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Using World History To Predict The Future Of The First Civilization, William Mcgaughey Oct 2006

Using World History To Predict The Future Of The First Civilization, William Mcgaughey

Comparative Civilizations Review

No abstract provided.

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Open Source, Openness, And Higher Education, David Wiley Oct 2006

Open Source, Openness, And Higher Education, David Wiley

Faculty Publications

With the growth of open source software and other related trends, a culture of openness is advancing from the edges of society to the core of academic culture. In this article I provide an overview of how the expansion of open source software in culture at large has affected the world of education, describe how the greater use of open source software in education has unfolded hand-in-hand with the development of open course content and open access research, and argue that this more comprehensive shift towards "openness" in academic practice is not only a positive trend, but a necessary one …

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The Emergence Of Global Civilization, A New Layer Of World Civilization, Andrew Targowski Oct 2006

The Emergence Of Global Civilization, A New Layer Of World Civilization, Andrew Targowski

Comparative Civilizations Review

No abstract provided.

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Adopted, Amy Scott Oct 2006

Adopted, Amy Scott

Inscape

No abstract provided.

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Effects Of Gap Open And Gap Extension Penalties, Hyrum Carroll, Mark J. Clement, Perry Ridge, Quinn O. Snell Oct 2006

Effects Of Gap Open And Gap Extension Penalties, Hyrum Carroll, Mark J. Clement, Perry Ridge, Quinn O. Snell

Faculty Publications

Fundamental to multiple sequence alignment algorithms is modeling insertions and deletions (gaps). The most prevalent model is to use gap open and gap extension penalties. While gap open and gap extension penalties are well understood conceptually, their effects on multiple sequence alignment, and consequently on phylogeny scores are not as well understood. We use exhaustive phylogeny searching to explore the effects of varying the gap open and gap extension penalties for three nuclear ribosomal data sets. Particular attention is given to optimal phylogeny scores for 200 alignments of a range of gap open and gap extension penalties and their respective …

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Large Grain Size Stochastic Optimization Alignment, Hyrum Carroll, Mark J. Clement, Perry Ridge, Dan Sneddon, Quinn O. Snell Oct 2006

Large Grain Size Stochastic Optimization Alignment, Hyrum Carroll, Mark J. Clement, Perry Ridge, Dan Sneddon, Quinn O. Snell

Faculty Publications

DNA sequence alignment is a critical step in identifying homology between organisms. The most widely used alignment program, ClustalW, is known to suffer from the local minima problem, where suboptimal guide trees produce incorrect gap insertions. The optimization alignment approach, has been shown to be effective in combining alignment and phylogenetic search in order to avoid the problems associated with poor guide trees. The optimization alignment algorithm operates at a small grain size, aligning each tree found, wasting time producing multiple sequence alignments for suboptimal trees. This research develops and analyzes a large grain size algorithm for optimization alignment that …

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Pharmacogenomics: Analyzing Snps In The Cyp2d6 Gene Using Amino Acid Properties, Wesley A. Beckstead, Mark J. Clement, Mark Ebbert, David Mcclellan, Timothy O'Connor Oct 2006

Pharmacogenomics: Analyzing Snps In The Cyp2d6 Gene Using Amino Acid Properties, Wesley A. Beckstead, Mark J. Clement, Mark Ebbert, David Mcclellan, Timothy O'Connor

Faculty Publications

Each year people suffer from complications of adverse drug reactions, but with pharmacogenomics there is hope to prevent thousands of these people from suffering or dying needlessly. The CYP2D6 gene is responsible for metabolizing a large portion of these drugs. Because of the gene’s importance, various approaches have been taken to analyze CYP2D6 and single nucleotide polymorphisms (SNPs) throughout its sequence. This study introduces a novel method to analyze the effects of SNPs on encoded protein complexes by focusing on the biochemical properties of each nonsynonymous substitution using the program TreeSAAP. We apply this technique to SNPs found in the …

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Mental Illness In The Family, Alexander B. Morrison Sep 2006

Mental Illness In The Family, Alexander B. Morrison

Marriage and Families

No abstract provided.

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Low-Frequency Ultrasound Increases Outer Membrane Permeability Of Pseudomonas Aeruginosa, Christopher M. Runyan, John C. Carmen, Benjamin L. Beckstead, Jared L. Nelson, Richard A. Robison, William G. Pitt Sep 2006

Low-Frequency Ultrasound Increases Outer Membrane Permeability Of Pseudomonas Aeruginosa, Christopher M. Runyan, John C. Carmen, Benjamin L. Beckstead, Jared L. Nelson, Richard A. Robison, William G. Pitt

Faculty Publications

Low-frequency ultrasound has been investigated as an adjuvant to antimicrobial therapy, targeted at both planktonic and biofilm (sessile) organisms. Our previous work showed that ultrasound (US) effectively enhances the bactericidal activity of certain antibiotics against planktonic cultures (Pitt et al., 1994; Rediske et al., 1999) and in vitro biofilms (Johnson et al., 1998; Qian et al., 1999) and in vivo biofilms (Carmen et al., 2004b, 2005; Rediske et al., 2000) of gram-positive and gram-negative bacteria. Ultrasound was shown to increase the transport of antibiotics through biofilms (Carmen et al., 2004a) which could account for some (or all) of the enhanced …

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Studies On Cyclooxygenase-1, Its Structure And Splice Variants, And Modulation Of Cyclooxygenase-2 By Inducible Nitric Oxide Synthase And Novel Phytochemicals., Yibing Xu Sep 2006

Studies On Cyclooxygenase-1, Its Structure And Splice Variants, And Modulation Of Cyclooxygenase-2 By Inducible Nitric Oxide Synthase And Novel Phytochemicals., Yibing Xu

Theses and Dissertations

Cyclooxygenases (COXs) are of important therapeutic value as they are the target site of aspirin-like drugs. Here I report nine new COX-1 splice variants in chapter 1, which I characterized with regard to heme-binding and other properties. Inducible NO synthase (iNOS) and cyclooxygenase-2 (COX-2) are co-inducible in many tissues following mitogenic and proinflammatory stimulation. In chapter 2, I investigate the physical and enzymatic properties of human COX-2 and iNOS and demonstrate that, despite reports to the contrary by another laboratory, they do not interact. The only reported COX-1 splice variant to exhibit cyclooxygenase activity has been isolated from …

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Multiplatform Genome-Wide Identification And Modeling Of Functional Human Estrogen Receptor Binding Sites, Chin-Yo Lin, Vinsensius B. Vega, Koon Siew Lai, Li Say Kong, Min Xie, Xiaodi Su, Huey Fang The, Jane S. Thomsen, Ai Li Yeo, Wing Kin Sung, Guillaume Bourque, Edison T. Liu Sep 2006

Multiplatform Genome-Wide Identification And Modeling Of Functional Human Estrogen Receptor Binding Sites, Chin-Yo Lin, Vinsensius B. Vega, Koon Siew Lai, Li Say Kong, Min Xie, Xiaodi Su, Huey Fang The, Jane S. Thomsen, Ai Li Yeo, Wing Kin Sung, Guillaume Bourque, Edison T. Liu

Faculty Publications

Transcription factor binding sites (TFBS) impart specificity to cellular transcriptional responses and have largely been defined by consensus motifs derived from a handful of validated sites. The low specificity of the computational predictions of TFBSs has been attributed to ubiquity of the motifs and the relaxed sequence requirements for binding. We posited that the inadequacy is due to limited input of empirically verified sites, and demonstrated a multiplatform approach to constructing a robust model. Results: Using the TFBS for the estrogen receptor (ER)alpha (estrogen response element [ERE]) as a model system, we extracted EREs from multiple molecular and genomic platforms …

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Design Of Piezoresistive Mems Force And Displacement Sensors, Tyler Lane Waterfall Sep 2006

Design Of Piezoresistive Mems Force And Displacement Sensors, Tyler Lane Waterfall

Theses and Dissertations

MEMS (MicroElectroMechanical Systems) sensors are used in acceleration, flow, pressure and force sensing applications on the micro and macro levels. Much research has focused on improving sensor precision, range, reliability, and ease of manufacture and operation. One exciting possibility for improving the capability of micro sensors lies in exploiting the piezoresistive properties of silicon, the material of choice in many MEMS fabrication processes. Piezoresistivity—the change of electrical resistance due to an applied strain—is a valuable material property of silicon due to its potential for high signal output and on-chip and feedback-control possibilities. However, successful design of piezoresistive micro sensors requires …

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Co-Variation In Soil Biodiversity And Biogeochemistry In Northern And Southern Victoria Land, Antarctica, Byron J. Adams, J. E. Barrett, Ross A. Virginia, Diana H. Wall, S. C. Cary, A. L. Hacker, J. M. Aislabie Sep 2006

Co-Variation In Soil Biodiversity And Biogeochemistry In Northern And Southern Victoria Land, Antarctica, Byron J. Adams, J. E. Barrett, Ross A. Virginia, Diana H. Wall, S. C. Cary, A. L. Hacker, J. M. Aislabie

Faculty Publications

Data from six sites in Victoria Land (72-77degrees S) investigating co-variation in soil communities (microbial and invertebrate) with biogeochemical properties show the influence of soil properties on habitat suitability varied among local landscapes as well as across climate gradients. Species richness of metazoan invertebrates (Nematoda, Tardigrada and Rotifera) was similar to previous descriptions in this region, though identification of three cryptic nematode species of Eudorylaimus through DNA analysis contributed to the understanding of controls over habitat preferences for individual species. Denaturing Gradient Gel Electrophoresis profiles revealed unexpectedly high diversity of bacteria. Distribution of distinct bacterial communities was associated with specific …

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Detection Of Proteins By Two-Photon Excitation Of Native Fluorescence, Li Li Aug 2006

Detection Of Proteins By Two-Photon Excitation Of Native Fluorescence, Li Li

Theses and Dissertations

Proteins are of primary importance to the structure and function of all living cells. Study of proteins relies on the ability to separate a complex mixture so that individual proteins can be more easily processed by other techniques. Since protein samples often exist at low concentration in a small volume, the trend in chemical analysis is toward micro total analysis systems (µTAS) or lab-on-a-chip devices. Among µTAS separation methods, the relatively new electric field gradient focusing (EFGF) technique has shown potential. It focuses and separates analytes based on their electrophoretic migration in an opposing hydrodynamic flow. The detection principles that …

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Experimental And Modeling Investigations Of Biomass Particle Combustion, Hong Lu Aug 2006

Experimental And Modeling Investigations Of Biomass Particle Combustion, Hong Lu

Theses and Dissertations

This investigation provides a comprehensive analysis of entrained-flow biomass combustion processes. Experimental and theoretical investigations indicate how particle shape and size influence biomass combustion rates. Experimental samples include flake-like, cylinder-like, and equant (nearly spherical) shapes with similar particle masses and volumes but different surface areas. Samples of small (less than 500 µm) particles were passed through a laboratory entrained-flow reactor in a nitrogen/air atmosphere and a maximum reactor wall temperature of 1600 K, while large samples were reacted in suspension in a single particle furnace operated at similar conditions as the entrained-flow reactor. A separately developed computer and image analysis …

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Construction Of A Col11a1 Transgene Vector, Cameron Mckell Beck Aug 2006

Construction Of A Col11a1 Transgene Vector, Cameron Mckell Beck

Theses and Dissertations

Background: Cartilage disorders affect millions of people in the United States alone, with effects ranging from poor skeletal development and joint pain to shortened lifespan and perinatal lethality. Many of these disorders have their root in defects of collagen, type XI collagen being among the most important. A mouse model of such a type XI collagen defect is the chondrodysplasia (cho) mutant. Mice homozygous for this null mutation in the Col11a1 gene do not express the α1 chain of type XI collagen. This results in a functional knockout of type XI collagen, leading to insufficient skeletal development and perinatal lethality. …

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Sources Of Variability In A Proteomic Experiment, Scott Daniel Crawford Aug 2006

Sources Of Variability In A Proteomic Experiment, Scott Daniel Crawford

Theses and Dissertations

The study of proteomics holds the hope for detecting serious diseases earlier than is currently possible by analyzing blood samples in a mass spectrometer. Unfortunately, the statistics involved in comparing a control group to a diseased group are not trivial, and these difficulties have led others to incorrect decisions in the past. This paper considers a nested design that was used to quantify and identify the sources of variation in the mass spectrometer at BYU, so that correct conclusions can be drawn from blood samples analyzed in proteomics. Algorithms were developed which detect, align, correct, and cluster the peaks in …

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Ravens And Other Raptors Occupy Winter Roosts With Bald Eagles In Utah, Bryan T. Brown, Dana G. Truman, Linda Jones, Thomas Sharp Aug 2006

Ravens And Other Raptors Occupy Winter Roosts With Bald Eagles In Utah, Bryan T. Brown, Dana G. Truman, Linda Jones, Thomas Sharp

Western North American Naturalist

No abstract provided.

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Effects Of Anthropogenic Land Use On Odonata In Playas Of The Southern High Plains, K. M. Hernandez, B. A. Reece, N. E. Mcintyre Aug 2006

Effects Of Anthropogenic Land Use On Odonata In Playas Of The Southern High Plains, K. M. Hernandez, B. A. Reece, N. E. Mcintyre

Western North American Naturalist

Playas are ephemeral wetlands that are the only source of aboveground freshwater in the southern Great Plains, making them of vital importance to aquatic and amphibious animals. Playas are also highly threatened from anthropogenic land use (chiefly agriculture, which decreases hydroperiod through increased sedimentation). We examined community structure of adult odonates (dragonflies and damselflies) in playas differing in the 2 main regional forms of surrounding land use (cropland vs. grassland). Analysis of odonate diversity revealed high overlap between cropland and grassland playas. Traditional species-area theory did not fit observed patterns, as there appears to be a threshold playa size that …

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Rclus, A New Program For Clustering Associated Species: A Demonstration Using A Mojave Desert Plant Community Dataset, Stewart C. Sanderson, Jeffrey E. Ott, E. Durant Mcarthur, Kimball T. Harper Aug 2006

Rclus, A New Program For Clustering Associated Species: A Demonstration Using A Mojave Desert Plant Community Dataset, Stewart C. Sanderson, Jeffrey E. Ott, E. Durant Mcarthur, Kimball T. Harper

Western North American Naturalist

This paper presents a new clustering program named RCLUS that was developed for species (R-mode) analysis of plant community data. RCLUS identifies clusters of co-occurring species that meet a user-specified cutoff level of positive association with each other. The "strict affinity" clustering algorithm in RCLUS builds clusters of species whose pairwise associations all exceed the cutoff level, whereas the "coalition" clustering algorithm only requires that the mean pairwise association of the cluster exceeds the cutoff level. Both algorithms allow species to belong to multiple clusters, thus accommodating both generalist and specialist species. Using a 60-plot dataset of perennial plants occurring …

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Naturalization Of Plains Cottonwood (Populus Deltoides Subsp. Monilifera) Along River Drainages West Of The Rocky Mountains, J. H. Braatne, S. J. Brunsfeld, V. D. Hipkins, B. L. Wilson Aug 2006

Naturalization Of Plains Cottonwood (Populus Deltoides Subsp. Monilifera) Along River Drainages West Of The Rocky Mountains, J. H. Braatne, S. J. Brunsfeld, V. D. Hipkins, B. L. Wilson

Western North American Naturalist

Historic botanical surveys documented that the natural distribution of the plains cottonwood (Populus deltoides subsp. monilifera) was limited to semiarid drainages east of the Rocky Mountains. Recently, a number of isolated populations of plains cottonwood have been found along the Kootenai, lower Snake, and Columbia Rivers and their tributaries. We used isozyme analysis to assess the genetic structure of these Pacific Northwest (PNW) populations in relation to native cottonwood populations east of the Rocky Mountains. These genetic data along with field surveys (dbh, age estimates) and cadastral field survey notes (mid-1800s) were used to understand the origin of …

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Influence Of Fire And Juniper Encroachment On Birds In High-Elevation Sagebrush Steppe, Anna C. Noson, Richard A. Schmitz, Richard F. Miller Aug 2006

Influence Of Fire And Juniper Encroachment On Birds In High-Elevation Sagebrush Steppe, Anna C. Noson, Richard A. Schmitz, Richard F. Miller

Western North American Naturalist

We examined relationships between high-elevation sagebrush (Artemisia spp.) steppe habitats altered by prescribed fire and western juniper (Juniperus occidentalis) encroachment on breeding distributions of Brewer's Sparrows (Spizella breweri), Vesper Sparrows (Pooecetes gramineus), Green-tailed Towhees (Pipilo chlorurus), and Sage Thrashers (Oreoscoptes montanus) on Steens Mountain in southeastern Oregon. In 2000 we conducted fixed-radius point count surveys at 172 sites encompassing burned and unburned sagebrush habitat and a range of juniper densities. For each bird species we developed habitat models using local variables measured in the field and landscape variables derived …

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Plant Composition And Erosion Potential Of A Grazed Wetland In The Salmon River Subbasin, Idaho, Kristine N. Hopfensperger, Joan Q. Wu, Richard A. Gill Aug 2006

Plant Composition And Erosion Potential Of A Grazed Wetland In The Salmon River Subbasin, Idaho, Kristine N. Hopfensperger, Joan Q. Wu, Richard A. Gill

Western North American Naturalist

Wetlands are dynamic habitats with many unique, important functions including filtering sediments and providing diverse habitats for fish and wildlife. Wetlands in the western United States are particularly important because they offer habitat for a number of protected runs of endangered fish species. Historically, livestock grazing has altered wetland and riparian area form and function by facilitating exotic species invasions, altering spatial heterogeneity of vegetation, and increasing erosion. In this study we examined vegetation structure and erosion potential in a wetland meadow exposed to unregulated grazing along Deer Creek in the Salmon River subbasin, Idaho. We characterized the vegetation composition …

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Distribution Of The Milliped Genus Narceus Rafinesque, 1820 (Spirobolida: Spirobolidae): Occurrences In New England And West Of The Mississippi River; A Summary Of Peripheral Localities; And First Records From Connecticut, Delaware, Maine, And Minnesota, Rowland M. Shelley, Chris T. Mcallister, Michael F. Medrano Aug 2006

Distribution Of The Milliped Genus Narceus Rafinesque, 1820 (Spirobolida: Spirobolidae): Occurrences In New England And West Of The Mississippi River; A Summary Of Peripheral Localities; And First Records From Connecticut, Delaware, Maine, And Minnesota, Rowland M. Shelley, Chris T. Mcallister, Michael F. Medrano

Western North American Naturalist

The milliped genus Narceus Rafinesque, 1820 (Spirobolida: Spirobolidae) occupies parts or all of 2 Canadian provinces, Québec and Ontario; every U.S. state east of the Mississippi River; and 9 states to the west including Minnesota, Iowa, Missouri, Arkansas, Louisiana, Nebraska, Kansas, Oklahoma, and Texas. Records are detailed for the "western" states and New England and include the first from Minnesota, Connecticut, Delaware, and Maine; occurrence is projected for southeastern Minnesota and the Delmarva Peninsula. The genus presently comprises 2 valid species that are endemic to Florida—N. gordanus (Chamberlin, 1943) and N. woodruffi Causey, 1959—and 2 of uncertain status that …

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Fish Remains Dominate Barn Owl Pellets In Northwestern Nevada, Raymond J. Bogiatto, Jack M. Broughton, Virginia I. Cannon, Kevin Dalton, Shannon Arnold Aug 2006

Fish Remains Dominate Barn Owl Pellets In Northwestern Nevada, Raymond J. Bogiatto, Jack M. Broughton, Virginia I. Cannon, Kevin Dalton, Shannon Arnold

Western North American Naturalist

No abstract provided.

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Great Salt Lake: An Anthology Edited By Gary Topping, C. Riley Nelson Aug 2006

Great Salt Lake: An Anthology Edited By Gary Topping, C. Riley Nelson

Western North American Naturalist

No abstract provided.

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Reviewers Needed Aug 2006

Reviewers Needed

Western North American Naturalist

No abstract provided.

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Survival And Reproduction Of Translocated Eastern Wild Turkeys In A Sparsely Wooded Landscape In Northeastern South Dakota, Roger D. Shields, Lester D. Flake Aug 2006

Survival And Reproduction Of Translocated Eastern Wild Turkeys In A Sparsely Wooded Landscape In Northeastern South Dakota, Roger D. Shields, Lester D. Flake

Western North American Naturalist

We studied the survival and reproduction of a newly introduced population of Eastern Wild Turkeys (Meleagris gallopavo silvestris) during 1999 and 2000 to determine the adaptability of this subspecies to a minimally wooded (<10%) region located north of their recorded historic distribution in South Dakota. During 1999 and 2000, the South Dakota Department of Game, Fish and Parks (SDGFP) released 111 female and 25 male turkeys from Iowa and Kentucky onto a study area in northeastern South Dakota. We used radio telemetry to monitor survival and reproduction of the females for 2 years after their initial release. Annual survival for 71 females averaged 67%. Seasonal survival was lowest in fall and highest in winter. Mortality agents included avian and mammalian predators, haying equipment, automobiles, and unknown causes. Nesting rate for the 2 years averaged 93%, and renesting rate of turkeys with failed 1st-nest attempts averaged 45%. Nest success for all nests was 50%, and 62% of females attempting to nest each year were successful in at least 1 attempt. Predation was the primary cause of nest failure during both years. Overall, 72% of brooding females successfully raised ≥1 poult to 4 weeks post-hatch while individual poult survival to 4 weeks post-hatch averaged 36%. Despite <10% woodland cover, Eastern Wild Turkeys appeared to thrive in a glacial escarpment topography north of their historic range in the northern plains.

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Production, Losses, And Germination Of Ceanothus Fendleri Seeds In An Arizona Ponderosa Pine Forest, David W. Huffman Aug 2006

Production, Losses, And Germination Of Ceanothus Fendleri Seeds In An Arizona Ponderosa Pine Forest, David W. Huffman

Western North American Naturalist

I quantified seed production and ovule losses for Ceanothus fendleri Gray (Fendler ceanothus) plants protected from large ungulate herbivores in a ponderosa pine (Pinus ponderosa [Laws]) forest of northern Arizona. I also tested seed germination responses to cold stratification and heat treatments in the laboratory. Fruit production on fecund stems ranged from 7.4 to 38.2 fruits per stem, which equated to 22.2–118.2 potential seeds based on 3 ovules per fruit. Stems that produced fruit were significantly large relative to their expected sizes. Predispersal ovule losses ranged from 70.7% to 91.4% across the 2 years studied. A chalcidoid seed parasite …

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Selection Of Dwarf Mistletoe–Infected Ponderosa Pines By Ips Species (Coleoptera, Scolytidae) In Northern Arizona, Shawn C. Kenaley, Robert L. Mathiasen, Carolyn M. Daugherty Aug 2006

Selection Of Dwarf Mistletoe–Infected Ponderosa Pines By Ips Species (Coleoptera, Scolytidae) In Northern Arizona, Shawn C. Kenaley, Robert L. Mathiasen, Carolyn M. Daugherty

Western North American Naturalist

Following an Ips bark beetle outbreak in 2002, mortality of ponderosa pine (Pinus ponderosa Douglas ex C. Lawson) was evaluated in 2 study areas infested with southwestern dwarf mistletoe (Arceuthobium vaginatum [Willd.] Presl subsp. cryptopodum [Engelm.] Hawksw. & Wiens) in the Coconino and Tonto National Forests, Arizona. A pairwise comparison of dwarf mistletoe ratings for live and dead ponderosa pines was conducted to determine whether dead ponderosa pines had higher dwarf mistletoe ratings than pines that were not attacked. In both study areas, dead ponderosa pines had significantly higher dwarf mistletoe ratings, indicating an association between the severity …

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