broader fish community from a freshwater lagoon. These findings highlight the importance of the floodplain in supporting the production of large fishes in spite of the episodic nature and relatively short duration of inundation compared to large river floodplains of humid tropical regions. They also illustrate the high degree of food web connectivity mediated by mobile fish in this system in the absence of human modification, and point to the potential consequences of water resource development that may reduce or eliminate hydrological connectivity between the river and its floodplain.

Small firm internet adoption: A market oriented approach

Fundamental to the development of new customer value offerings via web-based commerce is a small firm's ability to strategically acquire and exploit knowledge. The focus of this paper is the empirical testing of a normative web-based commerce adoption model developed from a review of the extant literature related to electronic marketing, the Internet and the diffusion of new innovations. A preliminary test of the model's theoretical contentions lent support to its overall focus, but found that the firm's existing learning capabilities were diminished during the adoption of web-based commerce. Consequently, sub-optimal adoption outcomes were associated with insufficient knowledge development.

Luottamuksenhallinta web-palveluympäristössä

Tutkielmassa käsitellään luottamuksenhallintaa web-palveluympäristössä. Dynaaminen toimintaympäristö asettaa vaatimuksia luottamuksenhallintajärjestelmälle, jota käytetään paitsi paikallisten pääsynhallintapäätösten tekemiseen, myös laajemman mittakaavan päätöksenteon tukena, useiden autonomisten toimijoiden muodostamien yhteisöjen hallinnassa. Tutkielma esittelee Trust Based on Evidence -projektissa kehitetyn luottamuksenhallintajärjestelmän tiedollisen ja toiminnallisen mallin, paikallisesta ja yhteisön näkökulmasta. Mallia selkeytetään web-palveluympäristöön sijoittuvan esimerkin avulla. Luottamuksen käsitteen rakentamiseksi esitellään myös eri osa-alueille sijoittuvia luottamuksen malleja ja luottamusta käyttäviä järjestelmiä. Avoimessa verkkoympäristössä palveluntarjoaja joutuu tasapainottelemaan kahden osin vastakkaisen tavoitteen välillä: toisaalta järjestelmän tulisi olla mahdollisimman avoin, jotta se houkuttelisi käyttäjiä, toisaalta liiallinen avoimuus kasvattaa tietomurron riskiä. Kompromissin löytäminen on hankaloitunut edelleen saavutettavien käyttäjien määrän kasvaessa ja tarjottavien palvelujen monimutkaistuessa. Tehtävä vaatii toisaalta erikoistapauksien käsittelyä, toisaalta yleistettävyyttä laajan käyttäjistön suhteen. Tietoturvan ylläpidon automatisointia ovat edistäneet muun muassa politiikkapäätösten erottaminen toteutuksesta ja mahdollisten tietomurron merkkien tarkkailun delegointi siihen erikoistuneille ohjelmille (IDS). Palvelujen käyttäjistön kasvaessa ja siirtyessä nimettömämmiksi kurinpito ja tarkkailu kuitenkin vaikeutuvat entisestään, eikä ylläpitäjiä riitä sidottavaksi jatkuvaan käyttäjien vahtimiseen. Monesti valvoja voikin vain poistaa käyttöoikeuden häiriköltä, jolloin esimerkiksi hieman lievemmälle sääntöjen ``venyttämiselle'' ei juuri voi tehdä mitään. Luottamuksenhallinta helpottaa rikkomuksiin ja toisaalta hyvään käytökseen reagoimista asteittain. Sen pohjalta käyttäjien valvontaan, pääsynhallintaan ja resurssien rajoitukseen liittyvä hienosäätö voidaan tuoda ymmärrettäväksi osaksi ylläpitoa ja pitkälti myös automatisoida. Avainsanat: luottamuksenhallinta, Web Services

Web-based active learning and frequent feedback: Engaging first-year university students

Web-based technology is particularly well-suited to promoting active student involvement in the processes of learning. All students enrolled in a first-year educational psychology unit were required to complete ten weekly online quizzes, ten weekly student-generated questions and ten weekly student answers to those questions. Results of an online survey of participating students strongly support the viability and perceived benefits of such an instructional approach. Although students reported that the 30 assessments were useful and reasonable, the most common theme to emerge from the professional reflections of participating lecturers was that the marking of questions and answers was unmanageable.

Web 2.0 technology: Social learning tools in higher education in Saudi Arabia

Information and communication technology (ICT) has created opportunities for students' online interaction in higher education throughout the world. Limited research has been done in this area in Saudi Arabia. This study investigated university students' engagement and perceptions of online collaborative learning using Social Learning Tools (SLTs). In addition, it explored the quality of knowledge construction that occurred in this environment. A mixed methods case study approach was adopted, and the data was gathered from undergraduate students (n=43) who were enrolled in a 15-week course at a Saudi university. The results showed that while the students had positive perceptions towards SLTs and their engagement, data gathered from their work also showed little evidence of high levels of knowledge construction.

An Optimal Mechanism for Sponsored Search Auctions on the Web and Comparison With Other Mechanisms

In this paper, we first describe a framework to model the sponsored search auction on the web as a mechanism design problem. Using this framework, we describe two well-known mechanisms for sponsored search auction-Generalized Second Price (GSP) and Vickrey-Clarke-Groves (VCG). We then derive a new mechanism for sponsored search auction which we call optimal (OPT) mechanism. The OPT mechanism maximizes the search engine's expected revenue, while achieving Bayesian incentive compatibility and individual rationality of the advertisers. We then undertake a detailed comparative study of the mechanisms GSP, VCG, and OPT. We compute and compare the expected revenue earned by the search engine under the three mechanisms when the advertisers are symmetric and some special conditions are satisfied. We also compare the three mechanisms in terms of incentive compatibility, individual rationality, and computational complexity. Note to Practitioners-The advertiser-supported web site is one of the successful business models in the emerging web landscape. When an Internet user enters a keyword (i.e., a search phrase) into a search engine, the user gets back a page with results, containing the links most relevant to the query and also sponsored links, (also called paid advertisement links). When a sponsored link is clicked, the user is directed to the corresponding advertiser's web page. The advertiser pays the search engine in some appropriate manner for sending the user to its web page. Against every search performed by any user on any keyword, the search engine faces the problem of matching a set of advertisers to the sponsored slots. In addition, the search engine also needs to decide on a price to be charged to each advertiser. Due to increasing demands for Internet advertising space, most search engines currently use auction mechanisms for this purpose. These are called sponsored search auctions. A significant percentage of the revenue of Internet giants such as Google, Yahoo!, MSN, etc., comes from sponsored search auctions. In this paper, we study two auction mechanisms, GSP and VCG, which are quite popular in the sponsored auction context, and pursue the objective of designing a mechanism that is superior to these two mechanisms. In particular, we propose a new mechanism which we call the OPT mechanism. This mechanism maximizes the search engine's expected revenue subject to achieving Bayesian incentive compatibility and individual rationality. Bayesian incentive compatibility guarantees that it is optimal for each advertiser to bid his/her true value provided that all other agents also bid their respective true values. Individual rationality ensures that the agents participate voluntarily in the auction since they are assured of gaining a non-negative payoff by doing so.

Towards web-based semantic enrichment of 3D insects

Natural history collections are an invaluable resource housing a wealth of knowledge with a long tradition of contributing to a wide range of fields such as taxonomy, quarantine, conservation and climate change. It is recognized however [Smith and Blagoderov 2012] that such physical collections are often heavily underutilized as a result of the practical issues of accessibility. The digitization of these collections is a step towards removing these access issues, but other hurdles must be addressed before we truly unlock the potential of this knowledge.

Harmful algae in the planktonic food web of the Baltic Sea

This study deals with algal species occurring commonly in the Baltic Sea: haptophyte Prymnesium parvum, dinoflagellates Dinophysis acuminata, D. norvegica and D. rotundata, and cyanobacterium Nodularia spumigena. The hypotheses are connected to the toxicity of the species, to the factors determining toxicity, to the consequences of toxicity and to the transfer of toxins in the aquatic food web. Since the Baltic Sea is severely eutrophicated, the fast-growing haptophytes have potential in causing toxic blooms. In our studies, the toxicity (as haemolytic activity) of the haptophyte P. parvum was highest under phosphorus-limited conditions, but the cells were toxic also under nitrogen limitation and under nutrient-balanced growth conditions. The cellular nutrient ratios were tightly related to the toxicity. The stoichiometric flexibility for cellular phosphorus quota was higher than for nitrogen, and nitrogen limitation led to decreased biomass. Negative allelopathic effects on another algae (Rhodomonas salina) could be observed already at low P. parvum cell densities, whereas immediate lysis of R. salina cells occurred at P. parvum cell densities corresponding to natural blooms. Release of dissolved organic carbon from the R. salina cells was measured within 30 minutes, and an increase in bacterial number and biomass was measured within 23 h. Because of the allelopathic effect, formation of a P. parvum bloom may accelerate after a critical cell density is reached and the competing species are eliminated. A P. parvum bloom indirectly stimulates bacterial growth, and alters the functioning of the planktonic food web by increasing the carbon transfer through the microbial loop. Our results were the first reports on DSP toxins in Dinophysis cells in the Gulf of Finland and on PTX-2 in the Baltic Sea. Cellular toxin contents in Dinophysis spp. ranged from 0.2 to 149 pg DTX-1 cell-1 and from 1.6 to 19.9 pg PTX-2 cell-1 in the Gulf of Finland. D. norvegica was found mainly around the thermocline (max. 200 cells L-1), whereas D. acuminata was found in the whole mixed layer (max. 7 280 cells L-1). Toxins in the sediment trap corresponded to 1 % of DTX-1 and 0.01 % PTX-2 of the DSP pool in the suspended matter. This indicates that the majority of the DSP toxins does not enter the benthic community, but is either decomposed in the water column, or transferred to higher trophic levels in the planktonic food chain. We found that nodularin, produced by Nodularia spumigena, was transferred to the copepod Eurytemora affinis through three pathways: by grazing on filaments of small Nodularia, directly from the dissolved pool, and through the microbial food web by copepods grazing on ciliates, dinoflagellates and heterotrophic nanoflagellates. The estimated proportion of the microbial food web in nodularin transfer was 22-45 % and 71-76 % in our two experiments, respectively. This highlights the potential role of the microbial food web in the transfer of toxins in the planktonic food web.