Sustaining your Open Source project through training: a Hydra case study

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Kramerius - Fedora based open source system for a digital library

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Software and Code Finder: making research outputs visible

Poster at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Assimilate partitioning in leaves of the raffinose-storing herb Lamium album L.: the effects of altering source-sink balance

In Lamium album, sucrose and raffinose-family oligosaccharides are the major products of photosynthesis that are stored in leaves. Using gas analysis and 14CO2 feeding, we compared photosynthesis and the partitioning of recently-fixed carbon in plants where sink activity was lowered by excision of flowers and chilling of roots with those where sink activity was not modified. Reduction in sink activity led to a reduction in the maximum rate of photosynthesis, to retention of fixed carbon in source leaves and to the progressive accumulation of raffinose-family oligosaccharides. This ultimately affected the extractable activities of invertase and sucrose phosphate synthase. At the end of the light period, invertase activity was significantly higher in treated plants. By contrast sucrose phosphate synthase activity was significantly lower in treated plants. We propose that reducing sink activity in L. album is associated with a shift in metabolism away from starch and sucrose synthesis and towards sucrose catabolism, galactinol utilisation and the synthesis of raffinose-family oligosaccharides.

Usability comparison of open source content management systems

The purpose of this thesis is to study, investigate and compare usability of open source cms. The thesis examines and compares usability aspect of some open source cms. The research is divided into two complementary parts –theoretical part and analytical part. The theoretical part mainly describes open source web content management systems, usability and the evaluation methods. The analytical part is to compare and analyze the results found from the empirical research. Heuristic evaluation method was used to measure usability problems in the interfaces. The study is fairly limited in scope; six tasks were designed and implemented in each interface for discovering defects in the interfaces. Usability problems were rated according to their level of severity. Time it took by each task, level of problem’s severity and type of heuristics violated will be recorded, analyzed and compared. The results of this study indicate that the comparing systems provide usable interfaces, and WordPress is recognized as the most usable system.

Identification of the main generator source of longitudinal muscle contraction in the earthworm ventral nerve cord

The main generator source of a longitudinal muscle contraction was identified as an M (mechanical-stimulus-sensitive) circuit composed of a presynaptic M-1 neuron and a postsynaptic M-2 neuron in the ventral nerve cord of the earthworm, Amynthas hawayanus, by simultaneous intracellular response recording and Lucifer Yellow-CH injection with two microelectrodes. Five-peaked responses were evoked in both neurons by a mechanical, but not by an electrical, stimulus to the mechanoreceptor in the shaft of a seta at the opposite side of an epidermis-muscle-nerve-cord preparation. This response was correlated to 84% of the amplitude, 73% of the rising rate and 81% of the duration of a longitudinal muscle contraction recorded by a mechano-electrical transducer after eliminating the other possible generator sources by partitioning the epidermis-muscle piece of this preparation. The pre- and postsynaptic relationship between these two neurons was determined by alternately stimulating and recording with two microelectrodes. Images of the Lucifer Yellow-CH-filled M-1 and M-2 neurons showed that both of them are composed of bundles of longitudinal processes situated on the side of the nerve cord opposite to stimulation. The M-1 neuron has an afferent process (A1) in the first nerve at the stimulated side of this preparation and the M-2 neuron has two efferent processes (E1 and E3) in the first and third nerves at the recording side where their effector muscle cell was identified by a third microelectrode.

Facilitation of the main generator source of earthworm muscle contraction by a peripheral neuron

A constant facilitation of responses evoked in the earthworm muscle contraction generator neurons by responses evoked in the neurons of its peripheral nervous system was demonstrated. It is based on the proposal that these two responses are bifurcations of an afferent response evoked by the same peripheral mechanical stimulus but converging again on this central neuron. A single-peaked generator response without facilitation was demonstrated by sectioning the afferent route of the peripheral facilitatory modulatory response, or conditioning response (CR). The multipeaked response could be restored by restimulating the sectioned modulatory neuron with an intracellular substitutive conditioning stimulus (SCS). These multi-peaked responses were proposed to be the result of reverberating the original single peaked unconditioned response (UR) through a parallel (P) neuronal circuit which receives the facilitation of the peripheral modulatory neuron. This peripheral modulatory neuron was named "Peri-Kästchen" (PK) neuron because it has about 20 peripheral processes distributed on the surface of a Kästchen of longitudinal muscle cells on the body wall of this preparation as revealed by the Lucifer Yellow-CH-filling method.

Evaluation of Location Intelligence exploitation in capital-intensive business

As technology has developed it has increased the number of data produced and collected from business environment. Over 80% of that data includes some sort of reference to geographical location. Individuals have used that information by utilizing Google Maps or different GPS devices, however such information has remained unexploited in business. This thesis will study the use and utilization of geographically referenced data in capital-intensive business by first providing theoretical insight into how data and data-driven management enables and enhances the business and how especially geographically referenced data adds value to the company and then examining empirical case evidence how geographical information can truly be exploited in capital-intensive business and what are the value adding elements of geographical information to the business. The study contains semi-structured interviews that are used to scan attitudes and beliefs of an organization towards the geographic information and to discover fields of applications for the use of geographic information system within the case company. Additionally geographical data is tested in order to illustrate how the data could be used in practice. Finally the outcome of the thesis provides understanding from which elements the added value of geographical information in business is consisted of and how such data can be utilized in the case company and in capital-intensive business.

Family ownership – a source of sustainable success in listed companies

Extant research on exchange-listed firms has acknowledged that the concentration of ownership and the identity of owners make a difference. In addition, studies indicate that firms with a dominant owner outperform firms with dispersed ownership. During the last few years, scholars have identified one group of owners, in particular, whose ownership stake in publicly listed firm is positively related to performance: the business family. While acknowledging that family firms represent a unique organizational form, scholars have identified various concepts and theories in order to understand how the family influences organizational processes and firm performance. Despite multitude of research, scholars have not been able to present clear results on how firm performance is actually impacted by the family. In other words, studies comparing the performance of listed family and other types of firms have remained descriptive in nature since they lack empirical data and confirmation from the family business representatives. What seems to be missing is a convincing theory that links the involvement and behavioral consequences. Accordingly, scholars have not yet come to a mutual understanding of what precisely constitutes a family business. The variety of different definitions and theories has made comparability of different results difficult for instance. These two issues have hampered the development of a rigorous theory of family business. The overall objective of this study is to describe and understand how the family as a dominant owner can enhance firm performance, and can act a source of sustainable success in listed companies. In more detail, in order to develop understanding of the unique factors that can act as competitive advantages for listed family firms, this study is based on a qualitative approach and aims at theory development, not theory verification. The data in this study consist of 16 thematic interviews with CEOs, members of the board, supervisory board chairs, and founders of Finnish listed-family firms. The study consists of two parts. The first part introduces the research topic, research paradigm, methods, and publications, and also discusses the overall outcomes and contributions of the publications. The second part consists of four publications that address the research questions from different viewpoints. The analyses of this study indicate that family ownership in listed companies represents a structure that differs from the traditional views of agency and stewardship, as well as from resource-based and stakeholder views. As opposed to these theories and shareholder capitalism which consider humans as individualistic, opportunistic, and self-serving, and assume that the behaviors of an investor are based on the incentives and motivations to maximize private profits, the family owners form a collective social unit that is motivated to act together toward their mutual purpose or benefit. In addition, socio-emotional and psychological elements of ownership define the family members as owners, rather than the legal and financial dimensions of ownership. That is, collective psychological ownership of family over the business (F-CPO) can be seen as a construct that comprehensively captures the fusion between the family and the business. Moreover, it captures the realized, rather than merely potential, family influence on and interaction with the business, and thereby brings more theoretical clarity of the nature of the fusion between the family and the business, and offers a solution to the problem of family business definition. This doctoral dissertation provides academics, policy-makers, family business practitioners, and the society at large with many implications considering family and business relationships.

Large-eddy simulation of wind flows over complex terrains for wind energy applications

Wind energy has obtained outstanding expectations due to risks of global warming and nuclear energy production plant accidents. Nowadays, wind farms are often constructed in areas of complex terrain. A potential wind farm location must have the site thoroughly surveyed and the wind climatology analyzed before installing any hardware. Therefore, modeling of Atmospheric Boundary Layer (ABL) flows over complex terrains containing, e.g. hills, forest, and lakes is of great interest in wind energy applications, as it can help in locating and optimizing the wind farms. Numerical modeling of wind flows using Computational Fluid Dynamics (CFD) has become a popular technique during the last few decades. Due to the inherent flow variability and large-scale unsteadiness typical in ABL flows in general and especially over complex terrains, the flow can be difficult to be predicted accurately enough by using the Reynolds-Averaged Navier-Stokes equations (RANS). Large- Eddy Simulation (LES) resolves the largest and thus most important turbulent eddies and models only the small-scale motions which are more universal than the large eddies and thus easier to model. Therefore, LES is expected to be more suitable for this kind of simulations although it is computationally more expensive than the RANS approach. With the fast development of computers and open-source CFD software during the recent years, the application of LES toward atmospheric flow is becoming increasingly common nowadays. The aim of the work is to simulate atmospheric flows over realistic and complex terrains by means of LES. Evaluation of potential in-land wind park locations will be the main application for these simulations. Development of the LES methodology to simulate the atmospheric flows over realistic terrains is reported in the thesis. The work also aims at validating the LES methodology at a real scale. In the thesis, LES are carried out for flow problems ranging from basic channel flows to real atmospheric flows over one of the most recent real-life complex terrain problems, the Bolund hill. All the simulations reported in the thesis are carried out using a new OpenFOAM® -based LES solver. The solver uses the 4th order time-accurate Runge-Kutta scheme and a fractional step method. Moreover, development of the LES methodology includes special attention to two boundary conditions: the upstream (inflow) and wall boundary conditions. The upstream boundary condition is generated by using the so-called recycling technique, in which the instantaneous flow properties are sampled on aplane downstream of the inlet and mapped back to the inlet at each time step. This technique develops the upstream boundary-layer flow together with the inflow turbulence without using any precursor simulation and thus within a single computational domain. The roughness of the terrain surface is modeled by implementing a new wall function into OpenFOAM® during the thesis work. Both, the recycling method and the newly implemented wall function, are validated for the channel flows at relatively high Reynolds number before applying them to the atmospheric flow applications. After validating the LES model over simple flows, the simulations are carried out for atmospheric boundary-layer flows over two types of hills: first, two-dimensional wind-tunnel hill profiles and second, the Bolund hill located in Roskilde Fjord, Denmark. For the twodimensional wind-tunnel hills, the study focuses on the overall flow behavior as a function of the hill slope. Moreover, the simulations are repeated using another wall function suitable for smooth surfaces, which already existed in OpenFOAM® , in order to study the sensitivity of the flow to the surface roughness in ABL flows. The simulated results obtained using the two wall functions are compared against the wind-tunnel measurements. It is shown that LES using the implemented wall function produces overall satisfactory results on the turbulent flow over the two-dimensional hills. The prediction of the flow separation and reattachment-length for the steeper hill is closer to the measurements than the other numerical studies reported in the past for the same hill geometry. The field measurement campaign performed over the Bolund hill provides the most recent field-experiment dataset for the mean flow and the turbulence properties. A number of research groups have simulated the wind flows over the Bolund hill. Due to the challenging features of the hill such as the almost vertical hill slope, it is considered as an ideal experimental test case for validating micro-scale CFD models for wind energy applications. In this work, the simulated results obtained for two wind directions are compared against the field measurements. It is shown that the present LES can reproduce the complex turbulent wind flow structures over a complicated terrain such as the Bolund hill. Especially, the present LES results show the best prediction of the turbulent kinetic energy with an average error of 24.1%, which is a 43% smaller than any other model results reported in the past for the Bolund case. Finally, the validated LES methodology is demonstrated to simulate the wind flow over the existing Muukko wind farm located in South-Eastern Finland. The simulation is carried out only for one wind direction and the results on the instantaneous and time-averaged wind speeds are briefly reported. The demonstration case is followed by discussions on the practical aspects of LES for the wind resource assessment over a realistic inland wind farm.

Auringon asemaa seuraavan aurinkopaneelijärjestelmän kehittäminen

Tässä diplomityössä käsitellään Aurinkoa seuraavan aurinkopaneelijärjestelmän kehittämistä Suomen olosuhteisiin. Työ on tehty osana Lappeenrannan teknillisen yliopiston Green Campus-projektia, jossa tarkoituksena on tuottaa yliopistolle energiaa uusiutuvilla menetelmillä ja käyttää niitä apuna tutkimuksessa sekä opetuksessa. Tavoitteena työssä on ymmärtää Auringon seuraamisen hyödyt sekä mahdolliset haitat aurinkopaneeli sovellutuksissa. Aikaisemman tutkimustiedon ollessa vähäistä, on työssä pyritty löytämään laskentamalli tuottavuuden laskentaan riippumatta siitä, missä päin maapalloa aurinkopaneelijärjestelmä sijaitsee. Työ alkaa kirjallisuustutkimuksella, jossa käydään läpi aurinkopaneelien toimintaperiaate, aurinkoenergian ja auringonpaistetuntien suuruusluokat Suomessa, sekä Suomen sääoloista johtuvat vaatimukset aurinkopaneelijärjestelmille. Tämän jälkeen on vertailtu kaupallisia järjestelmiä. Lopuksi järjestelmällistä tuotesuunnittelua hyväksikäyttäen suunnitellaan oma versio Aurinkoa seuraavasta aurinkopaneelijärjestelmästä. Oman suunnitelman järkevyyttä simuloidaan pienoismallilla Matlab-Arduino ympäristössä ja pyritään löytämään mahdollisia heikkouksia. Suomessa aurinkoenergiasta 90 % saadaan maalis – syyskuun aikana. Nykyisillä akkujärjestelmillä aurinkoenergia Suomessa ei sovellu kuin täydentäväksi energianlähteeksi. Aurinkoa seuraamalla voidaan saavuttaa 25-30 % tuottavuuden lisäys kesäaikana verrattuna staattiseen järjestelmään. Talvella hyöty tippuu 0-10 % luokkaan. Pienoismallilla simuloidut ohjaustavat osoittivat, että Aurinkoa on mahdollista seurata ilman sensoreita laskemalla Auringon paikka tähtitieteen kaavoista.

Allogeneic hematopoietic stem cell transplantation from an alternative stem cell source in Fanconi anemia patients: analysis of 47 patients from a single institution

We transplanted 47 patients with Fanconi anemia using an alternative source of hematopoietic cells. The patients were assigned to the following groups: group 1, unrelated bone marrow (N = 15); group 2, unrelated cord blood (N = 17), and group 3, related non-sibling bone marrow (N = 15). Twenty-four patients (51%) had complete engraftment, which was not influenced by gender (P = 0.87), age (P = 0.45), dose of cyclophosphamide (P = 0.80), nucleated cell dose infused (P = 0.60), or use of anti-T serotherapy (P = 0.20). Favorable factors for superior engraftment were full HLA compatibility (independent of the source of cells; P = 0.007) and use of a fludarabine-based conditioning regimen (P = 0.046). Unfavorable factors were > or = 25 transfusions pre-transplant (P = 0.011) and degree of HLA disparity (P = 0.007). Intensity of mucositis (P = 0.50) and use of androgen prior to transplant had no influence on survival (P = 0.80). Acute graft-versus-host disease (GVHD) grade II-IV and chronic GVHD were diagnosed in 47 and 23% of available patients, respectively, and infections prevailed as the main cause of death, associated or not with GVHD. Eighteen patients are alive, the Kaplan-Meyer overall survival is 38% at ~8 years, and the best results were obtained with related non-sibling bone marrow patients. Three recommendations emerged from the present study: fludarabine as part of conditioning, transplant in patients with <25 transfusions and avoidance of HLA disparity. In addition, an extended family search (even when consanguinity is not present) seeking for a related non-sibling donor is highly recommended.

The husk fiber of Cocos nucifera L. (Palmae) is a source of anti-neoplastic activity

In the present study, we investigated the in vitro anti-tumoral activities of fractions from aqueous extracts of the husk fiber of the typical A and common varieties of Cocos nucifera (Palmae). Cytotoxicity against leukemia cells was determined by the 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide (MTT) assay. Cells (2 x 104/well) were incubated with 0, 5, 50 or 500 µg/mL high- or low-molecular weight fractions for 48 h, treated with MTT and absorbance was measured with an ELISA reader. The results showed that both varieties have almost similar antitumoral activity against the leukemia cell line K562 (60.1 ± 8.5 and 47.5 ± 11.9% for the typical A and common varieties, respectively). Separation of the crude extracts with Amicon membranes yielded fractions with molecular weights ranging in size from 1-3 kDa (fraction A) to 3-10 kDa (fraction B) and to more than 10 kDa (fraction C). Cells were treated with 500 µg/mL of these fractions and cytotoxicity was evaluated by MTT. Fractions ranging in molecular weight from 1-10 kDa had higher cytotoxicity. Interestingly, C. nucifera extracts were also active against Lucena 1, a multidrug-resistant leukemia cell line. Their cytotoxicity against this cell line was about 50% (51.9 ± 3.2 and 56.3 ± 2.9 for varieties typical A and common, respectively). Since the common C. nucifera variety is extensively cultured in Brazil and the husk fiber is its industrial by-product, the results obtained in the present study suggest that it might be a very inexpensive source of new antineoplastic and anti-multidrug resistant drugs that warrants further investigation.

EEG spike source localization before and after surgery for temporal lobe epilepsy: a BOLD EEG-fMRI and independent component analysis study

Simultaneous measurements of EEG-functional magnetic resonance imaging (fMRI) combine the high temporal resolution of EEG with the distinctive spatial resolution of fMRI. The purpose of this EEG-fMRI study was to search for hemodynamic responses (blood oxygen level-dependent - BOLD responses) associated with interictal activity in a case of right mesial temporal lobe epilepsy before and after a successful selective amygdalohippocampectomy. Therefore, the study found the epileptogenic source by this noninvasive imaging technique and compared the results after removing the atrophied hippocampus. Additionally, the present study investigated the effectiveness of two different ways of localizing epileptiform spike sources, i.e., BOLD contrast and independent component analysis dipole model, by comparing their respective outcomes to the resected epileptogenic region. Our findings suggested a right hippocampus induction of the large interictal activity in the left hemisphere. Although almost a quarter of the dipoles were found near the right hippocampus region, dipole modeling resulted in a widespread distribution, making EEG analysis too weak to precisely determine by itself the source localization even by a sophisticated method of analysis such as independent component analysis. On the other hand, the combined EEG-fMRI technique made it possible to highlight the epileptogenic foci quite efficiently.