Changing Research Communication Practices and Open Scholarship: A Framework for Analysis

"It is important that academics’ research communication practices are explored to complement these system approaches. How do we think about these issues in order to investigate and illuminate changing forms of knowledge creation and communication? The project from which this paper is drawn was interested to answer three interrelated questions: • What are the research communication practices of academics? • What enables or constrains the flow of research communication within these practices? • How closed or open are academics’ scholarly communication practices? This paper describes our thinking as we developed the analytical framework that would enable us to answer these questions. The analytical framework was developed from the conceptual framework we used to shape our study through an iterative process with the data collected.

Seeking Impact and Visibility: Scholarly Communication in Southern Africa

The Scholarly Communication in Africa Programme (SCAP) was a three-year research and implementation initiative that took place between March 2010 and August 2013. Hosted by the University of Cape Town, the programme engaged the Universities of Botswana, Namibia and Mauritius in a process aimed at better understanding the dynamics around scholarly communication in the Southern African higher education environment and advancing the open access agenda for the purpose of increasing the visibility of African research. This work was made possible by a grant from the Canadian International Development Research Center (IDRC). This report synthesizes research and findings from the four institutional case studies conducted at the Universities of Botswana, Cape Town, Mauritius and Namibia. It provides an overview the scholarly communication activity systems at work in these four Southern African universities

Deterministic mathematical models of the cAMP pathway in Saccharomyces cerevisiae

<p>Abstract</p> <p>Background</p> <p>Cyclic adenosine monophosphate (cAMP) has a key signaling role in all eukaryotic organisms. In <it>Saccharomyces cerevisiae</it>, it is the second messenger in the Ras/PKA pathway which regulates nutrient sensing, stress responses, growth, cell cycle progression, morphogenesis, and cell wall biosynthesis. A stochastic model of the pathway has been reported.</p> <p>Results</p> <p>We have created deterministic mathematical models of the PKA module of the pathway, as well as the complete cAMP pathway. First, a simplified conceptual model was created which reproduced the dynamics of changes in cAMP levels in response to glucose addition in wild-type as well as cAMP phosphodiesterase deletion mutants. This model was used to investigate the role of the regulatory Krh proteins that had not been included previously. The Krh-containing conceptual model reproduced very well the experimental evidence supporting the role of Krh as a direct inhibitor of PKA. These results were used to develop the Complete cAMP Model. Upon simulation it illustrated several important features of the yeast cAMP pathway: Pde1p is more important than is Pde2p for controlling the cAMP levels following glucose pulses; the proportion of active PKA is not directly proportional to the cAMP level, allowing PKA to exert negative feedback; negative feedback mechanisms include activating Pde1p and deactivating Ras2 via phosphorylation of Cdc25. The Complete cAMP model is easier to simulate, and although significantly simpler than the existing stochastic one, it recreates cAMP levels and patterns of changes in cAMP levels observed experimentally <it>in vivo </it>in response to glucose addition in wild-type as well as representative mutant strains such as <it>pde1Δ, pde2Δ</it>, <it>cyr1Δ</it>, and others. The complete model is made available in SBML format.</p> <p>Conclusion</p> <p>We suggest that the lower number of reactions and parameters makes these models suitable for integrating them with models of metabolism or of the cell cycle in <it>S. cerevisiae</it>. Similar models could be also useful for studies in the human pathogen <it>Candida albicans </it>as well as other less well-characterized fungal species.</p

Methodology to prepare for UK's offshore wind Contract for Difference auctions

In the UK, the Contract for Difference (CfD) subsidies for renewable energy generation are awarded through a competitive auction process. This paper simulates the most recent CfD auction for offshore wind, using a novel methodology to assist developers in preparing their bid strategy and for policymakers to test auction efficiency. The simulation's results show developer's leading strategy is to shade their bid to increase auction pay-off. A developer's incentive to shade their bid depends on the project's capacity and minimum bid price; the offshore wind farm Hornsea 3 has the greatest incentive to shade its bid as its optimum bid price is further from its cost price, and results in the highest expected value of additional auction pay-off. The median strike price estimated by the model is £39.23/MWh, and the most likely winners, as predicted from the simulations, are Hornsea 3, Inch Cape, East Anglia 3 and Norfolk Boreas. Published auction results show that the estimated strike price from the simulation is 5% higher than the £37.35/MWh awarded strike price; however, the model successfully predicted the winners. Further analysis of results demonstrates that developers adopted a risk-averse bidding strategy, bidding at a pre-determined floor (coexist) price, guaranteeing subsidy. As a result, £38 million of the subsidy budget was unused

Developing a real time sensing system to monitor bacteria in wound dressings

Infection control is a key aspect of wound management strategies. Infection results in chemical imbalances and inflammation in the wound and may lead to prolonged healing times and degradation of the wound surface. Frequent changing of wound dressings may result in damage to healing tissues and an increased risk of infection. This paper presents the first results from a monitoring system that is being developed to detect presence and growth of bacteria in real time. It is based on impedance sensors that could be placed at the wound-dressing interface and potentially monitor bacterial growth in real time. As wounds can produce large volumes of exudate, the initial system reported here was developed to test for the presence of bacteria in suspension. Impedance was measured using disposable silver-silver chloride electrodes. The bacteria Staphylococcus aureus were chosen for the study as a species commonly isolated from wounds. The growth of bacteria was confirmed by plate counting methods and the impedance data were analysed for discernible differences in the impedance profiles to distinguish the absence and/or presence of bacteria. The main findings were that the impedance profiles obtained by silver-silver chloride sensors in bacterial suspensions could detect the presence of high cell densities. However, the presence of the silver-silver chloride electrodes tended to inhibit the growth of bacteria. These results indicate that there is potential to create a real time infection monitor for wounds based upon impedance sensing

Dynamic Contrast-Enhanced Ultrasound of Colorectal Liver Metastases as an Imaging Modality for Early Response Prediction to Chemotherapy

Our aim was to investigate whether dynamic contrast-enhanced ultrasound (DCE-US) can detect early changes in perfusion of colorectal liver metastases after initiation of chemotherapy. Newly diagnosed patients with colorectal cancer with liver metastases were enrolled in this explorative prospective study. Patients were treated with capecitabine or 5-fluorouracil-based chemotherapy with or without bevacizumab. DCE-US was performed before therapy (baseline) and again 10 days after initiation of treatment. Change in contrast-enhancement in one liver metastasis (indicator lesion) was measured. Treatment response was evaluated with a computed tomography (CT) scan after three cycles of treatment and the initially observed DCE-US change of the indicator lesion was related to the observed CT response. Eighteen patients were included. Six did not complete three series of chemotherapy and the evaluation CT scan, leaving twelve patients for analysis. Early changes in perfusion parameters using DCE-US did not correlate well with subsequent CT changes. A subgroup analysis of eight patients receiving bevacizumab, however, demonstrated a statistically significant correlation (p = 0.045) between early changes in perfusion measures of peak enhancement at DCE-US and tumor shrinkage at CT scan. The study indicates that early changes in DCE-US perfusion measures may predict subsequent treatment response of colorectal liver metastases in patients receiving bevacizumab

Scholarly Communication at the University of Cape Town: Case Study Report

This report, "Scholarly Communication at the University of Cape Town", is one of a series of four institutional case studies. It provides an overview the scholarly communication activity system at UCT

Scholarly Communication at the University of Botswana: Case Study Report

This report, "Scholarly Communication at the University of Botswana", is one of a series of four institutional case studies. It provides an overview the scholarly communication activity system at UB