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

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.

Suodattimen simulointi Aspen Plus simulointiohjelmistolla

Tässä työssä tutkittiin Aspen Plus-ohjelmiston soveltuvuutta suodattimen simulointiin. Tämän työn kirjallisuusosassa on esitelty eri suodatusmekanismit sekä joitain prosessisimulointiin soveltuvia ohjelmistoja lähdekirjallisuuden perusteella. Kokeellisessa osassa on tutkittu Aspen Plus-ohjelmiston soveltuvuutta suodattimen simuloimiseen. Simulointi suoritettiin käyttäen Aspenin suodatinmoduulin suunnittelumallia. Lähtökohtana käytettiin buchnersuppilolla ZnS-suspensiolle tehtyä koesuodatusta, jonka perusteella saatiin lähtöparametrien, kuten kakun- ja kankaan vastusten arvot. Simuloinnissa mitoitettiin samalle kapasiteetille rumpusuodatin, jonka suodatuspinta-alaa ja kiintoainekakun tilavuutta verrattiin koesuodatuksen vastaaviin arvoihin. Lisäksi vastaava simulointi suoritettiin filtration-and-separation.com sivuston omaa vakiopaineisen vakuumisuodattimen simulointiin tarkoitettua laskentapohjaa käyttäen, jonka tuloksia verrattiin myös Aspenilla saatuihin simulointituloksiin.

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.

Advanced analysis and design methods for preparative chromatographic separation processes

Preparative liquid chromatography is one of the most selective separation techniques in the fine chemical, pharmaceutical, and food industries. Several process concepts have been developed and applied for improving the performance of classical batch chromatography. The most powerful approaches include various single-column recycling schemes, counter-current and cross-current multi-column setups, and hybrid processes where chromatography is coupled with other unit operations such as crystallization, chemical reactor, and/or solvent removal unit. To fully utilize the potential of stand-alone and integrated chromatographic processes, efficient methods for selecting the best process alternative as well as optimal operating conditions are needed. In this thesis, a unified method is developed for analysis and design of the following singlecolumn fixed bed processes and corresponding cross-current schemes: (1) batch chromatography, (2) batch chromatography with an integrated solvent removal unit, (3) mixed-recycle steady state recycling chromatography (SSR), and (4) mixed-recycle steady state recycling chromatography with solvent removal from fresh feed, recycle fraction, or column feed (SSR–SR). The method is based on the equilibrium theory of chromatography with an assumption of negligible mass transfer resistance and axial dispersion. The design criteria are given in general, dimensionless form that is formally analogous to that applied widely in the so called triangle theory of counter-current multi-column chromatography. Analytical design equations are derived for binary systems that follow competitive Langmuir adsorption isotherm model. For this purpose, the existing analytic solution of the ideal model of chromatography for binary Langmuir mixtures is completed by deriving missing explicit equations for the height and location of the pure first component shock in the case of a small feed pulse. It is thus shown that the entire chromatographic cycle at the column outlet can be expressed in closed-form. The developed design method allows predicting the feasible range of operating parameters that lead to desired product purities. It can be applied for the calculation of first estimates of optimal operating conditions, the analysis of process robustness, and the early-stage evaluation of different process alternatives. The design method is utilized to analyse the possibility to enhance the performance of conventional SSR chromatography by integrating it with a solvent removal unit. It is shown that the amount of fresh feed processed during a chromatographic cycle and thus the productivity of SSR process can be improved by removing solvent. The maximum solvent removal capacity depends on the location of the solvent removal unit and the physical solvent removal constraints, such as solubility, viscosity, and/or osmotic pressure limits. Usually, the most flexible option is to remove solvent from the column feed. Applicability of the equilibrium design for real, non-ideal separation problems is evaluated by means of numerical simulations. Due to assumption of infinite column efficiency, the developed design method is most applicable for high performance systems where thermodynamic effects are predominant, while significant deviations are observed under highly non-ideal conditions. The findings based on the equilibrium theory are applied to develop a shortcut approach for the design of chromatographic separation processes under strongly non-ideal conditions with significant dispersive effects. The method is based on a simple procedure applied to a single conventional chromatogram. Applicability of the approach for the design of batch and counter-current simulated moving bed processes is evaluated with case studies. It is shown that the shortcut approach works the better the higher the column efficiency and the lower the purity constraints are.

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.

Intravenous dipyrone for the acute treatment of episodic tension-type headache: A randomized, placebo-controlled, double-blind study

Acute headaches are responsible for a significant percentage of the case load at primary care units and emergency rooms in Brazil. Dipyrone (metamizol) is easily available in these settings, being the most frequently used drug. We conducted a randomized, placebo-controlled, double-blind study to assess the effect of dipyrone in the acute treatment of episodic tension-type headache. Sixty patients were randomized to receive placebo (intravenous injection of 10 ml saline) or 1 g dipyrone in 10 ml saline. We used seven parameters of analgesic evaluation. The patients receiving dipyrone showed a statistically significant improvement (P<0.05) of pain compared to placebo up to 30 min after drug administration. The therapeutic gain was 30% in 30 min and 40% in 60 min. The number of patients needed to be treated for at least one to have benefit was 3.3 in 30 min and 2.2 in 60 min. There were statistically significant reductions in the recurrence (dipyrone = 25%, placebo = 50%) and use of rescue medication (dipyrone = 20%, placebo = 47.6%) for the dipyrone group. Intravenous dipyrone is an effective drug for the relief of pain in tension-type headache and its use is justified in the emergency room setting.

Effect of cocaine on periadolescent rats with or without early maternal separation

Cocaine-induced behavioral sensitization and weight loss were investigated in periadolescent Wistar rats kept with their mothers or subjected to repeated maternal separation. Litters allocated to the separation procedure were placed in a temperature-controlled (33ºC) chamber for 3 h per day from postnatal day 6 (P6) to P20. Non-handled rats were left undisturbed until weaning. Treatments were started on P30-31 and the test was performed on P36-37. Animals received injections of saline or cocaine (10 mg/kg, sc) twice daily for 5 days. On day 6 all animals received saline. On day 7 animals were challenged with 10 mg/kg cocaine and their locomotion was evaluated in activity cages. A third group received saline throughout the 7-day period. Body weights were recorded on P30-31 and P36-37. Two-way ANOVA on body weights showed a main effect of treatment group (F(1,35) = 10.446, P = 0.003; N = 10-12). Non-handled rats treated with cocaine for 5 days gained significantly less weight, while no significant effect was observed in maternally separated rats. Two-way ANOVA revealed a main effect of drug treatment on locomotor activity (F(2,32) = 15.209, P<0.001; N = 6-8), but not on rearing condition (F(1,32)<0.001, P = 0.998). Animals pretreated with cocaine showed a clear behavioral sensitization relative to the saline group. No difference in the magnitude of sensitization was found between separated and non-handled animals. Only the effect of cocaine on weight gain was significantly affected by repeated episodes of early maternal separation during the pre-weaning period.

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.

A randomized double-blind study of the short-time treatment of obese patients with nonalcoholic fatty liver disease with ursodeoxycholic acid

In order to determine the effect of ursodeoxycholic acid on nonalcoholic fatty liver disease, 30 patients with body mass indices higher than 25, serum levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST) or gamma-glutamyltransferase (gamma-GT) at least more than 1.5 times the upper limit of normality, and hepatic steatosis demonstrated by ultrasonography were randomized into two groups of 15 patients to receive placebo or 10 mg kg-1 day-1 ursodeoxycholic acid for three months. Abdominal computed tomography was performed to quantify hepatic fat content, which was significantly correlated with histological grading of steatosis (r s = -0.83, P < 0.01). Patient body mass index remained stable for both groups throughout the study, but a significant reduction in mean (± SEM) serum levels of ALT, AST and gamma-GT was observed only in the treated group (ALT = 81.2 ± 9.7, 44.8 ± 7.7, 48.1 ± 7.7 and 52.2 ± 6.3 IU/l at the beginning and after the first, second and third months, respectively, N = 14, P < 0.05). For the placebo group ALT values were 66.4 ± 9.8, 54.5 ± 7, 60 ± 7.6 and 43.7 ± 5 IU/l, respectively. No alterations in hepatic lipid content were observed in these patients by computed tomography examination (50.2 ± 4.2 Hounsfield units (HU) at the beginning versus 51.1 ± 4.1 HU at the third month). These results show that ursodeoxycholic acid is able to reduce serum levels of hepatic enzymes in patients with nonalcoholic fatty liver disease, but this effect is not related to modifications in liver fat content.

A randomized, double-blind, and placebo-controlled study with tranexamic acid of bleeding and fibrinolytic activity after primary coronary artery bypass grafting

Cardiopulmonary bypass is frequently associated with excessive blood loss. Platelet dysfunction is the main cause of non-surgical bleeding after open-heart surgery. We randomized 65 patients in a double-blind fashion to receive tranexamic acid or placebo in order to determine whether antifibrinolytic therapy reduces chest tube drainage. The tranexamic acid group received an intravenous loading dose of 10 mg/kg, before the skin incision, followed by a continuous infusion of 1 mg kg-1 h-1 for 5 h. The placebo group received a bolus of normal saline solution and continuous infusion of normal saline for 5 h. Postoperative bleeding and fibrinolytic activity were assessed. Hematologic data, convulsive seizures, allogeneic transfusion, occurrence of myocardial infarction, mortality, allergic reactions, postoperative renal insufficiency, and reopening rate were also evaluated. The placebo group had a greater postoperative blood loss (median (25th to 75th percentile) 12 h after surgery (540 (350-750) vs 300 (250-455) mL, P = 0.001). The placebo group also had greater blood loss 24 h after surgery (800 (520-1050) vs 500 (415-725) mL, P = 0.008). There was a significant increase in plasma D-dimer levels after coronary artery bypass grafting only in patients of the placebo group, whereas no significant changes were observed in the group treated with tranexamic acid. The D-dimer levels were 1057 (1025-1100) µg/L in the placebo group and 520 (435-837) µg/L in the tranexamic acid group (P = 0.01). We conclude that tranexamic acid effectively reduces postoperative bleeding and fibrinolysis in patients undergoing first-time coronary artery bypass grafting compared to placebo.

Isolation and Characterization of Ovomucin - a Bioactive Agent of Egg White

The hen’s egg is a source of new life. Therefore, it contains many biologically active compounds. In addition to being a very nutritious food and also commonly used in the food industry due to its many techno-functional properties, the egg can serve as a source of compounds used as nutra-, pharmaand cosmeceuticals. One such interesting compound is ovomucin, an egg white protein responsible for the gel-like properties of thick egg white. Previous studies have indicated that ovomucin and ovomucin-derived peptides have several different bioactive properties. The objectives of the present study were to develop isolation methods for ovomucin, to characterize the structure of ovomucin, to compare various egg fractions as sources of ovomucin, to study the effects of various dissolving methods for ovomucin, and to investigate the bioactive properties of ovomucin and ovomucin-derived peptides. A simple and rapid method for crude ovomucin separation was developed. By using this method crude ovomucin was isolated within hours, compared to the 1-2 days (including a dialysis step) needed when using several other methods. Structural characterization revealed that ovomucin is composed of two subunits, α- and β-ovomucin, as egg white protein formerly called α1-ovomucin seemed to be ovostatin. However, it might be possible that ovostatin is associated within β- and α-ovomucin. This interaction could even have some effect on the physical nature of various egg white layers. Although filtration by-product fraction was a very prominent source of both crude and β-ovomucin, process development has reduced its amount so significantly that it has no practical meaning anymore. Thus, the commercial liquid egg white is probably the best option, especially if it generally contains amounts of β-ovomucin as high as were found in these studies. Crude ovomucin was dissolved both by using physical and enzymic methods. Although sonication was the most effective physical method for ovomucin solubilisation, colloid milling seemed to be a very promising alternative. A milk-like, smooth and opaque crude ovomucin suspension was attained by using a colloid mill. The dissolved ovomucin fractions were further tested for bioactive properties, and it was found that three dissolving methods tested produced moderate antiviral activity against Newcastle disease virus, namely colloid milling, enzymatic hydrolysis and a combination of sonicaton and enzymatic hydrolysis. Moreover, trypsin-digested crude ovomucin was found to have moderate antiviral activity against avian influenza virus: both subtype H5 and H7.