On systems thinking, systems biology and the in Silico Plant

The recent summary report of a Department of Energy Workshop on Plant Systems Biology (P.V. Minorsky [2003] Plant Physiol 132: 404-409) offered a welcomed advocacy for systems analysis as essential in understanding plant development, growth, and production. The goal of the Workshop was to consider methods for relating the results of molecular research to real-world challenges in plant production for increased food supplies, alternative energy sources, and environmental improvement. The rather surprising feature of this report, however, was that the Workshop largely overlooked the rich history of plant systems analysis extending over nearly 40 years (Sinclair and Seligman, 1996) that has considered exactly those challenges targeted by the Workshop. Past systems research has explored and incorporated biochemical and physiological knowledge into plant simulation models from a number of perspectives. The research has resulted in considerable understanding and insight about how to simulate plant systems and the relative contribution of various factors in influencing plant production. These past activities have contributed directly to research focused on solving the problems of increasing biomass production and crop yields. These modeling approaches are also now providing an avenue to enhance integration of molecular genetic technologies in plant improvement (Hammer et al., 2002).

A study of business user based information systems development, and modelling success factors

This thesis describes research into business user involvement in the information systems application building process. The main interest of this research is in establishing and testing techniques to quantify the relationships between identified success factors and the outcome effectiveness of 'business user development' (BUD). The availability of a mechanism to measure the levels of the success factors, and quantifiably relate them to outcome effectiveness, is important in that it provides an organisation with the capability to predict and monitor effects on BUD outcome effectiveness. This is particularly important in an era where BUD levels have risen dramatically, user centred information systems development benefits are recognised as significant, and awareness of the risks of uncontrolled BUD activity is becoming more widespread. This research targets the measurement and prediction of BUD success factors and implementation effectiveness for particular business users. A questionnaire instrument and analysis technique has been tested and developed which constitutes a tool for predicting and monitoring BUD outcome effectiveness, and is based on the BUDES (Business User Development Effectiveness and Scope) research model - which is introduced and described in this thesis. The questionnaire instrument is designed for completion by 'business users' - the target community being more explicitly defined as 'people who primarily have a business role within an organisation'. The instrument, named BUD ESP (Business User Development Effectiveness and Scope Predictor), can readily be used with survey participants, and has been shown to give meaningful and representative results.

Trigger release liposome systems:local and remote controlled delivery?

Target-specific delivery has become an integral area of research in order to increase bioavailability and reduce the toxic effects of drugs. As a drug-delivery option, trigger-release liposomes offer sophisticated targeting and greater control-release capabilities. These are broadly divided into two categories; those that utilise the local environment of the target site where there may be an upregulation in certain enzymes or a change in pH and those liposomes that are triggered by an external physical stimulus such as heat, ultrasound or light. These release mechanisms offer a greater degree of control over when and where the drug is released; furthermore, targeting of diseased tissue is enhanced by incorporation of target-specific components such as antibodies. This review aims to show the development of such trigger release liposome systems and the current research in this field.

To what extent and in what manner do Chinese and Indian contract research organisation learn and upgrade with the unbundling the global pharmaceutical R&D value chain?

The paper applies the GVC framework to analyse the organisational and geographical reconfiguration of the global R&D function of leading US and European pharmaceutical MNCs. Though pharmaceutical MNCs have been outsourcing clinical trial activities since the mid-1990s, the outsourcing of discovery research tasks is a phenomenon of the 2000s (Ramirez 2013). Moreover, in the context of a crisis of R&D productivity and increasing pressure from shareholders, a number of US and European pharmaceutical MNCs are breaking up their R&D function in an attempt to increase flexibility and reduce risk as well as costs and are thereby restructuring the global architecture of their R&D function. This break-up, or unbundling (Sako 2006), of the R&D function is particularly interesting given the prevalence of market failure in innovation (Howells et al 2008), the non-modular nature of the R&D process in this industry (Pisano 2006) and the strategic important of this activity to the core competence and long-term competitive advantage of firms in this sector. The focus of this paper is on the outsourcing of R&D activities to Chinese and Indian independently-owned contract research organisations (CROs) and the way these firms are becoming integrated as service providers into the global R&D function (or R&D value chain) of pharmaceutical MNCs. Above all the paper is concerned with the development of capabilities of CROs from these two countries and the dynamics of upgrading in GVCs in knowledge-intensive functions. The paper therefore discusses the role of both knowledge flows within global pharmaceutical R&D value chains as well as national innovation systems on the development of capabilities of Chinese and Indian CROs. Our analysis is based on data from semi-structured interviews collected from senior R&D managers from a sample of ten US and European pharmaceutical MNCs and owners and senior R&D managers from five Chinese and five Indian CROs who are providing research services to MNCs in this industry. We discuss the emergence of R&D outsourcing in this industry and the nature and mechanisms of knowledge flows within R&D value chains. The embeddedness of CROS in the national innovation systems of their home countries is also discussed.

Next generation of recommender systems: Algorithms and applications

Personalized recommender systems aim to assist users in retrieving and accessing interesting items by automatically acquiring user preferences from the historical data and matching items with the preferences. In the last decade, recommendation services have gained great attention due to the problem of information overload. However, despite recent advances of personalization techniques, several critical issues in modern recommender systems have not been well studied. These issues include: (1) understanding the accessing patterns of users (i.e., how to effectively model users' accessing behaviors); (2) understanding the relations between users and other objects (i.e., how to comprehensively assess the complex correlations between users and entities in recommender systems); and (3) understanding the interest change of users (i.e., how to adaptively capture users' preference drift over time). To meet the needs of users in modern recommender systems, it is imperative to provide solutions to address the aforementioned issues and apply the solutions to real-world applications. ^ The major goal of this dissertation is to provide integrated recommendation approaches to tackle the challenges of the current generation of recommender systems. In particular, three user-oriented aspects of recommendation techniques were studied, including understanding accessing patterns, understanding complex relations and understanding temporal dynamics. To this end, we made three research contributions. First, we presented various personalized user profiling algorithms to capture click behaviors of users from both coarse- and fine-grained granularities; second, we proposed graph-based recommendation models to describe the complex correlations in a recommender system; third, we studied temporal recommendation approaches in order to capture the preference changes of users, by considering both long-term and short-term user profiles. In addition, a versatile recommendation framework was proposed, in which the proposed recommendation techniques were seamlessly integrated. Different evaluation criteria were implemented in this framework for evaluating recommendation techniques in real-world recommendation applications. ^ In summary, the frequent changes of user interests and item repository lead to a series of user-centric challenges that are not well addressed in the current generation of recommender systems. My work proposed reasonable solutions to these challenges and provided insights on how to address these challenges using a simple yet effective recommendation framework.^

Modelling nitrous oxide emissions from mown-grass and grain-cropping systems : Testing and sensitivity analysis of DailyDayCent using high frequency measurements

The lead author, Nimai Senapati (Post doc), was funded by the European community’s Seventh Framework programme (FP2012-2015) under grant agreement no. 262060 (ExpeER). The research leading to these results has received funding principally from the ANR (ANR-11-INBS-0001), AllEnvi, CNRS-INSU. We would like to thank the National Research Infrastructure ‘Agro-écosystèmes, Cycles Biogéochimique et Biodiversité (SOERE-ACBB http://www.soere-acbb.com/fr/) for their support in field experiment. We are deeply indebted to Christophe deBerranger, Xavier Charrier for their substantial technical assistance and Patricia Laville for her valuables suggestion regarding N2O flux estimation.

Essays on Energy Economics and Industrial Organization

The dissertation consists of three chapters related to the low-price guarantee marketing strategy and energy efficiency analysis. The low-price guarantee is a marketing strategy in which firms promise to charge consumers the lowest price among their competitors. Chapter 1 addresses the research question "Does a Low-Price Guarantee Induce Lower Prices'' by looking into the retail gasoline industry in Quebec where there was a major branded firm which started a low-price guarantee back in 1996. Chapter 2 does a consumer welfare analysis of low-price guarantees to drive police indications and offers a new explanation of the firms' incentives to adopt a low-price guarantee. Chapter 3 develops the energy performance indicators (EPIs) to measure energy efficiency of the manufacturing plants in pulp, paper and paperboard industry.

Chapter 1 revisits the traditional view that a low-price guarantee results in higher prices by facilitating collusion. Using accurate market definitions and station-level data from the retail gasoline industry in Quebec, I conducted a descriptive analysis based on stations and price zones to compare the price and sales movement before and after the guarantee was adopted. I find that, contrary to the traditional view, the stores that offered the guarantee significantly decreased their prices and increased their sales. I also build a difference-in-difference model to quantify the decrease in posted price of the stores that offered the guarantee to be 0.7 cents per liter. While this change is significant, I do not find the response in comeptitors' prices to be significant. The sales of the stores that offered the guarantee increased significantly while the competitors' sales decreased significantly. However, the significance vanishes if I use the station clustered standard errors. Comparing my observations and the predictions of different theories of modeling low-price guarantees, I conclude the empirical evidence here supports that the low-price guarantee is a simple commitment device and induces lower prices.

Chapter 2 conducts a consumer welfare analysis of low-price guarantees to address the antitrust concerns and potential regulations from the government; explains the firms' potential incentives to adopt a low-price guarantee. Using station-level data from the retail gasoline industry in Quebec, I estimated consumers' demand of gasoline by a structural model with spatial competition incorporating the low-price guarantee as a commitment device, which allows firms to pre-commit to charge the lowest price among their competitors. The counterfactual analysis under the Bertrand competition setting shows that the stores that offered the guarantee attracted a lot more consumers and decreased their posted price by 0.6 cents per liter. Although the matching stores suffered a decrease in profits from gasoline sales, they are incentivized to adopt the low-price guarantee to attract more consumers to visit the store likely increasing profits at attached convenience stores. Firms have strong incentives to adopt a low-price guarantee on the product that their consumers are most price-sensitive about, while earning a profit from the products that are not covered in the guarantee. I estimate that consumers earn about 0.3% more surplus when the low-price guarantee is in place, which suggests that the authorities should not be concerned and regulate low-price guarantees. In Appendix B, I also propose an empirical model to look into how low-price guarantees would change consumer search behavior and whether consumer search plays an important role in estimating consumer surplus accurately.

Chapter 3, joint with Gale Boyd, describes work with the pulp, paper, and paperboard (PP&PB) industry to provide a plant-level indicator of energy efficiency for facilities that produce various types of paper products in the United States. Organizations that implement strategic energy management programs undertake a set of activities that, if carried out properly, have the potential to deliver sustained energy savings. Energy performance benchmarking is a key activity of strategic energy management and one way to enable companies to set energy efficiency targets for manufacturing facilities. The opportunity to assess plant energy performance through a comparison with similar plants in its industry is a highly desirable and strategic method of benchmarking for industrial energy managers. However, access to energy performance data for conducting industry benchmarking is usually unavailable to most industrial energy managers. The U.S. Environmental Protection Agency (EPA), through its ENERGY STAR program, seeks to overcome this barrier through the development of manufacturing sector-based plant energy performance indicators (EPIs) that encourage U.S. industries to use energy more efficiently. In the development of the energy performance indicator tools, consideration is given to the role that performance-based indicators play in motivating change; the steps necessary for indicator development, from interacting with an industry in securing adequate data for the indicator; and actual application and use of an indicator when complete. How indicators are employed in EPA’s efforts to encourage industries to voluntarily improve their use of energy is discussed as well. The chapter describes the data and statistical methods used to construct the EPI for plants within selected segments of the pulp, paper, and paperboard industry: specifically pulp mills and integrated paper & paperboard mills. The individual equations are presented, as are the instructions for using those equations as implemented in an associated Microsoft Excel-based spreadsheet tool.

Commercial and Industrial Network Improvement and Programming Policy, Summary, 1991

The Commercial and Industrial Network improvement and programming policy reflected in this summary report was adopted for use in future highway programming by the Transportation Commission on November 5, 1991. The Iowa Department of Transportation, as directed by the Legislature, has established a 2,331-mile network of commercial and industrial highways and is directing a significant amount of primary construction funding resources toward improvements to this network. This summary outlines the technical needs assessment for improvements on the Commercial and Industrial Network for the next 20-year period. The portions of the network which require four-lane capacity, as well as major improvements to the two-lane sections, are graphically displayed. Detailed improvement needs and costs are listed in tabular form for the first two five-year periods (1992-1996 and 1997-2001). It is essential to note that these improvement needs are the result of a technical assessment and do not imply any funding commitment.

Influence of grinding operations on surface integrity and chloride induced stress corrosion cracking of stainless steels

Stainless steels were developed in the early 20th century and are used where both the mechanical properties of steels and corrosion resistance are required. There is continuous research to allow stainless steel components to be produced in a more economical way and be used in more harsh environments. A necessary component in this effort is to correlate the service performance with the production processes. The central theme of this thesis is the mechanical grinding process.  This is commonly used for producing stainless steel components, and results in varied surface properties that will strongly affect their service life. The influence of grinding parameters including abrasive grit size, machine power and grinding lubricant were studied for 304L austenitic stainless steel (Paper II) and 2304 duplex stainless steel (Paper I). Surface integrity was proved to vary significantly with different grinding parameters. Abrasive grit size was found to have the largest influence. Surface defects (deep grooves, smearing, adhesive/cold welding chips and indentations), a highly deformed surface layer up to a few microns in thickness and the generation of high level tensile residual stresses in the surface layer along the grinding direction were observed as the main types of damage when grinding stainless steels. A large degree of residual stress anisotropy is interpreted as being due to mechanical effects dominating over thermal effects. The effect of grinding on stress corrosion cracking behaviour of 304L austenitic stainless steel in a chloride environment was also investigated (Paper III). Depending on the surface conditions, the actual loading by four-point bend was found to deviate from the calculated value using the formula according to ASTM G39 by different amounts. Grinding-induced surface tensile residual stress was suggested as the main factor to cause micro-cracks initiation on the ground surfaces. Grinding along the loading direction was proved to increase the susceptibility to chloride-induced SCC, while grinding perpendicular to the loading direction improved SCC resistance. The knowledge obtained from this work can provide a reference for choosing appropriate grinding parameters when fabricating stainless steel components; and can also be used to help understanding the failure mechanism of ground stainless steel components during service.

HOG CHAINS AND MARK TWAINS: A STUDY OF LABOR HISTORY, ARCHAEOLOGY, AND INDUSTRIAL ETHNOGRAPHY OF THE STEAMBOAT ERA OF THE MONONGAHELA VALLEY 1811-1950

This dissertation examines a unique working class in the United States, the men and women who worked on the steamboats from the Industrial Revolution until the demise of steam-powered boats in the mid-20th century. The steamboat was the beginning of a technological system that was developed in America and used in such great numbers that it made the rapid population of the Trans-Appalachian West possible. The steamboat was forever romanticized by images of the antebellum South or the quick wit of Samuel Clemens and his sentimental book, Life on the Mississippi. The imagination swirls with thoughts of boats, bleach white, slowly churning the calm waters of some Spanish moss covered river. The reality of the boats and the experience of those who worked on them has been lost in this nostalgic vision. This research details the history of the western steamboat in the Monongahela Valley, the birthplace of the commercial steamboat industry. The first part of this dissertation examines the literature of authors in the field of labor history and Industrial Archaeology to place this work into the larger context of published literature. The second builds a framework for understanding the various eras that the steamboat went through both in terms of technological change, but also the change the workers experienced as their identity as a working class was being shaped. The third part details the excavations of two steamboat captains houses, those of Captain James Gormley and Captain Michael A. Cox. Both men represented a time in which the steamboat was in an era of transition. Excavations at their homes yield clues to their class status and how integrated they were in the local community. The fourth part of this study documents the oral histories of steamboat workers, both men and women, and their experience on the boats and on the river. Their rapidly declining population of those who lived and worked on the boats gives urgency for their lives to be documented. Finally, this study concludes with a synthesis of how worker identity solidified in the face of technological, socio-economic, and ideological change especially during their push for unionization and the introduction of the diesel towboat.

Waste Heat Recovery Systems: Numerical and Experimental Analysis of organic Rankine Cycle Solutions

This thesis aims to present the ORC technology, its advantages and related problems. In particular, it provides an analysis of ORC waste heat recovery system in different and innovative scenarios, focusing on cases from the biggest to the lowest scale. Both industrial and residential ORC applications are considered. In both applications, the installation of a subcritical and recuperated ORC system is examined. Moreover, heat recovery is considered in absence of an intermediate heat transfer circuit. This solution allow to improve the recovery efficiency, but requiring safety precautions. Possible integrations of ORC systems with renewable sources are also presented and investigated to improve the non-programmable source exploitation. In particular, the offshore oil and gas sector has been selected as a promising industrial large-scale ORC application. From the design of ORC systems coupled with Gas Turbines (GTs) as topper systems, the dynamic behavior of the GT+ORC innovative combined cycles has been analyzed by developing a dynamic model of all the considered components. The dynamic behavior is caused by integration with a wind farm. The electric and thermal aspects have been examined to identify the advantages related to the waste heat recovery system installation. Moreover, an experimental test rig has been realized to test the performance of a micro-scale ORC prototype. The prototype recovers heat from a low temperature water stream, available for instance in industrial or residential waste heat. In the test bench, various sensors have been installed, an acquisitions system developed in Labview environment to completely analyze the ORC behavior. Data collected in real time and corresponding to the system dynamic behavior have been used to evaluate the system performance based on selected indexes. Moreover, various operational steady-state conditions are identified and operation maps are realized for a completely characterization of the system and to detect the optimal operating conditions.

Supporting Scientific Research Through Machine and Deep Learning: Fluorescence Microscopy and Operational Intelligence Use Cases

Although the debate of what data science is has a long history and has not reached a complete consensus yet, Data Science can be summarized as the process of learning from data. Guided by the above vision, this thesis presents two independent data science projects developed in the scope of multidisciplinary applied research. The first part analyzes fluorescence microscopy images typically produced in life science experiments, where the objective is to count how many marked neuronal cells are present in each image. Aiming to automate the task for supporting research in the area, we propose a neural network architecture tuned specifically for this use case, cell ResUnet (c-ResUnet), and discuss the impact of alternative training strategies in overcoming particular challenges of our data. The approach provides good results in terms of both detection and counting, showing performance comparable to the interpretation of human operators. As a meaningful addition, we release the pre-trained model and the Fluorescent Neuronal Cells dataset collecting pixel-level annotations of where neuronal cells are located. In this way, we hope to help future research in the area and foster innovative methodologies for tackling similar problems. The second part deals with the problem of distributed data management in the context of LHC experiments, with a focus on supporting ATLAS operations concerning data transfer failures. In particular, we analyze error messages produced by failed transfers and propose a Machine Learning pipeline that leverages the word2vec language model and K-means clustering. This provides groups of similar errors that are presented to human operators as suggestions of potential issues to investigate. The approach is demonstrated on one full day of data, showing promising ability in understanding the message content and providing meaningful groupings, in line with previously reported incidents by human operators.

Understanding, defining and assessing food systems’ social and economic sustainability indicators: implementation of mixed methodologies for policy insights

Sustainability encompasses the presence of three dimensions that must coexist simultaneously, namely the environmental, social, and economic ones. The economic and social dimensions are gaining the spotlight in recent years, especially within food systems. To assess social and economic impacts, indicators and tools play a fundamental role in contributing to the achievements of sustainability targets, although few of them have deepen the focus on social and economic impacts. Moreover, in a framework of citizen science and bottom-up approach for improving food systems, citizen play a key role in defying their priorities in terms of social and economic interventions. This research expands the knowledge of social and economic sustainability indicators within the food systems for robust policy insights and interventions. This work accomplishes the following objectives: 1) to define social and economic indicators within the supply chain with a stakeholder perspective, 2) to test social and economic sustainability indicators for future food systems engaging young generations. The first objective was accomplished through the development of a systematic literature review of 34 social sustainability tools, based on five food supply chain stages, namely production, processing, wholesale, retail, and consumer considering farmers, workers, consumers, and society as stakeholders. The second objective was achieved by defining and testing new food systems social and economic sustainability indicators through youth engagement for informed and robust policy insights, to provide policymakers suggestions that would incorporate young generations ones. Future food systems scenarios were evaluated by youth through focus groups, whose results were analyzed through NVivo and then through a survey with a wider platform. Conclusion addressed the main areas of policy interventions in terms of social and economic aspects of sustainable food systems youth pointed out as in need of interventions, spanning from food labelling reporting sustainable origins to better access to online food services.

Governing the water conservation in the Urmia Lake Basin: addressing macro systems’ fit and micro users’ behavior

To change unadapted water governing systems, and water users’ traditional conducts in line with climate change, understanding of systems’ structures and users’ behaviors is necessary. To this aim, comprehensive and pragmatic research was designed and implemented in the Urmia Lake Basin where due to the severe droughts, and human-made influences, especially through the agricultural development, the lake has been shrunken drastically. To analyze the water governance and conservation issues in the basin, an innovative framework was developed based on mathematical physics concepts and pro-environmental behavior theories. Accordingly, in system level (macro/meso), the problem of fit of the early-shaped water governing system associating with the function of “political-security” and “political-economic” factors in the basin was identified through mean-field models. Furthermore, the effect of a “political-environmental” factor, the Urmia Lake Restoration Program (ULRP), on reforming the system structure and hence its fit was assessed. The analysis results revealed that by revising the provincial boundaries (horizontal alternation) for the entity of Kurdistan province to permit that interact with the headquarter of West Azerbaijan province for its water demand-supply initiatives, the system fit can increase. Also, the constitution of the ULRP (vertical arrangement) not only could increase the structural fit of the water governing system to the basin, but also significantly could enhance the system fit through its water-saving policy. Besides, in individual level (micro), the governing factors of water conservation behavior of the major users/farmers were identified through rational and moral socio-psychological models. In rational approach, incorporating PMT and TPB, the SEM results demonstrated that “Perceived Vulnerability”, “Self-Efficacy”, “Response Efficacy”, “Response Cost”, “Subjective Norms” and “Institutional Trust” significantly affect the water-saving intention/behavior. Likewise, NAM based analysis as a moral approach, uncovered the significant effects of “Awareness of Consequences”, “Appraisal of Responsibility”, “Personal Norms” as well as “Place Attachment” and “Emotions” on water-saving intention.