The role of electron transfer in DNA building blocks: evaluation of strand breaks and their implications

Dissertação para obtenção do Grau de Doutor em Engenharia Física

Late-medieval construction site management at the Monastery of Jerónimos in Lisbon

Through the analysis of the exceptional accounting documents of 1517 related to the construction of the Monastery of Jerónimos (Lisbon), this paper discusses the main characteristics of a new model of construction site organization. In the later Middle Ages we can find, among others, two main models of constructing site organization. One, older and more widespread, consisted in a centralized and pyramidal management model. The other, apparently more recent, was based in the existence of several autonomous teams working simultaneously, each one responsible for building a specific part or section of the building. This paper describes and discusses this new organizational model as it was adopted and implemented by João de Castilho (1470–1552) for the construction of the Monastery of Jerónimos in 1517, probably for the first time in Portugal, but with some parallels in other places in Europe.

IEA EBC Annex56 vision for cost effective energy and carbon emissions optimization in building renovation

Building sector has become an important target for carbon emissions reduction, energy consumption and resources depletion. Due to low rates of replacement of the existing buildings, their low energy performances are a major concern. Most of the current regulations are focused on new buildings and do not account with the several technical, functional and economic constraints that have to be faced in the renovation of existing buildings. Thus, a new methodology is proposed to be used in the decision making process for energy related building renovation, allowing finding a cost-effective balance between energy consumption, carbon emissions and overall added value.

An analysis of the use of photogrammetric sorting to audit construction and demolition waste production on site

This study analyses the area of construction and demolition waste (C & D W) auditing. The production of C&DW has grown year after year since the Environmental Protection Agency (EPA) first published a report in 1996 which provided data for C&D W quantities for 1995 (EPA, 1996a). The most recent report produced by the EPA is based on data for 2005 (EPA, 2006). This report estimated that the quantity of C&DW produced for that period to be 14 931 486 tonnes. However, this is a ‘data update’ report containing an update on certain waste statistics so any total provided would not be a true reflection of the waste produced for that period. This illustrates that a more construction site-specific form of data is required. The Department of Building and Civil Engineering in the Galway-Mayo Institute of Technology have carried out two recent research projects (Grimes, 2005; Kelly, 2006) in this area, which have produced waste production indicators based on site-specific data. This involved the design and testing of an original auditing tool based on visual characterisation and the application of conversion factors. One of the main recommendations of these studies was to compare this visual characterisation approach with a photogrammetric sorting methodology. This study investigates the application of photogrammetric sorting on a residential construction site in the Galway region. A visual characterisation study is also carried out on the same project to compare the two methodologies and assess the practical application in a construction site environment. Data collected from the waste management contractor on site was also used to provide further evaluation. From this, a set of waste production indicators for new residential construction was produced: □ 50.8 kg/m2 for new residential construction using data provided by the visual characterisation method and the Landfill Levy conversion factors. □ 43 kg/m2 for new residential construction using data provided by the photogrammetric sorting method and the Landfill Levy conversion factors. □ 23.8 kg/m2 for new residential construction using data provided by Waste Management Contractor (WMC). The acquisition of the data from the waste management contractor was a key element for testing of the information produced by the visual characterisation and photogrammetric sorting methods. The actual weight provided by the waste management contractor shows a significant difference between the quantities provided.

Nest site selection by Hypsiboas faber(Anura, Hylidae) in Southern Brazil

ABSTRACT Male gladiator frogs of Hypsiboas Wagler, 1830 build nests on available substrate surrounding ponds and streams where female spawn eggs during the breeding period. Although gladiator frogs seem to show plasticity in the way they construct their nests, there is no study reporting if these species present preferences about microhabitat conditions for nest-building (mainly under subtropical climate). Predation pressure and environmental conditions have been considered major processes shaping the great diversity of reproductive strategies performed by amphibians, but microhabitat conditions should explain where to build a nest as well as how nest looks. This study aimed to test nest site selection for nest-building by Hypsiboas faber(Wied-Neuwied, 1821), determining which factors are related to nest site selection and nest features. The survey was conducted at margins of two permanent ponds in Southern Brazil. Habitat factors were evaluated in 18 plots with nest and 18 plots in the surrounding without nest (control), describing vegetation structure and heterogeneity, and substrate characteristics. Water temperature was measured inside the nest and in its adjacency. Nest features assessed were area, depth and temperature. Habitat characteristics differed between plots with and without nest. Microhabitat selected for nest-building was characterized by great vegetation cover and height, as well as shallower water and lower cover of organic matter in suspension than in plots without nest. Differences between temperature inside nest and in its adjacency were not observed. No relationship between nest features and habitat descriptors was evidenced. Results revealed that Hypsiboas faber does not build nests anywhere. Males seem to prefer more protected habitats, probably avoiding predation, invasion of conspecific males and inclement weather. Lack of differences between temperature inside- and outside-nest suggest that nest do not improve this condition for eggs and tadpole development. Nest architecture was not related to habitat characteristics, which may be determined by other factors, as nest checking by females before amplexus. Nest site selection should increase offspring survival as well the breeding success of Hypsiboas faber.

Management of major accidents with on-site 144 dispatcher

Introduction: An excellent coordination between firefighters, policemen and medical rescue is the key to success in the management of major accidents. In order to improve and assist the medical teams engaged on site, the Swiss "medical command and control system" for rescue operations is based on a binomial set up involving one head emergency doctor and one head rescue paramedic, both trained in disaster medicine. We have recently experimented an innovative on-site "medical command and control system", based on the binomial team, supported by a dedicated 144 dispatcher. Methods: A major road traffic accident took place on the highway between Lausanne and Vevey on April 9th 2008. We have retrospectively collected all data concerning the victims as well as the logistics and dedicated structures, reported by the 144, the Hospitals, the Authority of the State and the Police and Fire Departments. Results: The 72-car pileup caused one death and 26 slightly injured patients. The management on the accident site was organized around a tripartite system, gathering together the medical command and control team with the police and fire departments. On the medical side, 16 ambulances, 2 medical response teams (SMUR), the Rega crew and the medical command and control team were dispatched by the 144. On that occasion an advanced medical command car equipped with communication devices and staffed with a 144 dispatcher was also engaged, allowing efficient medical regulation directly from the site. Discussion: The specific skills of one doctor and one paramedic both trained for disaster's management proved to be perfectly complementary. The presence of a dispatcher on site with a medical command car also proved to be useful, improving orders transmission from the medical command team to all other on- and off-site partners. It relieved the need of repeated back-and-forth communication with the 144, allowing both paramedic and doctor to focus on strategy and tactics rather than communication and logistics.

Building high technology complete products for the markets of humanitarian organizations and developing countries

Tämä tutkielma käsittelee high-tech kokonaisratkaisun rakentamista kehitysmaiden ja humanitääristen organisaatioiden markkinoille. Tavoitteena on löytää ne komponentit joita case-yritys Mediburner Ltd:n polttouuni tarvitsee rinnalleen. Jotta täydentävien elementtien määritteleminen olisi mahdollista, pitää ensin selvittää keitä ovat asiakkaat, ja mitkä ovat heidän tarpeensa. Tutkimusmetodina käytetään kuvailevaa case-tutkimusta. Empiirinen materiaali kerättiin henkilökohtaisissa- ja puhelinkeskusteluissa. Niihin henkilöihin, joiden tavoittaminen oli aikaeron vuoksi hankalaa, otettiin yhteyttä sähköpostitse. Toinen tietolähde olivat dokumentit. Tutkielmassa käytettiin internetsivuja, sairaalajätehuoltoon liittyvien kansainvälisten konferenssien ja kenttätutkimusten raportteja sekä humanitääristen organisaatioiden suosituksia ja lehdistötiedotteita. Tulokseksi saatiin kymmenen tarvittavaa tukevien elementtien ryhmää: lisälaitteet, astiat jätteen keräilyyn ja tilapäiseen varastointiin, polttoaine, sähkö, logistiset ratkaisut, asennus ja käyttöönotto, huolto- ja korjauspalvelut, koulutus, help-desk –palvelu ja rahoitus. Lisäksi tarvitaan imago, joka konkretisoi tarjotun ratkaisun hyödyt. Yksi toimivan imagotyylin perusta voisi olla vastuullisuus.

Building wood debris piles benefits avian seed dispersers in burned and logged Mediterranean pine forests

Salvage logging is a common practice carried out in burned forests worldwide, and intended to mitigate the economic losses caused by wildfires. Logging implies an additional disturbance occurring shortly after fire, although its ecological effects can be somewhat mitigated by leaving wood debris on site. The composition of the bird community and its capacity to provide ecosystem services such as seed dispersal offleshy-fruited plants have been shown to be affected by postfire logging. We assessedthe effects of the habitat structure resulting from different postfire management practices on the bird community, in three burned pine forests in Catalonia (western Mediterranean). For this purpose, we focused on the group of species that is responsible for seed dispersal, a process which takes place primarily during the winter in theMediterranean basin. In addition, we assessed microhabitat selection by seed disperser birds in such environments in relation to management practices. Our results showed a significant, positive relationship between the density of wood debris piles and the abundance of seed disperser birds. Furthermore, such piles were the preferredmicrohabitat of these species. This reveals an important effect of forest management on seed disperser birds, which is likely to affect the dynamics of bird-dependent seed dispersal. Thus, building wood debris piles can be a useful practice for the conservation of both the species and their ecosystem services, while also being compatible with timber harvesting

An analytic approach to distribution logistics strategic management

Logistics management is increasingly being recognised by many companies to be of critical concern. The logistics function includes directly or indirectly many of the new areas for achieving or maintaining competitive advantage that companies have been forced to develop due to increasing competitive pressures. The key to achieving a competitive advantage is to manage the logistics function strategically which involves determining the most cost effective method of providing the necessary customer service levels from the many combinations of operating procedures in the areas of transportation, warehousing, order processing and information systems, production, and inventory management. In this thesis, a comprehensive distribution logistics strategic management process is formed by integrating the periodic strategic planning process with a continuous strategic issues management process. Strategic planning is used for defining the basic objectives for a company and assuring co operation and synergy between the different functions of a company while strategic issues management is used on a continuous basis in order to deal with environmental and internal turbulence. The strategic planning subprocess consists of the following main phases: (1) situational analyses, (2) defining the vision and strategic goals for the logistics function, (3) determining objectives and strategies, (4) drawing up tactical action plans, and (5) evaluating the implementation of the plans and making the needed adjustments. The aim of the strategic issues management subprocess is to continuously scan the environment and the organisation for early identification of the issues having a significant impact on the logistics function using the following steps: (1) the identification of trends, (2) assessing the impact and urgency of the identified trends, (3) assigning priorities to the issues, and (4) planning responses to the, issues. The Analytic Hierarchy Process (AHP) is a systematic procedure for structuring any problem. AHP is based on the following three principles: decomposition, comparative judgements, and synthesis of priorities. AHP starts by decomposing a complex, multicriteria problem into a hierarchy where each level consists of a few manageable elements which are then decomposed into another set of elements. The second step is to use a measurement methodology to establish priorities among the elements within each level of the hierarchy. The third step in using AHP is to synthesise the priorities of the elements to establish the overall priorities for the decision alternatives. In this thesis, decision support systems are developed for different areas of distribution logistics strategic management by applying the Analytic Hierarchy Process. The areas covered are: (1) logistics strategic issues management, (2) planning of logistic structure, (3) warehouse site selection, (4) inventory forecasting, (5) defining logistic action and development plans, (6) choosing a distribution logistics strategy, (7) analysing and selecting transport service providers, (8) defining the logistic vision and strategic goals, (9) benchmarking logistic performance, and (10) logistic service management. The thesis demonstrates the potential of AHP as a systematic and analytic approach to distribution logistics strategic management.

Defining the location factors of new manufacturing site in chemical industry

The objective of this thesis is to examine the factors that have an impact on the location decision of new manufacturing site and to create the relative order of importance of these factors by analytic hierarchy process (AHP). The decision making process especially related to the location selection and the measurement of the location factors are also examined. In theoretical part the character of decision making process and the relevant methods are introduced. Based on the previous studies of other researchers, the location factors are examined and the main research method, analytic hierarchy process, is also introduced. The empirical part of the study mainly follows the phases of decision making process and is emphasized on the main stages of analytic hierarchy process; building the hierarchy, defining the priorities and analyzing the results. The hierarchy is constructed from seven main criteria which all have several sub criteria. The evaluation of the hierarchy is implemented at the group decision making –laboratory and there can be seen significant differences between the importance of criteria. The final stage in the study is to create the appropriate measurement scales to the chosen criteria.

Networks and partnerships in third party logistics service production

Third party logistics, and third party logistics providers and the services they offer have grown substantially in the last twenty years. Even though there has been extensive research on third party logistics providers, and regular industry reviews within the logistics industry, a closer research in the area of partner selection and network models in the third party logistics industry is missing. The perspective taken in this study was of expanding the network research into logistics service providers as the focal firm in the network. The purpose of the study is to analyze partnerships and networks in the third party logistics industry in order to define how networks are utilized in third party logistics markets, what have been the reasons for the partnerships, and whether there are benefits for the third party logistics provider that can be achieved through building networks and partnerships. The theoretical framework of this study was formed based on common theories in studying networks and partnerships in accordance with models of horizontal and vertical partnerships. The theories applied to the framework and context of this study included the strategic network view and the resource-based view. Applying these two network theories to the position and networks of third party logistics providers in an industrial supply chain, a theoretical model for analyzing the horizontal and vertical partnerships where the TPL provider is in focus was structured. The empirical analysis of TPL partnerships consisted of a qualitative document analysis of 33 partnership examples involving companies present in the Finnish TPL markets. For the research, existing documents providing secondary data on types of partnerships, reasons for the partnerships, and outcomes of the partnerships were searched from available online sources. Findings of the study revealed that third party logistics providers are evident in horizontal and vertical interactions varying in geographical coverage and the depth and nature of the relationship. Partnership decisions were found to be made on resource based reasons, as well as from strategic aspects. The discovered results of the partnerships in this study included cost reduction and effectiveness in the partnerships for improving existing services. In addition in partnerships created for innovative service extension, differentiation, and creation of additional value were discovered to have emerged as results of the cooperation. It can be concluded that benefits and competitive advantage can be created through building partnerships in order to expand service offering and seeking synergies.

Value of Information Logistics Integration in Digital Business Ecosystem

Digital business ecosystems (DBE) are becoming an increasingly popular concept for modelling and building distributed systems in heterogeneous, decentralized and open environments. Information- and communication technology (ICT) enabled business solutions have created an opportunity for automated business relations and transactions. The deployment of ICT in business-to-business (B2B) integration seeks to improve competitiveness by establishing real-time information and offering better information visibility to business ecosystem actors. The products, components and raw material flows in supply chains are traditionally studied in logistics research. In this study, we expand the research to cover the processes parallel to the service and information flows as information logistics integration. In this thesis, we show how better integration and automation of information flows enhance the speed of processes and, thus, provide cost savings and other benefits for organizations. Investments in DBE are intended to add value through business automation and are key decisions in building up information logistics integration. Business solutions that build on automation are important sources of value in networks that promote and support business relations and transactions. Value is created through improved productivity and effectiveness when new, more efficient collaboration methods are discovered and integrated into DBE. Organizations, business networks and collaborations, even with competitors, form DBE in which information logistics integration has a significant role as a value driver. However, traditional economic and computing theories do not focus on digital business ecosystems as a separate form of organization, and they do not provide conceptual frameworks that can be used to explore digital business ecosystems as value drivers—combined internal management and external coordination mechanisms for information logistics integration are not the current practice of a company’s strategic process. In this thesis, we have developed and tested a framework to explore the digital business ecosystems developed and a coordination model for digital business ecosystem integration; moreover, we have analysed the value of information logistics integration. The research is based on a case study and on mixed methods, in which we use the Delphi method and Internetbased tools for idea generation and development. We conducted many interviews with key experts, which we recoded, transcribed and coded to find success factors. Qualitative analyses were based on a Monte Carlo simulation, which sought cost savings, and Real Option Valuation, which sought an optimal investment program for the ecosystem level. This study provides valuable knowledge regarding information logistics integration by utilizing a suitable business process information model for collaboration. An information model is based on the business process scenarios and on detailed transactions for the mapping and automation of product, service and information flows. The research results illustrate the current cap of understanding information logistics integration in a digital business ecosystem. Based on success factors, we were able to illustrate how specific coordination mechanisms related to network management and orchestration could be designed. We also pointed out the potential of information logistics integration in value creation. With the help of global standardization experts, we utilized the design of the core information model for B2B integration. We built this quantitative analysis by using the Monte Carlo-based simulation model and the Real Option Value model. This research covers relevant new research disciplines, such as information logistics integration and digital business ecosystems, in which the current literature needs to be improved. This research was executed by high-level experts and managers responsible for global business network B2B integration. However, the research was dominated by one industry domain, and therefore a more comprehensive exploration should be undertaken to cover a larger population of business sectors. Based on this research, the new quantitative survey could provide new possibilities to examine information logistics integration in digital business ecosystems. The value activities indicate that further studies should continue, especially with regard to the collaboration issues on integration, focusing on a user-centric approach. We should better understand how real-time information supports customer value creation by imbedding the information into the lifetime value of products and services. The aim of this research was to build competitive advantage through B2B integration to support a real-time economy. For practitioners, this research created several tools and concepts to improve value activities, information logistics integration design and management and orchestration models. Based on the results, the companies were able to better understand the formulation of the digital business ecosystem and the importance of joint efforts in collaboration. However, the challenge of incorporating this new knowledge into strategic processes in a multi-stakeholder environment remains. This challenge has been noted, and new projects have been established in pursuit of a real-time economy.

(A) Photoregulation of DNA Functions by Cyclic Azobenzene-tethered Oligonucleotides (B) Site-specific Fluorescent Labeling of DNA using Inverse Electron Demand Diels-Alder Reaction between trans-Cyclooctene Derivatives and BODIPY-Tetrazine Adducts

(A) Most azobenzene-based photoswitches require UV light for photoisomerization, which limit their applications in biological systems due to possible photodamage. Cyclic azobenzene derivatives, on the other hand, can undergo cis-trans isomerization when exposed to visible light. A shortened synthetic scheme was developed for the preparation of a building block containing cyclic azobenzene and D-threoninol (cAB-Thr). trans-Cyclic azobenzene was found to thermally isomerize back to the cis-form in a temperature-dependent manner. cAB-Thr was transformed into the corresponding phosphoramidite and subsequently incorporated into oligonucleotides by solid phase synthesis. Melting temperature measurement suggested that incorporation of cis-cAB into oligonucleotides destabilizes DNA duplexes, these findings corroborate with circular dichroism measurement. Finally, Fluorescent Energy Resonance Transfer experiments indicated that trans-cAB can be accommodated in DNA duplexes. (B) Inverse Electron Demand Diels-Alder reactions (IEDDA) between trans-olefins and tetrazines provide a powerful alternative to existing ligation chemistries due to its fast reaction rate, bioorthogonality and mutual orthogonality with other click reactions. In this project, an attempt was pursued to synthesize trans-cyclooctene building blocks for oligonucleotide labeling by reacting with BODIPY-tetrazine. Rel-(1R-4E-pR)-cyclooct-4-enol and rel-(1R,8S,9S,4E)-Bicyclo[6.1.0]non-4-ene-9-ylmethanol were synthesized and then transformed into the corresponding propargyl ether. Subsequent Sonogashira reactions between these propargylated compounds with DMT-protected 5-iododeoxyuridine failed to give the desired products. Finally a methodology was pursued for the synthesis of BODIPY-tetrazine conjugates that will be used in future IEDDA reactions with trans-cyclooctene modified oligonucleotides.

How can strategic philanthropy contribute to innovation for companies

This investigation proposes to explore the existing link between a strategic conception of philanthropy and innovation. Indeed, the nature of the research question relies on an unexplored field in the CSR and Innovation management academic literature. It starts with the interest to know which the benefits are for a firm encouraged to invest strategically in philanthropy. In this regard, the analysis contributes in fitting this gap by following different objectives in an exploratory perspective. Throughout the research it will be analyzed the concept and the current and past contributions on the different branches of innovation (product innovation, managerial innovation, technological innovation), to accentuate the relation between an accurate strategic approach to philanthropy and the impact on the organizational value. Indeed, analyzing philanthropic innovation may provide insights about business opportunities and notions related to social investments and profit. That aspect includes the link between those strategic decisions that a firm can use to maximize those investments as it was part of their core business. It also proves the existing link between CSR and innovation, and the possibilities that the enterprises have towards this subject.

Perfil logístico del sector cemento en Colombia

Este proyecto caracteriza la logística del sector cemento en Colombia al identificar y describir los principales actores, procesos y materiales involucrados en la cadena de suministros del sector. Este documento compila la información logística relevante para la producción de cemento en Colombia. Esta información se obtuvo sintetizando estudios y reportes acerca de las prácticas logísticas y las condiciones en las que éstas se desarrollan. Adicionalmente se realizaron visitas empresariales en diferentes plantas de producción de cemento y entrevistas semiestructuradas a expertos en logística de los diferentes eslabones. Con la información primaria y secundaria se caracteriza del producto, las materias primas e insumos necesarios para la producción de cemento. Se identifican los principales agentes que componen el sector y se describen los procesos logísticos relacionados con el cemento en cada uno de ellos. Para las cementeras y canteras se hace un análisis de entradas y salidas de los procesos principales de su cadena de valor. Adicionalmente se expone la operación de transporte como un elemento clave en el sector y se presentan las simulaciones de fletes, rutas y cubicaje. Por último, se incluye un caso de optimización de transporte aplicando teorías de investigación de operaciones.