Prediction of 3D structure and ligand-binding properties : ABC transporters and flavodiiron proteins from Synechocystis sp. strain PCC 6803

Cyanobacteria are unicellular, non-nitrogen-fixing prokaryotes, which perform photosynthesis similarly as higher plants. The cyanobacterium Synechocystis sp. strain PCC 6803 is used as a model organism in photosynthesis research. My research described herein aims at understanding the function of the photosynthetic machinery and how it responds to changes in the environment. Detailed knowledge of the regulation of photosynthesis in cyanobacteria can be utilized for biotechnological purposes, for example in the harnessing of solar energy for biofuel production. In photosynthesis, iron participates in electron transfer. Here, we focused on iron transport in Synechocystis sp. strain PCC 6803 and particularly on the environmental regulation of the genes encoding the FutA2BC ferric iron transporter, which belongs to the ABC transporter family. A homology model built for the ATP-binding subunit FutC indicates that it has a functional ATPbinding site as well as conserved interactions with the channel-forming subunit FutB in the transporter complex. Polyamines are important for the cell proliferation, differentiation and apoptosis in prokaryotic and eukaryotic cells. In plants, polyamines have special roles in stress response and in plant survival. The polyamine metabolism in cyanobacteria in response to environmental stress is of interest in research on stress tolerance of higher plants. In this thesis, the potd gene encoding an polyamine transporter subunit from Synechocystis sp. strain PCC 6803 was characterized for the first time. A homology model built for PotD protein indicated that it has capability of binding polyamines, with the preference for spermidine. Furthermore, in order to investigate the structural features of the substrate specificity, polyamines were docked into the binding site. Spermidine was positioned very similarly in Synechocystis PotD as in the template structure and had most favorable interactions of the docked polyamines. Based on the homology model, experimental work was conducted, which confirmed the binding preference. Flavodiiron proteins (Flv) are enzymes, which protect the cell against toxicity of oxygen and/or nitric oxide by reduction. In this thesis, we present a novel type of photoprotection mechanism in cyanobacteria by the heterodimer of Flv2/Flv4. The constructed homology model of Flv2/Flv4 suggests a functional heterodimer capable of rapid electron transfer. The unknown protein sll0218, encoded by the flv2-flv4 operon, is assumed to facilitate the interaction of the Flv2/Flv4 heterodimer and energy transfer between the phycobilisome and PSII. Flv2/Flv4 provides an alternative electron transfer pathway and functions as an electron sink in PSII electron transfer.

Modeling of residual stresses and distortion due to welding in fillet welds

Welding has a growing role in modern world manufacturing. Welding joints are extensively used from pipes to aerospace industries. Prediction of welding residual stresses and distortions is necessary for accurate evaluation of fillet welds in relation to design and safety conditions. Residual stresses may be beneficial or detrimental, depending whether they are tensile or compressive and the loading. They directly affect the fatigue life of the weld by impacting crack growth rate. Beside theoretical background of residual stresses this study calculates residual stresses and deformations due to localized heating by welding process and subsequent rapid cooling in fillet welds. Validated methods are required for this purpose due to complexity of process, localized heating, temperature dependence of material properties and heat source. In this research both empirical and simulation methods were used for the analysis of welded joints. Finite element simulation has become a popular tool of prediction of welding residual stresses and distortion. Three different cases with and without preload have been modeled during this study. Thermal heat load set is used by calculating heat flux from the given heat input energy. First the linear and then nonlinear material behavior model is modeled for calculation of residual stresses. Experimental work is done to calculate the stresses empirically. The results from both the methods are compared to check their reliability. Residual stresses can have a significant effect on fatigue performance of the welded joints made of high strength steel. Both initial residual stress state and subsequent residual stress relaxation need to be considered for accurate description of fatigue behavior. Tensile residual stresses are detrimental and will reduce the fatigue life and compressive residual stresses will increase it. The residual stresses follow the yield strength of base or filler material and the components made of high strength steel are typically thin, where the role of distortion is emphasizing.

Prediction of transients and control reactions in a transonic wind tunnel

This work describes a lumped parameter mathematical model for the prediction of transients in an aerodynamic circuit of a transonic wind tunnel. Control actions to properly handle those perturbations are also assessed. The tunnel circuit technology is up to date and incorporates a novel feature: high-enthalpy air injection to extend the tunnel’s Reynolds number capability. The model solves the equations of continuity, energy and momentum and defines density, internal energy and mass flow as the basic parameters in the aerodynamic study as well as Mach number, stagnation pressure and stagnation temperature, all referred to test section conditions, as the main control variables. The tunnel circuit response to control actions and the stability of the flow are numerically investigated. Initially, for validation purposes, the code was applied to the AWT ("Altitude Wind Tunnel" of NASA-Lewis). In the sequel, the Brazilian transonic wind tunnel was investigated, with all the main control systems modeled, including injection.

The application of Process Management for reliability enhancement of the Taguchi method

The concept of Process Management has been used by managers and consultants that search for the improvement of both operational or managerial industrial processes. Its strength is in focusing on the external client and on the optimization of the internal process in order to fulfill their needs. By the time the needs of internal clients are being sought, a set of improvements takes place. The Taguchi method, because of its claim for knowledge share between design engineers and people engaged in the process, is a candidate for process management implementation. The objective of this paper is to propose that kind of application aiming for improvements related with reliability of results revealed by the robust design of Taguchi method.

A New Model to Determine the Dispersion of Fatigue Damage Evaluations

Reliable predictions of remaining lives of civil or mechanical structures subjected to fatigue damage are very difficult to be made. In general, fatigue damage is extremely sensitive to the random variations of material mechanical properties, environment and loading. These variations may induce large dispersions when the structural fatigue life has to be predicted. Wirsching (1970) mentions dispersions of the order of 30 to 70 % of the mean calculated life. The presented paper introduces a model to estimate the fatigue damage dispersion based on known statistical distributions of the fatigue parameters (material properties and loading). The model is developed by expanding into Taylor series the set of equations that describe fatigue damage for crack initiation.

Modeling of the Fluid-Structure Interaction in Inelastic Piping Systems

In many engineering applications, compliant piping systems conveying liquids are subjected to inelastic deformations due to severe pressure surges such as plastic tubes in modern water supply transmission lines and metallic pipings in nuclear power plants. In these cases the design of such systems may require an adequate modeling of the interactions between the fluid dynamics and the inelastic structural pipe motions. The reliability of the prediction of fluid-pipe behavior depends mainly on the adequacy of the constitutive equations employed in the analysis. In this paper it is proposed a systematic and general approach to consistently incorporate different kinds of inelastic behaviors of the pipe material in a fluid-structure interaction analysis. The main feature of the constitutive equations considered in this work is that a very simple numerical technique can be used for solving the coupled equations describing the dynamics of the fluid and pipe wall. Numerical examples concerning the analysis of polyethylene and stainless steel pipe networks are presented to illustrate the versatility of the proposed approach.

Impact of reliability of supply on long-term development approaches to electricity distribution networks

The Finnish electricity distribution sector, rural areas in particular, is facing major challenges because of the economic regulation, tightening supply security requirements and the ageing network asset. Therefore, the target in the distribution network planning and asset management is to develop and renovate the networks to meet these challenges in compliance with the regulations in an economically feasible way. Concerning supply security, the new Finnish Electricity Market Act limits the maximum duration of electricity supply interruptions to six hours in urban areas and 36 hours in rural areas. This has a significant impact on distribution network planning, especially in rural areas where the distribution networks typically require extensive modifications and renovations to meet the supply security requirements. This doctoral thesis introduces a methodology to analyse electricity distribution system development. The methodology is based on and combines elements of reliability analysis, asset management and economic regulation. The analysis results can be applied, for instance, to evaluate the development of distribution reliability and to consider actions to meet the tightening regulatory requirements. Thus, the methodology produces information for strategic decision-making so that DSOs can respond to challenges arising in the electricity distribution sector. The key contributions of the thesis are a network renovation concept for rural areas, an analysis to assess supply security, and an evaluation of the effects of economic regulation on the strategic network planning. In addition, the thesis demonstrates how the reliability aspect affects the placement of automation devices and how the reserve power can be arranged in a rural area network.

Reliability of SMD interconnections on flexible low-temperature substrates with inkjet-printed conductors

julkaisumaa: NLD

Linear prediction in optical spectroscopy

A linear prediction procedure is one of the approved numerical methods of signal processing. In the field of optical spectroscopy it is used mainly for extrapolation known parts of an optical signal in order to obtain a longer one or deduce missing signal samples. The first is needed particularly when narrowing spectral lines for the purpose of spectral information extraction. In the present paper the coherent anti-Stokes Raman scattering (CARS) spectra were under investigation. The spectra were significantly distorted by the presence of nonlinear nonresonant background. In addition, line shapes were far from Gaussian/Lorentz profiles. To overcome these disadvantages the maximum entropy method (MEM) for phase spectrum retrieval was used. The obtained broad MEM spectra were further underwent the linear prediction analysis in order to be narrowed.

Prediction of market switching and delisting events from OMX First North Nordic multilateral stock exchange

This thesis studies the predictability of market switching and delisting events from OMX First North Nordic multilateral stock exchange by using financial statement information and market information from 2007 to 2012. This study was conducted by using a three stage process. In first stage relevant theoretical framework and initial variable pool were constructed. Then, explanatory analysis of the initial variable pool was done in order to further limit and identify relevant variables. The explanatory analysis was conducted by using self-organizing map methodology. In the third stage, the predictive modeling was carried out with random forests and support vector machine methodologies. It was found that the explanatory analysis was able to identify relevant variables. The results indicate that the market switching and delisting events can be predicted in some extent. The empirical results also support the usability of financial statement and market information in the prediction of market switching and delisting events.

Reliability and validity of the interactive observation scale for psychiatric inpatients applied by nursing aides in daily ward practice

The main characteristic of the nursing Interactive Observation Scale for Psychiatric Inpatients (IOSPI) is the necessity of interaction between raters and patients during assessment. The aim of this study was to evaluate the reliability and validity of the scale in the "real" world of daily ward practice and to determine whether the IOSPI can increase the interaction time between raters and patients and influence the raters' opinion about mental illness. All inpatients of a general university hospital psychiatric ward were assessed daily over a period of two months by 9 nursing aides during the morning and afternoon shifts, with 273 pairs of daily observations. Once a week the patients were interviewed by a psychiatrist who filled in the Brief Psychiatric Rating Scale (BPRS). The IOSPI total score was found to show significant test-retest reliability (interclass correlation coefficient = 0.83) and significant correlation with the BPRS total score (r = 0.69), meeting the criteria of concurrent validity. The instrument can also discriminate between patients in need of further inpatient treatment from those about to be discharged (negative predictive value for discharge = 0.91). Using this scale, the interaction time between nursing aides and patients increased significantly (t = 2.93, P<0.05) and their opinion about the mental illness changed. The "social restrictiveness" factor of the opinion scale about mental illness showed a significant reduction (t = 4.27, P<0.01) and the "interpersonal etiology" factor tended to increase (t = 1.98, P = 0.08). The IOSPI was confirmed as a reliable and valid scale and as an efficient tool to stimulate the therapeutic attitudes of the nursing staff.

Early prediction of poor outcome in patients with acute asthma in the emergency room

Early identification of patients who need hospitalization or patients who should be discharged would be helpful for the management of acute asthma in the emergency room. The objective of the present study was to examine the clinical and pulmonary functional measures used during the first hour of assessment of acute asthma in the emergency room in order to predict the outcome. We evaluated 88 patients. The inclusion criteria were age between 12 and 55 years, forced expiratory volume in the first second below 50% of predicted value, and no history of chronic disease or pregnancy. After baseline evaluation, all patients were treated with 2.5 mg albuterol delivered by nebulization every 20 min in the first hour and 60 mg of intravenous methylprednisolone. Patients were reevaluated after 60 min of treatment. Sixty-five patients (73.9%) were successfully treated and discharged from the emergency room (good responders), and 23 (26.1%) were hospitalized or were treated and discharged with relapse within 10 days (poor responders). A predictive index was developed: peak expiratory flow rates after 1 h <=0% of predicted values and accessory muscle use after 1 h. The index ranged from 0 to 2. An index of 1 or higher presented a sensitivity of 74.0, a specificity of 69.0, a positive predictive value of 46.0, and a negative predictive value of 88.0. It was possible to predict outcome in the first hour of management of acute asthma in the emergency room when the index score was 0 or 2.

Reliability and clinical utility of a Portuguese version of the Abnormal Involuntary Movements Scale (AIMS) for tardive dyskinesia in Brazilian patients

The objective of the present study was to evaluate the reliability and clinical utility of a Portuguese version of the Abnormal Involuntary Movements Scale (AIMS). Videotaped interviews with 16 psychiatric inpatients treated with antipsychotic drugs for at least 5 years were evaluated. Reliability was assessed by the intraclass correlation coefficient (ICC) between three raters, two with and one without clinical training in psychopathology. Clinical utility was assessed by the difference between the scores of patients with (N = 11) and without (N = 5) tardive dyskinesia (TD). Patients with TD exhibited a higher severity of global evaluation by the AIMS (sum of scores: 4.2 ± 0.9 vs 0.4 ± 0.2; score on item 8: 2.3 ± 0.3 vs 0.4 ± 0.2, TD vs controls). The ICC for the global evaluation was fair between the two skilled raters (0.58-0.62) and poor between these raters and the rater without clinical experience (0.05-0.29). Thus, we concluded that the Portuguese version of the AIMS shows an acceptable inter-rater reliability, but only between clinically skilled raters, and that it is clinically useful.

Lightweight, liquid-cooled, direct-drive generator for highpower wind turbines: motivation, concept, and performance

Thesis: A liquid-cooled, direct-drive, permanent-magnet, synchronous generator with helical, double-layer, non-overlapping windings formed from a copper conductor with a coaxial internal coolant conduit offers an excellent combination of attributes to reliably provide economic wind power for the coming generation of wind turbines with power ratings between 5 and 20MW. A generator based on the liquid-cooled architecture proposed here will be reliable and cost effective. Its smaller size and mass will reduce build, transport, and installation costs. Summary: Converting wind energy into electricity and transmitting it to an electrical power grid to supply consumers is a relatively new and rapidly developing method of electricity generation. In the most recent decade, the increase in wind energy’s share of overall energy production has been remarkable. Thousands of land-based and offshore wind turbines have been commissioned around the globe, and thousands more are being planned. The technologies have evolved rapidly and are continuing to evolve, and wind turbine sizes and power ratings are continually increasing. Many of the newer wind turbine designs feature drivetrains based on Direct-Drive, Permanent-Magnet, Synchronous Generators (DD-PMSGs). Being low-speed high-torque machines, the diameters of air-cooled DD-PMSGs become very large to generate higher levels of power. The largest direct-drive wind turbine generator in operation today, rated just below 8MW, is 12m in diameter and approximately 220 tonne. To generate higher powers, traditional DD-PMSGs would need to become extraordinarily large. A 15MW air-cooled direct-drive generator would be of colossal size and tremendous mass and no longer economically viable. One alternative to increasing diameter is instead to increase torque density. In a permanent magnet machine, this is best done by increasing the linear current density of the stator windings. However, greater linear current density results in more Joule heating, and the additional heat cannot be removed practically using a traditional air-cooling approach. Direct liquid cooling is more effective, and when applied directly to the stator windings, higher linear current densities can be sustained leading to substantial increases in torque density. The higher torque density, in turn, makes possible significant reductions in DD-PMSG size. Over the past five years, a multidisciplinary team of researchers has applied a holistic approach to explore the application of liquid cooling to permanent-magnet wind turbine generator design. The approach has considered wind energy markets and the economics of wind power, system reliability, electromagnetic behaviors and design, thermal design and performance, mechanical architecture and behaviors, and the performance modeling of installed wind turbines. This dissertation is based on seven publications that chronicle the work. The primary outcomes are the proposal of a novel generator architecture, a multidisciplinary set of analyses to predict the behaviors, and experimentation to demonstrate some of the key principles and validate the analyses. The proposed generator concept is a direct-drive, surface-magnet, synchronous generator with fractional-slot, duplex-helical, double-layer, non-overlapping windings formed from a copper conductor with a coaxial internal coolant conduit to accommodate liquid coolant flow. The novel liquid-cooling architecture is referred to as LC DD-PMSG. The first of the seven publications summarized in this dissertation discusses the technological and economic benefits and limitations of DD-PMSGs as applied to wind energy. The second publication addresses the long-term reliability of the proposed LC DD-PMSG design. Publication 3 examines the machine’s electromagnetic design, and Publication 4 introduces an optimization tool developed to quickly define basic machine parameters. The static and harmonic behaviors of the stator and rotor wheel structures are the subject of Publication 5. And finally, Publications 6 and 7 examine steady-state and transient thermal behaviors. There have been a number of ancillary concrete outcomes associated with the work including the following. X Intellectual Property (IP) for direct liquid cooling of stator windings via an embedded coaxial coolant conduit, IP for a lightweight wheel structure for lowspeed, high-torque electrical machinery, and IP for numerous other details of the LC DD-PMSG design X Analytical demonstrations of the equivalent reliability of the LC DD-PMSG; validated electromagnetic, thermal, structural, and dynamic prediction models; and an analytical demonstration of the superior partial load efficiency and annual energy output of an LC DD-PMSG design X A set of LC DD-PMSG design guidelines and an analytical tool to establish optimal geometries quickly and early on X Proposed 8 MW LC DD-PMSG concepts for both inner and outer rotor configurations Furthermore, three technologies introduced could be relevant across a broader spectrum of applications. 1) The cost optimization methodology developed as part of this work could be further improved to produce a simple tool to establish base geometries for various electromagnetic machine types. 2) The layered sheet-steel element construction technology used for the LC DD-PMSG stator and rotor wheel structures has potential for a wide range of applications. And finally, 3) the direct liquid-cooling technology could be beneficial in higher speed electromotive applications such as vehicular electric drives.

Prediction of exposed domains of envelope glycoprotein in Indian HIV-1 isolates and experimental confirmation of their immunogenicity in humans

We describe the impact of subtype differences on the seroreactivity of linear antigenic epitopes in envelope glycoprotein of HIV-1 isolates from different geographical locations. By computer analysis, we predicted potential antigenic sites of envelope glycoprotein (gp120 and gp4l) of this virus. For this purpose, after fetching sequences of proteins of interest from data banks, values of hydrophilicity, flexibility, accessibility, inverted hydrophobicity, and secondary structure were considered. We identified several potential antigenic epitopes in a B subtype strain of envelope glycoprotein of HIV-1 (IIIB). Solid- phase peptide synthesis methods of Merrifield and Fmoc chemistry were used for synthesizing peptides. These synthetic peptides corresponded mainly to the C2, V3 and CD4 binding sites of gp120 and some parts of the ectodomain of gp41. The reactivity of these peptides was tested by ELISA against different HIV-1-positive sera from different locations in India. For two of these predicted epitopes, the corresponding Indian consensus sequences (LAIERYLKQQLLGWG and DIIGDIRQAHCNISEDKWNET) (subtype C) were also synthesized and their reactivity was tested by ELISA. These peptides also distinguished HIV-1-positive sera of Indians with C subtype infections from sera from HIV-negative subjects.