Browsing by Subject "Quantification"

Now showing 1 - 4 of 4
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    Closing the Divide: Exploring Meaningful Technology Use in the Technology Integration Matrix
    (2024) Seylar, John
    The purpose of this mixed-methods study is to investigate the suitability of Technology Integration Matrix Observations (TIM-O) extensity scores to serve as a quantitative proxy for meaningful technology use in K-12 public school settings across the United States. To do so, correlations between TIM-O extensity scores and various school-level socioeconomic indicators were explored using a Cumulative Link Mixed Model. Questions and observations gathered during the model-building process were then used to inform the development of an interview protocol, which was used to gather the experiences and perspectives of three middle school instructional coaches. My analysis uncovered evidence that TIM-O extensity scores could serve as a useful proxy for meaningful technology use, though improvements and further study will be necessary.
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    The importance of being proportional: a paradigm shift for intensity-based label free relative quantification in mass spectrometry proteomics
    (2013-05) Van Riper, Susan Kaye
    Biological variation not only provides insight into the molecular machinery of disease progression, but accurately informs clinicians about a patient's health status, both current and future. Researchers discover biological variation by conducting large scale comparative studies aimed at detecting differences in the molecular makeup (biomarkers) of samples in different states. Ideally suited for biomarkers are proteins because their cellular composition (proteome) and their degraded parts, endogenous peptides (peptidome), change in response to their environment and disease progression. For comparative proteomic studies, researchers commonly employ high performance liquid chromatography, coupled with electrospray ionization tandem mass spectrometry (HPLC-ESI-MS/MS) and labeled quantification. However, intensity-based label free relative quantification (iLFRQ) is more desirable than labeled quantification because iLFRQ is more cost effective and does not limit the number of samples in a study. Unfortunately, iLFRQ for proteins, and especially peptides, is challenging. Here, I highlight three challenges. 1) I contend that the current relative abundance paradigm is ill-suited to detect biological variation using iLFRQ. 2) HPLC-ESI-MS/ MS analyses produce poorly repeatable and reproducible results, and current normalization methods fail to mitigate localized extraneous variability (complex variability in measurements) from transient stochastic events occurring during an HPLC-ESI-MS/MS run. 3) Current software frameworks report protein level quantification rather than peptide level quantification. To overcome these challenges, I offer three contributions. 1) I propose to use the proportionality paradigm for iLFRQ instead of the relative abundance paradigm. 2) Proximity-based Intensity Normalization (PIN), an embodiment of the proportionality paradigm, normalizes a peptide's signal intensity by constructing its temporal neighborhood and computing its relative proportion within that neighborhood. 3) RIPPER, a new software framework that reports normalized peptide signal intensities rather than protein intensities. Evaluation results demonstrate that PIN dominates current normalization methods in reducing systematic bias and complex variability. Furthermore, RIPPER/PIN finds statistically significant biological variation which is now falsely reported or missed. I expect the proportionality paradigm for iLFRQ, embodied in PIN, and implemented in RIPPER, to change the way researchers analyze HPLC-ESI-MS/MS experimental data. The upshot will, I expect, will be reproducibility and repeatability improved, and otherwise falsely reported or missed, statistically significant biological variation discovered.
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    Quantification of magnetic components in sediments with applications in paleoenvironmental studies.
    (2011-12) Lascu, Ioan
    The present dissertation is a collection of papers investigating the magnetic properties of sediments. The main aim of the work presented here is to study the magnetic characteristics of sedimentary deposits by using a methodology that efficiently quantifies the contributions of various ferrimagnetic components in sediments, and to exemplify how this model can be used to make inferences about past climatic and environmental variability. Magnetic minerals in sediments have long been used as indicators of variability in the factors controlling sediment deposition, and sediment-magnetic properties can be interpreted in terms of the processes controlling the fluxes of various magnetic components. Ferrimagnetic minerals, such as magnetite, are strong magnetically, and tend to dominate the signal from bulk measurements. Two sedimentary ferrimagnetic components that play a major role in shaping the magnetic record with time: a detrital component and a biogenic component. The detrital component of magnetic assemblages probably accounts for the greater proportion of the magnetic signal in many records, and therefore has been the focus of most environmental magnetism studies. The processes that control detrital records are mostly tied to local hydrology, climate, and vegetation cover. However, there is strong evidence that many magnetic assemblages are dominated by autochthonous magnetic particles, which in most cases are produced as a result of direct biologic control. Knowing the contribution of each of these components to the total mass of ferrimagnetic material becomes important when making inferences about past climatic or environmental conditions. The theoretical mixing model devised here using the characteristics of detrital and biogenic end members was tested on lake sediments from Minnesota. The analysis incorporates both spatial and temporal effects on magnetic record. We have investigated the history of sediment flux to Deming Lake, Minnesota, for the past 1000 years. Our results reveal several episodes of reduced precipitation, during which less sediment is mobilized from the catchment by overland flow and runoff. The most prominent episode occurred at the end of the Little Ice Age, indicating that this time period was not only cold but might have been drier than previously thought. The spatial control on sediment-magnetic properties was established via a survey of the magnetic properties of surface sediments from several Minnesota lakes. The magnetic properties are controlled by the competing fluxes of detrital and biogenic particles, according to location in the basin, while the position of the oxic-anoxic interface controls whether biogenic magnetite is formed in the sediment or in the water column, with implications in the preservation of intact versus collapsed bacterial chains. The thesis concludes with an incursion into the magnetic properties of chemical sediments from caves, or speleothems. The magnetic recordings preserved in calcite speleothems hold enormous potential for paleomagnetic and paleoenvironmental reconstructions. Speleothems lock in magnetization instantly, are not affected by post-depositional effects, and can be dated with high precision. The natural remanence in speleothems is carried mainly by magnetite, and the main remanence acquisition mechanism is depositional, through physical alignment of detrital magnetic grains parallel to the Earth's magnetic field. Future speleothem magnetism studies should benefit from increasingly sensitive magnetometers, operating at high spatial resolution, that are able to resolve short-term geomagnetic variability, and characterize events such as geomagnetic excursions at an unprecedented scale.
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    Sucrose crystallinity quantification using FTIR spectroscopy
    (2014-10) Mortenson, Aimee Kwong
    Understanding sucrose crystallinity is important especially as the food industry has reduced sugar content in products. Robust quantification methods determine crystallinity effects from formulation and/or processing changes. Differential Scanning Calorimetry (DSC) quantifies crystallinity within products, albeit requiring sample destruction. Fourier Transform Infrared (FTIR) spectroscopy can quantify different materials and has the potential of mapping crystallizing areas within a complex food matrix. Additionally, this method can be used to quantify sucrose crystallinity by a non-destructive, rapid means.Currently the methods used to quantify for sucrose crystallinity have been explored in pharmaceutical, lower moisture systems, where complex food matrices are not a factor. The objectives were to create a FTIR method to quantify the amount of crystalline sucrose in mixtures at various concentrations and to determine feasibility of spatial analysis capabilities using FTIR microscope methods.The development of the method was built using model systems of sucrose and carbohydrate blends. Crystallinity was measured via both FTIR and DSC. Samples were freeze-dried and held at different humidity levels to determine which IR peaks were independent of moisture content. IR spectral peaks that correlated best with the DSC measured sucrose crystallinity content were identified. Different calibration methods were concurrently used to obtain the best statistical fit using TQ Analyst® software. FTIR spatial analyses were performed on samples to assess feasibility of the method and commercialized baking mixes were tested to determine efficacy of the bulk method on complex food matrices.Three regions of interest (1087 cm-1, 991 cm-1, and 909 cm-1) were found to have the best Partial Least Squares (PLS) correlation to the crystallinity percentage. A Performance Index of 96.3 and a Root Mean Square Error of Prediction 0.925 were achieved with the three regions. These results show the potential of a robust method to quantify heterogeneous microdomains within foods, without interference from complex matrices. The three regions were statistically comprehensive at defining the variables as a bulk method. The spatial analysis using the FTIR microscope was affected by sucrose orientation, beam intensity, and shifts in peaks. A lower magnification spatial method would be a more applicable use of this method in an inline FTIR technology. The future application of this technology is to combine observed microdomains and correlate them to events such as stickiness or drying rates, for example.