Applications of graph transformation in tools for domain-specific modeling languages

The use of domain-specific languages (DSLs) has been proposed as an approach to cost-e ectively develop families of software systems in a restricted application domain. Domain-specific languages in combination with the accumulated knowledge and experience of previous implementations, can in turn be used to generate new applications with unique sets of requirements. For this reason, DSLs are considered to be an important approach for software reuse. However, the toolset supporting a particular domain-specific language is also domain-specific and is per definition not reusable. Therefore, creating and maintaining a DSL requires additional resources that could be even larger than the savings associated with using them. As a solution, di erent tool frameworks have been proposed to simplify and reduce the cost of developments of DSLs. Developers of tool support for DSLs need to instantiate, customize or configure the framework for a particular DSL. There are di erent approaches for this. An approach is to use an application programming interface (API) and to extend the basic framework using an imperative programming language. An example of a tools which is based on this approach is Eclipse GEF. Another approach is to configure the framework using declarative languages that are independent of the underlying framework implementation. We believe this second approach can bring important benefits as this brings focus to specifying what should the tool be like instead of writing a program specifying how the tool achieves this functionality. In this thesis we explore this second approach. We use graph transformation as the basic approach to customize a domain-specific modeling (DSM) tool framework. The contributions of this thesis includes a comparison of di erent approaches for defining, representing and interchanging software modeling languages and models and a tool architecture for an open domain-specific modeling framework that e ciently integrates several model transformation components and visual editors. We also present several specific algorithms and tool components for DSM framework. These include an approach for graph query based on region operators and the star operator and an approach for reconciling models and diagrams after executing model transformation programs. We exemplify our approach with two case studies MICAS and EFCO. In these studies we show how our experimental modeling tool framework has been used to define tool environments for domain-specific languages.

Future revenue models: Transformation from textbooks to digital solutions in the educational publishing industry, Case Sanoma Learning

This study was conducted in order to learn how companies’ revenue models will be transformed due to the digitalisation of its products and processes. Because there is still only a limited number of researches focusing solely on revenue models, and particularly on the revenue model change caused by the changes at the business environment, the topic was initially approached through the business model concept, which organises the different value creating operations and resources at a company in order to create profitable revenue streams. This was used as the base for constructing the theoretical framework for this study, used to collect and analyse the information. The empirical section is based on a qualitative study approach and multiple-case analysis of companies operating in learning materials publishing industry. Their operations are compared with companies operating in other industries, which have undergone comparable transformation, in order to recognise either similarities or contrasts between the cases. The sources of evidence are a literature review to find the essential dimensions researched earlier, and interviews 29 of managers and executives at 17 organisations representing six industries. Based onto the earlier literature and the empirical findings of this study, the change of the revenue model is linked with the change of the other dimen-sions of the business model. When one dimension will be altered, as well the other should be adjusted accordingly. At the case companies the transformation is observed as the utilisation of several revenue models simultaneously and the revenue creation processes becoming more complex.

Combining Near-Field and Far-Field Microscopy: A new method for nanoscale super-resolution imaging

Lähikenttä- ja kaukokenttämikroskopian yhdistäminen: Uusi korkearesoluutioinen menetelmä nanokuvantamiseen. Osteoporoosi on sairaus, jossa luun uudistumisprosessi ei ole enää tasapainossa. Uuden luun muodostuminen on hitaampaa johtuen osteoblastien laskeneesta aktiivisuudesta. Yksi keino estää osteoporoosin syntyä on estää osteoklastien sitoutuminen luun pinnalle, jolloin ne eivät aloita luun syömisprosessia. Tämän Pro gradu -tutkielman tarkoituksena on luoda uusi työkalu osteoklastien sitoutumisen tutkimiseen samanaikaisesti fluoresenssi- ja atomivoimamikroskoopilla. Tätä tarkoitusta varten yhdistettiin atomivoimamikroskooppi sekä STED mikroskooppi. Kirjallisuuskatsauksessa käydään läpi yksityiskohtaisesti molempien mikroskooppitekniikoiden teoriat. Kokeellisessa osiossa esitetään käytetyt metodit ja alustavat tulokset uudella systeemillä. Lisäksi keskustellaan lyhyesti kuvan analysoinnista ImageJohjelmalla. Konfokaalisen fluoresenssimikroskoopin ja atomivoimamikroskoopin yhdistelmä on keksitty jo aikaisemmin, mutta tavallisen konfokaalimikroskoopin erottelukyvyn raja on noin 200 nanometriä johtuen valon diffraktioluonteesta. Yksityiskohdat eivät erotu, jos ne ovat pienempiä kuin puolet käytettävästä aallonpituudesta. STED mikroskooppi mahdollistaa fluoresenssikuvien taltioimisen solunsisäisistä prosesseista 50 nanometrin lateraalisella erotuskyvyllä ja atomivoimamikroskooppi antaa topografista tietoa näytteestä nanometrien erotuskyvyllä. Biologisia näytteitä kuvannettaessa atomivoimamikroskoopin erotuskyky kuitenkin huononee ja yleensä saavutetaan 30-50 nanometrin erotuskyky. Kuvien kerrostaminen vaatii vertauspisteitä ja tätä varten käytettiin atomivoimamikroskoopin kärjen tunnistamista ja referenssipartikkeleita. Kuva-analysointi suoritettiin ImageJ-kuvankäsittelyohjelmalla. Tuloksista nähdään, että referenssipartikkelit ovat hyviä, mutta niiden sijoittaminen tarkasti tietylle kohdealueelle on hankalaa nanoskaalassa. Tästä johtuen kärjen havaitseminen fluoresenssikuvassa on parempi metodi. Atomivoimamikroskoopin kärki voidaan päällystää fluoresoivalla aineella, mutta tämä lisää kärjen aiheuttamaa konvoluutiota mittausdataan. Myös valon takaisinsirontaa kärjestä voidaan tutkia, jolloin konvoluutio ei lisäänny. Ensimmäisten kuvien kerrostamisessa käytettiin hyväksi fluoresoivalla aineella päällystettyä kärkeä ja lopputuloksessa oli vain 50 nanometrin yhteensopimattomuus fluoresenssi- ja topografiakuvan kanssa. STED mikroskoopin avulla nähdään leimattujen proteiinien tarkat sijainnit tiettynä ajankohtana elävän solun sisällä. Samaan aikaan pystytään kuvantamaan solun fyysisiä muotoja tai mitata adheesiovoimia atomivoimamikroskoopilla. Lisäksi voidaan käyttää funktinalisoitua kärkeä, jolla voidaan laukaista signalointitapahtumia solun ja soluväliaineen välillä. Sitoutuminen soluväliaineeseen voidaan rekisteröidä samoin kuin adheesiomediaattorien sijainnit sitoutumisalueella. Nämä dynaamiset havainnot tuottavat uutta informaatiota solun signaloinnista, kun osteoklasti kiinnittyy luun pintaan. Tämä teknologia tarjoaa uuden näkökulman monimutkaisiin signalointiprosesseihin nanoskaalassa ja tulee ratkaisemaan lukemattoman määrän biologisia ongelmia.

PET and MR imaging in Parkinson’s disease patients with cognitive impairment. A study of dopaminergic dysfunction, amyloid deposition, cortical hypometabolism and brain atrophy

Parkinson’s disease (PD) is the second most common neurodegenerative disorder. It is characterized by a severe loss of substantia nigra dopaminergic neurons leading to dopamine depletion in the striatum. PD affects movement, producing motor symptoms such as rigidity, tremor and bradykinesia. Non-motor symptoms include autonomic dysfunction, neurobehavioral problems and cognitive impairment, which may lead to dementia. The pathophysiological basis of cognitive impairment and dementia in PD is unclear. The aim of this thesis was to study the pathophysiological basis of cognitive impairment and dementia in PD. We evaluated the relation between frontostriatal dopaminergic dysfunction and the cognitive symptoms in PD patients with [18F]Fdopa PET. We also combined [C]PIB and [¹⁸F]FDG PET and magnetic resonance imaging in PD patients with and without dementia. In addition, we analysed subregional striatal [¹⁸F]Fdopa PET data to find out whether a simple ratio approach would reliably separate PD patients from healthy controls. The impaired dopaminergic function of the frontostriatal regions was related to the impairment in cognitive functions, such as memory and cognitive processing in PD patients. PD patients with dementia showed an impaired glucose metabolism but not amyloid deposition in the cortical brain regions, and the hypometabolism was associated with the degree of cognitive impairment. PD patients had atrophy, both in the prefrontal cortex and in the hippocampus, and the hippocampal atrophy was related to impaired memory. A single 15-min scan 75 min after a tracer injection seemed to be sufficient for separating patients with PD from healthy controls in a clinical research environment. In conclusion, the occurrence of cognitive impairment and dementia in PD seems to be multifactorial and relates to changes, such as reduced dopaminergic activity, hypometabolism, brain atrophy and rarely to amyloid accumulation.

Genetic transformation of Eucalyptus camaldulensis by agrobalistic method

Eucalyptus stands in the setting of worldwide forestry due to its adaptability, rapid growth, production of high-quality and low cost of wood pulp fibers. The eucalyptus convetional breeding is impaired mainlly by the long life cycle making the genetic transformation systems an important tool for this purpose. However, this system requires in vitro eficient protocols for plant induction, regeneration and seletion, that allow to obtain transgenic plants from the transformed cell groups. The aim of this work was to evaluate the callus formation and to optimize the leaves and callus genetic transformation protocol by using the Agrobacterium tumefaciens system. Concerning callus formation, two different culture media were evaluated: MS medium supplemented with auxin, cytokinin (M1) and the MS medium with reduced nitrogen concentration and supplemented with auxin, cytokinin coconut water (M2). To establish the leave genetic transformation, those were exposed to agrobiolistics technique (gene gun), to tissue injury, and A. tumesfasciens EHA 105 contening the vetor pCambia 3301 (35S::GUS::NOS), for gene transference and to establish the callus transformation thoses were exposed only to A. tumefasciens. For both experiments, the influence of different infection periods was evaluated. The M2 medium provided the best values for callus sizea and fresh and dry weight. The leaves genetic transformation using the agrobiolistics technique was effective, the gus gene transient expression could be observed. No significant differences were obtained in the infection periods (4, 6 and 8 minutes). The callus genetic transformation with A. tumefaciens also promotend the gus gene transient expression on the callus co-cultiveted for 15 e 30 minutes. The transformed callus was transfered to a regeneration and selection medium and transformed plants were obtained.

In vivo imaging of vascular adhesion protein 1 - preclinical studies with positron emission tomography

The golden standard in nuclear medicine imaging of inflammation is the use of radiolabeled leukocytes. Although their diagnostic accuracy is good, the preparation of the leukocytes is both laborious and potentially hazardous for laboratory personnel. Molecules involved in leukocyte migration could serve as targets for the development of inflammation imaging agents. An excellent target would be a molecule that is absent or expressed at low level in normal tissues, but is induced or up-regulated at the site of inflammation. Vascular adhesion protein-1 (VAP-1) is a very promising target for in vivo imaging, since it is translocated to the endothelial cell surface when inflammation occurs. VAP-1 functions as an endothelial adhesion molecule that participates in leukocyte recruitment to inflamed tissues. Besides being an adhesion molecule, VAP-1 also has enzymatic activity. In this thesis, the targeting of VAP-1 was studied by using Gallium-68 (68Ga) labeled peptides and an Iodine-124 (124I) labeled antibody. The peptides were designed based on molecular modelling and phage display library searches. The new imaging agents were preclinically tested in vitro, as well as in vivo in animal models. The most promising imaging agent appeared to be a peptide belonging to the VAP-1 leukocyte ligand, Siglec-9 peptide. The 68Ga-labeled Siglec-9 peptide was able to detect VAP-1 positive vasculature in rodent models of sterile skin inflammation and melanoma by positron emission tomography. In addition to peptides, the 124I-labeled antibody showed VAP-1 specific binding both in vitro and in vivo. However, the estimated human radiation dose was rather high, and thus further preclinical studies in disease models are needed to clarify the value of this imaging agent. Detection of VAP-1 on endothelium was demonstrated in these studies and this imaging approach could be used in the diagnosis of inflammatory conditions as well as melanoma. These studies provide a proof-of-concept for PET imaging of VAP-1 and further studies are warranted.

Cadastral maps of irrigated areas by center pivots in the State of Minas Gerais, using CBERS-2B/CCD satellite imaging

Medium-resolution satellite images have been widely used for the identification and quantification of irrigated areas by center pivot. These areas, which present predominantly circular forms, can be easily identified by visual analyses of these images. In addition to identifying and quantifying areas irrigated by center pivot, other information that is associated to these areas is fundamental for producing cadastral maps. The goal of this work was to generate cadastral mapping of areas irrigated by center pivots in the State of Minas Gerais, Brazil, with the purpose of supplying information on irrigated agriculture. Using the satellite CBERS2B/CCD, images were used to identify and quantify irrigated areas and then associate these areas with a database containing information about: irrigated area, perimeter, municipality, path row, basin in which the pivot is located, and the date of image acquisition.3,781 center pivots systems were identified. The smallest area irrigated was 4.6 hectares and the largest one was 192.6 hectares. The total estimated value of irrigated area was 254,875 hectares. The largest number of center pivots appeared in the municipalities of Unaí and Paracatu, with 495 and 459 systems, respectively. Cadastral mapping is a very useful tool to assist and enhance information on irrigated agriculture in the State of Minas Gerais.

Influence of data acquisition geometry on soybean spectral response simulated by the prosail model

View angle and directional effects significantly affect reflectance and vegetation indices, especially when daily images collected by large field-of-view (FOV) sensors like the Moderate Resolution Imaging Spectroradiometer (MODIS) are used. In this study, the PROSAIL radiative transfer model was chosen to evaluate the impact of the geometry of data acquisition on soybean reflectance and two vegetation indices (Normalized Difference Vegetation Index - NDVI and Enhanced Vegetation Index -EVI) by varying biochemical and biophysical parameters of the crop. Input values for PROSAIL simulation were based on the literature and were adjusted by the comparison between simulated and real satellite soybean spectra acquired by the MODIS/Terra and hyperspectral Hyperion/Earth Observing-One (EO-1). Results showed that the influence of the view angle and view direction on reflectance was stronger with decreasing leaf area index (LAI) and chlorophyll concentration. Because of the greater dependence on the near-infrared reflectance, the EVI was much more sensitive to viewing geometry than NDVI presenting larger values in the backscattering direction. The contrary was observed for NDVI in the forward scattering direction. In relation to the LAI, NDVI was much more isotropic for closed soybean canopies than for incomplete canopies and a contrary behavior was verified for EVI.

White mold detection in common beans through leaf reflectance spectroscopy

ABSTRACT This study aimed to identify wavelengths based on leaf reflectance (400-1050 nm) to estimate white mold severity in common beans at different seasons. Two experiments were carried out, one during fall and another in winter. Partial Least Squares (PLS) regression was used to establish a set of wavelengths that better estimates the disease severity at a specific date. Therefore, observations were previously divided in two sub-groups. The first one (calibration) was used for model building and the second subgroup for model testing. Error measurements and correlation between measured and predicted values of disease severity index were employed to provide the best wavelengths in both seasons. The average indexes of each experiment were of 5.8% and 7.4%, which is considered low. Spectral bands ranged between blue and green, green and red, and red and infrared, being most sensitive for disease estimation. Beyond the transition ranges, other spectral regions also presented wavelengths with potential to determine the disease severity, such as red, green, and near infrared.

Neurobiology of pathological gambling. Brain imaging and epidemiological studies

Pathological gambling, a form of behavioral addiction, refers to maladaptive, compulsive gambling behavior severely interfering with an individual’s normal life. The prevalence of pathological gambling has been estimated to be 1–2% in western societies. The reward deficiency hypothesis of addiction assumes that individuals that have, or are prone, to addictions have blunted mesolimbic dopamine reward signaling, which leads to compulsive reward seeking in an attempt to compensate for the malfunctioning brain reward network. In this research project, the effects of gambling were measured using brain [11C] raclopride PET during slot machine gambling and possible brain structural changes associated with pathological gambling using MRI. The subjects included pathological gamblers and healthy volunteers. In addition, impulse control disorders associated with Parkinson’s disease were investigated by using brain [18F]fluorodopa PET and conducting an epidemiological survey. The results demonstrate mesolimbic dopamine release during gambling in both pathological gamblers and healthy volunteers. Striatal dopamine was released irrespective of the gambling outcome, whether the subjects won or not. There was no difference in gambling induced dopamine release between pathological gamblers and control subjects, although the magnitude of the dopamine release correlated with gambling related symptom severity in pathological gamblers. The results also show that pathological gambling is associated with extensive abnormality of brain white matter integrity, as measured with diffusion tensor imaging, similar to substance-addictions. In Parkinson’s disease patients with impulse control disorders, enhanced brain [18F] fluorodopa uptake in the medial orbitofrontal cortex was observed, indicating increased presynaptic monoamine function in this region, which is known to influence signaling in the mesolimbic system and reward processing. Finally, a large epidemiological survey in Finnish Parkinson’s disease patients showed that compulsive behaviors are very common in Parkinson disease and they are strongly associated with depression. These findings demonstrate the role of dopamine in pathological gambling, without support for the concept of reward deficiency syndrome.

Detection of the Vulnerable Atherosclerotic Plaque. Pre-Clinical Evaluation of Novel PET Imaging Probes With Experimental Models

Atherosclerosis is a life-long vascular inflammatory disease and the leading cause of death in Finland and in other western societies. The development of atherosclerotic plaques is progressive and they form when lipids begin to accumulate in the vessel wall. This accumulation triggers the migration of inflammatory cells that is a hallmark of vascular inflammation. Often, this plaque will become unstable and form vulnerable plaque which may rupture causing thrombosis and in the worst case, causing myocardial infarction or stroke. Identification of these vulnerable plaques before they rupture could save lives. At present, in the clinic, there exists no appropriated, non-invasive method for their identification. The aim of this thesis was to evaluate novel positron emission tomography (PET) probes for the detection of vulnerable atherosclerotic plaques and to characterize, two mouse models of atherosclerosis. These studies were performed by using ex vivo and in vivo imaging modalities. The vulnerability of atherosclerotic plaques was evaluated as expression of active inflammatory cells, namely macrophages. Age and the duration of high-fat diet had a drastic impact on the development of atherosclerotic plaques in mice. In imaging of atherosclerosis, 6-month-old mice, kept on high-fat diet for 4 months, showed matured, metabolically active, atherosclerotic plaques. [18F]FDG and 68Ga were accumulated in the areas representative of vulnerable plaques. However, the slow clearance of 68Ga limits its use for the plaque imaging. The novel synthesized [68Ga]DOTA-RGD and [18F]EF5 tracers demonstrated efficient uptake in plaques as compared to the healthy vessel wall, but the pharmacokinetic properties of these tracers were not optimal in used models. In conclusion, these studies resulted in the identification of new strategies for the assessment of plaque stability and mouse models of atherosclerosis which could be used for plaque imaging. In the used probe panel, [18F]FDG was the best tracer for plaque imaging. However, further studies are warranted to clarify the applicability of [18F]EF5 and [68Ga]DOTA-RGD for imaging of atherosclerosis with other experimental models.

Designing the transformation from a boiler supplier into a solution seller

Competition for customers in business-to-business markets is rough, and in order to survive a seller has to be able to deliver more value to its customers than its competitors. This thesis is done for the sales department of an energy technology company operating in business-to-business markets. The company is a relatively small in its field, and it aims to expand internationally and differ itself from its competitors by providing better service for its customers and selling solutions. This study aims to design the transformation from a product seller into a solution seller by defining what is a solution and how solutions are sold, and creating an action plan for sales. Data for the study is collected in ten theme interviews, and analyzed with thematic and content analysis. The action plan is constructed based both on the data and theory. According to the findings of the study, solution is defined as a specially designed unique combination of elements – such as products, services, knowledge, experience and thinking – that work with and complement each other, and bring value to a particular customer. Solution sales requires capabilities to anticipate; build relationships with customers; identify needs and define requirements; cocreate solutions by customizing and integrating elements; and provide postdeployment support. Vision for the change is to sell solution through sensing customers’ needs and responding to them, and the steps of the action plan are to (1) cascade customer-focus, (2) involve other departments in solution sales, (3) develop customer relationship management, and (4) involve the whole organization in solution business.