Three ionic liquids (ILs), trihexyltetradecylphosphonium tetrafluoroborate (TTPT), N-butyl-4-methylpyridinium tetrafluoroborate (BMPT), and 1-methyl-3- octylimidazolium tetrafluoroborate (MOIC), were utilized to prepare sol- gel sorbent coatings. Non-polar polydimethylsiloxane (PDMS) and polar poly(ethylene glycol) (PEG), poly(tetrahydrofuran) (PolyTHF) and bis[(3-methyldimethoxy-silyl)propyl] polypropylene oxide (BMPO) polymers were employed to develop novel ionic liquidmediated sol- gel hybrid organic- inorganic sorbents. The novel sorbents were first tested as coatings for capillary microextraction off-line hyphenated to gas chromatography. To gain an understanding of the role of the ionic liquids in the sol-gel process, the preconcentration abilities of these novel coatings were investigated for several classes of compounds utilizing CME-GC. This was accomplished by comparing GC peak areas of a series of analytes extracted on the ionic liquid mediated sol-gel CME coatings with that of analogous peak areas obtained on sol- gel coatings prepared without the ionic liquid. The morphology of these coatings was compared using scanning electron microscopy (SEM) imaging data. Overall, the ionic liquid-mediated sol- gel coatings had more porous morphologies than the sol-gel coatings prepared without ionic liquid. The PDMS andBMPO sol-gel coatings prepared with ionic liquid in the sol solution provided enhanced extraction sensitivity reflected in higher preconcentration effects and lower detection limits than the sol- gel coatings prepared without the ionic liquid. The polar IL-mediated BMPO sol- gel sorbent was further investigated by exploring the extraction profile and thermal stability of these coatings. A further application of ionic liquid-mediated sol-gel sorbents could be as stationary phases in a microchip-based separation system. Towards this goal, microfluidic channels were fabricated in glass substrates using microelectromechanical engineering. Spiral and serpentine channels were etched in Pyrex and fused silica wafers using wet and deep reactive ion etching (DRIE) techniques. Microfabrication protocols such as the use of hard mask and etching times were investigated for both techniques. DRIE produced microfluidic channels that had an etch quality that was superior to wet etched channels. Thus, the ultimate microchip-based separation system should by fabricated using DRIE.

<p>The analysis of low abundant biological molecules is often challenging due to their chemical properties, low concentration and limited sample volumes. Neuropeptides are one group of molecules that fits these criteria. Neuropeptides also play an important role in biological functions, which makes them extra interesting to analyze. A classic chemical analysis involves sampling, sample preparation, separation and detection. In this thesis, an enhanced solid supported microdialysis method was developed and used as a combined sampling- and preparation technique. In general, significantly increased extraction efficiency was obtained for all studied peptides. To be able to control the small sample volumes and to minimize the loss of neuropeptides because of unwanted adsorption onto surfaces, the subsequent analysis steps were miniaturized to a micro total analysis system (µ-TAS), which allowed sample pre-treatment, injection, separation, manipulation and detection. </p><p>In order to incorporate these analysis functions to a microchip, a novel microfabrication protocol was developed. This method facilitated three-dimensional structures to be fabricated without the need of clean room facilities. </p><p>The sample pre-treatment step was carried out by solid phase extraction from beads packed in the microchip. Femtomole levels of neuropeptides were detected from samples possessing the same properties as microdialysates. The developed injection system made it possible to conduct injections from a liquid chromatographic separation into a capillary electrophoresis channel, which facilitated for advanced multidimensional separations. An electrochemical sample manipulation system was also developed. In the last part, different electrospray emitter tip designs made directly from the edge of the microchip substrate were developed and evaluated. The emitters were proven to be comparable with conventional, capillary based emitters in stability, durability and dynamic flow range. Although additional developments remain, the analysis steps described in this thesis open a door to an integrated, on-line µ-TAS for neuropeptides analysis in complex biological samples.</p>

<p>Advances in life science require knowledge of active molecules in complex biological systems. These molecules are often only present for a certain time and at limited concentrations. Integrated micro-analytical tools for sampling, separation and mass spectrometric (MS) detection would meet these requests and are therefore continuously gaining interest. An on-line coupling of analytical functions provides shorter analysis time and less manual sample handling. In this thesis, improved compatibility of microdialysis sampling and multidimensional separations coupled to MS detection are developed and discussed.</p><p>Microdialysis was used <i>in vitro</i> for determination of the non-protein bound fraction of the drug ropivacaine. The sampling unit was coupled on-line to capillary column liquid chromatography (LC) followed by ultraviolet or MS detection. For MS detection, the system was extended with a desalting step and an addition of internal standard. A method for MS screening of microdialysates, collected <i>in vivo,</i> was also developed. The method involved sampling and measurements of the chemical pattern of molecules that generally are ignored in clinical investigations. Chemometric tools were used to extract the relevant information and to compare samples from stimulated and control tissues.</p><p>Complex samples often require separation in more than one dimension. On-line interfaces for sample transfer between LC and capillary electrophoresis (CE) were developed in soft poly(dimethylsiloxane) (PDMS). MS detection in the LC-CE system was optimised on frequent sampling of the CE peak or on high resolution in mass spectra using time-of-flight (TOF)MS or Fourier transform ion cyclotron resonance (FTICR)MS, respectively. Aspects on electrode positioning in the LC-CE interface led to development of an on-column CE electrode. A successful method for deactivation of the PDMS surface using a polyamine polymer was also developed. The systems were evaluated using peptides and proteins, molecules that are gaining increased attention in bioscience, and consequently also in chemical analysis. </p>

Today,   most traditional method used in the research of immune cells, such as flow   cytometry and microscopy, are based on average values of cell responses.   However, immune cells are heterogeneous and respond differently to a given   stimuli. There is also a risk that important, but rare, behaviors of   individual cells are missed when a larger population of immune cells is   analyzed. Also, flow cytometry and microscopy do not allow long-term survival   of cells; these methods lack the ability to do dynamic long-term analysis of   motile immune cells, i.e. studies of cell-cell interactions, morphology and proliferation.   In a   patient who is affected by cancer, the cell heterogeneity contributes to the   ability to battle various types of cancer or virus infections. In an   outbreak, immune cells recognize and kill tumor cells. However, the number of   specific immune cells is sometimes too few to kill all the tumor cells in a   successful way. One way to help these patients is to isolate, select out and   cultivate the active immune cells with capacity to kill tumor cells.   The   Cell Physic Laboratory (a part of the department of Applied Physics) at the   Royal Institute of Technology (KTH) has developed a method for single-cell   analysis where the immune cells are trapped in microwells in a silicon chip.   The immune cells are then studied by using fluorescence microscopy in an   inverted setup. The method enables high-throughput experiments due to the   parallelization. Furthermore, since the immune cells survive long periods in   the chip, the cells can be analyzed over several days up to weeks. The   research group has also developed a semi-automatic ‘cell-picker’. The   cell-picker will be used in combination with the developed method for   single-cell analysis, which enables picking of cells of interest. In this report, experiments for the characterization and evaluation of the biocompatibility of two generations of the cell-picker will be presented. The experiments include development of a protocol for the cell-picking process, studies of the survival time of transferred cells for both generation of the cell-picker and studies of surface coating in the chip in order to increase the biocompatibility. The preliminary results indicate that the cell-picker has potential to be used as a selection tool for immune cells of interest.

This paper presents an empirical case study of the company Elicom AB. Elicom AB is producing electrical devices that are mostly used in the telecom market where the main customers are. The data that was collected from this case was collected through observations, interviews and the study of company documents. This allowed the author to compare secondary and primary data, as well as quantitative and qualitative information. The problem, the company is facing in the logistical field, was discovered in the labeling production process. The production of the labels is unnecessarily complicated and inefficient due to incompatibility of the computer systems. Therefore some parts of the label design have to be made manually, even though the company has a scanning system. When analyzing the problem in detail it became clear to the author that it could be fixed easily and fast and that the key individuals involved in the process already knew the answer to the problem. Therefore the question of the underlying cause of the problem arose. Why has the company not yet fixed the problem if it is so obvious and also everybody in the organization is aware of it? When further reanalyzing the problem, the author discovered a second problem, which was not lying in the logistics of the production process, but had its roots in the organizational structure. The problem of interfering authorities and responsibilities made it impossible for the company to overcome the changes needed to solve the logistical problem in the labeling production process. Therefore this problem must be addressed first, together with overcoming the obstacles to change in the organization, to make a problem-solving-process in the logistical area possible. In general this paper shows the interrelation of logistics with organization and the highly complex environment manufacturing companies are facing when it comes to changes in the production process. / Denna uppsats är en empirisk fallstudie som gjordes på Elicom AB. Elicom AB är en tillverkare av elektrisk apparatur som till mestadels används inom Telecom-marknaden, vilket också är den marknad som de flesta av företagets kunder finns inom. Den data som författaren samlat in är igenom observationer, intervjuer samt analys av olika interna företagsdokument. Detta gjorde att författaren kunde jämföra sekundär-och primär-data samt kvalitativ-och kvantitativ-data. Problemet som företaget hade framför sig var av logistisk karaktär och upptäcktes i etikettproduktionsprocessen. Produktionen av etiketter är onödigt komplicerad och ineffektiv pga icke kompatibla datasystem. Därför sker visa delar av skapandet av etiketter manuellt, även om företaget har ett scanning system. Efter viss analys blev det dock klart för författaren att problemet var lätt att ordna upp och att huvudpersonerna som var involverade, i etikett hanteringen, visste om att problemet var lätt löst men gjorde inget åt situationen. Detta ledde till att författaren fråga sig vad den underliggande orsaken, till detta problem, kunde vara. Varför har inte företaget gjort något åt problemet om det har varit uppenbart för dem att problemet existerar? När all information sedan om analyserades, upptäckte författaren ett andra problem vilket inte var inom logistikområdet utan hade sina rötter i organisationens struktur. Problemet med överlappande auktoritet, samt ansvarsområden, gör det omöjligt för företaget att lösa deras logistiska problem inom etiketthanteringen. Därför måste detta problem ses över först, samtidigt som inställningen till förändring måste ändras för att göra det möjligt att skapa en ”problem-lösnings-process” i den logistiska delen. Generellt visar denna fallstudie på relationen mellan logistik- och organisation och på den mycket komplicerade miljön som tillverkande företag ställs inför vid en förändring av sina processer.

<p>This paper presents an empirical case study of the company Elicom AB. Elicom AB is producing electrical devices that are mostly used in the telecom market where the main customers are. The data that was collected from this case was collected through observations, interviews and the study of company documents. This allowed the author to compare secondary and primary data, as well as quantitative and qualitative information. The problem, the company is facing in the logistical field, was discovered in the labeling production process.</p><p>The production of the labels is unnecessarily complicated and inefficient due to incompatibility of the computer systems. Therefore some parts of the label design have to be made manually, even though the company has a scanning system. When analyzing the problem in detail it became clear to the author that it could be fixed easily and fast and that the key individuals involved in the process already knew the answer to the problem. Therefore the question of the underlying cause of the problem arose. Why has the company not yet fixed the problem if it is so obvious and also everybody in the organization is aware of it?</p><p>When further reanalyzing the problem, the author discovered a second problem, which was not lying in the logistics of the production process, but had its roots in the organizational structure. The problem of interfering authorities and responsibilities made it impossible for the company to overcome the changes needed to solve the logistical problem in the labeling production process. Therefore this problem must be addressed first, together with overcoming the obstacles to change in the organization, to make a problem-solving-process in the logistical area possible.</p><p>In general this paper shows the interrelation of logistics with organization and the highly complex environment manufacturing companies are facing when it comes to changes in the production process.</p> / <p>Denna uppsats är en empirisk fallstudie som gjordes på Elicom AB. Elicom AB är en tillverkare av elektrisk apparatur som till mestadels används inom Telecom-marknaden, vilket också är den marknad som de flesta av företagets kunder finns inom. Den data som författaren samlat in är igenom observationer, intervjuer samt analys av olika interna företagsdokument. Detta gjorde att författaren kunde jämföra sekundär-och primär-data samt kvalitativ-och kvantitativ-data. Problemet som företaget hade framför sig var av logistisk karaktär och upptäcktes i etikettproduktionsprocessen.</p><p>Produktionen av etiketter är onödigt komplicerad och ineffektiv pga icke kompatibla datasystem. Därför sker visa delar av skapandet av etiketter manuellt, även om företaget har ett scanning system. Efter viss analys blev det dock klart för författaren att problemet var lätt att ordna upp och att huvudpersonerna som var involverade, i etikett hanteringen, visste om att problemet var lätt löst men gjorde inget åt situationen. Detta ledde till att författaren fråga sig vad den underliggande orsaken, till detta problem, kunde vara. Varför har inte företaget gjort något åt problemet om det har varit uppenbart för dem att problemet existerar?</p><p>När all information sedan om analyserades, upptäckte författaren ett andra problem vilket inte var inom logistikområdet utan hade sina rötter i organisationens struktur. Problemet med överlappande auktoritet, samt ansvarsområden, gör det omöjligt för företaget att lösa deras logistiska problem inom etiketthanteringen. Därför måste detta problem ses över först, samtidigt som inställningen till förändring måste ändras för att göra det möjligt att skapa en ”problem-lösnings-process” i den logistiska delen.</p><p>Generellt visar denna fallstudie på relationen mellan logistik- och organisation och på den mycket komplicerade miljön som tillverkande företag ställs inför vid en förändring av sina processer.</p>

Les études génétiques, telles que les études de liaison ou d’association, ont permis d’acquérir une plus grande connaissance sur l’étiologie de plusieurs maladies affectant les populations humaines. Même si une dizaine de milliers d’études génétiques ont été réalisées sur des centaines de maladies ou autres traits, une grande partie de leur héritabilité reste inexpliquée. Depuis une dizaine d’années, plusieurs percées dans le domaine de la génomique ont été réalisées. Par exemple, l’utilisation des micropuces d’hybridation génomique comparative à haute densité a permis de démontrer l’existence à grande échelle des variations et des polymorphismes en nombre de copies. Ces derniers sont maintenant détectables à l’aide de micropuce d’ADN ou du séquençage à haut débit. De plus, des études récentes utilisant le séquençage à haut débit ont permis de démontrer que la majorité des variations présentes dans l’exome d’un individu étaient rares ou même propres à cet individu. Ceci a permis la conception d’une nouvelle micropuce d’ADN permettant de déterminer rapidement et à faible coût le génotype de plusieurs milliers de variations rares pour un grand ensemble d’individus à la fois. Dans ce contexte, l’objectif général de cette thèse vise le développement de nouvelles méthodologies et de nouveaux outils bio-informatiques de haute performance permettant la détection, à de hauts critères de qualité, des variations en nombre de copies et des variations nucléotidiques rares dans le cadre d’études génétiques. Ces avancées permettront, à long terme, d’expliquer une plus grande partie de l’héritabilité manquante des traits complexes, poussant ainsi l’avancement des connaissances sur l’étiologie de ces derniers. Un algorithme permettant le partitionnement des polymorphismes en nombre de copies a donc été conçu, rendant possible l’utilisation de ces variations structurales dans le cadre d’étude de liaison génétique sur données familiales. Ensuite, une étude exploratoire a permis de caractériser les différents problèmes associés aux études génétiques utilisant des variations en nombre de copies rares sur des individus non reliés. Cette étude a été réalisée avec la collaboration du Wellcome Trust Centre for Human Genetics de l’University of Oxford. Par la suite, une comparaison de la performance des algorithmes de génotypage lors de leur utilisation avec une nouvelle micropuce d’ADN contenant une majorité de marqueurs rares a été réalisée. Finalement, un outil bio-informatique permettant de filtrer de façon efficace et rapide des données génétiques a été implémenté. Cet outil permet de générer des données de meilleure qualité, avec une meilleure reproductibilité des résultats, tout en diminuant les chances d’obtenir une fausse association. / Genetic studies, such as linkage and association studies, have contributed greatly to a better understanding of the etiology of several diseases. Nonetheless, despite the tens of thousands of genetic studies performed to date, a large part of the heritability of diseases and traits remains unexplained. The last decade experienced unprecedented progress in genomics. For example, the use of microarrays for high-density comparative genomic hybridization has demonstrated the existence of large-scale copy number variations and polymorphisms. These are now detectable using DNA microarray or high-throughput sequencing. In addition, high-throughput sequencing has shown that the majority of variations in the exome are rare or unique to the individual. This has led to the design of a new type of DNA microarray that is enriched for rare variants that can be quickly and inexpensively genotyped in high throughput capacity. In this context, the general objective of this thesis is the development of methodological approaches and bioinformatics tools for the detection at the highest quality standards of copy number polymorphisms and rare single nucleotide variations. It is expected that by doing so, more of the missing heritability of complex traits can then be accounted for, contributing to the advancement of knowledge of the etiology of diseases. We have developed an algorithm for the partition of copy number polymorphisms, making it feasible to use these structural changes in genetic linkage studies with family data. We have also conducted an extensive study in collaboration with the Wellcome Trust Centre for Human Genetics of the University of Oxford to characterize rare copy number definition metrics and their impact on study results with unrelated individuals. We have conducted a thorough comparison of the performance of genotyping algorithms when used with a new DNA microarray composed of a majority of very rare genetic variants. Finally, we have developed a bioinformatics tool for the fast and efficient processing of genetic data to increase quality, reproducibility of results and to reduce spurious associations.

The analysis of low abundant biological molecules is often challenging due to their chemical properties, low concentration and limited sample volumes. Neuropeptides are one group of molecules that fits these criteria. Neuropeptides also play an important role in biological functions, which makes them extra interesting to analyze. A classic chemical analysis involves sampling, sample preparation, separation and detection. In this thesis, an enhanced solid supported microdialysis method was developed and used as a combined sampling- and preparation technique. In general, significantly increased extraction efficiency was obtained for all studied peptides. To be able to control the small sample volumes and to minimize the loss of neuropeptides because of unwanted adsorption onto surfaces, the subsequent analysis steps were miniaturized to a micro total analysis system (µ-TAS), which allowed sample pre-treatment, injection, separation, manipulation and detection. In order to incorporate these analysis functions to a microchip, a novel microfabrication protocol was developed. This method facilitated three-dimensional structures to be fabricated without the need of clean room facilities. The sample pre-treatment step was carried out by solid phase extraction from beads packed in the microchip. Femtomole levels of neuropeptides were detected from samples possessing the same properties as microdialysates. The developed injection system made it possible to conduct injections from a liquid chromatographic separation into a capillary electrophoresis channel, which facilitated for advanced multidimensional separations. An electrochemical sample manipulation system was also developed. In the last part, different electrospray emitter tip designs made directly from the edge of the microchip substrate were developed and evaluated. The emitters were proven to be comparable with conventional, capillary based emitters in stability, durability and dynamic flow range. Although additional developments remain, the analysis steps described in this thesis open a door to an integrated, on-line µ-TAS for neuropeptides analysis in complex biological samples.

Advances in life science require knowledge of active molecules in complex biological systems. These molecules are often only present for a certain time and at limited concentrations. Integrated micro-analytical tools for sampling, separation and mass spectrometric (MS) detection would meet these requests and are therefore continuously gaining interest. An on-line coupling of analytical functions provides shorter analysis time and less manual sample handling. In this thesis, improved compatibility of microdialysis sampling and multidimensional separations coupled to MS detection are developed and discussed. Microdialysis was used in vitro for determination of the non-protein bound fraction of the drug ropivacaine. The sampling unit was coupled on-line to capillary column liquid chromatography (LC) followed by ultraviolet or MS detection. For MS detection, the system was extended with a desalting step and an addition of internal standard. A method for MS screening of microdialysates, collected in vivo, was also developed. The method involved sampling and measurements of the chemical pattern of molecules that generally are ignored in clinical investigations. Chemometric tools were used to extract the relevant information and to compare samples from stimulated and control tissues. Complex samples often require separation in more than one dimension. On-line interfaces for sample transfer between LC and capillary electrophoresis (CE) were developed in soft poly(dimethylsiloxane) (PDMS). MS detection in the LC-CE system was optimised on frequent sampling of the CE peak or on high resolution in mass spectra using time-of-flight (TOF)MS or Fourier transform ion cyclotron resonance (FTICR)MS, respectively. Aspects on electrode positioning in the LC-CE interface led to development of an on-column CE electrode. A successful method for deactivation of the PDMS surface using a polyamine polymer was also developed. The systems were evaluated using peptides and proteins, molecules that are gaining increased attention in bioscience, and consequently also in chemical analysis.

Tato diplomová práce se zabývá návrhem elektronického informačního štítku, jehož základem je maticový LED displej. V teoretické části jsou probrány použitá rozhraní a periferie mikrokontroléru a PC a diskutuje se nad možnostmi kódování českých znaků. Dále se probírá krok za krokem návrh zařízení. Nejdříve jsou vytyčeny hlavní požadavky a funkcionalita zařízení, následuje výběr vhodných komponent a je navrženo elektrické schéma. Jádrem zařízení je mikrokontrolér Microchip PIC, pro který je dále navržen program. Nakonec je popsána a naprogramována aplikace pro MS Windows, která se se zařízením komunikuje.