Computational identification and analysis of noncoding RNAs - Unearthing the buried treasures in the genome

The central dogma of molecular biology states that the genetic information flows from DNA to RNA to protein. This dogma has exerted a substantial influence on our understanding of the genetic activities in the cells. Under this influence, the prevailing assumption until the recent past was that genes are basically repositories for protein coding information, and proteins are responsible for most of the important biological functions in all cells. In the meanwhile, the importance of RNAs has remained rather obscure, and RNA was mainly viewed as a passive intermediary that bridges the gap between DNA and protein. Except for classic examples such as tRNAs (transfer RNAs) and rRNAs (ribosomal RNAs), functional noncoding RNAs were considered to be rare. However, this view has experienced a dramatic change during the last decade, as systematic screening of various genomes identified myriads of noncoding RNAs (ncRNAs), which are RNA molecules that function without being translated into proteins [11], [40]. It has been realized that many ncRNAs play important roles in various biological processes. As RNAs can interact with other RNAs and DNAs in a sequence-specific manner, they are especially useful in tasks that require highly specific nucleotide recognition [11]. Good examples are the miRNAs (microRNAs) that regulate gene expression by targeting mRNAs (messenger RNAs) [4], [20], and the siRNAs (small interfering RNAs) that take part in the RNAi (RNA interference) pathways for gene silencing [29], [30]. Recent developments show that ncRNAs are extensively involved in many gene regulatory mechanisms [14], [17]. The roles of ncRNAs known to this day are truly diverse. These include transcription and translation control, chromosome replication, RNA processing and modification, and protein degradation and translocation [40], just to name a few. These days, it is even claimed that ncRNAs dominate the genomic output of the higher organisms such as mammals, and it is being suggested that the greater portion of their genome (which does not encode proteins) is dedicated to the control and regulation of cell development [27]. As more and more evidence piles up, greater attention is paid to ncRNAs, which have been neglected for a long time. Researchers began to realize that the vast majority of the genome that was regarded as “junk,” mainly because it was not well understood, may indeed hold the key for the best kept secrets in life, such as the mechanism of alternative splicing, the control of epigenetic variations and so forth [27]. The complete range and extent of the role of ncRNAs are not so obvious at this point, but it is certain that a comprehensive understanding of cellular processes is not possible without understanding the functions of ncRNAs [47]

Dynamic Leadership: Toolbox for the Values-Based Entrepreneur

Four entrepreneurship models are proposed which lend guidance in the development of a business, from birth to exit, each examining ways to maintain the business founder’s initial vision and to continue to infuse values and ethical decision-making at each stage of development

A legacy handbook for manufacturing

Legacy Handbook reviewing emda's experience of manufacturing activity. Identifies key achievements and draws out lessons learned that may be relevant to successor bodies active in this area

Performance in franchising: the effects of different management styles

Various theoretical approaches uphold the relevance of the relationship between the form of management and performance. Different management styles influence the relationships of agencies [Jensen, M.C. (1998). Foundations of organizational strategy. Cambridge, MA: Harvard University Press], the cost of governing transactions [Williamson, O.E. (1985). The economics institutions of capitalism: Firms, markets, relational contracting. New York, NY: Free Press], and the allocation of resources between the exploitation and exploration of activities [March, J.G. (1991). Exploration and exploitation in organizational learning. Organization Science, 2(1), 71-87], and this is manifested in firm performance. In light of these assumptions, this article presents an empirical verification of the relationship between the management of franchises and their performance, examining how different styles of management on the part of franchisers over their franchisees have significant effects on the growth and profits of franchiser firms.Peris-Ortiz, M.; Willoughby, MC.; Rueda Armengot, C. (2012). Performance in franchising: the effects of different management styles. Service Industries Journal. 32(16):2507-2525. doi:10.1080/02642069.2011.594876S250725253216Altinay, L., & Okumus, F. (2010). Franchise partner selection decision making. The Service Industries Journal, 30(6), 929-946. doi:10.1080/02642060802322275Child, J. (1972). Organizational Structure, Environment and Performance: The Role of Strategic Choice. Sociology, 6(1), 1-22. doi:10.1177/003803857200600101Combs, J. G., & Ketchen, D. J. (1999). CAN CAPITAL SCARCITY HELP AGENCY THEORY EXPLAIN FRANCHISING? REVISITING THE CAPITAL SCARCITY HYPOTHESIS. Academy of Management Journal, 42(2), 196-207. doi:10.2307/257092Combs, J. (2003). Why Do Firms Use Franchising as an Entrepreneurial Strategy?: A Meta-Analysis. Journal of Management, 29(3), 443-465. doi:10.1016/s0149-2063(03)00019-9COMBS, J. G., KETCHEN, D. J., & IRELAND, R. D. (2006). Effectively managing service chain organizations. Organizational Dynamics, 35(4), 357-371. doi:10.1016/j.orgdyn.2006.08.006Combs, J. G., Michael, S. C., & Castrogiovanni, G. J. (2009). Institutional Influences on the Choice of Organizational Form: The Case of Franchising. Journal of Management, 35(5), 1268-1290. doi:10.1177/0149206309336883Crook, T. R., Shook, C. L., Madden, T. M., & Morris, M. L. (2009). A review of current construct measurement in entrepreneurship. International Entrepreneurship and Management Journal, 6(4), 387-398. doi:10.1007/s11365-009-0114-7Fama, E. F., & Jensen, M. C. (1983). Agency Problems and Residual Claims. The Journal of Law and Economics, 26(2), 327-349. doi:10.1086/467038Fama, E. F., & Jensen, M. C. (1983). Separation of Ownership and Control. The Journal of Law and Economics, 26(2), 301-325. doi:10.1086/467037Gillis, W. E., & Combs, J. G. (2009). Franchisor strategy and firm performance: Making the most of strategic resource investments. Business Horizons, 52(6), 553-561. doi:10.1016/j.bushor.2009.07.001Gouldner, A. W. (1960). The Norm of Reciprocity: A Preliminary Statement. American Sociological Review, 25(2), 161. doi:10.2307/2092623Gupta, A. K., Smith, K. G., & Shalley, C. E. (2006). The Interplay Between Exploration and Exploitation. Academy of Management Journal, 49(4), 693-706. doi:10.5465/amj.2006.22083026Hambrick, D. C. (2007). Upper Echelons Theory: An Update. Academy of Management Review, 32(2), 334-343. doi:10.5465/amr.2007.24345254Hambrick, D. C., & Mason, P. A. (1984). Upper Echelons: The Organization as a Reflection of Its Top Managers. The Academy of Management Review, 9(2), 193. doi:10.2307/258434Hindle, K., & Moroz, P. (2009). Indigenous entrepreneurship as a research field: developing a definitional framework from the emerging canon. International Entrepreneurship and Management Journal, 6(4), 357-385. doi:10.1007/s11365-009-0111-xJensen, M. C., & Meckling, W. H. (1976). Theory of the firm: Managerial behavior, agency costs and ownership structure. Journal of Financial Economics, 3(4), 305-360. doi:10.1016/0304-405x(76)90026-xJensen, M. C., & Heckling, W. H. (1995). SPECIFIC AND GENERAL KNOWLEDGE, AND ORGANIZATIONAL STRUCTURE. Journal of Applied Corporate Finance, 8(2), 4-18. doi:10.1111/j.1745-6622.1995.tb00283.xKlein, B., Crawford, R. G., & Alchian, A. A. (1978). Vertical Integration, Appropriable Rents, and the Competitive Contracting Process. The Journal of Law and Economics, 21(2), 297-326. doi:10.1086/466922Liu, W., Lepak, D. P., Takeuchi, R., & Sims, H. P. (2003). Matching leadership styles with employment modes: strategic human resource management perspective. Human Resource Management Review, 13(1), 127-152. doi:10.1016/s1053-4822(02)00102-xMarch, J. G. (1991). Exploration and Exploitation in Organizational Learning. Organization Science, 2(1), 71-87. doi:10.1287/orsc.2.1.71Mitsuhashi, H., Shane, S., & Sine, W. D. (2008). Organization governance form in franchising: efficient contracting or organizational momentum? Strategic Management Journal, 29(10), 1127-1136. doi:10.1002/smj.702Orlikowski, W. J. (1992). The Duality of Technology: Rethinking the Concept of Technology in Organizations. Organization Science, 3(3), 398-427. doi:10.1287/orsc.3.3.398Ouchi, W. G. (1980). Markets, Bureaucracies, and Clans. Administrative Science Quarterly, 25(1), 129. doi:10.2307/2392231Gómez, R. S., González, I. S., & Vázquez, L. (2009). Multi-unit versus single-unit franchising: assessing why franchisors use different ownership strategies. The Service Industries Journal, 30(3), 463-476. doi:10.1080/02642060802252027Gómez, R. S., González, I. S., & Suárez, L. V. (2011). Service quality control mechanisms in franchise networks. The Service Industries Journal, 31(5), 713-723. doi:10.1080/02642060902833338Sarkees, M., & Hulland, J. (2009). Innovation and efficiency: It is possible to have it all. Business Horizons, 52(1), 45-55. doi:10.1016/j.bushor.2008.08.002Sebora, T. C., & Theerapatvong, T. (2009). Corporate entrepreneurship: a test of external and internal influences on managers’ idea generation, risk taking, and proactiveness. International Entrepreneurship and Management Journal, 6(3), 331-350. doi:10.1007/s11365-009-0108-5Shane, S., & Foo, M.-D. (1999). New Firm Survival: Institutional Explanations for New Franchisor Mortality. Management Science, 45(2), 142-159. doi:10.1287/mnsc.45.2.142Shane, S., Shankar, V., & Aravindakshan, A. (2006). The Effects of New Franchisor Partnering Strategies on Franchise System Size. Management Science, 52(5), 773-787. doi:10.1287/mnsc.1050.0449Shane, S. A. (1996). HYBRID ORGANIZATIONAL ARRANGEMENTS AND THEIR IMPLICATIONS FOR FIRM GROWTH AND SURVIVAL: A STUDY OF NEW FRANCHISORS. Academy of Management Journal, 39(1), 216-234. doi:10.2307/256637Shane, S. (2001). Organizational Incentives and Organizational Mortality. Organization Science, 12(2), 136-160. doi:10.1287/orsc.12.2.136.10108Tihula, S., & Huovinen, J. (2009). Incidence of teams in the firms owned by serial, portfolio and first-time entrepreneurs. International Entrepreneurship and Management Journal, 6(3), 249-260. doi:10.1007/s11365-008-0101-4TSUI, A. S., PEARCE, J. L., PORTER, L. W., & TRIPOLI, A. M. (1997). ALTERNATIVE APPROACHES TO THE EMPLOYEE-ORGANIZATION RELATIONSHIP: DOES INVESTMENT IN EMPLOYEES PAY OFF? Academy of Management Journal, 40(5), 1089-1121. doi:10.2307/256928Valliere, D. (2008). Reconceptualizing entrepreneurial framework conditions. 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(2003). Understanding dynamic capabilities. Strategic Management Journal, 24(10), 991-995. doi:10.1002/smj.318Yin, X., & Zajac, E. J. (2004). The strategy/governance structure fit relationship: theory and evidence in franchising arrangements. Strategic Management Journal, 25(4), 365-383. doi:10.1002/smj.38

High-resolution lidar mapping and analysis to quantify surface movement of Swift Creek landslide, Whatcom County, WA

I investigated the applicability of using terrestrial laser scanning (TLS) to quantify surface displacement of the Swift Creek landslide, an active earth flow in the foothills of northwest Washington State. Five surveys were completed from October, 2009-April, 2011 to identify and measure spatial and temporal changes in the movement of the landslide. The seasonally variable movement patterns at the site provide an ideal environment to test the effectiveness of newly emerging methods to measure surface displacement. Iterative closest point (ICP) analysis and image cross-correlation via particle image velocimetry (PIV) were applied to sequential TLS datasets to identify and match features in multi-temporal data. ICP utilizes a distance-based function to match point-cloud surfaces whereas PIV is essentially a pixel-matching algorithm applied to derived DEMs and slopegradient images. Results of the analysis revealed that the ICP and PIV methods applied to LiDAR data are suitable for measuring surface displacement on actively deforming landscapes. Total movement rates of 25 boulders on the toe ranged from 3.3 to 39.3 m/yr, with seasonal changes evident in their movement patterns. PIV analysis produced a spatially continuous displacement field when the time between surveys was less than about five months. Results show that the toe is a highly dynamic zone with as many as five discrete zones of movement. To gain a better understanding of the overall dynamics of the Swift Creek landslide, I applied PIV analysis to airborne LiDAR acquired in 2006 and 2011 that extended the spatial coverage to the entire basin. Movement rates on the main body of the landslide were 3.0 (+/- 0.9) m/yr over the five years. Using both terrestrial and airborne LiDAR data allowed me to circumvent the limitations of each to quantify movement across the whole landslide. My data suggests that the landslide undergoes a transition from a predominately sliding mass in its upper portion to a flow near the top of the unvegetated toe based on increasing velocity and more variable movement patterns observed in this area

Vide-omics : a genomics-inspired paradigm for video analysis

With the development of applications associated to ego-vision systems, smart-phones, and autonomous cars, automated analysis of videos generated by freely moving cameras has become a major challenge for the computer vision community. Current techniques are still not suitable to deal with real-life situations due to, in particular, wide scene variability and the large range of camera motions. Whereas most approaches attempt to control those parameters, this paper introduces a novel video analysis paradigm, 'vide-omics', inspired by the principles of genomics where variability is the expected norm. Validation of this new concept is performed by designing an implementation addressing foreground extraction from videos captured by freely moving cameras. Evaluation on a set of standard videos demonstrates both robust performance that is largely independent from camera motion and scene, and state-of-the-art results in the most challenging video. Those experiments underline not only the validity of the 'vide-omics' paradigm, but also its potential

Developing tools and models for evaluating geospatial data integration of official and VGI data sources

PhD ThesisIn recent years, systems have been developed which enable users to produce, share and update information on the web effectively and freely as User Generated Content (UGC) data (including Volunteered Geographic Information (VGI)). Data quality assessment is a major concern for supporting the accurate and efficient spatial data integration required if VGI is to be used alongside official, formal, usually governmental datasets. This thesis aims to develop tools and models for the purpose of assessing such integration possibilities. Initially, in order to undertake this task, geometrical similarity of formal and informal data was examined. Geometrical analyses were performed by developing specific programme interfaces to assess the positional, linear and polygon shape similarity among reference field survey data (FS); official datasets such as data from Ordnance Survey (OS), UK and General Directorate for Survey (GDS), Iraq agencies; and VGI information such as OpenStreetMap (OSM) datasets. A discussion of the design and implementation of these tools and interfaces is presented. A methodology has been developed to assess such positional and shape similarity by applying different metrics and standard indices such as the National Standard for Spatial Data Accuracy (NSSDA) for positional quality; techniques such as buffering overlays for linear similarity; and application of moments invariant for polygon shape similarity evaluations. The results suggested that difficulties exist for any geometrical integration of OSM data with both bench mark FS and formal datasets, but that formal data is very close to reference datasets. An investigation was carried out into contributing factors such as data sources, feature types and number of data collectors that may affect the geometrical quality of OSM data and consequently affect the integration process of OSM datasets with FS, OS and GDS. Factorial designs were undertaken in this study in order to develop and implement an experiment to discover the effect of these factors individually and the interaction between each of them. The analysis found that data source is the most significant factor that affects the geometrical quality of OSM datasets, and that there are interactions among all these factors at different levels of interaction. This work also investigated the possibility of integrating feature classification of official datasets such as data from OS and GDS geospatial data agencies, and informal datasets such as OSM information. In this context, two different models were developed. The first set of analysis included the evaluation of semantic integration of corresponding feature classifications of compared datasets. The second model was concerned with assessing the ability of XML schema matching of feature classifications of tested datasets. This initially involved a tokenization process in order to split up into single words classifications that were composed of multiple words. Subsequently, encoding feature classifications as XML schema trees was undertaken. The semantic similarity, data type similarity and structural similarity were measured between the nodes of compared schema trees. Once these three similarities had been computed, a weighted combination technique has been adopted in order to obtain the overall similarity. The findings of both sets of analysis were not encouraging as far as the possibility of effectively integrating feature classifications of VGI datasets, such as OSM information, and formal datasets, such as OS and GDS datasets, is concerned.Ministry of Higher Education and Scientific Research, Republic of Iraq