| 1. |
- Alizadeh Khameneh, Mohammad Amin, 1983-
(författare)
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Optimal Design in Geodetic GNSS-based Networks
- 2017
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- An optimal design of a geodetic network helps the surveying engineers maximise the efficiency of the network. A number of pre-defined quality requirements, i.e. precision, reliability, and cost, of the network are fulfilled by performing an optimisation procedure. Today, this is almost always accomplished by implementing analytical solutions, where the human intervention in the process cycle is limited to defining the requirements. Nevertheless, a trial and error method can be beneficial to some applications. In order to analytically solve an optimisation problem, it can be classified to different orders, where an optimal datum, configuration, and optimal observation weights can be sought such that the precision, reliability and cost criteria are satisfied.In this thesis, which is a compilation of six peer-reviewed papers, we optimised and redesigned a number of GNSS-based monitoring networks in Sweden by developing new methodologies. In addition, optimal design and efficiency of total station establishment with RTK-GNSS is investigated in this research.Sensitivity of a network in detecting displacements is of importance for monitoring purposes. In the first paper, a precision criterion was defined to enable a GNSS-based monitoring network to detect 5 mm displacements at each network point. Developing an optimisation model by considering this precision criterion, reliability and cost yielded a decrease of 17% in the number of observed single baselines implying a reliable and precise network at lower cost. The second paper concerned a case, where the precision of observations could be improved in forthcoming measurements. Thus a new precision criterion was developed to consider this assumption. A significant change was seen in the optimised design of the network for subsequent measurements. As yet, the weight of single baselines was subject to optimisation, while in the third paper, the effect of mathematical correlations between GNSS baselines was considered in the optimisation. Hence, the sessions of observations, including more than two receivers, were optimised. Four out of ten sessions with three simultaneous operating receivers were eliminated in a monitoring network with designed displacement detection of 5 mm. The sixth paper was the last one dealing with optimisation of GNSS networks. The area of interest was divided into a number of three-dimensional elements and the precision of deformation parameters was used in developing a precision criterion. This criterion enabled the network to detect displacements of 3 mm at each point.A total station can be set up in the field by different methods, e.g. free station or setup over a known point. A real-time updated free station method uses RTK-GNSS to determine the coordinates and orientation of a total station. The efficiency of this method in height determination was investigated in the fourth paper. The research produced promising results suggesting using the method as an alternative to traditional levelling under some conditions. Moreover, an optimal location for the total station in free station establishment was studied in the fifth paper. It was numerically shown that the height component has no significant effect on the optimal localisation.
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| 2. |
- Alvarsson, Jonathan, 1981-
(författare)
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Ligand-based Methods for Data Management and Modelling
- 2015
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Drug discovery is a complicated and expensive process in the billion dollar range. One way of making the drug development process more efficient is better information handling, modelling and visualisation. The majority of todays drugs are small molecules, which interact with drug targets to cause an effect. Since the 1980s large amounts of compounds have been systematically tested by robots in so called high-throughput screening. Ligand-based drug discovery is based on modelling drug molecules. In the field known as Quantitative Structure–Activity Relationship (QSAR) molecules are described by molecular descriptors which are used for building mathematical models. Based on these models molecular properties can be predicted and using the molecular descriptors molecules can be compared for, e.g., similarity. Bioclipse is a workbench for the life sciences which provides ligand-based tools through a point and click interface. The aims of this thesis were to research, and develop new or improved ligand-based methods and open source software, and to work towards making these tools available for users through the Bioclipse workbench. To this end, a series of molecular signature studies was done and various Bioclipse plugins were developed.An introduction to the field is provided in the thesis summary which is followed by five research papers. Paper I describes the Bioclipse 2 software and the Bioclipse scripting language. In Paper II the laboratory information system Brunn for supporting work with dose-response studies on microtiter plates is described. In Paper III the creation of a molecular fingerprint based on the molecular signature descriptor is presented and the new fingerprints are evaluated for target prediction and found to perform on par with industrial standard commercial molecular fingerprints. In Paper IV the effect of different parameter choices when using the signature fingerprint together with support vector machines (SVM) using the radial basis function (RBF) kernel is explored and reasonable default values are found. In Paper V the performance of SVM based QSAR using large datasets with the molecular signature descriptor is studied, and a QSAR model based on 1.2 million substances is created and made available from the Bioclipse workbench.
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| 3. |
- Andersson, David E.
(författare)
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The Emergence of Markets for Technology : Patent Transfers and Patenting in Sweden, 1819–1914
- 2016
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis is concerned with the emergence of markets for technology and studies the evolution of patent transfers and its determinants, patent agencies and independent versus firm patenting in Sweden during the 19th century and the turn of 20th century. It explores how and why markets for technology emerge and under what circumstances by investigating the evolution of Swedish patent legislation and the patterns of patent transfers between individuals and firms. It presents a three-pronged framework studying: structure and actors, technology and transactions.Using a new and unique database covering every Swedish privilege and patent over the 1819–1914 period the empirical analysis reveals that although the transferability of intellectual property goes all the way back to the 18th century patent transfers did not start to increase significantly until the first modern Swedish patent law was passed in 1884. Along with the new law a market for patenting services also emerged where actors such as patent agents and the firms they founded, patent agencies, functioned as intermediaries in the market for patents and international networks of patenting. A few older patent agencies managed to create an oligopolistic setting where they introduced price controls through special interest groups.The thesis also questions the current dichotomous classification of independent and firm patenting. The methodological contribution lies in showing that research that depend too much on patent statistics run the risk of underestimating the importance of the firm when patents granted to individuals actually cover inventive activities that has taken place inside the boundaries of firms.Finally, the study shows that special marketplaces for the sale of patented and unpatented technology were created to help inventors find buyers and financiers for their invention and to help firms find new technology. The patent law of 1884 made it possible to trade in several submarkets of technology where the right to patent a certain invention could be bought, ideas could be financed, pending patent applications or the priority right to foreign markets could be bought and sold.The results lend support to the research emphasizing the role of intellectual property as a disclosure and diffusion mechanism for new technology.
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| 4. |
- Dini, Hoda, 1984-
(författare)
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As-cast AZ91D magnesium alloy properties : Effects of microstructure and temperature
- 2017
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Today, there is an essential need for lightweight, energy-efficient, environmentally benign engineering systems, and this is the driving force behind the development of a wide range of structural and functional materials for energy generation, energy storage, propulsion, and transportation. These challenges have motivated the use of magnesium alloys for lightweight structural systems. Magnesium has a density of 1.74 g/cm3, which is almost 30% less than that of aluminium, one quarter of steel, and almost identicalto polymers. The ease of recycling magnesium alloys as compared to polymers makes them environmentally attractive, but their poor mechanical performance is the primary reason for the limited adoption of these alloys for structural applications.The Mg-Al-Zn alloy AZ91D exhibits an excellent combination of strength, die-castability, and corrosion resistance. However, its mechanical performance with regard to creep strength, for example, at evaluated temperatures is poor. Moreover, very little is known about the correlation between its mechanical properties and microstructural features. This thesis aims to provide new knowledge regarding the role played by microstructure in the mechanical performance of the magnesium alloy. The properties/performance of the material in relation to process parameters became of great interest during the investigation.An exhaustive characterisation of the grain size, secondary dendrite arm spacing (SDAS) distribution, and fraction of Mg17Al12 was performed using optical and electron backscatter diffraction (EBSD). These microstructural parameters were correlated to the offset yield point (Rp0.2), fracture strength, and elongation to failure of the material. It was proposed that the intermetallic phase, Mg17Al12, plays an important role in determining the mechanical and physical properties of the alloy in a temperature range of room temperature to 190°C by forming a rigid network of intermetallic. The presence of this network was confirmed by studying the thermal expansion behaviour of samples of the alloy containing different amounts of Mg17Al12.A physically based constitutive model with a wide validity range was successfully adapted to describe the flow stress behaviour of AZ91D with various microstructures. The temperature-dependent variables of the model correlated quite well with the underlying physics of the material. The model was validated through comparison with dislocation densities obtained using EBSD.The influence of high-pressure die-cast parameters on the distortion and residual stress of the cast components was studied, as were distortion and residual stress in components after shot peening and painting. Interestingly, it was found that intensification pressure has a major effect on distortion and residual stresses, and that the temperature of the fixed half of the die had a slight influence on the component's distortion and residual stress.
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| 5. |
- Mahajan, Mayank
(författare)
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Evolution of cellular complexity and other remarkable features in Gemmataceae : Complex bacterial lineages defy prokaryotic trends
- 2019
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Bacteria of the family Gemmataceae belong the phylum Planctomycetes and are remarkable because of their complex cellular architectures, previously considered to be traits exclusive to eukaryotes. This thesis provides clues to the atypical cell envelope, the enhanced radiotolerance and the amazing cellular complexity of these bacteria.A comparative genomics study of these bacteria revealed massive duplications and new combinations of structural domains that are highly abundant in eukaryotes but rare in bacteria. These domains are known to facilitate signalling and protein interactions. The proteins of these bacteria also contain long regions with no predicted domains. On average, eukaryotic proteins are longer and more disordered than prokaryotic proteins. Intriguingly, the length and fraction of disordered regions in proteins of some bacteria are higher than in many other prokaryotes, and these bacteria also have complex lifestyles. Many bacteria in the Planctomycetes, including the Gemmataceae, are among these few bacteria. This suggests that there is no sharp boundary between prokaryotes and eukaryotes with respect to protein length and domain composition patterns, as previously thought.A bioinformatics analysis revealed the loss of genes for the peptidoglycan cell wall in some lineages of the Planctomycetes. Loss of the gene for the FtsZ protein, the major cell division protein in bacteria, may have facilitated the evolution of budding in the Planctomycetales and led to the gradual loss of the cell wall and cell division gene cluster. These changes may have enabled the expansion of the inner membrane and triggered adaptive changes in conserved membrane proteins and transport systems. The loss of the peptidoglycan cell wall may also explain the altered cell morphology. A subcellular proteomics study showed that the DNA replication and repair proteins are associated with the cell envelope, which supports the cell factory model of DNA replication.T. immobilis, which has the simplest genome of all members of the Gemmataceae, was found to be naturally competent and most suitable for transformation experiments. T. immobilis was transformed to produce mutants in which the gene for DdrA, a double stranded break DNA repair protein, has been inactivated. The DdrA-null mutant showed a major loss in radiotolerance.
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| 6. |
- Tamarit, Daniel, 1988-
(författare)
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Evolution of symbiotic lineages and the origin of new traits
- 2016
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis focuses on the genomic study of symbionts of two different groups of hymenopterans: bees and ants. Both groups of insects have major ecological impact, and investigating their microbiomes increases our understanding of their health, diversity and evolution.The study of the bee gut microbiome, including members of Lactobacillus and Bifidobacterium, revealed genomic processes related to the adaptation to the gut environment, such as the expansion of genes for carbohydrate metabolism and the acquisition of genes for interaction with the host. A broader genomic study of these genera demonstrated that some lineages evolve under strong and opposite substitution biases, leading to extreme GC content values. A comparison of codon usage patterns in these groups revealed ongoing shifts of optimal codons.In a separate study we analysed the genomes of several strains of Lactobacillus kunkeei, which inhabits the honey stomach of bees but is not found in their gut. We observed signatures of genome reduction and suggested candidate genes for host-interaction processes. We discovered a novel type of genome architecture where genes for metabolic functions are located in one half of the genome, whereas genes for information processes are located in the other half. This genome organization was also found in other Lactobacillus species, indicating that it was an ancestral feature that has since been retained. We suggest mechanisms and selective forces that may cause the observed organization, and describe processes leading to its loss in several lineages independently.We also studied the genome of a species of Rhizobiales bacteria found in ants. We discuss its metabolic capabilities and suggest scenarios for how it may affect the ants’ lifestyle. This genome contained a region with homology to the Bartonella gene transfer agent (GTA), which is a domesticated bacteriophage used to transfer bacterial DNA between cells. We propose that its unique behaviour as a specialist GTA, preferentially transferring host-interaction factors, originated from a generalist GTA that transferred random segments of chromosomal DNA.These bioinformatic analyses of previously uncharacterized bacterial lineages have increased our understanding of their physiology and evolution and provided answers to old and new questions in fundamental microbiology.
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