The View from LU Cooperative Extension, October 2014

Volume 1, Issue 6

The View from LU Cooperative Extension, December 2014

Volume 2, Issue 1

The Contribution of Agriculture, Forestry and other Land Use activities to Global Warming, 1990-2012

Date of Acceptance: 16/12/2014 Acknowledgements: This work was carried out with generous funding by the Governments of Germany (GCP/GLO/286/GER) and Norway (GCP/GLO/325/NOR) to the ‘Monitoring and Assessment of GHG Emissions and Mitigation Potential from Agriculture’ Project of the FAO Climate, Energy and Tenure Division. P. Smith is a Royal Society Wolfson Merit Award holder, and his input contributes to the University of Aberdeen Environment and Food Security Theme and to Scotland's ClimateXChange. J. House was funded by a Leverhulme Research Fellowship. The FAO Statistics Division maintains the FAOSTAT Emissions database with regular program funds allocated through Strategic Objective 6. © 2015 John Wiley & Sons Ltd.

Nuclear Activities of Basic Fibroblast Growth Factor: Potentiation of Low-Serum Growth Mediated by Natural or Chimeric Nuclear Localization Signals

Human basic fibroblast growth factor (FGF-2) occurs in four isoforms: a low molecular weight (LMW FGF-2, 18 kDa) and three high molecular weight (HMW FGF-2, 22, 22.5, and 24 kDa) forms. LMW FGF-2 is primarily cytoplasmic and functions in an autocrine manner, whereas HMW FGF-2s are nuclear and exert activities through an intracrine, perhaps nuclear, pathway. Selective overexpression of HMW FGF-2 forms in fibroblasts promotes growth in low serum, whereas overexpression of LMW FGF-2 does not. The HMW FGF-2 forms have two functional domains: an amino-terminal extension and a common 18-kDa amino acid sequence. To investigate the role of these regions in the intracrine signaling of HMW FGF-2, we produced stable transfectants of NIH 3T3 fibroblasts overexpressing either individual HMW FGF-2 forms or artificially nuclear-targeted LMW FGF-2. All of these forms of FGF-2 localize to the nucleus/nucleolus and induce growth in low serum. The nuclear forms of FGF-2 trigger a mitogenic stimulus under serum starvation conditions and do not specifically protect the cells from apoptosis. These data indicate the existence of a specific role for nuclear FGF-2 and suggest that LMW FGF-2 represents the biological messenger in both the autocrine/paracrine and intracrine FGF-2 pathways.

DNA-binding and strand-annealing activities of human Mre11: implications for its roles in DNA double-strand break repair pathways

DNA double-strand breaks (DSBs) in eukaryotic cells can be repaired by non-homologous end-joining or homologous recombination. The complex containing the Mre11, Rad50 and Nbs1 proteins has been implicated in both DSB repair pathways, even though they are mechanistically different. To get a better understanding of the properties of the human Mre11 (hMre11) protein, we investigated some of its biochemical activities. We found that hMre11 binds both double- and single-stranded (ss)DNA, with a preference for ssDNA. hMre11 does not require DNA ends for efficient binding. Interestingly, hMre11 mediates the annealing of complementary ssDNA molecules. In contrast to the annealing activity of the homologous recombination protein hRad52, the activity of hMre11 is abrogated by the ssDNA binding protein hRPA. We discuss the possible implications of the results for the role(s) of hMre11 in both DSB repair pathways.

A database and tools for 3-D protein structure comparison and alignment using the Combinatorial Extension (CE) algorithm

The database reported here is derived using the Combinatorial Extension (CE) algorithm which compares pairs of protein polypeptide chains and provides a list of structurally similar proteins along with their structure alignments. Using CE, structure–structure alignments can provide insights into biological function. When a protein of known function is shown to be structurally similar to a protein of unknown function, a relationship might be inferred; a relationship not necessarily detectable from sequence comparison alone. Establishing structure–structure relationships in this way is of great importance as we enter an era of structural genomics where there is a likelihood of an increasing number of structures with unknown functions being determined. Thus the CE database is an example of a useful tool in the annotation of protein structures of unknown function. Comparisons can be performed on the complete PDB or on a structurally representative subset of proteins. The source protein(s) can be from the PDB (updated monthly) or uploaded by the user. CE provides sequence alignments resulting from structural alignments and Cartesian coordinates for the aligned structures, which may be analyzed using the supplied Compare3D Java applet, or downloaded for further local analysis. Searches can be run from the CE web site, http://cl.sdsc.edu/ce.html, or the database and software downloaded from the site for local use.

Multiple Perspectives on Academic Service-Learning Partnerships at the American University in Cairo: A Mixed Method Study

This mixed method study aimed to redress the gap in the literature on academic service-learning partnerships, especially in Eastern settings. It utilized Enos and Morton's (2003) theoretical framework to explore these partnerships at the American University in Cairo (AUC). Seventy-nine community partners, administrators, faculty members, and students from a diverse range of age, citizenship, racial, educational, and professional backgrounds participated in the study. Qualitative interviews were conducted with members of these four groups, and a survey with both close-ended and open-ended questions administered to students yielded 61 responses. Qualitative analyses revealed that the primary motivators for partners' engagement in service-learning partnerships included contributing to the community, enhancing students' learning and growth, and achieving the civic mission of the University. These partnerships were characterized by short-term relationships with partners' aspiring to progress toward long-term commitments. The challenges to these partnerships included issues pertaining to the institution, partnering organizations, culture, politics, pedagogy, students, and faculty members. Key strategies for improving these partnerships included institutionalizing service-learning in the University and cultivating an institutional culture supportive of community engagement. Quantitative analyses showed statistically significant relationships between students' scores on the Community Awareness and Interpersonal Effectiveness scales and their overall participation in community service activities inside and outside the classroom, as well as a statistically significant difference between their scores on the Community Awareness scale and department offering service-learning courses. The study's outcomes underscore the role of the local culture in shaping service-learning partnerships, as well as the role of both curricular and extracurricular activities in boosting students' awareness of their community and interpersonal effectiveness. Cultivating a culture of community engagement and building support mechanisms for engaged scholarship are among the critical steps required by public policy-makers in Egypt to promote service-learning in Egyptian higher education. Institutionalizing service-learning partnerships at AUC and enhancing the visibility of these partnerships on campus and in the community are essential to the future growth of these collaborations. Future studies should explore factors affecting community partners' satisfaction with these partnerships, top-down and bottom-up support to service-learning, the value of reflection to faculty members, and the influence of students' economic backgrounds on their involvement in service-learning partnerships.

Review and extension of the McCabe-Thiele method covering multiple feeds, products and heat transfer stages

The McCabe-Thiele method is a classical approximate graphical method for the conceptual design of binary distillation columns which is still widely used, mainly for didactical purposes, though it is also valuable for quick preliminary calculations. Nevertheless, no complete description of the method has been found and situations such as different thermal feed conditions, multiple feeds, possibilities to extract by-products or to add or remove heat, are not always considered. In the present work we provide a systematic analysis of such situations by developing the generalized equations for: a) the operating lines (OL) of each sector, and b) the changeover line that provides the connection between two consecutive trays of the corresponding sectors separated by a lateral stream of feed, product, or a heat removal or addition.

Developing Semantic Rich Internet Applications with the Sm4RIA Extension for OIDE

This paper introduces the Sm4RIA Extension for OIDE, which implements the Sm4RIA approach in OIDE (OOH4RIA Integrated Development Environment). The application, based on the Eclipse framework, supports the design of the Sm4RIA models as well as the model-to-model and model-to-text transformation processes that facilitate the generation of Semantic Rich Internet Applications, i.e., RIA applications capable of sharing data as Linked data and consuming external data from other sources in the same manner. Moreover, the application implements mechanisms for the creation of RIA interfaces from ontologies and the automatic generation of administration interfaces for a previously design application.

A Cloud-based Framework for Security Analysis of Browser Extensions

In today's internet world, web browsers are an integral part of our day-to-day activities. Therefore, web browser security is a serious concern for all of us. Browsers can be breached in different ways. Because of the over privileged access, extensions are responsible for many security issues. Browser vendors try to keep safe extensions in their official extension galleries. However, their security control measures are not always effective and adequate. The distribution of unsafe extensions through different social engineering techniques is also a very common practice. Therefore, before installation, users should thoroughly analyze the security of browser extensions. Extensions are not only available for desktop browsers, but many mobile browsers, for example, Firefox for Android and UC browser for Android, are also furnished with extension features. Mobile devices have various resource constraints in terms of computational capabilities, power, network bandwidth, etc. Hence, conventional extension security analysis techniques cannot be efficiently used by end users to examine mobile browser extension security issues. To overcome the inadequacies of the existing approaches, we propose CLOUBEX, a CLOUd-based security analysis framework for both desktop and mobile Browser EXtensions. This framework uses a client-server architecture model. In this framework, compute-intensive security analysis tasks are generally executed in a high-speed computing server hosted in a cloud environment. CLOUBEX is also enriched with a number of essential features, such as client-side analysis, requirements-driven analysis, high performance, and dynamic decision making. At present, the Firefox extension ecosystem is most susceptible to different security attacks. Hence, the framework is implemented for the security analysis of the Firefox desktop and Firefox for Android mobile browser extensions. A static taint analysis is used to identify malicious information flows in the Firefox extensions. In CLOUBEX, there are three analysis modes. A dynamic decision making algorithm assists us to select the best option based on some important parameters, such as the processing speed of a client device and network connection speed. Using the best analysis mode, performance and power consumption are improved significantly. In the future, this framework can be leveraged for the security analysis of other desktop and mobile browser extensions, too.

Possible Approaches to Commercializing Applied University Research: a Russian Case Study

This paper discusses the environment around universities in Russia and possible approaches to analyzing and choosing the method for applied research results commercialization as well as selecting promising applied research areas in that environment. Conceptual foundations for decision making during the commercialization and roadmap/action plan creation processes are outlined. These can be useful to both universities for planning their activities aswell as for organizations that plan to cooperate with universities or that are interested in university generated research. This being said, obtained models and used evaluation parameters may be unique and may depend upon the particular project, university, region, and personal preferences of decision makers. Thus, consideration of these parameters and characteristics only has merit when making decisions in the dynamics of change of these parameters. For this purpose statistical information is needed that characterizes the competencies of the research organization (university) inquestion, needs of partner organizations, governmental and societal requirements, and science and technology prospects. After determining the promising research areas it’s time to look at particular projects, which in turn are also characterized by various parameters dependent upon their objectives. Considering the values of these parameters in their dynamics allows control of project parameters in the course of its execution. This in turn allows prediction of negative situations and alleviation of such by setting the target values of parameters and using best practices and standardization of management processes to achieve those values.

Publication activities of German junior researchers in academic medicine: which factors impact impact factors?

Previous studies have shown medical students in Germany to have little interest in research while at the same time there is a lack of physician scientists. This study’s aim is to investigate factors influencing publication productivity of physicians during and after finishing their medical doctorate. We conducted a PubMed search for physicians having received their doctoral degree at Ludwig-Maxmilians-University Munich Faculty of Medicine between 2011 and 2013 (N = 924) and identified the appropriate impact factor (IF) for each journal the participants had published in. Gender, age, final grade of the doctorate, participation in a structured doctoral study program and joint publication activities between graduate and academic supervisor were defined as factors. For analyses we used nonparametric procedures. Men show significantly more publications than women. Before their doctoral graduation men publish 1.98 (SD ± 3.64) articles on average, women 1.15 (±2.67) (p < 0.0001, d = 0.27). After completion of the doctorate (up to 06/2015), 40 % of men still publish, while only 24.3 % of women (p < 0.0001, φ = 0.17) continue to publish. No differences were found concerning the value of IFs. Similar results were found regarding the variable ‘participation in a structured doctoral study program’. Until doctoral graduation, program participants publish 2.82 (±5.41) articles, whereas participants doing their doctorate individually only publish 1.39 (±2.87) articles (p < 0.0001, d = 0.46). These differences persist in publication activities after graduation (45.5 vs. 29.7 %, p = 0.008, φ = 0.09). A structured doctorate seems to have positive influence on IFs (4.33 ± 2.91 vs. 3.37 ± 2.82, p = 0.006, d = 0.34). Further significant results concern the variables ‘final grade’ and ‘age’: An early doctoral graduation and an excellent or very good grade for the doctoral thesis positively influence publication productivity. Finally, joint publication activities between the graduate and his/her academic supervisor result in significantly higher IFs (3.64 ± 3.03 vs. 2.84 ± 2.25, p = 0.007, d = 0.28). The study’s results support the assumption about women’s underrepresentation in science as well as the relevance of structured doctoral study programs for preparing and recruiting young academics in medicine for scientific careers. Promoting women and further development of structured doctoral study programs are highly recommended.