Clustering techniques play an important role in exploratory pattern analysis, unsupervised pattern recognition and image segmentation applications. Clustering algorithms are computationally intensive in nature. This thesis proposes new parallel algorithms for Single Link and Complete Link hierarchical clustering. The parallel algorithms have been mapped on a SIMD machine model with a linear interconnection network. The model consists of a linear array of N (number of patterns to be clustered) processing elements (PEs), interfaced to a host machine and the interconnection network provides inter-PE and PE-to-host/host-to-PE communication. For single link clustering, each PE maintains a sorted list of its first logN nearest neighbors and the host maintains a heap of the root elements of all the PEs. The determination of the smallest entry in the distance matrix and update of the distance matrix is achieved in O(logN) time. In the case of complete link clustering, each PE maintains a heap data structure of the inter pattern distances. This significantly reduces the computation time for the determination of the smallest entry in the distance matrix during each iteration, from O(N2) to O(N), as the root element in each PE gives its nearest neighbor. The proposed algorithms are faster and simpler than previously known algorithms for hierarchical clustering. For clustering a data set with N patterns, using N PEs, the computation time for the single link clustering algorithm is shown to be O(NlogN) and the time complexity for the complete link clustering algorithm is shown to be O(N2). The parallel algorithms have been verified through simulations on the Intel iPSC/2 parallel machine.

<p>In this thesis I have done a discourse analysis of the documentary movie <em>A Jihad for Love</em>. <em>A Jihad for Love </em>came out 2007 and is directed by Parvez Sharma. The documentary movie is about homosexual Muslims and their jihad, struggle, for love and to be accepted in a world where they are barely recognized as a group. My aim of the thesis was to see how the movie portrays the persons who are in the film and their relationship to Islam and who gets access to the religion. I have also analyzed if Islam can be used to strengthen the sexual identity or if it works in the opposite way. I have used the theoretical instrument of intersectionality and religious proximity with a gender perspective with focus on sexuality and religion to analyze my material.</p><p>My conclusions of the thesis are that the men in the movie are often more portrayed as active subjects that can use the religion as a tool to strengthen the sexuality. The women are more portrayed as inactive objects that cannot use the religion to strengthen their sexual identity because of different power axes, like gender and sexuality, which collide and with each other. Another conclusion is that men have a higher grade of religious proximity which makes them closer to God, whereas the women traditionally don’t have the same closeness to God and cannot therefore have the same power in the religious hierarchy.</p><p> </p>

<p>Proximity ligation is a recently established technique that can provide answers to questions about the concentration, localization, interactions, modifications and functions of proteins. The method enables sensitive protein measurements with a detection limit in the low femtomolar range in complex biological samples. In proximity ligation, the challenge of detecting specific proteins is converted to the analysis of specific DNA sequences. Proximity probes containing oligonucleotide extensions are designed to bind pairwise to target proteins, and to form amplifiable tag sequences upon ligation when brought in proximity. Protocols for the conversion of monoclonal or polyclonal antibodies into proximity probes through the attachment of oligonucleotide sequences are described in the thesis. In addition, the thesis describes the adaptation of the proximity ligation technology for detection of microbial pathogens, analysis of interactions between proteins and nucleic acids, and of inhibition of receptor-ligand interactions. </p><p>Nucleic acid amplification allows specific detection of pathogens with single-copy sensitivity. There are many circumstances, however, when analysis of pathogen surface antigens or the antibody response can provide increased diagnostic value. Proximity ligation reactions were used to measure numbers of virus and bacteria by detection of viral or bacterial surface proteins. Detection sensitivities similar to those of nuclear acid-based detection reactions were achieved directly in infected samples for a parvovirus and for an intracellular bacterium. </p><p>Biological processes are orchestrated by interactions of proteins with molecules in their environment, and investigations of interactions between proteins and other biomolecules are thus of great importance. Protocols were established for very specific and sensitive homogeneous-phase analysis of interactions between proteins and specific nucleic acid sequences. Finally, the proximity ligation mechanism was used to monitor interactions between VEGF-A and two of its receptors, VEGFR-1 and VEGFR-2, and to characterize the effects of agents disrupting this interaction.</p>

<p>Improved methods are needed to interrogate the genome and the proteome. Methods with high selectivity, wide dynamic range, and excellent precision, capable of simultaneously analyzing many biomolecules are required to decipher cellular function. This thesis describes a molecular and microfluidic toolbox designed with those criteria in mind. It also presents a tool for graphical representation of nucleic acid sequences.</p><p>Proximity ligation is a novel protein detection method that requires dual and proximate binding of two oligonucleotide-tagged affinity reagents to a protein or protein complex in order to elicit a signal. The responses from such recognition reactions are the formation of specific nucleic acid reporter molecules that are subsequently amplified and quantitatively detected. </p><p>A scalable microfluidic platform suitable for fluorescence detection, cell culture, and actuation is also described. The platform uses rapid injection molding to produce microstructures in thermoplastic materials. By applying a thin layer of silica to the structures, a lid made of silicone rubber coated onto a thermoplastic support can be covalently bonded to generate enclosed channels.</p><p>A method is presented for precise biomolecule counting, termed “amplified single-molecule detection”. The method preserves the discrete nature of biomolecules, converting specific molecular recognition events to fluorescence-labeled micrometer-sized objects that are enumerated in microfluidic channels. </p><p>I also present a novel microarray-based detection method. To attain high selectivity and a wide dynamic range, the method is based on dual recognition with enzymatic discrimination and amplification. Upon target recognition in solution, DNA probes are subjected to thousand-fold amplification in solution, followed by selective detection on arrays and another hundred-fold amplification of reporter molecule created from the first amplification reaction. </p><p>Lastly, I describe a novel graphical representation of nucleic acid sequences using TrueType fonts that can be of value for visual inspection of DNA sequences and for teaching purposes</p>

<p>Padlock probes and proximity ligation are two powerful molecular tools for detection of nucleic acids and proteins, respectively. Both methods result in the formation of DNA reporter molecules upon recognition of specific target molecules. These reporter molecules can be designed to include tag sequences that can be analyzed by techniques for nucleic acid analysis. Herein, I present a dual-tag microarray (DTM) platform that is suitable for high-performance analyses of DNA reporter molecule libraries, generated by padlock and proximity probing reactions. The DTM platform was applied for analysis of mRNA transcripts using padlock probes, and of cytokines using proximity ligation. The platform drastically improved specificity of detection, and it allowed precise measurements of proteins and nucleic acids over wide dynamic ranges.</p><p>The thesis also presents two techniques for multi-probe analyses of biomolecules: the triple-specific proximity ligation assay (3PLA) for protein analyses, and the spliceotyping assay for mRNA analyses. 3PLA allows highly specific measurements of as little as hundreds of target protein molecules by interrogating three target epitopes simultaneously. In spliceotyping the exon composition of individual transcripts are represented as a series of tag sequences in DNA reporter molecules, via a series of target-dependent ligation reactions. Next, the splicing patterns along individual transcripts can be revealed by amplified single molecule detection and step-wise decoding.</p>

This thesis aims to explore the importance of proximity and mobility, respectively, for individuals’ accessibility, as well as the relationship between these two key spatial dimensions of accessibility in the context of everyday life. The thesis is based upon three empirical research papers which focus on accessibility-related preferences, actual accessibility conditions, and travel patterns. Focus is directed towards the spatial relationships between individuals’ residential location vis-à-vis the location of a selection of different amenities including work, education, service and leisure functions as well as social relations. The analyses are based on a wide range of quantitative data, including questionnaire surveys as well as official register data for the Swedish population.      The first paper shows that residential proximity to amenities was most valued by individuals in the case of social relations and basic daily activities. The level of satisfaction with current accessibility conditions was generally high, with the exception of social relations where the findings suggest the existence of a ‘proximity deficit’. The second paper shows that observed average distances to most amenities have decreased over time (1995–2005). Concerning service amenities, the increases in proximity over the period were primarily due to a restructuring of the localization patterns within the service sector. A comparison of potential accessibility conditions and actual travel patterns revealed that people tend to travel farther than to the nearest amenity options, presumably to a large extent because of selective individual preferences, which may downplay the importance of distance in destination choice. The third paper shows that although the numerical supply of amenities within different spatial ranges has a significant influence on how far individuals travel for service errands, supply size alone is not sufficient for explaining travel length. The findings also suggest that although people tend to utilize the supply of amenities available locally, they are also willing to extend their travel distance in order to reach the amenity supply available within the region. Thus, even when there is a local supply, a rich regional supply may induce longer trips.      A juxtaposition of the findings of the three empirical studies suggests the existence of an ‘accessibility paradox’ with several facets. First, although people express an affinity for residential proximity to many amenities, this is not necessarily reflected in actual destination choices, since minimization of travel distance is apparently not always a key criterion. This is also suggested by the conclusion that the spatial structure of the amenity supply alone accounts for only a relatively small part of the explanation of travel length, which is influenced by many other factors. In addition, actual travel distances show an increasing trend over time despite the concurrent reductions in potential distances. Second, the development over time indicates that the proximity deficit regarding social relations may be increasing in the sense that average distances have increased to many of the amenities considered important to have nearby, for instance adult children, but have decreased to those where proximity is not considered particularly important. Third, there is a discrepancy between the observed trend towards increased proximity to many amenities and much of the general discourse on accessibility, which tends to emphasize deteriorating conditions.

Ethical issues and problems in business are receiving increasing attention, both in terms of criticism of examples of "bad" behaviour of business actors and in terms of the development of ethical codes of conduct in certain companies, ethical visions for businesses etc. In general, ethical problems seem to be increasingly prevalent in business, but ethics tend to be disre­garded by traditional organisational and managerial theory. This calls for the development of an ethical perspective on business. This study adopts a stakeholder approach to the problem, meaning that the empirical focus lies on how business actors deal with the ethical issues that arise in their daily work in relation to various stakeholder groups. Two empirical studies have been conducted: one is a survey study of the attitudes of Swedish managing directors, and the other a case study of the ethical values and behaviour of two companies. These studies resulted in the formulation of concepts which reflect contextually interpreted moral views on the individual and organisational levels, respectively. On the individual level, a distinction was made between humanitarian morality, meaning that ethical problems in business are judged according to what is best for individuals, and organisational morality, where economic and practical concerns for the company are considered. On the organisational level, I found a principled, individually based morality where rule-following, voluntary agreements and personal moral norms were important, and an instrumental, collectively based morality, which meant that company goals dictated the way stakeholder relations and ethical dilemmas were taken care of. Overall, it was possible to make a distinction between two basic ethical criteria business actors use when judging ethical dilemmas: principles versus objectives. The results indicate that the use of principles and moral rules presuppose an intimate and personal handling of stakeholder relations. On the other hand, when business actors acquire a more professional way of managing their activi­ties, stakeholder relationships are handled in accordance with objectives and economic utility, these usually being the same as company goals. One of the major contributions of this thesis is the concept of the ethical contract, as a meta­phor for the relationship between a company and any one particular stakeholder with special focus on the informal and implicit aspects of the relationship. The contract is characterised by two opposing forces: the striving for self-interest, which underpins ethical problems, and the development of self-imposed duties, which are necessary if instrumentally based interaction is to be "good". The mutual development of such duties is stimulated by proximity and personal relations. / digitalisering@umu

Proximity ligation is a recently established technique that can provide answers to questions about the concentration, localization, interactions, modifications and functions of proteins. The method enables sensitive protein measurements with a detection limit in the low femtomolar range in complex biological samples. In proximity ligation, the challenge of detecting specific proteins is converted to the analysis of specific DNA sequences. Proximity probes containing oligonucleotide extensions are designed to bind pairwise to target proteins, and to form amplifiable tag sequences upon ligation when brought in proximity. Protocols for the conversion of monoclonal or polyclonal antibodies into proximity probes through the attachment of oligonucleotide sequences are described in the thesis. In addition, the thesis describes the adaptation of the proximity ligation technology for detection of microbial pathogens, analysis of interactions between proteins and nucleic acids, and of inhibition of receptor-ligand interactions. Nucleic acid amplification allows specific detection of pathogens with single-copy sensitivity. There are many circumstances, however, when analysis of pathogen surface antigens or the antibody response can provide increased diagnostic value. Proximity ligation reactions were used to measure numbers of virus and bacteria by detection of viral or bacterial surface proteins. Detection sensitivities similar to those of nuclear acid-based detection reactions were achieved directly in infected samples for a parvovirus and for an intracellular bacterium. Biological processes are orchestrated by interactions of proteins with molecules in their environment, and investigations of interactions between proteins and other biomolecules are thus of great importance. Protocols were established for very specific and sensitive homogeneous-phase analysis of interactions between proteins and specific nucleic acid sequences. Finally, the proximity ligation mechanism was used to monitor interactions between VEGF-A and two of its receptors, VEGFR-1 and VEGFR-2, and to characterize the effects of agents disrupting this interaction.

Padlock probes and proximity ligation are two powerful molecular tools for detection of nucleic acids and proteins, respectively. Both methods result in the formation of DNA reporter molecules upon recognition of specific target molecules. These reporter molecules can be designed to include tag sequences that can be analyzed by techniques for nucleic acid analysis. Herein, I present a dual-tag microarray (DTM) platform that is suitable for high-performance analyses of DNA reporter molecule libraries, generated by padlock and proximity probing reactions. The DTM platform was applied for analysis of mRNA transcripts using padlock probes, and of cytokines using proximity ligation. The platform drastically improved specificity of detection, and it allowed precise measurements of proteins and nucleic acids over wide dynamic ranges. The thesis also presents two techniques for multi-probe analyses of biomolecules: the triple-specific proximity ligation assay (3PLA) for protein analyses, and the spliceotyping assay for mRNA analyses. 3PLA allows highly specific measurements of as little as hundreds of target protein molecules by interrogating three target epitopes simultaneously. In spliceotyping the exon composition of individual transcripts are represented as a series of tag sequences in DNA reporter molecules, via a series of target-dependent ligation reactions. Next, the splicing patterns along individual transcripts can be revealed by amplified single molecule detection and step-wise decoding.

Airborne CW doppler proximity sensors are very sensitive, but leaks precise height measurement. It may be possible to estimate the heigth at the terminal phase (the case where the sensor is at a heigth close to ground) precisely by using the doppler shift and amplitude information. The thesis includes this novel concept with theoritical analysis and simulation results.