Geo-enabling repositories - techniques, tools, and challenges

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

Segmentation of overlapping convex objects

This thesis presents a framework for segmentation of clustered overlapping convex objects. The proposed approach is based on a three-step framework in which the tasks of seed point extraction, contour evidence extraction, and contour estimation are addressed. The state-of-art techniques for each step were studied and evaluated using synthetic and real microscopic image data. According to obtained evaluation results, a method combining the best performers in each step was presented. In the proposed method, Fast Radial Symmetry transform, edge-to-marker association algorithm and ellipse fitting are employed for seed point extraction, contour evidence extraction and contour estimation respectively. Using synthetic and real image data, the proposed method was evaluated and compared with two competing methods and the results showed a promising improvement over the competing methods, with high segmentation and size distribution estimation accuracy.

Algorithmic Techniques in Gene Expression Processing. From Imputation to Visualization

The amount of biological data has grown exponentially in recent decades. Modern biotechnologies, such as microarrays and next-generation sequencing, are capable to produce massive amounts of biomedical data in a single experiment. As the amount of the data is rapidly growing there is an urgent need for reliable computational methods for analyzing and visualizing it. This thesis addresses this need by studying how to efficiently and reliably analyze and visualize high-dimensional data, especially that obtained from gene expression microarray experiments. First, we will study the ways to improve the quality of microarray data by replacing (imputing) the missing data entries with the estimated values for these entries. Missing value imputation is a method which is commonly used to make the original incomplete data complete, thus making it easier to be analyzed with statistical and computational methods. Our novel approach was to use curated external biological information as a guide for the missing value imputation. Secondly, we studied the effect of missing value imputation on the downstream data analysis methods like clustering. We compared multiple recent imputation algorithms against 8 publicly available microarray data sets. It was observed that the missing value imputation indeed is a rational way to improve the quality of biological data. The research revealed differences between the clustering results obtained with different imputation methods. On most data sets, the simple and fast k-NN imputation was good enough, but there were also needs for more advanced imputation methods, such as Bayesian Principal Component Algorithm (BPCA). Finally, we studied the visualization of biological network data. Biological interaction networks are examples of the outcome of multiple biological experiments such as using the gene microarray techniques. Such networks are typically very large and highly connected, thus there is a need for fast algorithms for producing visually pleasant layouts. A computationally efficient way to produce layouts of large biological interaction networks was developed. The algorithm uses multilevel optimization within the regular force directed graph layout algorithm.

Liquid cooling solutions for rotating permanent magnet synchronous machines

In the design of electrical machines, efficiency improvements have become very important. However, there are at least two significant cases in which the compactness of electrical machines is critical and the tolerance of extremely high losses is valued: vehicle traction, where very high torque density is desired at least temporarily; and direct-drive wind turbine generators, whose mass should be acceptably low. As ever higher torque density and ever more compact electrical machines are developed for these purposes, thermal issues, i.e. avoidance of over-temperatures and damage in conditions of high heat losses, are becoming of utmost importance. The excessive temperatures of critical machine components, such as insulation and permanent magnets, easily cause failures of the whole electrical equipment. In electrical machines with excitation systems based on permanent magnets, special attention must be paid to the rotor temperature because of the temperature-sensitive properties of permanent magnets. The allowable temperature of NdFeB magnets is usually significantly less than 150 ˚C. The practical problem is that the part of the machine where the permanent magnets are located should stay cooler than the copper windings, which can easily tolerate temperatures of 155 ˚C or 180 ˚C. Therefore, new cooling solutions should be developed in order to cool permanent magnet electrical machines with high torque density and because of it with high concentrated losses in stators. In this doctoral dissertation, direct and indirect liquid cooling techniques for permanent magnet synchronous electrical machines (PMSM) with high torque density are presented and discussed. The aim of this research is to analyse thermal behaviours of the machines using the most applicable and accurate thermal analysis methods and to propose new, practical machine designs based on these analyses. The Computational Fluid Dynamics (CFD) thermal simulations of the heat transfer inside the machines and lumped parameter thermal network (LPTN) simulations both presented herein are used for the analyses. Detailed descriptions of the simulated thermal models are also presented. Most of the theoretical considerations and simulations have been verified via experimental measurements on a copper tooth-coil (motorette) and on various prototypes of electrical machines. The indirect liquid cooling systems of a 100 kW axial flux (AF) PMSM and a 110 kW radial flux (RF) PMSM are analysed here by means of simplified 3D CFD conjugate thermal models of the parts of both machines. In terms of results, a significant temperature drop of 40 ̊C in the stator winding and 28 ̊C in the rotor of the AF PMSM was achieved with the addition of highly thermally conductive materials into the machine: copper bars inserted in the teeth, and potting material around the end windings. In the RF PMSM, the potting material resulted in a temperature decrease of 6 ̊C in the stator winding, and in a decrease of 10 ̊C in the rotor embedded-permanentmagnets. Two types of unique direct liquid cooling systems for low power machines are analysed herein to demonstrate the effectiveness of the cooling systems in conditions of highly concentrated heat losses. LPTN analysis and CFD thermal analysis (the latter being particularly useful for unique design) were applied to simulate the temperature distribution within the machine models. Oil-immersion cooling provided good cooling capability for a 26.6 kW PMSM of a hybrid vehicle. A direct liquid cooling system for the copper winding with inner stainless steel tubes was designed for an 8 MW directdrive PM synchronous generator. The design principles of this cooling solution are described in detail in this thesis. The thermal analyses demonstrate that the stator winding and the rotor magnet temperatures are kept significantly below their critical temperatures with demineralized water flow. A comparison study of the coolant agents indicates that propylene glycol is more effective than ethylene glycol in arctic conditions.

Minimizing Conducted RF-Emissions in Switch Mode Power Supplies Using Spread-Spectrum Techniques

Switching power supplies are usually implemented with a control circuitry that uses constant clock frequency turning the power semiconductor switches on and off. A drawback of this customary operating principle is that the switching frequency and harmonic frequencies are present in both the conducted and radiated EMI spectrum of the power converter. Various variable-frequency techniques have been introduced during the last decade to overcome the EMC problem. The main objective of this study was to compare the EMI and steady-state performance of a switch mode power supply with different spread-spectrum/variable-frequency methods. Another goal was to find out suitable tools for the variable-frequency EMI analysis. This thesis can be divided into three main parts: Firstly, some aspects of spectral estimation and measurement are presented. Secondly, selected spread spectrum generation techniques are presented with simulations and background information. Finally, simulations and prototype measurements from the EMC and the steady-state performance are carried out in the last part of this work. Combination of the autocorrelation function, the Welch spectrum estimate and the spectrogram were used as a substitute for ordinary Fourier methods in the EMC analysis. It was also shown that the switching function can be used in preliminary EMC analysis of a SMPS and the spectrum and autocorrelation sequence of a switching function correlates with the final EMI spectrum. This work is based on numerous simulations and measurements made with the prototype. All these simulations and measurements are made with the boost DC/DC converter. Four different variable-frequency modulation techniques in six different configurations were analyzed and the EMI performance was compared to the constant frequency operation. Output voltage and input current waveforms were also analyzed in time domain to see the effect of the spread spectrum operation on these quantities. According to the results presented in this work, spread spectrum modulation can be utilized in power converter for EMI mitigation. The results from steady-state voltage measurements show, that the variable-frequency operation of the SMPS has effect on the voltage ripple, but the ripple measured from the prototype is still acceptable in some applications. Both current and voltage ripple can be controlled with proper main circuit and controller design.

Graphene from Graphite by Chemical and Physical Techniques.

Graphene is a material with extraordinary properties. Its mechanical and electrical properties are unparalleled but the difficulties in its production are hindering its breakthrough in on applications. Graphene is a two-dimensional material made entirely of carbon atoms and it is only a single atom thick. In this work, properties of graphene and graphene based materials are described, together with their common preparation techniques and related challenges. This Thesis concentrates on the topdown techniques, in which natural graphite is used as a precursor for the graphene production. Graphite consists of graphene sheets, which are stacked together tightly. In the top-down techniques various physical or chemical routes are used to overcome the forces keeping the graphene sheets together, and many of them are described in the Thesis. The most common chemical method is the oxidisation of graphite with strong oxidants, which creates a water-soluble graphene oxide. The properties of graphene oxide differ significantly from pristine graphene and, therefore, graphene oxide is often reduced to form materials collectively known as reduced graphene oxide. In the experimental part, the main focus is on the chemical and electrochemical reduction of graphene oxide. A novel chemical route using vanadium is introduced and compared to other common chemical graphene oxide reduction methods. A strong emphasis is placed on electrochemical reduction of graphene oxide in various solvents. Raman and infrared spectroscopy are both used in in situ spectroelectrochemistry to closely monitor the spectral changes during the reduction process. These in situ techniques allow the precise control over the reduction process and even small changes in the material can be detected. Graphene and few layer graphene were also prepared using a physical force to separate these materials from graphite. Special adsorbate molecules in aqueous solutions, together with sonic treatment, produce stable dispersions of graphene and few layer graphene sheets in water. This mechanical exfoliation method damages the graphene sheets considerable less than the chemical methods, although it suffers from a lower yield.

Surface studies of limestones and dolostones : characterisation using various techniques and batch dissolution experiments with hydrochloric acid solutions

In this thesis, stepwise titration with hydrochloric acid was used to obtain chemical reactivities and dissolution rates of ground limestones and dolostones of varying geological backgrounds (sedimentary, metamorphic or magmatic). Two different ways of conducting the calculations were used: 1) a first order mathematical model was used to calculate extrapolated initial reactivities (and dissolution rates) at pH 4, and 2) a second order mathematical model was used to acquire integrated mean specific chemical reaction constants (and dissolution rates) at pH 5. The calculations of the reactivities and dissolution rates were based on rate of change of pH and particle size distributions of the sample powders obtained by laser diffraction. The initial dissolution rates at pH 4 were repeatedly higher than previously reported literature values, whereas the dissolution rates at pH 5 were consistent with former observations. Reactivities and dissolution rates varied substantially for dolostones, whereas for limestones and calcareous rocks, the variation can be primarily explained by relatively large sample standard deviations. A list of the dolostone samples in a decreasing order of initial reactivity at pH 4 is: 1) metamorphic dolostones with calcite/dolomite ratio higher than about 6% 2) sedimentary dolostones without calcite 3) metamorphic dolostones with calcite/dolomite ratio lower than about 6% The reactivities and dissolution rates were accompanied by a wide range of experimental techniques to characterise the samples, to reveal how different rocks changed during the dissolution process, and to find out which factors had an influence on their chemical reactivities. An emphasis was put on chemical and morphological changes taking place at the surfaces of the particles via X-ray Photoelectron Spectroscopy (XPS) and Scanning Electron Microscopy (SEM). Supporting chemical information was obtained with X-Ray Fluorescence (XRF) measurements of the samples, and Inductively Coupled Plasma-Mass Spectrometry (ICP-MS) and Inductively Coupled Plasma-Optical Emission Spectrometry (ICP-OES) measurements of the solutions used in the reactivity experiments. Information on mineral (modal) compositions and their occurrence was provided by X-Ray Diffraction (XRD), Energy Dispersive X-ray analysis (EDX) and studying thin sections with a petrographic microscope. BET (Brunauer, Emmet, Teller) surface areas were determined from nitrogen physisorption data. Factors increasing chemical reactivity of dolostones and calcareous rocks were found to be sedimentary origin, higher calcite concentration and smaller quartz concentration. Also, it is assumed that finer grain size and larger BET surface areas increase the reactivity although no certain correlation was found in this thesis. Atomic concentrations did not correlate with the reactivities. Sedimentary dolostones, unlike metamorphic ones, were found to have porous surface structures after dissolution. In addition, conventional (XPS) and synchrotron based (HRXPS) X-ray Photoelectron Spectroscopy were used to study bonding environments on calcite and dolomite surfaces. Both samples are insulators, which is why neutralisation measures such as electron flood gun and a conductive mask were used. Surface core level shifts of 0.7 ± 0.1 eV for Ca 2p spectrum of calcite and 0.75 ± 0.05 eV for Mg 2p and Ca 3s spectra of dolomite were obtained. Some satellite features of Ca 2p, C 1s and O 1s spectra have been suggested to be bulk plasmons. The origin of carbide bonds was suggested to be beam assisted interaction with hydrocarbons found on the surface. The results presented in this thesis are of particular importance for choosing raw materials for wet Flue Gas Desulphurisation (FGD) and construction industry. Wet FGD benefits from high reactivity, whereas construction industry can take advantage of slow reactivity of carbonate rocks often used in the facades of fine buildings. Information on chemical bonding environments may help to create more accurate models for water-rock interactions of carbonates.

Optimization and Measuring Techniques for Collect-and-Place Machines in Printed Circuit Board Industry

This thesis considers optimization problems arising in printed circuit board assembly. Especially, the case in which the electronic components of a single circuit board are placed using a single placement machine is studied. Although there is a large number of different placement machines, the use of collect-and-place -type gantry machines is discussed because of their flexibility and increasing popularity in the industry. Instead of solving the entire control optimization problem of a collect-andplace machine with a single application, the problem is divided into multiple subproblems because of its hard combinatorial nature. This dividing technique is called hierarchical decomposition. All the subproblems of the one PCB - one machine -context are described, classified and reviewed. The derived subproblems are then either solved with exact methods or new heuristic algorithms are developed and applied. The exact methods include, for example, a greedy algorithm and a solution based on dynamic programming. Some of the proposed heuristics contain constructive parts while others utilize local search or are based on frequency calculations. For the heuristics, it is made sure with comprehensive experimental tests that they are applicable and feasible. A number of quality functions will be proposed for evaluation and applied to the subproblems. In the experimental tests, artificially generated data from Markov-models and data from real-world PCB production are used. The thesis consists of an introduction and of five publications where the developed and used solution methods are described in their full detail. For all the problems stated in this thesis, the methods proposed are efficient enough to be used in the PCB assembly production in practice and are readily applicable in the PCB manufacturing industry.

Intensification of Operation of Inclined Plate Settler at Fertilizer Plant

Fertilizer plant’s process waters contain high concentrations of nitrogen compounds, such as ammonium and nitrate. Phosphorus and fluorine, which originate from phosphoric acid and rock phosphate (apatite) used in fertilizer production, are also present. Phosphorus and nitrogen are the primary nutrients causing eutrophication of surface waters. At fertilizer plant process waters are held in closed internal circulation. In a scrubber system process waters are used for washing exhaust gases from fertilizer reactors and dry gases from granulation drums as well as for cooling down the fertilizer slurry in neutralization reactor. Solids in process waters are separated in an inclined plate settler by gravitational sedimentation. However, the operation of inclined plate settler has been inadequate. The aim of this thesis was to intensify the operation of inclined plate settler and thus the solids separation e.g. through coagulation and/or flocculation process. Chemical precipitation was studied to reduce the amount of dissolved species in process waters. Specific interest was in precipitation of nitrogen, phosphorus, and fluorine containing specimens. Amounts of phosphorus and fluorine were reduced significantly by chemical precipitation. When compared to earlier studies, annual chemical costs were almost eight times lower. Instead, nitrogen compounds are readily dissolved in water, thus being difficult to remove by precipitation. Possible alternative techniques for nitrogen removal are adsorption, ion exchange, and reverse osmosis. Settling velocities of pH adjusted and flocculated process waters were sufficient for the operation of inclined plate settler. Design principles of inclined plate settler are also presented. In continuation studies, flow conditions in inclined plate settler should be modelled with computational fluid dynamics and suitability of adsorbents, ion exchange resins, and membranes should be studied in laboratory scale tests.

Novel Interaction Techniques for Mobile Augmented Reality applications. A Systematic Literature Review

This study reviews the research on interaction techniques and methods that could be applied in mobile augmented reality scenarios. The review is focused on themost recent advances and considers especially the use of head-mounted displays. Inthe review process, we have followed a systematic approach, which makes the reviewtransparent, repeatable, and less prone to human errors than if it was conducted in amore traditional manner. The main research subjects covered in the review are headorientation and gaze-tracking, gestures and body part-tracking, and multimodality– as far as the subjects are related to human-computer interaction. Besides these,also a number of other areas of interest will be discussed.

Accelerating food safety and quality control: The use of antibody engineering techniques in the detec-tion of low-molecular weight food contaminants

The increased awareness and evolved consumer habits have set more demanding standards for the quality and safety control of food products. The production of foodstuffs which fulfill these standards can be hampered by different low-molecular weight contaminants. Such compounds can consist of, for example residues of antibiotics in animal use or mycotoxins. The extremely small size of the compounds has hindered the development of analytical methods suitable for routine use, and the methods currently in use require expensive instrumentation and qualified personnel to operate them. There is a need for new, cost-efficient and simple assay concepts which can be used for field testing and are capable of processing large sample quantities rapidly. Immunoassays have been considered as the golden standard for such rapid on-site screening methods. The introduction of directed antibody engineering and in vitro display technologies has facilitated the development of novel antibody based methods for the detection of low-molecular weight food contaminants. The primary aim of this study was to generate and engineer antibodies against low-molecular weight compounds found in various foodstuffs. The three antigen groups selected as targets of antibody development cause food safety and quality defects in wide range of products: 1) fluoroquinolones: a family of synthetic broad-spectrum antibacterial drugs used to treat wide range of human and animal infections, 2) deoxynivalenol: type B trichothecene mycotoxin, a widely recognized problem for crops and animal feeds globally, and 3) skatole, or 3-methyindole is one of the two compounds responsible for boar taint, found in the meat of monogastric animals. This study describes the generation and engineering of antibodies with versatile binding properties against low-molecular weight food contaminants, and the consecutive development of immunoassays for the detection of the respective compounds.

Spectral Retinal Images Reconstruction

While red-green-blue (RGB) image of retina has quite limited information, retinal multispectral images provide both spatial and spectral information which could enhance the capability of exploring the eye-related problems in their early stages. In this thesis, two learning-based algorithms for reconstructing of spectral retinal images from the RGB images are developed by a two-step manner. First, related previous techniques are reviewed and studied. Then, the most suitable methods are enhanced and combined to have new algorithms for the reconstruction of spectral retinal images. The proposed approaches are based on radial basis function network to learn a mapping from tristimulus colour space to multi-spectral space. The resemblance level of reproduced spectral images and original images is estimated using spectral distance metrics spectral angle mapper, spectral correlation mapper, and spectral information divergence, which show a promising result from the suggested algorithms.