Computational models for and from biology : simple gene assembly and reaction systems

The advancement of science and technology makes it clear that no single perspective is any longer sufficient to describe the true nature of any phenomenon. That is why the interdisciplinary research is gaining more attention overtime. An excellent example of this type of research is natural computing which stands on the borderline between biology and computer science. The contribution of research done in natural computing is twofold: on one hand, it sheds light into how nature works and how it processes information and, on the other hand, it provides some guidelines on how to design bio-inspired technologies. The first direction in this thesis focuses on a nature-inspired process called gene assembly in ciliates. The second one studies reaction systems, as a modeling framework with its rationale built upon the biochemical interactions happening within a cell. The process of gene assembly in ciliates has attracted a lot of attention as a research topic in the past 15 years. Two main modelling frameworks have been initially proposed in the end of 1990s to capture ciliates’ gene assembly process, namely the intermolecular model and the intramolecular model. They were followed by other model proposals such as templatebased assembly and DNA rearrangement pathways recombination models. In this thesis we are interested in a variation of the intramolecular model called simple gene assembly model, which focuses on the simplest possible folds in the assembly process. We propose a new framework called directed overlap-inclusion (DOI) graphs to overcome the limitations that previously introduced models faced in capturing all the combinatorial details of the simple gene assembly process. We investigate a number of combinatorial properties of these graphs, including a necessary property in terms of forbidden induced subgraphs. We also introduce DOI graph-based rewriting rules that capture all the operations of the simple gene assembly model and prove that they are equivalent to the string-based formalization of the model. Reaction systems (RS) is another nature-inspired modeling framework that is studied in this thesis. Reaction systems’ rationale is based upon two main regulation mechanisms, facilitation and inhibition, which control the interactions between biochemical reactions. Reaction systems is a complementary modeling framework to traditional quantitative frameworks, focusing on explicit cause-effect relationships between reactions. The explicit formulation of facilitation and inhibition mechanisms behind reactions, as well as the focus on interactions between reactions (rather than dynamics of concentrations) makes their applicability potentially wide and useful beyond biological case studies. In this thesis, we construct a reaction system model corresponding to the heat shock response mechanism based on a novel concept of dominance graph that captures the competition on resources in the ODE model. We also introduce for RS various concepts inspired by biology, e.g., mass conservation, steady state, periodicity, etc., to do model checking of the reaction systems based models. We prove that the complexity of the decision problems related to these properties varies from P to NP- and coNP-complete to PSPACE-complete. We further focus on the mass conservation relation in an RS and introduce the conservation dependency graph to capture the relation between the species and also propose an algorithm to list the conserved sets of a given reaction system.

Quadcopter assistant for a mobile assembly robot

Science has revolutionized the human life. The advance progress in science and research is making human life easier and more comfortable. The new and emerging technology of micro drone is penetrating and widening the scientific research. This thesis is a part of work in which a unique work is carried out, although related research paper and journal are available. Design and development of automatic charging station for a ready to fly quadcopter is rare and unusual work. The work is carried out as an standard engineering process that include requirements gathering, creating the required document (this thesis is a part of required document as well), selection of suitable hardware, configuring the hardware, generate the code for software, uploading code to the microcontroller, troubleshooting and rectification, finalized prototype and testing. Thesis describe how mechatronics engineering is useful in generating a customized and unique project. At the starting phase of this project (before purchasing a ready to fly quadcopter) every single aspect of this work was known. The only unknown alternatives was a battery and charger. Several task was achieved including design and development of automatic charging station, accurate landing and telecast a live video on additional screen. At starting it was decided that quadcopter should follow the mobile robot, during study it was concluded there is no such quadcopter available in market to auto follow a robot indoor. This works starts with a market survey and comparing the different brands of quadcopter that meets all the requirements and specifications of the mobile robot assembly. Selection of quadcopter is a result of discussion and meeting with the team members, supervisor, professor and project manage.

Corporate Entrepreneurship in Healthcare Organizations: An explorative study of employees’ corporate entrepreneurial behavior, job satisfaction and turnover intention

The Finnish healthcare industry is currently facing significant challenges due to economic crises, aging population and major structural reforms, which have resulted in decreased job satisfaction and increased levels of turnover. This proposes that healthcare organizations need to come up with new, creative means to tackle these issues. Several researchers have argued that corporate entrepreneurship may be the necessary means to achieve this. As previous research has mainly focused on examining this concept from organizational perspective, this study looks at how it occurs on the level of individual employees. The purpose of this study is to examine how corporate entrepreneurship is manifested in individual behavior, and how this type of behavior is associated with the individual’s job satisfaction and turnover intention. Additionally, this study will examine the differences in corporate entrepreneurial behavior between private and public sector organizations, as previous research suggests that these two may be characterized differently. Data was collected with the help of a literature review as well as a survey study, which was sent out to a number of employees of four different healthcare organizations, out of which three were public and one was a private sector organization. Six distinct behavioral characteristics were recognized in previous research, which make up the measure for corporate entrepreneurial behavior. Principal components were formed from the different areas of the survey (corporate entrepreneurial behavior, job satisfaction, turnover intention), after which the association of these components were examined with linear regression analysis, which proved that corporate entrepreneurial behavior is positively correlated with both job satisfaction and intention to leave the organization. Differences between sectors were analyzed with analysis of variance and cross tabulation analysis, but neither of these suggested that any significant differences would occur. These results suggest that employees who behave entrepreneurially tend to be more satisfied with their jobs, but also consider leaving their current organizations more often than others. This may be due to the fact that healthcare organizations are not fertile for entrepreneurial behavior, which will drive entrepreneurial individuals looking for employers who may be more supportive of this type of behavior. With growing levels of dissatisfaction as well as little room for entrepreneurial behavior, the studied organizations may actually be in the process of losing those employees who have the ability and desire to behave in such manner, and who could very well be those who will eventually come up with solutions for the major challenges that these organizations are facing.

Design and implementation of machine vision system for the mobile assembly robot

The review of intelligent machines shows that the demand for new ways of helping people in perception of the real world is becoming higher and higher every year. This thesis provides information about design and implementation of machine vision for mobile assembly robot. The work has been done as a part of LUT project in Laboratory of Intelligent Machines. The aim of this work is to create a working vision system. The qualitative and quantitative research were done to complete this task. In the first part, the author presents the theoretical background of such things as digital camera work principles, wireless transmission basics, creation of live stream, methods used for pattern recognition. Formulas, dependencies and previous research related to the topic are shown. In the second part, the equipment used for the project is described. There is information about the brands, models, capabilities and also requirements needed for implementation. Although, the author gives a description of LabVIEW software, its add-ons and OpenCV which are used in the project. Furthermore, one can find results in further section of considered thesis. They mainly represented by screenshots from cameras, working station and photos of the system. The key result of this thesis is vision system created for the needs of mobile assembly robot. Therefore, it is possible to see graphically what was done on examples. Future research in this field includes optimization of the pattern recognition algorithm. This will give less response time for recognizing objects. Presented by author system can be used also for further activities which include artificial intelligence usage.

De novo transcriptome assembly and annotation of the isopod Idotea balthica

The Baltic Sea is a unique environment that contains unique genetic populations. In order to study these populations on a genetic level basic molecular research is needed. The aim of this thesis was to provide a basic genetic resource for population genomic studies by de novo assembling a transcriptome for the Baltic Sea isopod Idotea balthica. RNA was extracted from a whole single adult male isopod and sequenced using Illumina (125bp PE) RNA-Seq. The reads were preprocessed using FASTQC for quality control, TRIMMOMATIC for trimming, and RCORRECTOR for error correction. The preprocessed reads were then assembled with TRINITY, a de Bruijn graph-based assembler, using different k-mer sizes. The different assemblies were combined and clustered using CD-HIT. The assemblies were evaluated using TRANSRATE for quality and filtering, BUSCO for completeness, and TRANSDECODER for annotation potential. The 25-mer assembly was annotated using PANNZER (protein annotation with z-score) and BLASTX. The 25-mer assembly represents the best first draft assembly since it contains the most information. However, this assembly shows high levels of polymorphism, which currently cannot be differentiated as paralogs or allelic variants. Furthermore, this assembly is incomplete, which could be improved by sampling additional developmental stages.

Viability of part cargoes in tramp shipping company’s routing and scheduling decisions

Operational excellence of individual tramp shipping companies is important in today’s market, where competition is intense, freight revenues are modest and capital costs high due to global financial crisis, and tighter regulatory framework is generating additional costs and challenges to the industry. This thesis concentrates on tramp shipping, where a tramp operator in a form of an individual case company, specialized in short-sea shipping activities in the Baltic Sea region, is searching ways to map their current fleet operations and better understand potential ways to improve the overall routing and scheduling decisions. The research problem is related to tramp fleet planning where several cargoes are carried on board at the same time, which are here systematically referred to as part cargoes. The purpose is to determine the pivotal dimensions and characteristics of these part cargo operations in tramp shipping, and offer both the individual case company and wider research community better understanding of potential risks and benefits related to utilization of part cargo operations. A mixed method research approach is utilized in this research, as the objectives are related to complex, real-life business practices in the field of supply chain management and more specifically, maritime logistics. A quantitative analysis of different voyage scenarios is executed, including alternative voyage legs with varying cost structure and customer involvement. An on-line-based questionnaire designed and prepared by case company’s decision group again provides desired data of predominant attitudes and views of most important industrial customers regarding the part cargo-related operations and potential future utilization of this business model. The results gained from these quantitative methods are complied with qualitative data collection tools, along with suitable secondary data sources. Based on results and logical analysis of different data sources, a framework for characterizing the different aspects of part cargo operations is developed, utilizing both existing research and empirical investigation of the phenomenon. As conclusions, part cargoes have the ability to be part of viable fleet operations, and even increase flexibility among the fleet to a certain extent. Naturally, several hinderers for this development is recognized as well, such as potential issues with information gathering and sharing, inefficient port activities, and increased transit times.

Job cum glossa ordinaria, pars.

Job I,3-XLII,16 (2).

S. Gregorius Magnus, Moralia in Job, libri 1-16.

Claude Joly, chantre de Notre-Dame, a inscrit sa signature au f. 2v (XVIIe s.). Ce ms. a appartenu à la cathédrale Notre-Dame de Paris, dont il porte l'ex-libris "A la bibliotheque de l'Eglise de Paris" (XVIIe s., f. 2v). Notre-Dame.

Vetus testamentum, pars (Genesis-Job).

Ce ms. a été légué au chapitre de Notre-Dame par Pierre du Jardin, prêtre du diocèse de Limoges et chapelain de Notre-Dame de Paris, mort en 1431, comme l'indique la note au f. 251v: "Venerabilis et discretus vir deffunctus dominus Petrus de Orto, alias dictus Mallerat, presbiter Lemovicensis diocesis, quondam cappellanus hujus venerabilis eccelesie Parisiensis, qui obiit anno M° CCCC° XXXI° die XXIII° mensis aprilis, legavit per suum testamentum supra dicte ecclesie hunc presentem librum..." (XVe s.). Au f. 1 figure l'ex-libris "A la bibliotheque de l'Eglise de Paris" (XVIIe s.). Notre-Dame.

Livres sapientiaux et Job, avec glose.

Augustins.

Expositio Philippi in Job.

A la fin, fragment d'un rouleau mortuaire.

Morales de S. Grégoire sur Job.

Dans les gardes, fragments d'un compte champenois contenant l'état de divers débiteurs.