1,720,969 research outputs found
Data warehousing in the age of big data
No full textData Warehousing in the Age of the Big Data will help you and your organization make the most of unstructured data with your existing data warehouse. As Big Data continues to revolutionize how we use data, it doesn't have to create more confusion. Expert author Krish Krishnan helps you make sense of how Big Data fits into the world of data warehousing in clear and concise detail. The book is presented in three distinct parts. Part 1 discusses Big Data, its technologies and use cases from early adopters. Part 2 addresses data warehousing, its shortcomings, and new architectur
Residues N133 and E54 are important for maintaining the Escherichia coli camp receptor protein inactive in the absence of camp
No full textThe cyclic adenosine monophosphate(cAMP) receptor protein (CRP) from Escherichia coli is a transcriptional activator which regulates genes required for catabolizing carbon sources other than glucose. CRP exists in equilibrium between active and inactive conformations. In the absence of cAMP, the protein conformational equilibrium is poised towards the inactive form, leading to low basal CRP activity. Few studies have been conducted on the inactive CRP form to show what residue interactions stabilize this form. The Youn lab has previously identified 25 residues that form charge interactions with other residues only in the inactive form by comparing active and inactive structures of CRP. Alanine scanning mutagenesis analysis showed that N133A/A144T CRP had an exceptionally increased cAMP-free CRP activity, suggesting that N133 plays a role in CRP activation. The objectives of this thesis are : i) to distinguish between the absence of the asparagine or the introduction of alanine as the basis for enhanced CRP activity of N133A/A144T CRP, ii) to determine if substitution of N133's interaction partner E54 leads to enhanced CRP activity and iii) to create charge swapped mutants in order to validate the importance of the interaction N133-E54 in stabilizing the inactive CRP form in the absence of cAMP. To this end, N133 and E54 were subjected to codon randomization in the A144T CRP mutant background. At position 133, multiple mutants besides N133A/A144T were selected, displaying enhanced CRP activity: N133H/A144T, N133Q/A144T, and N133M/A144T CRP. Similarly, at position 54, E54K/A144T, E54S/A144T, E54N/A144T E54T/A144T CRP mutants were selected, which display enhanced CRP activity compared to A144T ii mutant by itself. These results suggest that the absence of the original amino acid N133 and E54 leads to enhancement of CRP activity, which we speculate is caused by shifting the equilibrium towards the active form. The charge-swapped mutant N133D/E54K/A144T displayed similar CRP activity as the two parental double mutants N133D/A144T and E54K/A144T. Hence we cannot conclusively suggest that the proposed N133-E54 interaction stabilizes the inactive CRP form. This work revealed the importance of N133 and E54 as residues that keep CRP inactive in the absence of cAMP. In the future, CRP mutants described here need to be purified for in vitro analyses
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Development of fluorinated peroxyl radical clock
Full text linkPeroxidation or autoxidation is the major chemical process behind degradation of hydrocarbon (petroleum) products, biomolecules, polymers, and foodstuffs. Peroxidation is a free-radical chain reaction where the hydrogen atom transfer reaction from the substrate to peroxyl radical is the rate-determining step in the overall process. The discovery of new methods that measure the rate constants of H-atom transfer is an integral part of the development process of radical-trapping antioxidants (RTAs), small molecules that limit peroxidation and have long been a focus of research in this field. Radical clocks are kinetic competition experiments that have long been the standard methods for measuring rate constants of radical-mediated reactions. Existing radical clock methods utilize chromatography techniques (GC, HPLC) for product analysis. However, chromatography-based methods require that all parameters of the method (column, flow rate, mobile phase, detector) are strictly met. Quantitative NMR (qNMR) offers an alternative way of quantifying oxidation products all with minimal or no modification to existing instrumentation since there is no actual separation of the analyzed mixture. 19F NMR is particularly suitable due to the high abundance of paramagnetic isotope (sensitivity) and a very wide window of chemical shifts (signal resolution). The research goal of the thesis was the development of an NMR-based peroxyl radical clock methodology based on 4-fluoroallylbenzene. Synthesis, characterization of standards, as well as calibration experiments, will be discussed
Measurements of the criegee intermediates and oh radical in alkene ozonolysis
Full text linkThe hydroxyl radical is an important atmosphere oxidant, which controls the chemical lifetimes of many atmospheric trace gases and it is involved in the formation of tropospheric ozone and secondary organic aerosols. Alkene ozonolysis is one of the pathways of producing OH radicals through the generation of Criegee intermediates (carbonyl oxides). Criegee intermediates are removed from the atmosphere through various reactions, which are dependent on pressure and relative humidity. In this work, two model alkenes were used to study the formation of Criegee intermediates and OH radical as a function of pressure, through chamber studies using Infrared spectroscopy. Similarly, the chemistry of Criegee intermediates was studied as a function of relative humidity; hydroperoxides and organic acid products were measured by using Proton Transfer Reaction Mass Spectrometry and High-Performance Liquid Chromatography. Through this work, the yields of stabilized Criegee intermediate and OH radical were found to be 0.39±0.06 and 0.60±0.04 in 2,3-dimethyl-2-butene ozonolysis. The yields of stabilized Criegee intermediate and OH radical were found to be 0.45±0.02 and 0.19±0.01 in ethylene ozonolysis. The pressure dependence measurements suggested an increase in the OH radical yields and a significant decrease in the Criegee intermediate yields, as the pressured was increased. Increasing the relative humidity, increased the production of hydroperoxides and organic acids from the Criegee intermediates. The fate of Criegee intermediates is important because the balance of radicals versus formation of products, influences the chemical composition of the atmosphere, which in turn has implications for climate change and health impacts from air pollutants
Ab initio computational analysis of molecular excitation data
Full text linkElectronically excited state data varies significantly between different types of molecules, which makes it difficult to store and process. Interpretation often requires molecular orbital visualization, but this becomes labor-intensive. One alternative is to analyze data associated with excited states. This thesis hypothesizes that instead of using molecular orbitals, a computer database program can be developed to use excited state data to compare the excitation properties of different molecules. A testing database was created using Q-Chem and simple excited state methods. Python scripts were developed to extract excited state data from each calculation output file. Using hierarchical clustering, the molecules were first manually grouped via dendrograms using orbital images. Then, another set of dendrograms were generated using simple data from the output files and compared to the manual grouping. While both approaches share some similarities, there are still discrepancies that may be resolved using additional excited state information such as orbital energies. After applying the program to a small set of phenylurea compounds, the clustering of the compounds in the resulting dendrogram appeared sound and were easily supported by analyzing the molecular orbitals of each compound. Ultimately, this project marks the first attempt of analyzing excited states using hierarchical clustering dendrograms
Effects of divalent metals on the dynamic equilibria between bmaa and its carbamate species
Full text linkβ-N-methyl-amino-L-alanine (BMAA) in the presence of bicarbonate (HCO3-) undergoes structural modifications generating two carbamate species, α-carbamate and β-carbamate. The presence of these carbamate species is thought to be a causative agent in neurodegenerative disorders. Interestingly, BMAA shares structural similarity to the bidentate ligand ethylenediamine. The two nitrogen atoms on ethylenediamine are known to exhibit high affinity for divalent metal ions ( Ni2+, Zn2+, Cu2+, Co2+) and form stable metal complexes in solution. Because BMAA is able to cross the blood brain barrier and has structural similarities to ethylenediamine, it is hypothesized that BMAA and its carbamate adducts are able to chelate divalent metals (Mg2+, Zn2+, and Cu2+) present within the neuronal environment. By using Nuclear Magnetic Resonance Spectroscopy (NMR), solutions of BMAA in the presence of HCO3- with either Mg2+, Zn2+, or Cu2+ were analyzed to derive the (%) population, kinetic rate constants, diffusion coefficients, ΔG*, and equilibrium constant (K*) for each species. Circular Dichroism was then performed on each solution to observe the nπ interaction in the presence of divalent metals and a UV-Vis was performed to verify the affinity of BMAA to Cu2+. The data obtained demonstrate that BMAA interacts with both Cu2+ and Zn2+ and causes subsequent disruptions in the formation of carbamate species. 2D NMR data reveals Zn2+ causes a decrease in the formation of both carbamate species (ΔG>0). In addition, population of BMAA is increased in solution presumably because Zn2+ is binding to BMAA. UV-Vis data of Cu2+-containing solutions indicates the formation of Cu-BMAA complexes in solution, while circular dichroism suggest Cu2+, similar to Zn2+, interacts with the amine groups on BMAA. In contrast, 1D and 2D NMR of Mg2+-containing solutions did not show any significant changes to the population of BMAA and its carbamate adducts in solution. Furthermore, Mg2+ does not interact with the amine groups on BMAA, as evidenced by the circular dichroism spectra, suggesting that Mg2+ interacts weakly with BMAA
Measurements of quinones in fine particulate matter
Full text linkInhalation of fine particulate matter (PM) has been shown to be harmful to human health and well-being. One of the main mechanisms of particle toxicity in the lungs is the generation of reactive oxygen species (ROS) which contributes to respiratory diseases such as asthma and lung cancer. Specific chemical constituents of PM have been implicated in the conversion of molecular oxygen to the harmful ROS but the extent of contribution by these chemical species is not well understood. Quinones are a class of organic molecules found in the complex composition of fine PM that have been shown to undergo a potentially indefinite catalytic process generating ROS in the lungs. Fine particles were collected for two weeks in winter of 2013 in Fresno California, analyzed for the presence of specific quinones, and compared with measurements of ROS formation. Four quinones were identified using gas chromatography mass spectrometry (GCMS): 9,10-phenanthraquinone, 9,10-anthraquinone, 1,4-napthoquinone, and 1,2-naphthoquinone. Comparison with ROS generated by particles in a cell-free, surrogate lung fluid show some contribution of quinones to the production of ROS but the contributions are shown to be minimal
The effects of calcium carbonate product OR-244B on the nutrient content and storability of table grapes
Full text linkGrapes are non-climacteric which means they will not ripen after being harvested. With this comes a short cold-storage time of 4 weeks and proneness to diseases and physiological and parasitic disorders. Essential nutrients such as calcium have been seen to inhibit such diseases and disorders. Common calcium treatments include calcium chloride or calcium nitrate which come with risks such as chloride necrosis or nitrate leaching to groundwater posing a human health risk. This project evaluated the effects of a more environmentally friendly calcium carbonate product called OR-244B developed by ORO AGRI. To measure the effect on nutrient content, storability, and berry juice composition, OR-244B was applied on Sweet Scarlet and Autumn Royal Table grapes and compared to commercial treatments as well as treatments of individual components from OR-244B. Leaf, soil, and berry samples were collected throughout the season and analyzed using various qualitative and quantitative tests. Results from this study showed the importance of having a surfactant delivery system and the proper particle size of calcium. OR-244B was shown to increase calcium concentration in some of the sample collections. OR-244B also decreased shatter and the occurrence of waterberry after a cold storage period of 4 weeks. All of these benefits were seen without compromising the berry juice composition. These results point to a promising future for OR-244B in the table grape market to increase calcium and improve storability without sacrificing quality
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