Automating database curation with workflow technology

The entire thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file; a non-technical public abstract appears in the public.pdf file.Title from PDF of title page (University of Missouri--Columbia, viewed February 12, 2010).Thesis advisor: Dr. Toni Kazic.Includes bibliographical references.M.S. University of Missouri--Columbia 2005.Dissertations, Academic -- University of Missouri--Columbia -- Computer science.Building scientific databases is extremely difficult and expensive. Costs could be reduced if the experts who curate the deposited data, are provided with data that are reviewed by other experts at lower levels for accuracy and consistency. Since expertise is distributed around the world, a common platform that implements a well-accepted work process is needed to support such community curation. The workflow is complicated because there are many different types of biochemical data and the relationships among the data are complex; different data types need different kinds of checks; procedures to deposit, review, revise, and accept data; and the volume of data is very large. We have automated the workflow used in curating several types of biochemical data. This model is flexible enough to accommodate additional processes idiosyncratic to particular groups of curators, such as those for enzymatic reactions, biochemical terms, and molecular structures. This work demonstrates the application of workflow technology to intellectually complex, geographically distributed, multidisciplinary scientific processe

Sonoluminescence and sonochemiluminescence from a microreactor

Micromachined pits on a substrate can be used to nucleate and stabilize microbubbles in a liquid exposed to an ultrasonic field. Under suitable conditions, the collapse of these bubbles can result in light emission (sonoluminescence, SL). Hydroxyl radicals (OH*) generated during bubble collapse can react with luminol to produce light (sonochemiluminescence, SCL). SL and SCL intensities were recorded for several regimes related to the pressure amplitude (low and high acoustic power levels) at a given ultrasonic frequency (200 kHz) for pure water, and aqueous luminol and propanol solutions. Various arrangements of pits were studied, with the number of pits ranging from no pits (comparable to a classic ultrasound reactor), to three-pits. Where there was more than one pit present, in the high pressure regime the ejected microbubbles combined into linear (two-pits) or triangular (three-pits) bubble clouds (streamers). In all situations where a pit was present on the substrate, the SL was intensified and increased with the number of pits at both low and high power levels. For imaging SL emitting regions, Argon (Ar) saturated water was used under similar conditions. SL emission from aqueous propanol solution (50 mM) provided evidence of transient bubble cavitation. Solutions containing 0.1 mM luminol were also used to demonstrate the radical production by attaining the SCL emission regions.Comment: http://www.sciencedirect.com/science/article/pii/S1350417712000855; ISSN 1350-417

Broad and potent cross clade neutralizing antibodies with multiple specificities in the plasma of HIV-1 subtype C infected individuals.

Broadly Cross clade Neutralizing (BCN) antibodies are recognized as potential therapeutic tools and leads for the design of a vaccine that can protect human beings against various clades of Human Immunodeficiency Virus (HIV). In the present study, we screened plasma of 88 HIV-1 infected ART naïve individuals for their neutralization potential using a standard panel of 18 pseudoviruses belonging to different subtypes and different levels of neutralization. We identified 12 samples with good breadth of neutralization (neutralized >90% of the viruses). Four of these samples neutralized even the difficult-to-neutralize tier-3 pseudoviruses with great potency (GMT > 600). Analysis of neutralization specificities indicated that four samples had antibodies with multiple epitope binding specificities, viz. CD4-binding site (CD4BS), glycans in the V1/V2 and V3 regions and membrane proximal external region (MPER). Our findings indicate the strong possibility of identifying highly potent bNAbs with known or novel specificities from HIV-1 subtype C infected individuals from India that can be exploited as therapeutic tools or lead molecules for the identification of potential epitopes for design of a protective HIV-1 vaccine

Glucose-induced down regulation of thiamine transporters in the kidney proximal tubular epithelium produces thiamine insufficiency in diabetes

Increased renal clearance of thiamine (vitamin B1) occurs in experimental and clinical diabetes producing thiamine insufficiency mediated by impaired tubular re-uptake and linked to the development of diabetic nephropathy. We studied the mechanism of impaired renal re-uptake of thiamine in diabetes. Expression of thiamine transporter proteins THTR-1 and THTR-2 in normal human kidney sections examined by immunohistochemistry showed intense polarised staining of the apical, luminal membranes in proximal tubules for THTR-1 and THTR-2 of the cortex and uniform, diffuse staining throughout cells of the collecting duct for THTR-1 and THTR-2 of the medulla. Human primary proximal tubule epithelial cells were incubated with low and high glucose concentration, 5 and 26 mmol/l, respectively. In high glucose concentration there was decreased expression of THTR-1 and THTR-2 (transporter mRNA: −76% and −53% respectively, p<0.001; transporter protein −77% and −83% respectively, p<0.05), concomitant with decreased expression of transcription factor specificity protein-1. High glucose concentration also produced a 37% decrease in apical to basolateral transport of thiamine transport across cell monolayers. Intensification of glycemic control corrected increased fractional excretion of thiamine in experimental diabetes. We conclude that glucose-induced decreased expression of thiamine transporters in the tubular epithelium may mediate renal mishandling of thiamine in diabetes. This is a novel mechanism of thiamine insufficiency linked to diabetic nephropathy

Comparison of voltage regulation between SST and conventional transformers in high penetration PV power systems

Solid state transformers (SST) are power electronic transformers combined with high-frequency conventional transformers and control circuitry capable of delivering high performance and flexible power control capabilities. This thesis focuses on analyzing the performance of SSTs in a distribution system with photovoltaic (PV) injection. In order to validate the performance of SSTs, average value models are used on the IEEE 34 bus distribution feeder network scaled to 12.47 kV. SST voltage profiles on the load side are analyzed and the unity power factor capabilities are demonstrated. This is followed by the study of voltage profiles on the primary side of the SST. Additionally, distributed energy resources such as PV systems tend to cause power quality issues which are handled using the SST\u27s volt-var control capabilities. In this case, both AC and DC side integration of PV systems in SST is demonstrated. DC side integration is one of the advantages of this type of solid state device. To compare this system to a conventional distribution system, the IEEE 34 bus system with similar load and PV injection profiles is built using conventional single-phase distribution transformers. By comparing the results of the SST (with AC and DC side PV integration) with a conventional transformer, the performance of the SST can be reviewed. To provide a complete analysis, voltage regulators are redesigned for the scaled IEEE 34 distribution feeder network using PSCAD while mounting conventional transformers, and its comparison is provided. Further, the impacts and performance of SST with PV penetration greater than 100% is studied and its results are presented and contrasted with conventional transformers --Abstract, page iii

Spatial and Temporal Variations in Population Dynamics of few Key Rocky Intertidal Macrofauna at Anthropogenically Influenced Intertidal shoreline

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