Digital Commons Network^™

Combined Supervised And Unsupervised Learning In Genomic Data Mining, Jack Y. Yang, Okan K. Ersoy

Department of Electrical and Computer Engineering Technical Reports

Since the discoveries of Overhauser effects and DNA double helix structure, many protein structures have been determined experimentally, especially by utilizing the Overhauser effects. Biologists are not only able to describe the life phenomena but also to seek the understanding of life mechanisms at molecular level. With the advent of high-throughput genome sequencing technology, more and more genomes are available; consequently our ability to sequence genomes has outstripped our ability to analyze the resulting data in order to determine the functions and structures of proteins encoded in the genomes. Determination of protein structures and functions using traditional laboratory methods is …

Profit + Capital (Chapter 6), Anwar Shaikh Phd

Archives of Anwar Shaikh

This collection includes:

• Shaikh, A. (n.d.). Ch 10 commodity prices / industrial prices (Unpublished manuscript notes) (p. 1).
• Shaikh, A. (2011, January 11). Fixcapesample.xmcd (Unpublished manuscript notes) (p. 2).
• Shaikh, A. (n.d.). Production function notes.docx (Unpublished manuscript notes) (p. 4).
• Shaikh, A. (2010, August 28). Petri reswitching.xmcd (Unpublished manuscript notes) (p. 22).
• Shaikh, A. (2013, November 24). Price and value aggregates (Unpublished manuscript notes) (p. 26).
• Shaikh, A. (2009, January 6). Three lines of inquiry w/r linear std prices (Unpublished manuscript notes) (p. 27).
• Shaikh, A. (2010, January 20). Subdominant eigenvalues of a (Unpublished manuscript notes) (p. 28).
• Shaikh, A. …

Potential Chemicals To Manage Llght Goose Populations, John Cummings, Pete Poulos

United States Department of Agriculture Wildlife Services: Staff Publications

Over-abundant light geese are having long-term negative effects on the Arctic tundra ecosystem. Significant damage to native plants, increases in soil degradation and impacts on bird communities are likely to be the main consequences (Batt 1998). The extent of which over-abundant light geese reduce food and cover for other wildlife on wintering grounds and migration routes is not well documented, although anecdotal observations suggest that light geese could compete with wintering waterfowl for food, i.e. Louisiana rice fields (J. L. Curnmings, National Wildlife Research Center, personal observation).

Efficacy Of Zinc Phosphide For Controlling Norway Rats, Roof Rats, House Mice, Peromyscus Spp., Prairie Dogs And Ground Squirrels: A Literature Review (1942-2000), John D. Eisemann, Brett E. Petersen, Kathleen A. Fagerstone

United States Department of Agriculture Wildlife Services: Staff Publications

Zinc phosphide has been used as a control agent for commensal rodents for over 60 years. Studies utilizing zinc phosphide as a population control agent were gathered and summarized to determine its efficacy when baiting the Norway rat, roof rat, house mouse, Peromyscus spp., prairie dog and ground squirrel. Efficacy information was abundant for rats, squirrels, and prairie dogs. However, efficacy data for baiting mice with zinc phosphide was limited. Overall the data show that in both laboratory and field testing, control levels of greater than 70% can be achieved for commensal rodent pests. Bait acceptance appeared to be …

Wildlife Road-Kills In An Urban Park In Florida, Henry T. Smith, Robert M. Barry, Richard M. Engeman, Stephanie A. Shwiff, William J.B. Miller

United States Department of Agriculture Wildlife Services: Staff Publications

Wildlife mortality due to collisions with motor vehicles is a problem within managed natural areas in Florida and worldwide (Skoog 1982; Smith et al. 1994; Foster and Humphrey 1995; Jackson 1996; Bertwistle 1999; Brown et al. 1999; Evink 1999; Gunther and Biel 1999; Phillips 1999; Trombulak and Frissell 2000; Hels and Buchwald 2001; Bard et al. 2002a,b; Fahrig et al. 2002; Foresman 2002; Gilbert et al. 2002). We here report wildlife mortality due to collisions with vehicles during 1997-2000 at John U. Lloyd State Park (JULSP), a 125.75-ha, mixed-use, urban state park located approximately 8 km south of Fort Lauderdale, …

Challenges Of Implementing The Double-Crested Cormorant Environmental Impact Statement, Kristina Casscles Godwin, D. Tommy King, Peter Butchko, Richard Chipman

United States Department of Agriculture Wildlife Services: Staff Publications

Double-crested cormorant populations have increased over the last 20 years within the continental United States. Problems associated with this increase include impacts to commercial aquaculture, damage to property, vegetation, recreational fisheries, and natural resources, as well as concerns over inter-specific competition. Implementation of the forthcoming Environmental Impact Statement for the management of double-crested cormorants will be a monumental task. Several state and federal agencies, along with private citizens and various interest groups will have parts to play. USDA/APHIS/Wildlife Services is expected to have a large part in the implementation of the plan. We discuss the proposed actions to be taken …

Fear And Loathing: The Modulatory Affect Of Stress On Memory Formation And Its Wildlife Management Implications, Arla G. Hile

United States Department of Agriculture Wildlife Services: Staff Publications

An ongoing challenge for wildlife managers is that target species habituate to or forget about hazing, even though the animals must be somewhat stressed by the hazing. Although stress and efficient memory formation/retrieval are considered to be incompatible, research suggests that the effect of stress on memory is complex. Mild and intense stress can impair memory formation and chronic stress can disrupt memory retrieval. Intermediate stress, however, actually enhances the formation of new memories, particularly long-term memories. Unfortunately, these conclusions are based data from only a very few domesticated species under highly controlled conditions. In nature the variation in baseline …

Oral Rabies Vaccination: Reducing Economic Uncertainty Via Response Surface Analysis, Ray T. Sterner, Matthew A. Kling, Stephanie A. Shwiff, Dennis Slate

United States Department of Agriculture Wildlife Services: Staff Publications

Economic uncertainty surrounds the distribution of Raboral V-RG7 as an oral rabies vaccine (ORV) bait for the containment or elimination of raccoon-variant rabies in the United States. This paper describes a costs-savings model of ORV. It also describes Excel XP7 code that was prepared to compute potential net savings (NS) and benefit-cost ratios (BCRs) associated with Raboral V-RG7 bait distributions. Currently, baits and bait distributions are relatively expensive; individual baits are produced at a cost of $1.27 for federal use and typically dispensed at >75 baits/km2. Distribution is estimated at $8.62/km², $15.80/km², and $33.30/km² for …

Mycobacterial Diseases In Wildlife, Gary W. Witmer, Thomas Deliberto, Kurt C. Vercauteren, Peter Butchko

United States Department of Agriculture Wildlife Services: Staff Publications

Mycobacterium infections occur in numerous wildlife species worldwide and this bacterial genus can also cause disease in humans and livestock. Two Mycobacterium species and one subspecies that infect wildlife are important from a wildlife damage management perspective. Mycobacterium avium, avian tuberculosis, is a ubiquitous and cosmopolitan disease of wild and domestic birds. Wild and domestic ruminants are host to M. avium paratuberculosis, also known as Johne’s disease. Finally, Mycobaterium bovis, bovine tuberculosis, is primarily associated with domestic and wild bovines and ungulates, but also infects many other species of mammals. Eradicating these diseases from wildlife populations is …

Status Of Double-Crested Cormorant Phalacrocorax Auritus Research And Management In North America, Scott J. Werner, Shauna L. Hanisch

United States Department of Agriculture Wildlife Services: Staff Publications

The Double-crested Cormorant, the most abundant of North America’s six cormorant species, has rebounded to high numbers after new extirpation in the 1960s and early 1970s. Enhanced environmental regulations and the availability of prey fishes facilitated the resurgence of Double-crested Cormorant populations by the mid-1970s and numbers have continued to increase steadily in most geographic regions through the present. The North American population of Double-crested Cormorants has been estimated at one to two million birds. Concerns about impacts of Double-crested Cormorants on aquacultural stock, sport fish populations, other birds, vegetation, private property, and local economies have been raised. Economic impacts …

Web Orientation Of The Banded Garden Spider Argiope Trifasciata (Araneae, Araneidae) In A California Coastal Population, Martina G. Ramirez

Biology Faculty Works

Magnetic heading (direction the spider’s ventrum faced) and web inclination (degree of slant from the vertical) in Argiope trifasciata Forska°l, a diurnal orb-weaving spider, were studied at a coastal site in southern California for nine weeks in fall 1999. Throughout the study, A. trifasciata largely occupied east-west oriented webs with their venters facing south and southwest. Mean magnetic heading was unaffected by ambient temperature extremes. Inclination levels varied from week to week over an approximately 58 range. However, these changes followed no discernible pattern and were independent both of the sun’s decrease in maximum altitude during the course of the …

Proteasome Inhibition Stabilizes Tau Inclusions In Oligodendroglial Cells That Occur After Treatment With Okadaic Acid, Deepa V. Dabir

Biology Faculty Works

Tau-positive inclusions in oligodendrocytes are consistent neuropathological features of corticobasal degeneration, progressive supranuclear palsy, and frontotemporal dementias with Parkinsonism linked to chromosome 17. Here we show by immunohistochemistry that tau-positive oligodendroglial inclusion bodies also contain the small heat-shock protein (HSP) αB-crystallin but not H HSP70. To study the molecular mechanisms underlying inclusion body formation, we engineered an oligodendroglia cell line (OLN-t40) to overexpress the longest human tau isoform. Treatment of OLN-t40 cells with okadaic acid (OA), an inhibitor of protein phosphatase 2A, caused tau hyperphosphorylation and a decrease in the binding of tau to microtubules. Simultaneously, tau-positive aggregates that also …

Evaluation Of Nitrate Nitrogen Fluxes From A Tile-Drained Watershed In Central Iowa, M. D. Tomer, D. W. Meek, D. B. Jaynes, J. L. Hatfield

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Nitrate Nfluxes fromtile-drained watersheds have been implicated in water quality studies of the Mississippi River basin, but actual NO₃–N loads from small watersheds during long periods are poorly documented. We evaluated discharge and NO₃–N fluxes passing the outlet of an Iowa watershed (5134 ha) and two of its tile-drained subbasins (493 and 863 ha) from mid-1992 through 2000. The cumulative NO₃–N load from the catchment was 168 kg ha^-1, and 176 and 229 kg ha^-1 from the subbasins. The outlet had greater total discharge (1831 mm) and smaller flow-weighted mean NO …

Time-Mortality Relationships For Tribolium Castaneum (Coleoptera: Tenebrionidae) Life Stages Exposed To Elevated Temperatures, Rizana Mahroof, Bhadriraju Subramanyam, James E. Throne, Anil Menon

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

The use of elevated temperatures (≥40-60°C) or heat treatments for managing insects in food-processing facilities is a viable alternative to space fumigation with methyl bromide. Quantitative data are lacking on the responses of life stages of the red flour beetle, Tribolium castaneum (Herbst), an important pest of food-processing facilities worldwide, to elevated temperatures used during heat treatments. We determined time-mortality relationships for eggs, young (neonate) larvae, old larvae, pupae, and adults of T. castaneum, exposed to constant temperatures of 42, 46, 50, 54, 58, and 60°C. Generally, mortality of each stage increased with an increase in temperature and exposure …

Efficacy Of Diatomaceous Earth To Control Internal Infestations Of Rice Weevil And Maize Weevil (Coleoptera: Curculionidae), Frank H. Arthur, James E. Throne

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Densities of 10, 20, and 30 hard red winter wheat kernels, Triticum aestivum L., were infested with different life stages of the rice weevil, Sitophilus oryzae (L.), mixed with 35 g of wheat treated with 300 ppm of the Protect-It (Mississauga, Ontario, Canada) formulation of diatomaceous earth (DE), and held at 22, 27, and 32°C. A similar test was conducted by exposing densities of 6, 12, and 18 corn kernels infested with different life stages of the maize weevil, Sitophilus zeamais Motschulsky, mixed with 30 g of corn, Zea mays L., treated with 300 ppm of DE. Mortality of adults …

A Less Tragic Commons?: Using Harvester And Processor Quotas To Address Crab Overfishing, Avi Brisman

Seattle University Law Review

Part II of this Comment provides a brief overview of the history of the Magnuson Act. Part III describes the current status of the BSAI crab fisheries and the need for crab rationalization. In Part IV, this Comment examines NPFMC's preferred alternative—the three-pie voluntary cooperative program as set forth in its Bering Sea Crab Rationalization Program Alternatives: Public Review Draft (May, 2002) and Summary of the North Pacific Fishery Management Council's Bering Sea and Aleutian Islands Crab Rationalization Program Submitted to the United States Congress, August, 2002. Part V looks at the legal issues surrounding processor quotas, focusing specifically on …

The Use Of Web Services In Bioinformatics, Sheng Lu

Electronic Theses and Dissertations

No abstract provided.

'Preferences Of The Platonic Age': Male Homosocial Desire In Quida's Novels Of The 1860s, Lorraine Dubuisson

Electronic Theses and Dissertations

No abstract provided.

Phytotoxins From The Leaves Of Ruta Graveolens, Amber L. Hale

Electronic Theses and Dissertations

No abstract provided.

Through A Glass Darkly : Reflections Of Southern Culture In South Carolina's Domestic Violence Policy, Ellen Barbara Meacham

Electronic Theses and Dissertations

No abstract provided.

Bifurcation Analysis Of Hiv-1 Dynamics In Vivo, Revanth Babu Mutyala

Electronic Theses and Dissertations

No abstract provided.

Detection Of Insect Fragments In Wheat Flour By Near-Infrared Spectroscopy, J. Perez-Mendoza, James E. Throne, F. E. Dowell, J. E. Baker

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Insect fragments in commercial wheat flour are a major concern to the milling industry because consumers expect high quality and wholesome products at the retail level. Thus, the US Food and Drug Administration (FDA) has established a defect action level of 75 insect fragments per 50 g of flour. Millers routinely test their wheat flour to comply with this federal requirement and to deliver sound flour to their consumers. The current standard flotation method for detecting fragments in flour is expensive and labor intensive. Therefore, we examined the possible use of a rapid, near-infrared spectroscopy (NIRS) method for detecting insect …

Post-Harvest Entomology Research In The United States Department Of Agriculture–Agricultural Research Service, James E. Throne, Guy J. Hallman, Judy A. Johnson, Peter A. Follett

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

This is a review of current post-harvest entomology research conducted by the Agricultural Research Service, the research branch of the US Department of Agriculture. The review covers both durable and perishable commodities. Research on biochemistry, genetics, physiology, monitoring and control of insects infesting stored grain, dried fruits and nuts, and processed commodities is reviewed. Research on development of quarantine treatments, particularly for fruit flies, is also reviewed, including research on thermal and irradiation treatments and a discussion of risk management for quarantine pests. Two areas of research are covered more extensively: a project to map the genome of the red …

Entomological Applications Of Near-Infrared Spectroscopy, James E. Throne, Floyd E. Dowell, Joel Perez-Mendoza, James E. Baker

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Our recent work on applications of near-infrared spectroscopy (NIRS) to entomological problems is reviewed. 1. Using an auto-mated NIRS system scanning individual wheat kernels at the rate of 15 per minute we were able to differentiate between uninfested kernels and kernels infested with late-instar larvae of Rhyzoperthadominica, Sitophilus orzyae. or Sitotroga cerealella. The ability to rapidly scan individual kernels indicates potential for automated segregation of infested kernels from bulk grain. 2. The automated MRS system was used to differentiate uninfested wheat kernels,kernels infested with rice weevils, and kernels that contained rice weevils that were parasitised by Anisopteromalus …

Impact Of Egg Storage On Carbonic Anhydrase Activity During Early Embryogenesis In The Turkey, M. R. Bakst, L. Holm

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Carbonic anhydrase is an enzyme that plays important roles in the conversion of carbon dioxide to bicarbonate, acid-base balance, and in subembryonic fluid formation in the early Japanese quail embryo. While turkey egg storage longer than 10 d is known to increase the rate of embryo mortality, little is known of the biological mechanisms that contribute to this phenomenon. In this study, we examined the impact of turkey egg storage on carbonic anhydrase activity in the freshly laid egg through 72 h of incubation. Carbonic anhydrase activity, which was not affected by egg storage for 21 d at 18°C, was …

Detection Of Enterohemorrhagic Escherichia Coli O157:H7 By Using A Multiplex Real-Time Pcr Assay For Genes Encoding Intimin And Shiga Toxins, Vijay K. Sharma, Evelyn A. Dean-Nystrom

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

A multiplex real-time PCR (R-PCR) assay was designed and evaluated on the ABI 7700 sequence detection system (TaqMan) to detect enterohemorrhagic Escherichia coli (EHEC) O157:H7 in pure cultures, feces, and tissues. Three sets of primers and fluorogenic probes were used for amplification and real-time detection of a 106-bp region of the eae gene encoding EHEC O157:H7-specific intimin, and 150-bp and 200-bp segments of genes stx1 and stx2 encoding Shiga toxins 1 and 2, respectively. Analysis of 67 bacterial strains demonstrated that the R-PCR assay successfully distinguished EHEC O157:H7 serotype from non-O157 serotypes and provided accurate profiling of genes encoding intimin …

Using Electrical Conductivity Classification And Within-Field Variability To Design Field-Scale Research, Cinthia K. Johnson, Kent M. Eskridge, Brian J. Wienhold, John W. Doran, Gary A. Peterson, Gerald W. Buchleiter

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Agronomic researchers are increasingly accountable for research programs and outcomes relevant to producers. Participatory research—where farmers assume leadership roles in identifying, designing, and managing on-farm field-scale research—addresses this directive. However, replication is often unfeasible at this level of scale, underscoring a need for alternative methods to estimate experimental error. We compared mean square errors to evaluate: (i) within-field variability for estimating experimental error (in lieu of replication) and (ii) classified within-field variability, using apparent electrical conductivity (EC_a), for estimating plot-scale experimental error. Eight 31-ha fields, within a contiguous section of farmland (250 ha), were managed as two replicates …

Watershed Vulnerability To Herbicide Transport In Northern Missouri And Southern Iowa Streams, R. N. Lerch, P. E. Blanchard

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Herbicide contamination of streams has been well documented, but little is currently known about the specific factors affecting watershed vulnerability to herbicide transport. The primary objectives of this study were (1) to document herbicide occurrence and transport from watersheds in the northern Missouri/ southern Iowa region; (2) to quantify watershed vulnerability to herbicide transport and relate vulnerability to soil properties; and (3) to compute the contribution of this region to the herbicide load of the Missouri and Mississippi Rivers. Grab samples were collected under baseflow and runoff conditions at 21 hydrologic monitoring stations between April 15 and July 15 from …

Exploratory Surveys In Australia And Asia For Natural Enemies Of Old World Climbing Fern, Lygodium Microphyllum: Lygodiaceae, John A. Goolsby, Anthony D. Wright, Robert W. Pemberton

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Lygodium microphyllum, Old World climbing fern, is native to the wet tropics and subtropics of the Old World and an invasive weed in southern Florida. Exploration for natural enemies of this weed was conducted between 1997 and 2002 in Australia, China, India, Indonesia, Japan, Malaysia, New Caledonia, Singapore, Taiwan, Thailand, and Vietnam. Two species of mites and 20 insect species were collected. The eriophyid mite, Floracarus perrepae Knihinicki and Boczek, was the most widely distributed and appeared to cause significant damage to the plant over time. Several unique geographical genotypes of F. perrepae were identified. Other promising candidates for …

Enhanced Bioremediation Of Soil Containing 2,4-Dinitrotoluene By A Genetically Modified Sinorhizobium Meliloti, Sisir K. Dutta, Gail P. Hollowell, Fawzy M. Hashem, L. David Kuykendall

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

The symbiotic nitrogen-fixing soil bacterium, Sinorhizobium meliloti, is well known for its ability to interact with the leguminous plant Medicago sativa L. It has, however, not been reported that this species possesses the capability to degrade toxic nitroaromatic compounds, such as 2,4-dinitrotoluene (DNT) which is commonly associated with the degradation of the explosive trinitrotoluene (TNT). In this study, the pJS1 DNT-biodegradative plasmid was genetically transferred to S. meliloti strain USDA 1936, which was confirmed by plasmid profile analysis. Several standard analytical and chemical tests including high performance liquid chromatography (HPLC), nitrite (NO2) release assays, rhizosphere population and plant greenhouse …