GPFlow: an intuitive environment for web-based scientific workflow

Increasingly scientists are using collections of software tools in their research. These tools are typically used in concert, often necessitating laborious and error-prone manual data reformatting and transfer. We present an intuitive workflow environment to support scientists with their research. The workflow, GPFlow, wraps legacy tools, presenting a high level, interactive web-based front end to scientists. The workflow backend is realized by a commercial grade workflow engine (Windows Workflow Foundation). The workflow model is inspired by spreadsheets and is novel in its support for an intuitive method of interaction enabling experimentation as required by many scientists, e.g. bioinformaticians. We apply GPFlow to two bioinformatics experiments and demonstrate its flexibility and simplicity.

Microscopic and spectroscopic investigation of poly(3-hexylthiophene) interaction with carbon nanotubes

The inclusion of carbon nanotubes in polymer matrix has been proposed to enhance the polymer’s physical and electrical properties. In this study, microscopic and spectroscopic techniques are used to investigate the interaction between poly(3-hexylthiophene) (P3HT) and nanotubes and the reciprocal modification of physical properties. The presence of P3HT-covered nanotubes dispersed in the polymer matrix has been observed by atomic force microscopy and transmission electron microscopy. Then, the modification of P3HT optical properties due to nanotube inclusion has been evidenced with spectroscopic techniques like absorption and Raman spectroscopy. The study is completed with detailed nanoscale analysis by scanning probe techniques. The ordered self assembly of polymer adhering on the nanotube is unveiled by showing an example of helical wrapping of P3HT. Scanning tunneling spectroscopy study provides information on the electronic structure of nanotube-polymer assembly, revealing the charge transfer from P3HT to the nanotube.

Bending and bundling of metal-free vertically aligned ZnO nanowires due to electrostatic interaction

Bending and bundling was observed from vertically aligned arrays of ZnO nanowires with flat (0001) top surfaces, which were synthesized using a vapor-phase method without metal catalysts. Sufficient evidence was found to exclude electron-beam bombardment during scanning electron microscopy as a cause for bending and bundling. We attribute the bending and bundling to electrostatic interactions due to charged (0001) polar surfaces, and also discussed the threshold surface charge densities for the bending and bundling based on a simple cantilever-bending model. Some growth features were indicative of the operation of electrostatic interactions during the growth.

Aggravation of ADAMTS and MMP production and ERK1/2 pathway in the interaction of osteoarthritic subchondral bone osteoblasts and articular cartilage chondrocytes : a possible pathogenic role in osteoarthritis

Introduction: Degradative enzymes, such as A disintegrin and metalloproteinase with thrombospondin motifs (ADAMTS) and matrix metalloproteinases (MMPs), play key roles in osteoarthritis (OA) development. The aim of the present study was to investigate if cross-talk between subchondral bone osteoblasts (SBOs) and articular cartilage chondrocytes (ACCs) in OA alters the expression and regulation of ADAMTS5, ADAMTS4, MMP-1, MMP-2, MMP-3, MMP-8, MMP-9 and MMP-13, and also to test the possible involvement of mitogen activated protein kinase (MAPK) signaling pathway during this process. Methods: ACCs and SBOs were isolated from normal and OA patients. An in vitro co-culture model was developed to study the regulation of ADAMTS and MMPs under normal and OA joint cross-talk conditions. MAPK-ERK inhibitor, PD98059 was applied to delineate the involvement of specific pathway during this interaction process. Results: Indirect co-culture of OA SBOs with normal ACCs resulted in significantly increased expression of ADAMTS5, ADAMTS4, MMP-2, MMP-3 and MMP-9 in ACCs, whereas co-culture of OA ACCs led to increased MMP-1 and MMP-2 expression in normal SBOs. The upregulation of ADAMTS and MMPs under these conditions was correlated with activation of the MAPK-ERK1/2 signaling pathway and the addition of the MAPK-ERK inhibitor, PD98059, reversed the overexpression of ADAMTS and MMPs in co-cultures. Conclusion: In summary, we believe, these results add to the evidence that in human OA, altered bi-directional signals transmitted between SBOs and ACCs significantly impacts the critical features of both cartilage and bone by producing abnormal levels of ADAMTS and MMPs. Furthermore, we have demonstrated for the first time that this altered cross-talk was mediated by the phosphorylation of MAPK-ERK1/2 signaling pathway.

Bridging the representation and interaction challenges of mobile context-aware computing: designing agile ridesharing

The increasing capability of mobile devices and social networks to gather contextual and social data has led to increased interest in context-aware computing for mobile applications. This paper explores ways of reconciling two different viewpoints of context, representational and interactional, that have arisen respectively from technical and social science perspectives on context-aware computing. Through a case study in agile ridesharing, the importance of dynamic context control, historical context and broader context is discussed. We build upon earlier work that has sought to address the divide by further explicating the problem in the mobile context and expanding on the design approaches.

Researching intuitive interaction

Intuitive interaction is based on past experience and is fast and often non conscious. We have conducted ten studies into this issue over the past ten years, involving more than 400 participants. Data collection methods have included questionnaires, interviews, observations, concurrent and retrospective protocols, and cognitive measures. Coding schemes have been developed to suit each study and involve robust, literature based heuristics. Some other researchers have investigated this issue and their methods are also examined. The paper traces the development of the methods and compares the various approaches used over the years.

Web searcher interaction with the Dogpile.com metasearch engine

Metasearch engines are an intuitive method for improving the performance of Web search by increasing coverage, returning large numbers of results with a focus on relevance, and presenting alternative views of information needs. However, the use of metasearch engines in an operational environment is not well understood. In this study, we investigate the usage of Dogpile.com, a major Web metasearch engine, with the aim of discovering how Web searchers interact with metasearch engines. We report results examining 2,465,145 interactions from 534,507 users of Dogpile.com on May 6, 2005 and compare these results with findings from other Web searching studies. We collect data on geographical location of searchers, use of system feedback, content selection, sessions, queries, and term usage. Findings show that Dogpile.com searchers are mainly from the USA (84% of searchers), use about 3 terms per query (mean = 2.85), implement system feedback moderately (8.4% of users), and generally (56% of users) spend less than one minute interacting with the Web search engine. Overall, metasearchers seem to have higher degrees of interaction than searchers on non-metasearch engines, but their sessions are for a shorter period of time. These aspects of metasearching may be what define the differences from other forms of Web searching. We discuss the implications of our findings in relation to metasearch for Web searchers, search engines, and content providers.

Designing an immersive environment for public use

Bystander is a multi-user, immersive, interactive environment intended for public display in a museum or art gallery. It is designed to make available heritage collections in novel and culturally responsible ways. We use its development as a case study to examine the role played in that process by a range of tools and techniques from participatory design traditions. We describe how different tools were used within the design process, specifically: the ways in which the potential audience members were both included and represented; the prototypes that have been constructed as a way of envisioning how the final work might be experienced; and how these tools have been brought together in ongoing designing and evaluation. We close the paper with some reflections on the extension of participatory commitments into still-emerging areas of technology design that prioritise the design of spaces for human experience and reflective interaction.

Status of current research on the implication of climate change on built environment

The cycling interaction between climate change and building performance is of dynamic nature and both are essentially the cause and the effect of each other. On one hand, buildings contribute significantly to the global warming process. On the other hand, climate change is also expected to impact on many aspects of building performance. In this paper, the status of current research on the implication of climate change on built environment is reviewed. It is found that although the present research has covered broad areas of research, they are generally only limited to the qualitative analyses. It is also highlighted that although it is widely realized that reducing greenhouse gas emissions from the building sector is very important, the adoption of complementary adaptation strategy to prepare the building for a range of climate change scenarios is also necessary. Due to the lack of holistic approach to generate future hourly weather data, various approaches have been used to generate different key weather variables. This ad hoc situation has seriously hindered the application of building simulation technique to the climate change impact study, in particular, to provide quantitative information for policy and design development.

Intuitive interaction and older people

Older people often struggle with using contemporary products and interfaces. They show slower, less intuitive interaction with more errors. This paper reports on a large project designed to investigate why older people have these difficulties and what strategies could be used to mitigate them. The project team found that older people are less familiar with products that they own than younger ones, while both older and middle aged people are less familiar with products that they do not own than younger ones. Age related cognitive decline is also related to slower and less intuitive performance with contemporary products and interfaces. Therefore, the reasons behind the problems that older people demonstrate with contemporary technologies involve a mix of familiarity and capability. Redundancy applied to an interface in the form of symbols and words is helpful for middle aged and younger old people but the oldest age group performed better with a words only interface. Also, older people showed faster and more intuitive use with a flat interface than a nested one, although there was no difference in errors. Further work is ongoing in order to establish ways in which these findings can be usefully applied in the design process.

Multi-cursor multi-user mobile interaction with a large shared display

When using a mobile device to control a cursor on a large shared display, the interaction must be carefully planned to match the environment and purpose of the systems use. We describe a ‘democratic jukebox’ system that revealed five recommendations that should be considered when designing this type of interaction relating to providing feedback to the user; how to represent users in a multi-cursor based system; where people tend to look and their expectation of how to move their cursor; the orientation of screens and the social context; and, the use of simulated users to give the real users a sense that they are engaging with a greater audience.

Power system stability enhancement in a deregulated environment using FACTS devices

In deregulated versions of free-market electricity, producers will be free to send power along other utilities. The price of power strongly depends and fluctuates according to mutual benefit index of both supplier and consumer. In such a situation, strong interaction among utilities may cause instabilities in the system. As the frequency of market-based dispatch increases market forces tend to destabilize the stable system dynamics depending on the value of Ks/τλ(market dependent parameter) ratio. This tends to destabilize the coupled dynamics. The implementation of TCSC can effectively damp the inter area modes of oscillations of the coupled market system.

Systematics and biology of the iconic Australian scribbly gum moths Ogmograptis Meyrick (Lepidoptera: Bucculatricidae) and their unique insect-plant interaction

The larvae of particular Ogmograptis spp. produce distinctive scribbles on some smooth-barked Eucalyptus spp. which are a common feature on many ornamental and forest trees in Australia. However, although they are conspicuous in the environment the systematics and biology of the genus has been poorly studied. This has been addressed through detailed field and laboratory studies of their biology of three species (O. racemosa Horak sp. nov., O. fraxinoides Horak sp. nov., O. scribula Meyrick), in conjunction with a comprehensive taxonomic revision support by a molecular phylogeny utilising the mitochondrial Cox1 and nuclear 18S genes. In brief, eggs are laid in bark depressions and the first instar larvae bore into the bark to the level where the future cork cambium forms (the phellegen). Early instar larvae bore wide, arcing tracks in this layer before forming a tighter zig-zag shaped pattern. The second last instar turns and bores either closely parallel to the initial mine or doubles its width, along the zig-zag shaped mine. The final instar possesses legs and a spinneret (unlike the earlier instars) and feeds exclusively on callus tissue which forms within the zig-zag shaped mine formed by the previous instar, before emerging from the bark to pupate at the base of the tree. The scars of mines them become visible scribble following the shedding of bark. Sequence data confirm the placement of Ogmograptis within the Bucculatricidae, suggest that the larvae responsible for the ‘ghost scribbles’ (unpigmented, raised scars found on smooth-barked eucalypts) are members of the genus Tritymba, and support the morphology-based species groups proposed for Ogmograptis. The formerly monotypic genus Ogmograptis Meyrick is revised and divided into three species groups. Eleven new species are described: Ogmograptis fraxinoides Horak sp. nov., Ogmograptis racemosa Horak sp. nov. and Ogmograptis pilularis Horak sp. nov. forming the scribula group with Ogmograptis scribula Meyrick; Ogmograptis maxdayi Horak sp. nov., Ogmograptis barloworum Horak sp. nov., Ogmograptis paucidentatus Horak sp. nov., Ogmograptis rodens Horak sp. nov., Ogmograptis bignathifer Horak sp. nov. and Ogmograptis inornatus Horak sp. nov. as the maxdayi group; Ogmograptis bipunctatus Horak sp. nov., Ogmograptis pulcher Horak sp. nov., Ogmograptis triradiata (Turner) comb. nov. and Ogmograptis centrospila (Turner) comb. nov. as the triradiata group. Ogmograptis notosema (Meyrick) cannot be assigned to a species group as the holotype has not been located. Three unique synapomorphies, all derived from immatures, redefine the family Bucculatricidae, uniting Ogmograptis, Tritymba Meyrick (both Australian) and Leucoedemia Scoble & Scholtz (African) with Bucculatrix Zeller, which is the sister group of the southern hemisphere genera. The systematic history of Ogmograptis and the Bucculatricidae is discussed.

Soil-pile interaction in deep layered marine sediment under seismic excitation

Under seismic loads neither the response of the pile nor the response of ground are independent of each other, contrary what is normally assumed. In seismic design of buildings, dynamic response of a structure is determined by assuming a fixed base on sub-grade and neglecting the physical interaction between foundation and soil profile in which it is embedded. However, the seismic response of pile foundations in vibration sensitive soil profiles is significantly affected by the behaviour of supporting soil. This research uses validated Finite Element techniques to simulate the seismic behaviour of pile foundations embedded in multilayered vibration sensitive soils.