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  • About
  • The Global ETD Search service is a free service for researchers to find electronic theses and dissertations. This service is provided by the Networked Digital Library of Theses and Dissertations.
    Our metadata is collected from universities around the world. If you manage a university/consortium/country archive and want to be added, details can be found on the NDLTD website.
371

Development of a Microchip-Based Flow Cytometer with Integrated Optics – Device Design, Fabrication, and Testing

Watts, Benjamin 04 1900 (has links)
<p>Lab-on-a-chip technologies have created a burgeoning number of new and novel devices designed to automate biological processes on-chip in an efficient and inexpensive format for far reaching point-of-care (POC) medicine and diagnostic treatments and for remote and on-line monitoring functions. This work designed a device that integrated advanced optical functionality on-chip with the microfluidics to relieve the reliance on traditional bulky and expensive free-space optics and a high-quality light source. The multimodal input beam was reshaped into an optimized geometry in the microchannel via a 2D system of lenses - improving the quality and reliability of detection through uniform detection of particles. A uniform beam geometry across the sample stream with a uniform beam width will allow repeatable excitation and burst duration to allow for more reliable and predictable detection. Numerous beam geometries were created and the quality and illumination properties confirmed by testing each with a couple sizes of fluorescent and non-fluorescent microspheres to test the effect of beam geometry and particle size combination on device performance. The measured coefficient of variation (CV) for fluorescent beads was found to have a particular beam geometry that yielded best device performance based on the bead size. Fluorescent beads 2.5µm in diameter had a CV of 8.5% for a 3.6 µm beam waist while 6 µm beads yielded a 14.6% CV with a 10 µm beam waist. When measuring scatter and fluorescence signal from a 10 µm the 2.5- and 6.0 µm beads gave 11.4% and 15.8% and 15.9% and 20.4% fluorescent and scatter CVs for each set of beads, respectively. Separately testing each beam geometry with 1-, 2-, and 5 µm beads did not yield any predictable ideal beam-bead ideal pairing for best performance. Lastly, further integration of optical function was shown through the on-chip collection of signals; CVs of 29% and 30% were measured for side scatter and forward scatter, respectively, for 5 µm beads. The reliability of this all-optically guided scheme was confirmed by comparing it to a simultaneously recorded free-space collection scheme. The coincidence rate was found to be 94% and 96% for the side scatter and forward scatter schemes. Both had very low false positive rates – below 0.5% - with missed detection rates that were satisfactory but in need of improvement. Sources of noise and device improvements were identified and suggested.</p> / Doctor of Philosophy (PhD)
372

DOES CALCIUM INFLUX THROUGH T-TYPE CALCIUM CHANNEL INDUCE CARDIOMYOCYTE PROLIFERATION?

Wang, Fang January 2012 (has links)
Cardiovascular disease remains the number one cause or mortally in the western world. Heart failure is the most rapidly growing cardiovascular disease (Hobbs, 2004; Levy, et al., 2002). Heart failure, by definition, is progressive deteriorating function of the heart due to progressive cardiac myocytes loss. Though after decades of endeavor of searching the pathophysiology and treatments for heart failure, it remains highly lethal. Therefore, it is vital to find novel therapies to help treat such chronic disease. Replace the lost cardiomyocyte with new ones could restore cardiac function and reduce mortality. The purpose of this study is to investigate on how TTCCs (T-type calcium channels) affect cardiomyocyte proliferation. In mice after birth, the major TTCC expressed in the heart is Cav3.1/α1G, and therefore we used Cav3.1/α1G transgenic (TG), knockout (-/-) and wild type mice respectively to define the role of TTCC in cardiomyocyte proliferation. In neonatal mouse ventricular myocyte (NMVMs) right after birth, there is almost no TTCC after birth in α1G-/- NMVMs, whereas there are around 35% NMVMs in wild type (WT) show TTCC. On day 7 after birth, there are no T-type calcium currents in both α1G-/- NMVMs and WT NMVMs. Using BrdU, a DNA synthesis marker, we identified plenty of BrdU positive cardiomyocyte during the first seven days after birth. Cardiomyocyte is special due to its double nucleation property. Our cell cycle studies showed that there is significant difference in cell cycle distribution between α1G-/- and WT NMVMs on day seven after birth. Significantly more NMVMs are arrested in G1 phase in α1G-/-, compared to WT NMVMs. Even until 2 month old, there are still significantly more mono-nucleated cardiomyocyte in α1G-/- than in WT. In conclusion, all these evidence showed that blocking T-type calcium channel could partially prevent binucleation from happening and stop cardiomyocytes withdrawal from cell cycle. Mononucleated cardiomyocyte is still able to proliferate. Hence, mononucleated cardiomyocytes in adult still have potential to proliferation because these cardiomyoctes are arrested in their cell-cycle before their terminal differentiation, which could offer a novel approach for cardiac repair. / Physiology
373

Bovine Coccidiosis: Dynamics of infection in grazing cattle and the potential role of stress and immunity

Lucas, Aaron Scott 08 September 2011 (has links)
Eimerian parasites infect cattle worldwide. Information on the infection dynamics of these parasites is lacking in the central Appalachian region of the United States. Studies aimed at characterizing the seasonal dynamics of eimerian parasites in this region were carried out in order to assess the impact of these organisms in grazing systems. In these studies the prevalence of Eimeria spp. infection was highest in calves less than one year of age and subsequently decreased to stable levels in older animals. Although E. bovis was the most common species identified in calves, heifers and cows, mixed species infections dominated. Additional studies were carried out to investigate the effect of stress on Eimeria spp. infection in beef calves. Lower stress, two-stage, weaning methods had no effect on Eimeria spp. infection dynamics in beef calves. These findings must be interpreted in light of the fact that calves used in this study were not managed in a way typical of many calves in the U.S.A. The fact that they were only transported short distances, never commingled, or exposed to a livestock market may explain why a rise in post weaning FOC was not observed. A model of stress- induced coccidiosis was developed using dexamethasone and E. bovis challenge. In this model, an oral challenge of at least 500,000 sporulated E. bovis oocysts in addition to dexamethasone injection at 7 days post challenge increased subsequent FOC. Further investigation of the immune response to E. bovis challenge during times of stress indicates that stress-induced suppression of cell mediated immunity and E. bovis challenge are required to increase subsequent oocyst shedding. These findings may represent the mechanism associated with stress-induced outbreaks of coccidiosis reported to occur in beef cattle in the United States. / Ph. D.
374

Increases in Cortisol due to Weaning Stress and the Subsequent Alterations to Immune Function in Beef Calves

Gilbertie, Jessica 10 August 2010 (has links)
Weaning is defined as the physical separation of the cow-calf pair and the end of milk feeding. Natural weaning occurs between 7 and 14 months and is a gradual process. However, domestic weaning occurs between 6 and 8 months and occurs rapidly. Calves that are abruptly separated from their dam respond with increased vocalization and walking, and decreased eating and resting. The psychological stress the calf undergoes during weaning causes elevated glucocorticoid and catecholamine hormone concentrations that may predispose to increased morbidity and/or mortality from infectious diseases such as Bovine Respiratory Disease Complex. As an attempt to counter these changes, alternative weaning methods have been implemented and normally occur in two stages. Two-stage weaning begins with the cessation of milk feeding for approximately one week with the calf maintaining some contact with their dam and then permanent separation occurs. One of these methods uses a single fence to separate the cow-calf pair; this process allows the calf to see, hear and smell their dam, but does not allow the calf to suckle from its dam. Increases in cortisol, a glucocorticoid, have been linked to immunological alterations. Most notably, elevated cortisol concentrations decrease neutrophil function by down regulating the gene expression of CD62L and Fas. Cortisol also alters lymphocyte phenotype by decreasing ?δ T cells and increasing°? T cells in the circulation. Lastly, increases in cortisol can modify T cell cytokine production. The cytokines IL-12 and IFN? are secreted from T helper 1 cells while T helper 2 cells secrete IL-4 and IL-10; these T cells subsets also inhibit one another. During higher cortisol concentrations, these T cells are biased toward T helper 2 cytokine production. All these changes in immune function can lead to increased susceptibility to disease around the time of weaning. Therefore, two trials were conducted to test the hypotheses that abrupt weaning results in elevated concentrations of cortisol and subsequently alters immunological functions, and that fenceline weaning alleviates the increase in cortisol and alterations to immune function associated with weaning. In the fall of 2008, 12 Angus and Angus-X heifers (186°21 kgs; 174°16 days of age) were blocked by age and weight and randomly allotted into two groups, fenceline and abrupt. Blood samples were taken on day -7, 0, 7, 14, 21, and 42; fecal samples were taken on day -7, 0, and 3. All calves were weighed on day -7, 0, 7, 14, and 42. On day -1 all calves were separated from their dam and transported for 2 hours to another facility. On day 0 all calves were vaccinated with Brucella abortus (strain RB51). Serum was analyzed for IFN? and IL-4 as well as IgG1 and IgG2 specific antibodies to RB51. Fecal samples were analyzed for cortisol metabolites. Both IgG1 and IgG2 antibodies to RB51 increased from day 0 to day 14 (P<0.05), however no differences were detected between treatment groups. Fecal cortisol metabolites were higher on day 0 in abruptly weaned calves (P< 0.001) but did not differ between groups on day -7 or day 3. Fenceline calves had higher concentrations of IFN? in the serum on day -7 and day 0 as compared to the abruptly weaned calves (P<0.04). In the fall of 2009, forty-four Angus and Angus-X calves (19 heifers and 25 steers; 181°27 kgs; 148°17 days old) were blocked by age and gender and randomly allotted within block into two treatment groups, fenceline (FL) and abrupt (AB). Approximately half the fenceline calves were separated from their dams by a single fence at day -7 and the rest of the fenceline group at day -6; all calves were removed from their dam at day 0. Calves were vaccinated with Histophilus somni on day 1. Blood samples were taken at day -6, 1, 3, 8, 15, and 22. Fecal samples were taken on day -7, -6, 1 and 3. All calves were weighed on day -7, 0, 8, and 22. Serum samples were analyzed for IgG1 and IgG2 specific-H. somni antibodies, white blood cells were analyzed for lymphocyte phenotypes, and gene expression using 18S as the housekeeper gene. Fecal samples were analyzed for cortisol metabolites. Abruptly weaned calves had higher concentrations of cortisol metabolites in the feces than fenceline calves at day 1 (P<0.0001). No difference in average daily gain or H. somni specific antibodies between treatment groups was detected. There was a treatment*date interaction in lymphocyte and neutrophil populations (P<0.05); neutrophils from fenceline calves dropped from day -6 to day 1, but increased from day 1 to day 3, while abrupt calves decreased from day -6 to day 3. Lymphocytes from fenceline calves increased from day -6 to day 1, but decreased from day 1 to day 3, while lymphocytes from abrupt calves increased from day -6 to day 3. No difference in treatment groups was detected for lymphocyte phenotypes or gene expression; however, a date effect was detected. The CD4 and CD8 cell populations increased over time (P<0.0001) and WC1 and TcR1 decreased over time (P=0.0243 and P=0.0027 respectively) for both treatment groups. A decrease was detected over time for expression of GAPDH and CD62L (P<0.0001). The gene expression for the cytokines IFN?, IL-4 and IL-10 had no change over time. Results from the two studies suggest that fenceline weaning decreases the cortisol response associated with cow-calf separation, but does not have a significant effect on immunological parameters measured in this study. / Master of Science
375

Subacute immunotoxic effects of the environmental contaminants 7,12-dimethylbenzanthracene (DMBA), hexachlorocyclohexane (lindane), and 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) on spleen and pronephros cellularity and morphology and functional activity of macrophages contained in these hemotopoietic organs in the cichlid fish tilapia (<i>Oreochromis niloticus</i>)

Hart, Laura J. 18 September 2008 (has links)
Alterations of immune parameters were investigated in fish exposed to non-overtly toxic levels of three different environmentally relevant chemicals, 7,12-dimethylbenzanthracene (DMBA), hexachlorocyclohexane (lindane), and 2,3,7,8- tetrachlorodibenzo-p -dioxin (TCDD). Each chemical agent was administered to tilapia in separate experiments by intraperitoneal injection for five consecutive days. Following the final dose, total cellularity and histology of the spleen and pronephros were assessed, as were activity of phagocytic celis contained in these hematopoietic organs. <p>Using chemical doses which produced no clinical toxicity, tilapia exposed to each chemical agent displayed a significant reduction in total cell number of both spleen and pronephros, in most cases in a dose-related manner. Consistent with this observation, splenic and pronephric hypocellularity was confirmed upon histological examination of chemical-treated fish. However, neither superoxide radical production or phagocytosis of splenic or pronephric macrophages was inhibited in either DMBA, lindane, or TCDD exposed fish. Results of this study indicate that depressed total cell number in fish hematopoietic organs may be a more sensitive indicator of exposure to these environmental contaminants than is the activity of macrophages contained within these organs. / Master of Science
376

Verification of ADAM rWBC2 – An instrument for quantifying residual leukocytes in leukocyte reduced blood components

Myron, Amanda January 2024 (has links)
To reduce the risk of transfusion related complications, blood components should, according to European guidelines, contain less than 1 x 106 leukocytes per unit. To verify that these guidelines are upheld, residual leukocytes are measured in randomly selected blood components as means of quality control. At Uppsala University Hospital, the method currently used for this is flow cytometry (FCM). However, the hospital recently purchased a new instrument, ADAM rWBC2, for this purpose. The aim of this study was to verify ADAM rWBC2 as a replacement method for FCM and investigate whether the type of test tube chosen for the instrument (EDTA or micro test tube) would affect the leukocyte concentration. To conduct the study, 30 red blood cell units (RBCs), 30 platelet units (PLTs) and 30 plasma units were analyzed on both the ADAM rWBC2 instrument and with FCM. In addition to this, each RBC and PLT unit was allocated into both an EDTA tube and a micro test tube before analysis on the ADAM rWBC2 instrument. Results from both methods and tubes were compared using statistical analysis. The results from ADAM rWBC2 tended to be higher than the results from FCM, and the difference turned out to be statistically significant (p&lt;0,001). No significant difference could be detected between the results from the different test tubes. The assessment is that ADAM rWBC2 will replace FCM for quality control of residual leukocytes in blood components. According to the results, the type of test tube used does not affect the leukocyte concentration.
377

Coabitação com um parceiro doente: conseqüências sobre o comportamento, a atividade imune inata e o crescimento tumoral / Cohabiting with a sick mate: consequences on behavior, innate immune activity, and tumor growht

Alves, Glaucie Jussilane 16 August 2005 (has links)
A atividade do sistema nervoso central (SNC) afeta aquela do sistema imune e esta por sua vez, através de produtos originados em células imunes, como por exemplo, as citocinas modificam a atividade cerebral e, portanto, alguns comportamentos. O ato de conviver com pessoas portadoras de um tumor ou de patologias crônicas debilitantes tem sido estudado por vários pesquisadores, os quais têm relatado evidencias que mostram ser algumas condições psicológicas experimentadas por ?caregivers? associadas com variações de comportamento e de imunidade. Manifestações de estresse têm sido intensamente estudadas nestas pessoas. Neste sentido, e guardado os devidos cuidados com as extrapolações, não existe um modelo animal especificamente desenvolvido para analisar, em laboratório, as eventuais alterações imunes que possam ocorrer em animais que convivem com um outro doente. Este foi o objeto do presente trabalho. Mais especificamente, avaliou-se a existência de uma possível interação neuroimune em camundongas que coabitaram com outras portadoras de um tumor de Ehrlich, através da análise de parâmetros hematológicos, imunológicos, hormonais, comportamentais e neuroquímicos. Os resultados obtidos mostraram que a convivência por 11 dias com um animal portador do tumor de Ehrlich produziu em camundongas: 1) leucopenia; 2) diminuição do burst oxidativo induzido por PMA e por S. aureus e da porcentagem e, também da intensidade de fagocitose de neutrófilos sanguíneos; 3) aumento do burst oxidativo e redução da porcentagem, mas não alterou a intensidade de fagocitose de macrófagos ativados pelo ONCO-BCG; 4) diminuição da resistência ao crescimento de um tumor de Ehrlich, isto é, aumentou a concentração de células tumorais/ml de líquido ascítico e o número total de células tumorais; 5) redução do número de leucócitos circulantes em animais inoculados com o tumor de Ehrlich; 6) diminuição dos níveis hipotalâmicos de noradrenalina e aumento daqueles de dopamina e de MHPG; 7) aumento do ?turnover? de noradrenalina no hipotálamo e de dopamina no córtex frontal; 8) aumento dos efeitos da anfetamina sobre alguns parâmetros da atividade locomotora dos animais observados no campo aberto; 9) potenciou os efeitos de um tratamento com diazepam, reduzindo ainda mais o burst oxidativo induzido por PMA e por S. aureus assim como os efeitos do fármaco sobre a porcentagem e a intensidade de fagocitose de neutrófilos sanguíneos. No entanto, esta convivência não modificou a média do número de eritrócitos, a porcentagem do hematócrito e o volume corpuscular médio, assim como a atividade de macrófagos peritoneais residentes e, não interferiu com os níveis de corticosterona sérica dos animais. Em seu conjunto, os presentes resultados mostraram que a convivência com animais portadores de um tumor ascítico de Ehrlich produziu alterações comportamentais, neuroquímicas e imunológicas, que guardam grande similaridade com sinais e sintomas relatados em caregivers. Estas alterações foram interpretadas como decorrentes de uma situação de estresse psicológico prolongado vivenciado pelas camundongas companheiras de conspecíficas portadoras de um tumor. Mais especificamente, postulou-se, neste trabalho, sejam as alterações observadas decorrentes de um aumento de atividade catecolaminérgica no SNC e/ou de ativação do SNAS. A semelhança dos resultados obtidos em companheiras de animais doentes com aqueles de caregivers permitiu sugerir, tomados os devidos cuidados com extrapolações, seja o modelo experimental agora usado de alguma utilidade para a compreensão da situação vivenciada por estes caregivers / The activity of the central nervous system (CNS) affects the immune system, which by means of products molecules synthesized by its cells, modify the activity of the CNS, and, consequently, animal behavior. People that care for and support the needs of patients bearing tumors or with chronic, debilitating diseases, have been studied by many groups, with evidences pointing towards an association between some psychological conditions experienced by caregivers and changes in behavior and immunity. Stress-associated symptoms have been intensely studied in these people. Thus, taking into account the required grounds reasonable comparisons, there was no description of a suitable model for laboratory analysis of possible changes in immunity of animals cohabiting with a sick cage-mate. Therefore, the objective of this study was to establish a suitable model for this purpose. We particularly aimed on possible neuroimmune interaction in female mice that had cohabited with Ehrlich tumor-bearing mice, using for comparison hematological, immune, hormonal, behavioral, and neurochemical parameters. The results of this study show that cohabiting with a sick mate - mice bearing the Ehrlich tumor - for 11 days induced, in female mice: 1) leukopenia; 2) decrease in PMA- or S. aureus-induced oxidative burst, and also of the percentage and intensity of phagocytosis by circulating neutrophils; 3) increase in oxidative burst and reduction in the percentage, but did not influence intensity of phagocytosis by ONCO-BCG-activated macrophages; 4) decrease in the resistance to the progression of the Ehrlich tumor, shown by the enhanced concentration of tumor cells per ml of the ascitic fluid, and total number of tumor cells; 5) reduction in the number of circulating leukocytes in animals injected with the Ehrlich tumor; 6) diminished hypothalamic levels of noradrenaline and increased those of dopamine and MHPG in the same region; 7) increased the turnover of noradrenaline in the hypothalamus, and of dopamine in the frontal cortex; 8) enhanced the effects of amphetamine on several parameters of motor activity observed in the open field arena; 9) potentiated the effects of diazepam, reducing the PMA- or S. aureus-induced oxidative burst, and on the percentage and intensity of phagocytosis by circulating neutrophils even further. Nonetheless, cohabiting with the sick mate did not alter the red cell count, the hematocrit, or the mean cell volume, nor did it influence the activity of resident peritoneal macrophages or interfere with serum corticosterone levels. Altogether, these findings show that cohabiting with animals bearing the ascitic Ehrlich tumor caused behavioral, neurochemical, and immunological changes compatible with those presented and described by caregivers. These changes are interpreted as related to a sustained, long-term situation of psychological stress experienced by the conspecific female healthy mates of the tumor-bearing mice. In particular, we postulate in this study that the changes observed might be driven by the increased cathecolaminergic activity in the CNS and/or by the activation of the sympathetic branch of the autonomic nervous system (SANS). The resemblance of the results obtained here and those seen in human caregivers allows the careful suggestion that this model may be relevant to help understanding the situation experienced by caregivers
378

Etude des altérations morphologiques et biochimiques des érythrocytes au cours du sepsis / Studies of the alterations of shape and biochemistry of erythrocytes during sepsis.

Piagnerelli, Michaël 05 November 2009 (has links)
La microcirculation est rapidement altérée dans le sepsis et la persistance de ces altérations est associée à un mauvais pronostic. La microcirculation est composée de vaisseaux invisibles à l’œil (< 100 µm), de l’endothélium, du glycocalyx, des cellules musculaires lisses et des éléments sanguins dont les GR. <p>De nombreuses études animales et humaines ont rapporté des altérations rhéologiques des GR dans le sepsis. Ces modifications comprennent une diminution de la déformabilité, une augmentation de l’agrégation et de l’adhérence globulaire. <p>De plus, l’altération de la déformabilité peut induire des altérations du flux microcirculatoire dans des modèles expérimentaux animaux. Ces mêmes altérations rhéologiques sont rapportées dans le diabète. Dans cette pathologie, les GR présentent une diminution du contenu membranaire en AS, comme dans les processus de sénescence. <p>La déformabilité des GR dépend des caractéristiques cellulaires incluant surtout les propriétés de la membrane, la géométrie cellulaire et dans une moindre mesure la viscosité cellulaire. Malgré la connaissance des altérations de la rhéologie dans le sepsis, peu de travaux, au contraire du diabète, s’interessent aux modifications de la membrane.<p>Nous avons étudié, par analogie aux altérations globulaires rapportées dans le diabète, la membrane des GR de patients admis en soins intensifs pour un sepsis, et comparé à des GR de patients non septiques et de volontaires sains. Le contenu membranaire en AS était significativement diminué chez les patients septiques par rapport aux patients non-septiques et aux volontaires sains. De plus, les GR des patients septiques, analysés par une technique de cytométrie en flux indépendante de la température de l’échantillon, étaient rapidement plus sphériques (dans les 24 heures du sepsis) et incapables de modifier leurs formes en hypoosmolalité. Cette technique de cytométrie a par ailleurs aussi été utilisée pour l’analyse de GR de patients diabétiques et en insuffisance rénale terminale. <p> La diminution du contenu en AS est aussi rapidement observée sur la transferrine, suggérant une augmentation de la concentration et/ou de l’activité de la neuraminidase, enzyme clivant l’AS. Dans un modèle de choc septique induit chez l’ovin, nous avons confirmé la rapidité de ce phénomène. En effet, la concentration en AS libre augmente dès la 15ième heure après induction du sepsis.<p>In-vitro, nous avons pu reproduire les modifications de forme des GR observés chez les patients septiques par incubation de GR de volontaire avec de la neuraminidase, et ce en 10 heures, quelles que soient les concentrations utilisées. Ces modifications de forme et de membrane s’accompagnent d’une augmentation significative du contenu en lactate, suggérant une stimulation de la glycolyse érythrocytaire et en 2,3-DPG, facilitant la libération de l’O2 de l’Hb vers les tissus. <p>Toutes ces modifications touchant la membrane des GR des patients de soins intensifs, surtout septiques, peuvent être responsables des altérations de rhéologie que nous avons observé grâce au LORCA sur une large population admis aux soins intensifs.<p>Une meilleure compréhension des mécanismes conduisant aux altérations rhéologiques des GR dans le sepsis, et ses effets potentiellement déletères sur la microcirculation, sont nécessaires avant d’envisager les GR comme cible thérapeutique.<p><p><p> / Doctorat en Sciences médicales / info:eu-repo/semantics/nonPublished
379

Computational Analysis of Flow Cytometry Data

Irvine, Allison W. 12 July 2013 (has links)
Indiana University-Purdue University Indianapolis (IUPUI) / The objective of this thesis is to compare automated methods for performing analysis of flow cytometry data. Flow cytometry is an important and efficient tool for analyzing the characteristics of cells. It is used in several fields, including immunology, pathology, marine biology, and molecular biology. Flow cytometry measures light scatter from cells and fluorescent emission from dyes which are attached to cells. There are two main tasks that must be performed. The first is the adjustment of measured fluorescence from the cells to correct for the overlap of the spectra of the fluorescent markers used to characterize a cell’s chemical characteristics. The second is to use the amount of markers present in each cell to identify its phenotype. Several methods are compared to perform these tasks. The Unconstrained Least Squares, Orthogonal Subspace Projection, Fully Constrained Least Squares and Fully Constrained One Norm methods are used to perform compensation and compared. The fully constrained least squares method of compensation gives the overall best results in terms of accuracy and running time. Spectral Clustering, Gaussian Mixture Modeling, Naive Bayes classification, Support Vector Machine and Expectation Maximization using a gaussian mixture model are used to classify cells based on the amounts of dyes present in each cell. The generative models created by the Naive Bayes and Gaussian mixture modeling methods performed classification of cells most accurately. These supervised methods may be the most useful when online classification is necessary, such as in cell sorting applications of flow cytometers. Unsupervised methods may be used to completely replace manual analysis when no training data is given. Expectation Maximization combined with a cluster merging post-processing step gives the best results of the unsupervised methods considered.
380

Development of Enhanced Molecular Diagnostic Tools for Protein Detection and Analysis

Ebai, Tonge January 2017 (has links)
Improved diagnosis, prognosis and disease follow-up is a fundamental procedure and a constant challenge in medicine.  Among the different molecular biomarkers, proteins are the essential regulatory component in blood; hence, by developing enhanced specific and sensitive molecular tools will gives great insight into the different processes in disease treatment.  In this thesis, we build on the proximity ligation assay to develop and apply new adaptable methods to facilitate protein detection. In paper I, I present a variant of the proximity ligation assay (we call PLARCA) using micro titer plate for detection and quantification of protein using optical density as readout in the fluorometer. PLARCA detected femtomolar levels of these proteins in patient samples, which was considerably below the detection threshold for ELISA. In paper II, we developed and adapted a new method into the in situ PLA methods for detection and identification of extracellular vesicles (EVs) using flow cytometry as readout (a method we call ExoPLA).  We identified five target proteins on the surface of the Evs and using three colors, we identified the EV using flow cytometer. In paper III, we aim to improve the efficiency of in situ PLA by creating and developing new designs and versions of the assay we called Unfold probes Through comparison of detection of protein using in situ PLA versus Unfold probes, we observed considerable decrease in non-specific signals, and also a lower detection threshold. In paper IV, we describe the development of a solid phase proximity extension (sp-PEA) assay for protein detection and quantification. We compared detection of IL-8, TNF-alpha, IL-10 and IL-6 using spPEA and PEA; spPEA demonstrations over 2 orders of magnitudes in the lower detection concentrations by decreased in background noise.

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