NADPH-Dependent Thioredoxin System In Regulation of Chloroplast Functions

Photosynthesis, the process in which carbon dioxide is converted into sugars using the energy of sunlight, is vital for heterotrophic life on Earth. In plants, photosynthesis takes place in specific organelles called chloroplasts. During chloroplast biogenesis, light is a prerequisite for the development of functional photosynthetic structures. In addition to photosynthesis, a number of other metabolic processes such as nitrogen assimilation, the biosynthesis of fatty acids, amino acids, vitamins, and hormones are localized to plant chloroplasts. The biosynthetic pathways in chloroplasts are tightly regulated, and especially the reduction/oxidation (redox) signals play important roles in controlling many developmental and metabolic processes in chloroplasts. Thioredoxins are universal regulatory proteins that mediate redox signals in chloroplasts. They are able to modify the structure and function of their target proteins by reduction of disulfide bonds. Oxidized thioredoxins are restored via the action of thioredoxin reductases. Two thioredoxin reductase systems exist in plant chloroplasts, the NADPHdependent thioredoxin reductase C (NTRC) and ferredoxin-thioredoxin reductase (FTR). The ferredoxin-thioredoxin system that is linked to photosynthetic light reactions is involved in light-activation of chloroplast proteins. NADPH can be produced via both the photosynthetic electron transfer reactions in light, and in darkness via the pentose phosphate pathway. These different pathways of NADPH production enable the regulation of diverse metabolic pathways in chloroplasts by the NADPH-dependent thioredoxin system. In this thesis, the role of NADPH-dependent thioredoxin system in the redox-control of chloroplast development and metabolism was studied by characterization of Arabidopsis thaliana T-DNA insertion lines of NTRC gene (ntrc) and by identification of chloroplast proteins regulated by NTRC. The ntrc plants showed the strongest visible phenotypes when grown under short 8-h photoperiod. This indicates that i) chloroplast NADPH-dependent thioredoxin system is non-redundant to ferredoxinthioredoxin system and that ii) NTRC particularly controls the chloroplast processes that are easily imbalanced in daily light/dark rhythms with short day and long night. I identified four processes and the redox-regulated proteins therein that are potentially regulated by NTRC; i) chloroplast development, ii) starch biosynthesis, iii) aromatic amino acid biosynthesis and iv) detoxification of H₂O₂. Such regulation can be achieved directly by modulating the redox state of intramolecular or intermolecular disulfide bridges of enzymes, or by protecting enzymes from oxidation in conjunction with 2-cysteine peroxiredoxins. This thesis work also demonstrated that the enzymatic antioxidant systems in chloroplasts, ascorbate peroxidases, superoxide dismutase and NTRC-dependent 2-cysteine peroxiredoxins are tightly linked up to prevent the detrimental accumulation of reactive oxygen species in plants.

Novel force control methods in a teleoperation system of a hydraulic slider

The objective of the this research project is to develop a novel force control scheme for the teleoperation of a hydraulically driven manipulator, and to implement an ideal transparent mapping between human and machine interaction, and machine and task environment interaction. This master‘s thesis provides a preparatory study for the present research project. The research is limited into a single degree of freedom hydraulic slider with 6-DOF Phantom haptic device. The key contribution of the thesis is to set up the experimental rig including electromechanical haptic device, hydraulic servo and 6-DOF force sensor. The slider is firstly tested as a position servo by using previously developed intelligent switching control algorithm. Subsequently the teleoperated system is set up and the preliminary experiments are carried out. In addition to development of the single DOF experimental set up, methods such as passivity control in teleoperation are reviewed. The thesis also contains review of modeling of the servo slider in particular reference to the servo valve. Markov Chain Monte Carlo method is utilized in developing the robustness of the model in presence of noise.

Feature selection using Fuzzy Entropy measures with Yu's Similarity measure

In this study, feature selection in classification based problems is highlighted. The role of feature selection methods is to select important features by discarding redundant and irrelevant features in the data set, we investigated this case by using fuzzy entropy measures. We developed fuzzy entropy based feature selection method using Yu's similarity and test this using similarity classifier. As the similarity classifier we used Yu's similarity, we tested our similarity on the real world data set which is dermatological data set. By performing feature selection based on fuzzy entropy measures before classification on our data set the empirical results were very promising, the highest classification accuracy of 98.83% was achieved when testing our similarity measure to the data set. The achieved results were then compared with some other results previously obtained using different similarity classifiers, the obtained results show better accuracy than the one achieved before. The used methods helped to reduce the dimensionality of the used data set, to speed up the computation time of a learning algorithm and therefore have simplified the classification task

Nonlinear dynamics and control of multibody systems

The dynamics of flexible systems, such as robot manipulators , mechanical chains or multibody systems in general, is becoming increasingly important in engineering. This article deals with some nonlinearities that arise in the study of dynamics and control of multibody systems in connection to large rotations. Specifically, a numerical scheme that adresses the conservation of fundamental constants is presented in order to analyse the control-structure interaction problems.

Variable structure position control of an industrial robotic manipulator

The use of a robust position controller for a robotic manipulator moving in free space is presented. The aim is to implement in practice a controller that is robust to uncertainties in the model of the system, as well as being inexpensive from a computational point of view. Variable structure theory provides the technique for the design of such controller. The design steps are presented, first from a theoretical perspective and then applied to the control of a two degree-of-freedom manipulator. Simulation results that backed the implementation are presented, followed by the experiments conducted and the results that were obtained. The conclusion is that variable structure control is readily applicable to industrial robots for the robust control of positions.

On-site calibration of a phase fraction meter by an inverse technique

The formal calibration procedure of a phase fraction meter is based on registering the outputs resulting from imposed phase fractions at known flow regimes. This can be straightforwardly done in laboratory conditions, but is rarely the case in industrial conditions, and particularly for on-site applications. Thus, there is a clear need for less restrictive calibration methods regarding to the prior knowledge of the complete set of inlet conditions. A new procedure is proposed in this work for the on-site construction of the calibration curve from total flown mass values of the homogeneous dispersed phase. The solution is obtained by minimizing a convenient error functional, assembled with data from redundant tests to handle the intrinsic ill-conditioned nature of the problem. Numerical simulations performed for increasing error levels demonstrate that acceptable calibration curves can be reconstructed, even from total mass measured within a precision of up to 2%. Consequently, the method can readily be applied, especially in on-site calibration problems in which classical procedures fail due to the impossibility of having a strict control of all the input/output parameters.

m-Equine : IS support for the horse industry

The horse industry is in many ways still operating the same way as it did in the beginning of the 20th century. At the same time the role of the horse has changed dramatically, from a beast of burden to a top athlete, a production animal or a beloved pet. A racehorse or an equestrian sport horse is trained and taken care of like any other athlete, but unlike its human counterpart, it might end up on our plate. According to European and many other countries’ laws, a horse is a production animal. The medical data of a horse should be known if it is to be slaughtered, to ensure that the meat is safe for human consumption. Today this vital medical information should be noted in the horse’s passport, but this paperbased system is not reliable. If a horse gets sold, depending on the country’s laws, the medical records might not be transferred to the new owner, the horse’s passport might get lost etc. Thus the system is not fool proof. It is not only the horse owners who have to struggle with paperwork; veterinarians as well as other officials often use much time on redundant paperwork. The main research question of this thesis is if IS could be used to help the different stakeholders within the horse industry? Veterinarians in particular who travel to stables to treat horses cannot always take with them their computers, since the somewhat unsanitary environment is not suitable for a sensitive technological device. Currently there is no common medical database developed for horses, although such a database with a support system could help with many problems. These include vaccination and disease control, food-safety, as well as export and import problems. The main stakeholders within the horse industry, including equine veterinarians and horse owners, were studied to find out their daily routines and needs for a possible support system. The research showed that there are different aspects within the horse industry where IS could be used to support the stakeholders daily routines. Thus a support system including web and mobile accessibility for the main stakeholders is under development. Since veterinarians will be the main users of this support system, it is very important to make sure that they find it useful and beneficial in their daily work. To ensure a desired result, the research and development of the system has been done iteratively with the stakeholders following the Action Design Research methodology.

Potential of macrophyte for removing arsenic from aqueous solution

The potential of three aquatic macrophytes, Azoll caroliniana, Salvinia minima and Lemna gibba, was evaluated in this work aimed at selection of plants to be used in remediation of environments contaminated by arsenic (As). The experiments were carried out in a greenhouse during six days in pots containing Hoagland solution (¼ ionic strength) at As concentrations of 0.5; 2.5 and 5.0 mg L-1. The three species showed greater As accumulation as the concentration of the metalloid in solution increased. However, a reduction was detected in fresh and dry mass gain when the plants were exposed to high As concentrations. The macrophytes showed differences in efficiency of removal of As in solution. A. caroliniana, S. minima and L. gibba accumulated, on average, 0.130; 0.200; and 1.397 mg mDM-1, respectively, when exposed to 5.0 mg L-1 of As. The macrophytes absorbed a greater quantity of As in solution with low phosphate content. The greater As concentration in L. gibba tissues lowered the chlorophyll and carotenoid contents as shown by the high chlorosis incidence. Lemna gibba also exhibited a decrease in leaf size, with the total chlorophyll and carotenoid synthesis not being affected by As in A. caroliniana. This species exhibited purplish leaves with high concentration of anthocyanin, whose presence suggested association to phosphate deficiency. Marginal necrosis occurred on S. minima floating leaves, with the released daughter-plants not showing any visual symptoms during the treatment. The percentage of As removed from the solution decreased when the plants were exposed to high concentrations of the pollutant. Among the three species studied, only L. gibba could be considered an As hyper-accumulator. The use of this plant species for remediation of aquatic environments was shown to be limited and requires further investigation.

Toward a-state-of-the-art IR copyright management system: a needs assessment

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

Chemokines, lymphocytes, and HIV

Chemokines are members of a family of more than 30 human cytokines whose best-described activities are as chemotactic factors for leukocytes and that are presumed to be important in leukocyte recruitment and trafficking. While many chemokines can act on lymphocytes, the roles of chemokines and their receptors in lymphocyte biology are poorly understood. The recent discoveries that chemokines can suppress infection by HIV-1 and that chemokine receptors serve, along with CD4, as obligate co-receptors for HIV-1 entry have lent urgency to studies on the relationships between chemokines and lymphocytes. My laboratory has characterized Mig and Crg-2/IP-10, chemokines that are induced by IFN-g and that specifically target lymphocytes, particularly activated T cells. We have demonstrated that the genes for these chemokines are widely expressed during experimental infections in mice with protozoan and viral pathogens, but that the patterns of mig and crg-2 expression differed, suggesting non-redundant roles in vivo. Our related studies to identify new chemokine receptors from activated lymphocytes resulted in the cloning of STRL22 and STRL33. We and others have shown that STRL22 is a receptor for the CC chemokine MIP-3a, and STRL22 has been re-named CCR6. Although STRL33 remains an orphan receptor, we have shown that it can function as a co-receptor for HIV-1 envelope glycoproteins, and that it is active with a broader range of HIV-1 envelope glycoproteins than the major co-receptors described to date. The ability of STRL33 to function with a wide variety of envelope glycoproteins may become particularly important if therapies are instituted to block other specific co-receptors. We presume that investigations into the roles of chemokines and their receptors in lymphocyte biology will provide information important for understanding the pathogenesis of AIDS and for manipulating immune and inflammatory responses for clinical benefit

Stiffness based trajectory planning and feedforward based vibration suppression control of parallel robot machines

The dissertation proposes two control strategies, which include the trajectory planning and vibration suppression, for a kinematic redundant serial-parallel robot machine, with the aim of attaining the satisfactory machining performance. For a given prescribed trajectory of the robot's end-effector in the Cartesian space, a set of trajectories in the robot's joint space are generated based on the best stiffness performance of the robot along the prescribed trajectory. To construct the required system-wide analytical stiffness model for the serial-parallel robot machine, a variant of the virtual joint method (VJM) is proposed in the dissertation. The modified method is an evolution of Gosselin's lumped model that can account for the deformations of a flexible link in more directions. The effectiveness of this VJM variant is validated by comparing the computed stiffness results of a flexible link with the those of a matrix structural analysis (MSA) method. The comparison shows that the numerical results from both methods on an individual flexible beam are almost identical, which, in some sense, provides mutual validation. The most prominent advantage of the presented VJM variant compared with the MSA method is that it can be applied in a flexible structure system with complicated kinematics formed in terms of flexible serial links and joints. Moreover, by combining the VJM variant and the virtual work principle, a systemwide analytical stiffness model can be easily obtained for mechanisms with both serial kinematics and parallel kinematics. In the dissertation, a system-wide stiffness model of a kinematic redundant serial-parallel robot machine is constructed based on integration of the VJM variant and the virtual work principle. Numerical results of its stiffness performance are reported. For a kinematic redundant robot, to generate a set of feasible joints' trajectories for a prescribed trajectory of its end-effector, its system-wide stiffness performance is taken as the constraint in the joints trajectory planning in the dissertation. For a prescribed location of the end-effector, the robot permits an infinite number of inverse solutions, which consequently yields infinite kinds of stiffness performance. Therefore, a differential evolution (DE) algorithm in which the positions of redundant joints in the kinematics are taken as input variables was employed to search for the best stiffness performance of the robot. Numerical results of the generated joint trajectories are given for a kinematic redundant serial-parallel robot machine, IWR (Intersector Welding/Cutting Robot), when a particular trajectory of its end-effector has been prescribed. The numerical results show that the joint trajectories generated based on the stiffness optimization are feasible for realization in the control system since they are acceptably smooth. The results imply that the stiffness performance of the robot machine deviates smoothly with respect to the kinematic configuration in the adjacent domain of its best stiffness performance. To suppress the vibration of the robot machine due to varying cutting force during the machining process, this dissertation proposed a feedforward control strategy, which is constructed based on the derived inverse dynamics model of target system. The effectiveness of applying such a feedforward control in the vibration suppression has been validated in a parallel manipulator in the software environment. The experimental study of such a feedforward control has also been included in the dissertation. The difficulties of modelling the actual system due to the unknown components in its dynamics is noticed. As a solution, a back propagation (BP) neural network is proposed for identification of the unknown components of the dynamics model of the target system. To train such a BP neural network, a modified Levenberg-Marquardt algorithm that can utilize an experimental input-output data set of the entire dynamic system is introduced in the dissertation. Validation of the BP neural network and the modified Levenberg- Marquardt algorithm is done, respectively, by a sinusoidal output approximation, a second order system parameters estimation, and a friction model estimation of a parallel manipulator, which represent three different application aspects of this method.

Bariatric and Post-Bariatric Surgery: from Metabolic Surgery to Plastic Surgery Indications

Background: Controversy exists concerning indications and outcomes of major bariatric surgery procedures. Massive weight loss after bariatric surgery leads to excess skin with functional and aesthetic impairments. The aim of this study was to investigate the major bariatric surgery procedures and their outcomes in two specific subgroups of morbidly obese patients, ≥55-year-olds and the superobese. Further aims were to evaluate whether the preoperative weight loss correlates with laparoscopic gastric bypass complications. The prevalence and impact of excess skin and the desire for body contouring after bariatric surgery were also studied. Patients and Methods: Data from patients who underwent Laparoscopic Adjustable Gastric Banding (LAGB) and Laparoscopic Roux-en-Y Gastric Bypass (LRYGB) at Vaasa Central Hospital were collected and postoperative outcomes were evaluated according to the BMI, age and preoperative weight loss. Patients who had undergone bariatric surgery procedures were asked to complete a questionnaire to estimate any impairment due to redundant skin and to analyse each patient’s desire for body contouring by area. Results: No significant difference was found in operative time, hospital stay, or overall early postoperative morbidity between LAGB and LRYGB. Mean excess weight loss percents (EWL%) at 6 and 12 months after LRYGB were significantly higher. A significant difference was found in operative time favouring patients <55 years. Intraoperative complications were significantly more frequent in the group aged >55 years. No significant difference was detected in overall postoperative morbidity rates. A significant difference was found in operative time and hospital stay favouring all patients who lost weight preoperatively. Most patients reported problems with redundant skin, especially on the abdomen, upper arms and rear/buttocks, which impaired daily physical activity in half of them. Excess skin was significantly associated with female gender, weight loss and ΔBMI. Patients with a WL >20 kg, ΔBMI ≥10 kg/m2 and an EWL % > 50 showed a significantly surplus skin discomfort (p < 0.001). Most patients desired body contouring surgery, with high or very high desire for waist/abdomen (62.2%), upper arm (37.6%), chest/breast (28.3%), and rear/buttock (35.6%) contouring. Conclusions: LRYGB is effective and safe in superobese (BMI >50) and elderly (>55 years) patients. A preoperative weight loss >5% is recommended to improve the outcomes and reduce complications. A WL >20 kg, ΔBMI ≥10 kg/m2 and an EWL % > 50 are associated with a higher functional discomfort due to redundant skin and to a stronger desire for body contouring plastic surgery.

Tuotekehitysprosessin alkupään järjestäminen pelialan yrityksessä

Tämän diplomityön tarkoitus on rakentaa mobiilipeliyritykselle tuotekehitysprosessin alkupään prosessi tuotekehityksen tehostamiseksi. Toimialan dynaamisuudesta ja hyperkilpailullisuudesta johtuen sekä projektien abstraktin luonteen takia tulee mobiilipelikehitysyritysten erityisesti panostaa tuotekehityksen alkuvaiheisiin. Työ tutkii yleisiä tuotekehityksen periaatteita sekä yleisiä olemassaolevia tuotekehitysprosesseja. Tarkastelun kohteena ovat erityisesti innovatiivinen organisaatio ja benchmarking tuotekehityksen apuna. Yleisesti tuotekehitysprosesseista tutustutaan yleisimpiin malleihin, jotka ovat olleet valtavirran käytössä jo pitkään. Prosessien tarkastelun lisäksi niitä tutkitaan kriittisesti ja löydetään osa-alueita, joihin tulee keskittyä erityisesti tuotekehitysprosessin alkupään järjestämisessä. Lisäksi työssä paneudutaan alan menestyneiden yritysten toimintatapoihin, joista haetaan oppia rakennettavaan malliin. Työssä käsitellään myös toimialan ominaispiirteitä, joista johtuen perinteiset tuotekehitysprosessit eivät ole optimaalisia alalle. Työn tuloksena saadaan virtaviivainen prosessimalli, joka maksimoi luovuuden, mutta säästää resursseja ja luo selkeät linjat prosessin läpivientiin. Rakennettuun malliin pohditaan myös kehitysehdotuksia, ja sille on laadittu kevyt jatkokehityssuunnitelma. Malli menee suoraan yrityksen käyttöön, joten lopullinen malli tulee myös hioutumaan tuotekehitysprojektien edetessä. Työssä on erityistä se, että työn tekijä on toiminut alalla työtehtävissä, ja malli on hioutunut pitkän ajan kuluessa. Täten suuri osa työstä on tekijän hiljaisen tiedon avaamista ja pohtimista.

Health in early adulthood: the contribution of the 1978/79 Ribeirão Preto birth cohort

The increase in non-communicable chronic diseases of adults is due to demographic changes and changes in the risk factors related to physical activity, smoking habits and nutrition. We describe the methodology for the evaluation of persons at 23/25 years of age of a cohort of individuals born in Ribeirão Preto in 1978/79. We present their socioeconomic characteristics and the profile of some risk factors for chronic diseases. A total of 2063 participants were evaluated by means of blood collection, standardized questionnaires, anthropometric and blood pressure measurements, and methacholine bronchoprovocation tests. The sexes were compared by the chi-square test, with alpha = 0.05. Obesity was similar among men and women (12.8 and 11.1%); overweight was almost double in men (30.3 vs 17.7%). Weight deficit was higher among women than among men (8.6 and 2.6%). Women were more sedentary and consumed less alcohol and tobacco. Dietary fat consumption was similar between sexes, with 63% consuming large amounts (30 to 39.9 g/day). Metabolic syndrome was twice more frequent among men than women (10.7 vs 4.8%), hypertension was six times more frequent (40.9 vs 6.4%); altered triglyceride (16.1 vs 9.8%) and LDL proportions (5.4 vs 2.7%) were also higher in men, while women had a higher percentage of low HDL (44.7 vs 39.5%). Asthma and bronchial hyper-responsiveness were 1.7 and 1.5 times more frequent, respectively, among women. The high prevalence of some risk factors for chronic diseases among young adults supports the need for investments in their prevention.

Nucleotide-sugar transporters: structure, function and roles in vivo

The glycosylation of glycoconjugates and the biosynthesis of polysaccharides depend on nucleotide-sugars which are the substrates for glycosyltransferases. A large proportion of these enzymes are located within the lumen of the Golgi apparatus as well as the endoplasmic reticulum, while many of the nucleotide-sugars are synthesized in the cytosol. Thus, nucleotide-sugars are translocated from the cytosol to the lumen of the Golgi apparatus and endoplasmic reticulum by multiple spanning domain proteins known as nucleotide-sugar transporters (NSTs). These proteins were first identified biochemically and some of them were cloned by complementation of mutants. Genome and expressed sequence tag sequencing allowed the identification of a number of sequences that may encode for NSTs in different organisms. The functional characterization of some of these genes has shown that some of them can be highly specific in their substrate specificity while others can utilize up to three different nucleotide-sugars containing the same nucleotide. Mutations in genes encoding for NSTs can lead to changes in development in Drosophila melanogaster or Caenorhabditis elegans, as well as alterations in the infectivity of Leishmania donovani. In humans, the mutation of a GDP-fucose transporter is responsible for an impaired immune response as well as retarded growth. These results suggest that, even though there appear to be a fair number of genes encoding for NSTs, they are not functionally redundant and seem to play specific roles in glycosylation.