Design and Evaluation of a BLAST Ungapped Extension Accelerator, Master\u27s Thesis

The amount of biosequence data being produced each year is growing exponentially. Extracting useful information from this massive amount of data is becoming an increasingly difficult task. This thesis focuses on accelerating the most widely-used software tool for analyzing genomic data, BLAST. This thesis presents Mercury BLAST, a novel method for accelerating searches through massive DNA databases. Mercury BLAST takes a streaming approach to the BLAST computation by offloading the performance-critical sections onto reconfigurable hardware. This hardware is then used in combination with the processor of the host system to deliver BLAST results in a fraction of the time of the general-purpose processor alone. Mercury BLAST makes use of new algorithms combined with reconfigurable hardware to accelerate BLAST-like similarity search. An evaluation of this method for use in real BLAST-like searches is presented along with a characterization of the quality of results associated with using these new algorithms in specialized hardware. The primary focus of this thesis is the design of the ungapped extension stage of Mercury BLAST. The architecture of the ungapped extension stage is described along with the context of this stage within the Mercury BLAST system. The design is compact and performs over 20× faster than that of the standard software ungapped extension, yielding close to 50× speedup over the complete software BLAST application. The quality of Mercury BLAST results is essentially equivalent to the standard BLAST results

THE USE OF NEAR INFRARED REFLECTANCE FOR EVALUATING COTTON FINENESS AND MATURITY

The U.S. Department of Agriculture has proposed to develop Ii new high speed, high volume technique to assess cotton quality. This goal has led us to investigate the feasibility of near infrared reflectance spectroscopy as a technique for evaluating cotton fiber perimeter size and wall thickness, two of the physical characteristics used in the evaluation of cotton fineness and maturity. In order to isolate the effects of perimeter size and wall thickness, nineteen cotton samples were selected on the basis of their having a nonsignificant correlation between these 2 measurements. The reflectance spectra from 1100 to 2500 nanometers was recorded at every other wavelength. The 700 independent variables were transformed by log (1/ reflectance). Due to the multicollinearity of the independent variables, the principle components were used in a multiple regression with data obtained from the reference method (arealometer) for the two dependent variables, perimeter size and wall thickness. The regression analysis of perimeter size and wall thickness on the principle components gave R2\u27S of 0.229 and 0.943 respectively

True Metabolizable Energy of Two Southern Aquatic Plants

In order to improve the accuracy of energetic models used to set habitat objectives, estimates of energy availability and metabolizability for a variety of aquatic plants are needed. While true metabolizable energy (TME) values are available for many species of moist-soil seeds, hard mast, agricultural grains, and invertebrates, few TME values exist in the published literature for submersed aquatic vegetation (SAV), despite SAV being a significant food item of many dabbling and diving duck species. Moreover, neither of the two plant species previous analyzed (i.e., shoalgrass [Halodule wrightii], Ballard et al. 2004; widgeon grass [Ruppia maritime], Coluccy et al. 2015) have values near means of other natural foods (Kaminski et al. 2003). Thus, there may exist significant energetic tradeoffs in managing wetland for SAV as opposed to moist-soil or agricultural crops. Moreover, TME values for both native and non-native species such as wild celery (Vallisneria americana) and hydrilla (Hydrilla verticillata) have not been previously published and are needed to assess the value for ducks and the 3 energetic tradeoffs of their control. Orth et al. (2017) suggested that scientists critically evaluate the ecosystem services provided by invasive vs native species before undertaking substantial efforts to manage an invasive. Therefore, we developed the following objectives aimed at estimating the TME of hydrilla for two waterfowl species and providing a comparison native vegetation for ring-necked ducks (Aythya collaris). Objectives 1)Estimate true metabolizable energy of hydrilla shoots and tubers for mallards (Anas platyrhynchos), and 2)Estimate true metabolizable energy of hydrilla and wild celery shoots for ring-necked ducks.Aquatic Ecosystems Restoration FoundationFlorida Fish and Wildlife Conservation Commissionunpublishednot peer reviewedOpe

Illinois Waterfowl Surveys and Investigations W-43-R-64 Annual Progress Report FY2017 Period: 1 July 2016 – 30 June 2017

Objectives 1) Inventory abundance and distribution of waterfowl, shorebirds, and other waterbirds (a minimum of 10 species and guilds) during autumn migration at a minimum of 30 sites along and nearby the Illinois and central Mississippi rivers, 2) Estimate waterfowl and other waterbird population sizes (a minimum of 10 species and guilds) during autumn migration using an aerial quadrat survey in the central Illinois River Valley for comparison with aerial inventories (Objective 1), 3) Investigate movement and population ecology of lesser scaup, canvasback, and other diving ducks by trapping and leg-banding a minimum of 1,000 individuals during spring migration along the Illinois and Mississippi rivers, 4) Investigate the ecology of American green-winged teal and gadwall by radio-marking a minimum of 40 individuals of each species during spring migration in and nearby the central Illinois River Valley, 5) Investigate movements and home range size of a minimum of 10 Canada geese during winter in and near the Greater Chicago Metropolitan Area (GCMA) of Illinois, 6) Determine habitat quality of a minimum of 50 wetland and deepwater polygons during spring, summer, and early autumn for migrating dabbling ducks, breeding wetland birds, and migrating shorebirds in Illinois, and 7) Distribute results and findings to site managers and biologists of the Illinois Department of Natural Resources (IDNR) and other state agencies, the Mississippi Flyway Technical Section, the Upper Mississippi River and Great Lakes Region (UMRGLR) Joint Venture, the U.S. Fish and Wildlife Service, other scientists and collaborators as requested, and the general public through oral presentations, popular articles, technical reports, and peer reviewed publications; make recommendations for future wetland management practices and research needs based on results and related research; contribute to regional conservation planning efforts during the project period as appropriate and requested.Illinois Department of Natural Resources, Division of Wildlife & U.S. Fish and Wildlife Service Contract Number: RC09-13FWUIUCunpublishednot peer reviewedOpe

Blazars in the Fermi Era: The OVRO 40-m Telescope Monitoring Program

The Large Area Telescope (LAT) aboard the Fermi Gamma-ray Space Telescope provides an unprecedented opportunity to study gamma-ray blazars. To capitalize on this opportunity, beginning in late 2007, about a year before the start of LAT science operations, we began a large-scale, fast-cadence 15 GHz radio monitoring program with the 40-m telescope at the Owens Valley Radio Observatory (OVRO). This program began with the 1158 northern (declination>-20 deg) sources from the Candidate Gamma-ray Blazar Survey (CGRaBS) and now encompasses over 1500 sources, each observed twice per week with a ~4 mJy (minimum) and 3% (typical) uncertainty. Here, we describe this monitoring program and our methods, and present radio light curves from the first two years (2008 and 2009). As a first application, we combine these data with a novel measure of light curve variability amplitude, the intrinsic modulation index, through a likelihood analysis to examine the variability properties of subpopulations of our sample. We demonstrate that, with high significance (7-sigma), gamma-ray-loud blazars detected by the LAT during its first 11 months of operation vary with about a factor of two greater amplitude than do the gamma-ray-quiet blazars in our sample. We also find a significant (3-sigma) difference between variability amplitude in BL Lacertae objects and flat-spectrum radio quasars (FSRQs), with the former exhibiting larger variability amplitudes. Finally, low-redshift (z<1) FSRQs are found to vary more strongly than high-redshift FSRQs, with 3-sigma significance. These findings represent an important step toward understanding why some blazars emit gamma-rays while others, with apparently similar properties, remain silent.Comment: 23 pages, 24 figures. Submitted to ApJ

Bodyweight Perceptions among Texas Women: The Effects of Religion, Race/Ethnicity, and Citizenship Status

Despite previous work exploring linkages between religious participation and health, little research has looked at the role of religion in affecting bodyweight perceptions. Using the theoretical model developed by Levin et al. (Sociol Q 36(1):157–173, 1995) on the multidimensionality of religious participation, we develop several hypotheses and test them by using data from the 2004 Survey of Texas Adults. We estimate multinomial logistic regression models to determine the relative risk of women perceiving themselves as overweight. Results indicate that religious attendance lowers risk of women perceiving themselves as very overweight. Citizenship status was an important factor for Latinas, with noncitizens being less likely to see themselves as overweight. We also test interaction effects between religion and race. Religious attendance and prayer have a moderating effect among Latina non-citizens so that among these women, attendance and prayer intensify perceptions of feeling less overweight when compared to their white counterparts. Among African American women, the effect of increased church attendance leads to perceptions of being overweight. Prayer is also a correlate of overweight perceptions but only among African American women. We close with a discussion that highlights key implications from our findings, note study limitations, and several promising avenues for future research

Updating a systematic review – what difference did it make? Case study of nicotine replacement therapy

AIMS: To examine the effect of updating a systematic review of nicotine replacement therapy on its contents and conclusions. METHODS: We examined the effects of regular updating of a systematic review of nicotine replacement therapy for smoking cessation. We considered two outcomes. First, we assessed the effect of adding new data to meta-analyses, comparing results in 2000 with the results in 1994. Second, we assessed qualitatively the ways inwhich the nature of the questions addressed by the review had changed between the two dates. For the first outcome, we compared the number of trials, the pooled estimate of effect using the odds ratio, and the results of pre-specified subgroup analyses, for nicotine gum and patch separately. Using a test for interaction, we assessed whether differences between estimates were statistically significant. RESULTS: There were ten new trials of nicotine gum between 1994 and 2000, and the meta-analytic effect changed little. For the nicotine patch the number of trials increased from 9 to 30, and the meta-analytic effect fell from 2.07 (95% CI 1.64 – 2.62) to 1.73 (95% CI 1.56 – 1.93). Apparent differences in relative effect in sub-groups found in 1994 were not found in 2000. The updated systematic review addressed a number of questions not identified in the original version. CONCLUSIONS: Updating the meta-analyses lead to a more precise estimate of the likely effect of the nicotine patch, but the clinical message was unchanged. Further placebo controlled NRT trials are not likely to add to the evidence base. It is questionable whether updating the meta-analyses to include them is worthwhile. The content of the systematic review has, however, changed, with the addition of data addressing questions not considered in the original review. There is a tension between the principle of identifying the important questions prior to conducting a review, and keeping the review up to date as primary research identifies new avenues of enquiry

True metabolizable energy of submersed aquatic vegetation in semi-permanent marshes for dabbling ducks in the upper Midwest

Our primary objectives were to 1) estimate true metabolizable energy of common species of submersed aquatic vegetation in semi-permanent marsh habitats of the Upper Midwest for gadwall and mallards during autumns 2015–2017, and 2) use current and historic estimates of semi-permanent marsh vegetation communities during autumn within the IRV to document the net change in energetic carrying capacity for dabbling ducks and compare with habitat use by waterfowl using long-term aerial surveys of the Illinois Natural History Survey. We assayed seven species of SAV common in the Midwest that have been documented as waterfowl foods: coontail (Ceratophyllum demersum), wild celery (Vallisneria americana), Canadian waterweed (Elodea canadensis),southern naiad (Najas guadalupensis), Eurasian watermilfoil (Myriophyllum spicatum), widgeon grass (Ruppia maritima), and sago pondweed (Stuckenia pectinate; Anderson 1959, Stewart 1962, Bergman 1973, Havera 1999, Benedict and Hepp 2000, Hitchcock 2009, Baldassarre 2014). Understanding the energetic value of SAV for dabbling ducks will allow wetland managers to accurately evaluate wetland management practices and conservation planners to develop more accurate energetic carrying capacity models. We predicted that the energetic carrying capacity of semi-permanent marshes containing SAV will be slightly less than if the same wetlands were managed for moist-soil vegetation (Bowyer et al. 2005). We hypothesized that the TME of SAV per unit biomass will be less than that of moist-soil seeds and agricultural grains. Further, we hypothesized that the TME of SAV will be independent of sex and trial week.Unites States Fish and Wildlife Service Contract Number: F15AP00687unpublishednot peer reviewedOpe

Illinois Waterfowl Surveys and Investigations W-43-R-65-B Annual Progress Report FY2018

We monitored cellular-collared Canada geese in the Greater Chicago Metropolitan Area, specifically their use of space near Midway International Airport(MWD).Extensions of runways 13 and 31 were intersected more frequently (13.26% of transitional movements, x = 225) than extensions of runways 4 and 22 (2.52% of transitional movements, x = 76). We recorded 18 instances of movements intersecting airspace over runways at MDW (0.60% of transitional movements).The majority of transmittered Canada geese bred within the range of the temperate-nesting, Mississippi Flyway Giant Population with the exception of one male that appeared to be part of the subarctic-nesting, Mississippi Valley Population based on timing of migration and movement pattern indicating nesting. On average, 24.6% of transmittered geese underwent molt migrations during 2015–2017.We monitored the chronology and distribution of shorebirds aerially in the IRV during autumn and spring migration. Total number of shorebirds peaked in the IRV during autumn 2017 at 18,120, and averaged 12,024 birds/flight. We noted a positive trend with shorebird abundance and mudflat availability as river levels decreased in the IRV during August 2017. We documented lower shorebird numbers during spring 2018 in the IRV with a peak of 3,320 birds and an average of 2,527 birds/flight.Fluctuating water levels during migration drastically reduced the availability of shorebird habitat in the IRV during spring.Aerial detection of shorebird flocks was 97% and aerial count bias was 89.1% (range 0–250%) for total shorebirds. Count bias averaged 101.1% for large shorebirds and 80.4% for small shorebirds.Illinois Department of Natural Resources, Division of WildlifeU.S. Fish and Wildlife Service, Federal Aid in Wildlife Restoration W-43-R-65-Bunpublishednot peer reviewedOpe

True metabolizable energy of submersed aquatic vegetation in semi-permanent marshes for dabbling ducks in the Upper Midwest

We completed 186 TME assays with mallards (n = 72) and gadwall (n = 114) between 2015 and 2018. Bioavailable energy (i.e., TME) of submersed aquatic vegetation was highly variable among duck and vegetation species as supported by their interaction in the most parsimonious model (wi = 0.42; R2m = 0.33, R2c = 0.47). For gadwall, mean TME (± SE; kcal/g[dry]) was greatest for Eurasian watermilfoil (0.77 ± 0.32, n = 19), followed by Canadian waterweed (0.70 ± 0.31, n = 20), coontail (0.55 ± 0.28, n = 18), southern naiad (–0.61 ± 0.34, n = 17), wild celery (–0.98 ± 0.39, n = 20), sago pondweed (–1.07 ± 0.33, n = 20). Mallards assimilated greatest energy from Canadian waterweed (1.66 ± 0.26, n = 13), followed by coontail (1.51 ± 0.28, n = 8), southern naiad (1.37 ± 0.39, n = 14), sago pondweed (0.50 ± 0.22, n = 14), wild celery (0.05 ± 0.42, n = 11), and Eurasian watermilfoil (–0.13 ± 0.26, n = 12). There was evidence from a competing model (wi = 0.11; R2m = 0.34, R2c = 0.47) that females acquired 0.52 kcal/g (± 0.34) more energy from vegetation than males and that TME declined 0.20 kcal/g (± 0.16) for every 100 g increase in initial mass. We estimated energetic carrying capacity at 318 random points within 20 wetlands across three years (2015–2017) in the Midwest, USA (Simpson et al. 2017). Across all points, Ceratophyllum spp. was the most commonly encountered genera (n = 188) of submersed aquatic vegetation, followed by Myriophyllum spp. (n = 64), Najas spp. (n = 47), Elodea spp. (n = 41), and Stuckenia spp. (n = 36). These five genera comprised 91.5% of the total energy density across all points and years. Extrapolated energy density estimated at sample points ranged from 0 to 5,624 EUD/ha (̅ = 426 ± 52) and biomass estimates ranged from 0 to 2,340 kg/ha (dry) (̅ = 204 ± 22). Evidenced from the best supported model (wi = 0.68; R2m = 0.19, R2c = 0.27), energy density was 195 EUD/ha (85% CI = 39 – 964) greater at managed points than unmanaged points, decreased 2 EUD/ha (85% CI = 1 – 3) for every 100 cm increase in water depth, increased 9 EUD/ha (85% CI = 6 – 12) for every 100 cm increase in Secchi depth, and increased 3 EUD/ha (85% CI = 0 – 11) if emergent vegetation was present.Upper Mississippi River and Great Lakes Joint Venture U.S. Fish and Wildlife Service, Region 3, Contract Number F15AP00687unpublishednot peer reviewedOpe