Improvement of in silico strain engineering methods in Saccharomyces cerevisiae

PhD thesis in Bioengineering

Ashbya gossypii beyond industrial riboflavin production: a historical perspective and emerging biotechnological applications

The filamentous fungus Ashbya gossypii has been safely and successfully used for more than two decades in the commercial production of riboflavin (vitamin B2). Its industrial relevance combined with its high genetic similarity with Saccharomyces cerevisiae together promoted the accumulation of fundamental knowledge that has been efficiently converted into a significant molecular and in silico toolbox for its genetic engineering. This synergy has enabled a directed and sustained exploitation of A. gossypii as an industrial riboflavin producer. Although there is still room for optimizing riboflavin production, the recent years have seen an abundant advance in the exploration of A. gossypii for other biotechnological applications, such as the production of recombinant proteins, single cell oil and flavour compounds. Here, we will address the biotechnological potential of A. gossypii beyond riboflavin production by presenting (a) a physiological and metabolic perspective over this fungus; (b) the molecular toolbox available for its manipulation; and (c) commercial and emerging biotechnological applications for this industrially important fungus, together with the approaches adopted for its engineering.

In vitro mechanical fatigue behavior of poly-ε-caprolactone macroporous scaffolds for cartilage tissue engineering: Influence of pore filling by a poly(vinyl alcohol) gel

Polymeric scaffolds used in regenerative therapies are implanted in the damaged tissue and subjected to repeated loading cycles. In the case of articular cartilage engineering, an implanted scaffold is typically subjected to long term dynamic compression. The evolution of the mechanical properties of the scaffold during bioresorption has been deeply studied in the past, but the possibility of failure due to mechanical fatigue has not been properly addressed. Nevertheless, the macroporous scaffold is susceptible to failure after repeated loading-unloading cycles. In this work fatigue studies of polycaprolactone scaffolds were carried by subjecting the scaffold to repeated compression cycles in conditions simulating the scaffold implanted in the articular cartilage. The behaviour of the polycaprolactone sponge with the pores filled with a poly(vinyl alcohol) gel simulating the new formed tissue within the pores was compared with that of the material immersed in water. Results were analyzed with Morrow’s criteria for failure and accurate fittings are obtained just up to 200 loading cycles. It is also shown that the presence of poly(vinyl alcohol) increases the elastic modulus of the scaffolds, the effect being more pronounced with increasing the number of freeze/thawing cycles.

Development of a model for occupational risk acceptance criteria definition in industrial settings

Doctoral Dissertation for PhD degree in Industrial and Systems Engineering

Upgrade of an industrial building: BIM model of the as-built situation and evaluation of modifications

Dissertação de mestrado integrado in Civil Engineering

Evaluation of work-related volatile organic compounds (VOCs) exposition in automotive painting cabins industrial cleanings

Automotive painting cabins are cleaned with several solvents, being great part of them mixtures of volatile organic compounds (VOCs), where the three xylene isomers are the most important constituents. To evaluate the work-related exposition of the cleaners that use these mixtures of solvents, xylenes have been determined in the working ambient air as well as its metabolite, o-m-p-methyl hippuric acid, has been analysed in urine to establish the dermal and respiratory exposition. This evaluation has been done in order to assess the occupational exposure to VOCs and to know the working conditions of the cleaners, but also to evaluate the effectiveness of personal protective equipment (PPE), the engineering control and the work practices.The xylenes have been chosen as indicators of exposition because they are the main components in the cleaning solvents used, with a level of concentration between 50% and 85%.The Xylenes have an occupational exposure limit (8 h TWA) of 50 ppm (221 mg/m3) and a short-term exposure limit (STEL) of 100 ppm (442 mg/m3). On the other hand, the biological exposure index (BEI) for xylenes is the sum of the total methyl hippuric acids in urine at the end of the work-shift, being the value 1500 mg/g creatinine.

Theimpact of industry collaboration on research: Evidence from engineering academics in the UK

We study the impact of university-industry research collaborations on academicoutput, in terms of productivity and direction of research. We report findings froma longitudinal dataset on all the researchers from the engineering departments inthe UK in the last 20 years. We control for the endogeneity caused by the dynamicnature of research and the existence of reverse causality. Our results indicate thatresearchers with industrial links publish significantly more. Productivity, though,is higher for low levels of industry involvement. Moreover, growing ties with theindustry skew research towards a more applied approach.

Three essays on major trends in a slow clockspeed industry : the case of industrial automation

The motivation for this research initiated from the abrupt rise and fall of minicomputers which were initially used both for industrial automation and business applications due to their significantly lower cost than their predecessors, the mainframes. Later industrial automation developed its own vertically integrated hardware and software to address the application needs of uninterrupted operations, real-time control and resilience to harsh environmental conditions. This has led to the creation of an independent industry, namely industrial automation used in PLC, DCS, SCADA and robot control systems. This industry employs today over 200'000 people in a profitable slow clockspeed context in contrast to the two mainstream computing industries of information technology (IT) focused on business applications and telecommunications focused on communications networks and hand-held devices. Already in 1990s it was foreseen that IT and communication would merge into one Information and communication industry (ICT). The fundamental question of the thesis is: Could industrial automation leverage a common technology platform with the newly formed ICT industry? Computer systems dominated by complex instruction set computers (CISC) were challenged during 1990s with higher performance reduced instruction set computers (RISC). RISC started to evolve parallel to the constant advancement of Moore's law. These developments created the high performance and low energy consumption System-on-Chip architecture (SoC). Unlike to the CISC processors RISC processor architecture is a separate industry from the RISC chip manufacturing industry. It also has several hardware independent software platforms consisting of integrated operating system, development environment, user interface and application market which enables customers to have more choices due to hardware independent real time capable software applications. An architecture disruption merged and the smartphone and tablet market were formed with new rules and new key players in the ICT industry. Today there are more RISC computer systems running Linux (or other Unix variants) than any other computer system. The astonishing rise of SoC based technologies and related software platforms in smartphones created in unit terms the largest installed base ever seen in the history of computers and is now being further extended by tablets. An underlying additional element of this transition is the increasing role of open source technologies both in software and hardware. This has driven the microprocessor based personal computer industry with few dominating closed operating system platforms into a steep decline. A significant factor in this process has been the separation of processor architecture and processor chip production and operating systems and application development platforms merger into integrated software platforms with proprietary application markets. Furthermore the pay-by-click marketing has changed the way applications development is compensated: Three essays on major trends in a slow clockspeed industry: The case of industrial automation 2014 freeware, ad based or licensed - all at a lower price and used by a wider customer base than ever before. Moreover, the concept of software maintenance contract is very remote in the app world. However, as a slow clockspeed industry, industrial automation has remained intact during the disruptions based on SoC and related software platforms in the ICT industries. Industrial automation incumbents continue to supply systems based on vertically integrated systems consisting of proprietary software and proprietary mainly microprocessor based hardware. They enjoy admirable profitability levels on a very narrow customer base due to strong technology-enabled customer lock-in and customers' high risk leverage as their production is dependent on fault-free operation of the industrial automation systems. When will this balance of power be disrupted? The thesis suggests how industrial automation could join the mainstream ICT industry and create an information, communication and automation (ICAT) industry. Lately the Internet of Things (loT) and weightless networks, a new standard leveraging frequency channels earlier occupied by TV broadcasting, have gradually started to change the rigid world of Machine to Machine (M2M) interaction. It is foreseeable that enough momentum will be created that the industrial automation market will in due course face an architecture disruption empowered by these new trends. This thesis examines the current state of industrial automation subject to the competition between the incumbents firstly through a research on cost competitiveness efforts in captive outsourcing of engineering, research and development and secondly researching process re- engineering in the case of complex system global software support. Thirdly we investigate the industry actors', namely customers, incumbents and newcomers, views on the future direction of industrial automation and conclude with our assessments of the possible routes industrial automation could advance taking into account the looming rise of the Internet of Things (loT) and weightless networks. Industrial automation is an industry dominated by a handful of global players each of them focusing on maintaining their own proprietary solutions. The rise of de facto standards like IBM PC, Unix and Linux and SoC leveraged by IBM, Compaq, Dell, HP, ARM, Apple, Google, Samsung and others have created new markets of personal computers, smartphone and tablets and will eventually also impact industrial automation through game changing commoditization and related control point and business model changes. This trend will inevitably continue, but the transition to a commoditized industrial automation will not happen in the near future.

Introducing Basic Systematic Requirements Engineering Practices in Small Organizations with an Easy to Adopt Method

Requirements-relatedissues have been found the third most important risk factor in software projects and as the biggest reason for software project failures. This is not a surprise since; requirements engineering (RE) practices have been reported deficient inmore than 75% of all; enterprises. A problem analysis on small and low maturitysoftware organizations revealed two; central reasons for not starting process improvement efforts: lack of resources and uncertainty; about process improvementeffort paybacks.; In the constructive part of the study a basic RE method, BaRE, was developed to provide an; easy to adopt way to introduce basic systematic RE practices in small and low maturity; organizations. Based on diffusion of innovations literature, thirteen desirable characteristics; were identified for the solution and the method was implemented in five key components:; requirements document template, requirements development practices, requirements; management practices, tool support for requirements management, and training.; The empirical evaluation of the BaRE method was conducted in three industrial case studies. In; this evaluation, two companies established a completely new RE infrastructure following the; suggested practices while the third company conducted continued requirements document; template development based on the provided template and used it extensively in practice. The; real benefits of the adoption of the method were visible in the companies in four to six months; from the start of the evaluation project, and the two small companies in the project completed; their improvement efforts with an input equal to about one person month. The collected dataon; the case studies indicates that the companies implemented new practices with little adaptations; and little effort. Thus it can be concluded that the constructed BaRE method is indeed easy to; adopt and it can help introduce basic systematic RE practices in small organizations.

Application Architecture Design for an Industrial Service Company

Työssä oli tavoitteena suunnitella globaali sovellusarkkitehtuuri, joka ohjaa teollisen huoltoyrityksen sovellusten kehitystyötä. Sovellusarkkitehtuuri kuvaa tietokoneohjelmien toiminnallisuuteen loppukäyttäjien näkökulmasta ja sen laatiminen on osa strategista tietojärjestelmäsuunnittelua. Arkkitehtuurin tehtävänä on varmistaa, että tietojärjestelmät suunnitellaan kokonaisuutena tukemaan organisaation toimintaa. Arkkitehtuurin tekemistä ohjasi strategisen tietojärjestelmäsuunnittelun periatteet ja mallit. Tekniikat olivat samoja kuin projektikohtaisessa tietojärjestelmäsuunnittelussa. Sovellusarkkitehtuurin tekeminen alkoi tutustumalla yrityksessä vallitsevaan tilanteeseen sekä liiketoiminta- ja tietotekniikkastrategioihin. Tarkastelun kohteena olivat pääasiassa liiketoimintaprosessit ja käytössä olevat sovellukset. Tutustuminen tapahtui lähinnä haastatteluin ja dokumentteihin tutustumalla. Seuraavaksi johdettiin vaatimukset tulevaisuuden sovelluksille haastatteluista ja edellisen vaiheen materiaalin perusteella. Liiketoiminnan kannalta tärkeimmät vaatimukset valittiin täytettäväksi arkkitehtuurilla. Varsinaisen arkitehtuurin tekeminen oli lähinnä sovellusten valitsemisesta ja niiden keskinäisten suhteiden määrittelyä. Arkkitehtuurin perusteella määritettiin kehityshankeet.

Industrial emissions abatement: Untangling the impact of the EU ETS and the economic crisis

In this study we use historical emission data from installations under the European Union Emissions Trading System, -EU ETS- to evaluate the impact of this policy on industrial greenhouse gas emissions during the first two trading phases, 2005-2012. As such the analysis seeks to disentangle two causes of emission abatement: that attributable to the EU ETS and that attributable to the economic crisis that hit the EU in 2008/09. Using a panel data approach the estimated emissions reduction attributable to the EU ETS is about 21 per cent of the total emission abatement during the observation period. These results suggest therefore that the lion’s share of abatement was attributable to the effects of the economic crisis, a finding that has serious implications for future policy adjustments affecting core elements of the EU ETS, including the distribution of EU emission allowances.

Competitive flexibility in systems supplier companies in mechanical engineering industry

Systems suppliers are focal actors in mechanical engineering supply chains, in between general contractors and component suppliers. This research concentrates on the systems suppliers’ competitive flexibility, as a competitive advantage that the systems supplier gains from independence from the competitive forces of the market. The aim is to study the roles that power, dependence relations, social capital, and interorganizational learning have on the competitive flexibility. Research on this particular theme is scarce thus far. The research method applied here is the inductive multiple case study. Interviews from four case companies were used as main source of the qualitative data. The literature review presents previous literature on subcontracting, supply chain flexibility, supply chain relationships, social capital and interorganizational learning. The result of this study are seven propositions and consequently a model on the effects that the dominance of sales of few customers, power of competitors, significance of the manufactured system in the end product, professionalism in procurement and the significance of brand products in the business have on the competitive flexibility. These relationships are moderated by either social capital or interorganizational learning. The main results obtained from this study revolve around social capital and interorganizational learning, which have beneficial effects on systems suppliers’ competitive flexibility, by moderating the effects of other constructs of the model. Further research on this topic should include quantitative research to provide the extent to which the results can be reliably generalized. Also each construct of the model gives possible focus for more thorough research.

Quitosana: biopolímero funcional com potencial industrial biomédico

The importance of chitosan has grown significantly over the last two decades due to its renewable and biodegradable source, and also because of the recent increase in the knowledge of its functionality in the technological and biomedical applications. The present article reviews the biopolymer chitosan and its derivatives as versatile biomaterials for potential drug delivery systems, as well as tissue engineering applications, analgesia and treatment of arthritis.

Industrial solid waste (whitewash mud) use in forest road pavements

The objective of the present study was to evaluate the effects of industrial solid waste (whitewash mud) on geotechnical properties considering the following engineering parameters: California Bearing Ratio (CBR), Atterberg limits and Permeability test. Seven soil samples derived from Alagoinhas, Bahia - Brazil, were classified by the Transportation Research Board (TRB) system. Two were selected as having a great geotecnical potential classified as A-3 (0) and A-2-4 (0), whitewash mud contents 10%, 15%, 20% and 25% dry weight and medium compaction effort were studied in the laboratory testing program. The results indicated the soil denominated good gravel as being the most promising one, when stabilized with whitewash mud, reaching the best results with the dosage of 20 and 25% of whitewash mud.

Integration in project business : mechanisms for integrating customers and the project network during the life-cycle of industrial projects

This thesis focuses on integration in project business, i.e. how projectbased companies organize their product and process structures when they deliver industrial solutions to their customers. The customers that invest in these solutions run their businesses in different geographical, political and economical environments, which should be acknowledged by the supplier when providing solutions comprising of larger and more complex scopes than previously supplied to these customers. This means that the suppliers are increasing their supply range by taking over some of the activities in the value chain that have traditionally been handled by the customer. In order to be able to provide the functioning solutions, including more engineering hours, technical equipment and a wider project network, a change is needed in the mindset in order to be able to carry out and take the required responsibility that these new approaches bring. For the supplier it is important to be able to integrate technical products, systems and services, but the supplier also needs to have the capabilities to integrate the cross-functional organizations and departments in the project network, the knowledge and information between and within these organizations and departments, along with inputs from the customer into the product and process structures during the lifecycle of the project under development. Hence, the main objective of this thesis is to explore the challenges of integration that industrial projects meet, and based on that, to suggest a concept of how to manage integration in project business by making use of integration mechanisms. Integration is considered the essential process for accomplishing an industrial project, whereas the accomplishment of the industrial project is considered to be the result of the integration. The thesis consists of an extended summary and four papers, that are based on three studies in which integration mechanisms for value creation in industrial project networks and the management of integration in project business have been explored. The research is based on an inductive approach where in particular the design, commissioning and operations functions of industrial projects have been studied, addressing entire project life-cycles. The studies have been conducted in the shipbuilding and power generation industries where the scopes of supply consist of stand-alone equipment, equipment and engineering, and turnkey solutions. These industrial solutions include demanding efforts in engineering and organization. Addressing the calls for more studies on the evolving value chains of integrated solutions, mechanisms for inter- and intra-organizational integration and subsequent value creation in project networks have been explored. The research results in thirteen integration mechanisms and a typology for integration is proposed. Managing integration consists of integrating the project network (the supplier and the sub-suppliers) and the customer (the customer’s business purpose, operations environment and the end-user) into the project by making use of integration mechanisms. The findings bring new insight into research on industrial project business by proposing integration of technology and engineering related elements with elements related to customer oriented business performance in contemporary project environments. Thirteen mechanisms for combining products and the processes needed to deliver projects are described and categorized according to the impact that they have on the management of knowledge and information. These mechanisms directly relate to the performance of the supplier, and consequently to the functioning of the solution that the project provides. This thesis offers ways to promote integration of knowledge and information during the lifecycle of industrial projects, enhancing the development towards innovative solutions in project business.