Digital Commons Network^™

1,3,7,10,14,17,21,28,31,42,52,55-Dodeca­Kis(Trifluoro­Meth­Yl)- 1,3,7,10,14,17,21,28,31,42,52,55-Dodeca­Hydro­(C60-IH)[5,6]Fullerene, Natalia B. Shustova Prof. Dr., O.P. Anderson, O. V. Boltalina, S. H. Strauss, I. E. Kareev

Faculty Publications

The title compound, C₇₂F₃₆, is one of four isomers of C₆₀(CF₃)₁₂ for which crystal structures have been obtained. The fullerene mol­ecule has an idealized I_h C₆₀ core with the 12 CF₃ groups arranged in an asymmetric fashion on two ribbons of edge-sharing C₆(CF₃)₂ hexa­gons, a para–meta–para–para–para–meta–para ribbon and a para–meta–para ribbon, giving an overall pmp ³ mp,pmp structure. There are no cage Csp ^{3 …}

Compressed Data Structures: Dictionaries And Data-Aware Measures, Ankur Gupta, Wing Kai Hon, Rahul Shah, Jeffrey Scott Vitter

Faculty Publications

In this paper, we propose measures for compressed data structures, in which space usage is measured in a data-aware manner. In particular, we consider the fundamental dictionary problem on set data, where the task is to construct a data structure for representing a set S of n items out of a universe U = {0, ..., u - 1} and supporting various queries on S. We use a well-known data-aware measure for set data called gap to bound the space of our data structures. We describe a novel dictionary structure that requires gap + O (n log (u / n) …

Relationship Between Vegetation Biophysical Properties And Surface Temperature Using Multisensor Satellite Data, Seungbum Hong, Venkataraman Lakshmi, Eric Small

Faculty Publications

Vegetation is an important factor in global climatic variability and plays a key role in the complexinteractions between the land surface and the atmosphere. This study focuses on the spatial and temporalvariability of vegetation and its relationship with land–atmosphere interactions. The authors have analyzedthe vegetation water content (VegWC) from the Advanced Microwave Scanning Radiometer for EOS(AMSR-E), the leaf area index (LAI), the normalized difference vegetation index (NDVI), the land surfacetemperature (Ts), and the Moderate Resolution Imaging Spectroradiometer (MODIS). Three regions,which have climatically differing characteristics, have been selected: the North America Monsoon System(NAMS) region, the Southern Great Plains (SGP) region, and …

Reproductive Function For A C-Terminus Extended, Male-Transmitted Cytochrome C Oxidase Subunit Ii Protein Expressed In Both Spermatozoa And Eggs, Rumela Chakrabarti, Jennifer M. Walker, E.G. Chapman, S.P. Shepardson, R.J. Trdan, J.P. Curole, G.T. Watters, D.T. Stewart, S. Vijayaraghavan, W.R. Hoeh

Faculty Publications

Our previous study documented expression of a male-transmitted cytochrome c oxidase subunit II protein (MCOX2), with a C-terminus extension (MCOX2e), in unionoidean bivalve testes and sperm mitochondria. Here, we present evidence demonstrating that MCOX2 is seasonally expressed in testis, with a peak shortly before fertilization that is independent of sperm density. MCOX2 is localized to the inner and outer sperm mitochondrial membranes and the MCOX2 antibody’s epitope is conserved across >65 million years of evolution. We also demonstrate the presence of male-transmitted mtDNA and season-specific MCOX2 spatial variation in ovaries. We hypothesize …

A Nondestructive Technique For Determining Complex Permittivity And Permeability Of Magnetic Sheet Materials Using Two Flanged Rectangular Waveguides, Milo W. Hyde Iv, Michael J. Havrilla

Faculty Publications

In this paper, a nondestructive technique for determining the complex permittivity and permeability of magnetic sheet materials using two flanged rectangular waveguides is presented. The technique extends existing single probe methods by its ability to simultaneously measure reflection and transmission coefficients imperative for extracting both permittivity and permeability over all frequencies. Using Love’s Equivalence Principle, a system of coupled magnetic field integral equations (MFIEs) is formed. Evaluation of one of the two resulting spectral domain integrals via complex plane integration is discussed. The system, solved via the Method of Moments (MoM),yields theoretical values for the reflection and transmission coefficients. These …

Role Of Adiponectin And Inflammation In Insulin Resistance Of Mc3r And Mc4r Knockout Mice, James L. Trevaskis, Barbara Gawronska-Kozak, Gregory M. Sutton, Michele Mcneil, Jacqueline M. Stephens, Steven R. Smith, Andrew A. Butler

Faculty Publications

Objective: To investigate the involvement of hypoadiponectinemia and inflammation in coupling obesity to insulin resistance in melanocortin-3 receptor and melanocortin-4 receptor knockout (KO) mice (Mc3/4rKO). Research Methods and Procedures: Sera and tissue were collected from 6-month-old Mc3rKO, Mc4rKO, and wild-type C57BL6J litter mates maintained on low-fat diet or exposed to high-fat diet (HFD) for 1 or 3 months. Inflammation was assessed by both real-time polymerase chain reaction analysis of macrophage-specific gene expression and immunohistochemistry. Results: Mc4rKO exhibited hypoadiponectinemia, exacerbated by HFD and obesity, previously reported in murine models of obesity. Mc4r deficiency was also associated with high levels of macrophage …

Is A 3-Mm Intrafractional Margin Sufficient For Daily Image-Guided Intensity-Modulated Radiation Therapy Of Prostate Cancer?, Adam D. Melancon, Jennifer C. O'Daniel, Lifei Zhang, Rajat J. Kudchadker, Deborah A. Kuban, Andrew K. Lee, Rex M. Cheung, Renaud De Crevoisier, Susan L. Tucker, Wayne D. Newhauser, Radhe Mohan, Lei Dong

Faculty Publications

Purpose: To determine whether a 3-mm isotropic target margin adequately covers the prostate and seminal vesicles (SVs) during administration of an intensity-modulated radiation therapy (IMRT) treatment fraction, assuming that daily image-guided setup is performed just before each fraction. Materials and methods: In-room computed tomographic (CT) scans were acquired immediately before and after a daily treatment fraction in 46 patients with prostate cancer. An eight-field IMRT plan was designed using the pre-fraction CT with a 3-mm margin and subsequently recalculated on the post-fraction CT. For convenience of comparison, dose plans were scaled to full course of treatment (75.6 Gy). Dose coverage …

Capillary Electrophoretic Screening For The Inhibition Of Homocysteine Thiolactone-Induced Protein Oligomerization, Arther T. Gates, Mark Lowry, Kristin A. Fletcher, Abitha Murugeshu, Oleksandr Rusin, James W. Robinson, Robert M. Strongin, Isiah M. Warner

Faculty Publications

We report the first demonstration of rapid electrophoretic monitoring of homocysteine thiolactone-induced protein oligomerization (HTPO), a unique type of post-translational protein modification that may have clinical significance as an indicator of cardiovascular and neurovascular diseases. HTPO of the model protein bovine cytochrome c was initiated in vitro. The relative monomer and aggregate levels of the resultant protein mixtures were determined following separation using capillaries coated with the cationic polymer, poly(diallyldimethylammonium chloride). UV detection provided adequate sensitivity for the monitoring of higher order species, which exist at relatively low concentrations in the protein reaction mixture as compared to the monomelic species. …

Sound Production And Spectral Hearing Sensitivity In The Hawaiian Sergeant Damselfish, Abudefduf Abdominalis, Karen P. Maruska, Kelly S. Boyle, Laura R. Dewan, Timothy C. Tricas

Faculty Publications

Sounds provide important signals for inter- and intraspecific communication in fishes, but few studies examine fish acoustic behavior in the context of coevolution of sound production and hearing ability within a species. This study characterizes the acoustic behavior in a reproductive population of the Hawaiian sergeant fish, Abudefduf abdominalis, and compares acoustic features to hearing ability, measured by the auditory evoked potential (AEP) technique. Sergeant fish produce sounds at close distances to the intended receiver (≤1-2 body lengths), with different pulse characteristics that are associated primarily with aggression, nest preparation and courtship-female-visit behaviors. Energy peaks of all sounds were between …

Cloning, Analysis And Functional Annotation Of Expressed Sequence Tags From The Earthworm Eisenia Fetida, Mehdi Pirooznia, Ping Gong, Xin Guan, Laura S. Inouye, Kuan Yang, Edward J. Perkins, Youping Deng

Faculty Publications

Background

Eisenia fetida, commonly known as red wiggler or compost worm, belongs to the Lumbricidae family of the Annelida phylum. Little is known about its genome sequence although it has been extensively used as a test organism in terrestrial ecotoxicology. In order to understand its gene expression response to environmental contaminants, we cloned 4032 cDNAs or expressed sequence tags (ESTs) from two E. fetida libraries enriched with genes responsive to ten ordnance related compounds using suppressive subtractive hybridization-PCR.

Results

A total of 3144 good quality ESTs (GenBank dbEST accession number EH669363–EH672369 and EL515444–EL515580) were obtained from the raw clone …

Comparison Of Probabilistic Boolean Network And Dynamic Bayesian Network Approaches For Inferring Gene Regulatory Networks, Peng Li, Chaoyang Zhang, Edward J. Perkins, Ping Gong, Youping Deng

Faculty Publications

Background: The regulation of gene expression is achieved through gene regulatory networks (GRNs) in which collections of genes interact with one another and other substances in a cell. In order to understand the underlying function of organisms, it is necessary to study the behavior of genes in a gene regulatory network context. Several computational approaches are available for modeling gene regulatory networks with different datasets. In order to optimize modeling of GRN, these approaches must be compared and evaluated in terms of accuracy and efficiency.

Results: In this paper, two important computational approaches for modeling gene regulatory networks, …

Characterization Of Polymorphic Microsatellite Loci For The Invasive Monk Parakeet (Myiopsitta Monachus), M. A. Russello, V. Saranathan, S. Buhrman-Deever, J. Eberhard, A. Caccone

Faculty Publications

Microsatellite loci were characterized for the monk parakeet (Myiopsitta monachus) from a GTn-enriched genomic library. Twelve of 14 microsatellite loci were polymorphic, averaging 6.7 alleles per locus across the 20 individuals genotyped. Mean expected heterozygosity was 0.72, with locus-specific values ranging from 0.53 to 0.90. An equally high multilocus probability of identity (2.48 × 10-12) was revealed for this set of loci. In addition, all 12 loci were demonstrated to cross-amplify to varying extents within three additional parrot genera suggesting their potential utility for population-level studies in a broad range of Neotropical psittacines. © 2007 The Authors.

Are There Rearrangement Hotspots In The Human Genome?, Max A. Alekseyev, Pavel A. Pevzner

Faculty Publications

In a landmark paper, Nadeau and Taylor [18] formulated the random breakage model (RBM) of chromosome evolution that postulates that there are no rearrangement hotspots in the human genome. In the next two decades, numerous studies with progressively increasing levels of resolution made RBM the de facto theory of chromosome evolution. Despite the fact that RBM had prophetic prediction power, it was recently refuted by Pevzner and Tesler [4], who introduced the fragile breakage model (FBM), postulating that the human genome is a mosaic of solid regions (with low propensity for rearrangements) and fragile regions (rearrangement hotspots). However, the rebuttal …

Undergraduate Use Of Federated Searching: A Survey Of Preferences And Perceptions Of Value-Added Functionality, C. Jeffrey Belliston, Jared L. Howland, Brian C. Roberts

Faculty Publications

Randomly selected undergraduates at Brigham Young University, Brigham Young University-Idaho and Brigham Young University-Hawaii, all private universities sponsored by The Church of Jesus Christ of Latter-day Saints, participated in a study that investigated four questions regarding federated searching: (1) Does it save time? (2) Do undergraduates prefer it? (3) Are undergraduates satisfied with the results they get from it? (4) Does it yield higher quality results than non-federated searching? Federated searching was, on average, 11% faster than non-federated searching. Undergraduates rated their satisfaction with the citations gathered by federated searching 17% higher than their satisfaction using non-federated search methods. A …

Analyzing Gene Relationships For Down Syndrome With Labeled Transition Graphs, Hyrum Carroll, Mark J. Clement, Eric G. Mercer, Neha Rungta, Quinn O. Snell, Randall J. Roper

Faculty Publications

The relationship between changes in gene expression and physical characteristics associated with Down syndrome is not well understood. Chromosome 21 genes interact with nonchromosome 21 genes to produce Down syndrome characteristics. This indirect influence, however, is difficult to empirically define due to the number, size, and complexity of the involved gene regulatory networks. This work links chromosome 21 genes to non-chromosome 21 genes known to interact in a Down syndrome phenotype through a reachability analysis of labeled transition graphs extracted from published gene regulatory network databases. The analysis provides new relations in a recently discovered link between a specific gene …

Exceptionally Preserved Jellyfishes From The Middle Cambrian, Paulyn Cartwright, Susan L. Halgedahl, Jonathan R. Hendricks, Richard D. Jarrard, Antonio C. Marques, Allen G. Collins, Bruce S. Lieberman

Faculty Publications

Cnidarians represent an early diverging animal group and thus insight into their origin and diversification is key to understanding metazoan evolution. Further, cnidarian jellyfish comprise an important component of modern marine planktonic ecosystems. Here we report on exceptionally preserved cnidarian jellyfish fossils from the Middle Cambrian (~505 million years old) Marjum Formation of Utah. These are the first described Cambrian jellyfish fossils to display exquisite preservation of soft part anatomy including detailed features of structures interpreted as trailing tentacles and subumbrellar and exumbrellar surfaces. If the interpretation of these preserved characters is correct, their presence is diagnostic of modern jellyfish …

Tarphonomus, A New Genus Of Ovenbird (Aves: Passeriformes: Furnariidae) From South America, R. Terry Chesser, Robb T. Brumfield

Faculty Publications

Tarphonomus, a new genus of ovenbird (Aves: Passeriformes: Furnariidae) from South America, is described. Species included in the new genus, formerly placed in Upucerthia, are T. certhioides and T. harterti.

The Chlamydomonas Genome Reveals The Evolution Of Key Animal And Plant Functions, Sabeeha S. Merchant, Simon E. Prochnik, Olivier Vallon, Elizabeth H. Harris, Steven J. Karpowicz, George B. Witman, Astrid Terry, Asaf Salamov, Lillian K. Fritz-Laylin, Laurence Maréchal-Drouard, Wallace F. Marshall, Liang Hu Qu, David R. Nelson, Anton A. Sanderfoot, Martin H. Spalding, Vladimir V. Kapitonov, Qinghu Ren, Patrick Ferris, Erika Lindquist, Harris Shapiro, Susan M. Lucas, Jane Grimwood, Jeremy Schmutz, Igor V. Grigoriev, Daniel S. Rokhsar, Arthur R. Grossman, Pierre Cardol, Heriberto Cerutti, Guillaume Chanfreau, Chun Long Chen, Valérie Cognat, Martin T. Croft, Rachel Dent

Faculty Publications

Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the ∼120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, …

Habitat Fragmentation, Variable Edge Effects, And The Landscape-Divergence Hypothesis, William F. Laurance, Henrique E.M. Nascimento, Susan G. Laurance, Ana Andrade, Robert M. Ewers, Kyle E. Harms, Regina C.C. Luizão, José E. Ribeiro

Faculty Publications

Edge effects are major drivers of change in many fragmented landscapes, but are often highly variable in space and time. Here we assess variability in edge effects altering Amazon forest dynamics, plant community composition, invading species, and carbon storage, in the world's largest and longest-running experimental study of habitat fragmentation. Despite detailed knowledge of local landscape conditions, spatial variability in edge effects was only partially foreseeable: relatively predictable effects were caused by the differing proximity of plots to forest edge and varying matrix vegetation, but windstorms generated much random variability. Temporal variability in edge phenomena was also only partially predictable: …

Sammd: Staphylococcus Aureus Microarray Meta-Database, Vijayaraj Nagarajan, Mohamed O. Elasri

Faculty Publications

Background

Staphylococcus aureus is an important human pathogen, causing a wide variety of diseases ranging from superficial skin infections to severe life threatening infections. S. aureus is one of the leading causes of nosocomial infections. Its ability to resist multiple antibiotics poses a growing public health problem. In order to understand the mechanism of pathogenesis of S. aureus, several global expression profiles have been developed. These transcriptional profiles included regulatory mutants of S. aureus and growth of wild type under different growth conditions. The abundance of these profiles has generated a large amount of data without a uniform annotation …

Hypoxia In The Northern Gulf Of Mexico: Does The Science Support The Plan To Reduce, Mitigate, And Control Hypoxia?, Nancy N. Rabalais, R. Eugene Turner, B.K. Sen Gupta, D. F. Boesch, P. Chapman, M. C. Murrell

Faculty Publications

We update and reevaluate the scientific information on the distribution, history, and causes of continental shelf hypoxia that supports the 2001 Action Plan for Reducing, Mitigating, and Controlling Hypoxia in the Northern Gulf of Mexico (Mississippi River/Gulf of Mexico Watershed Nutrient Task Force 2001), incorporating data, publications, and research results produced since the 1999 integrated assessment. The metric of mid-summer hypoxic area on the Louisiana-Texas shelf is an adequate and suitable measure for continued efforts to reduce nutrients loads from the Mississippi River and hypoxia in the northern Gulf of Mexico as outlined in the Action Plan. More frequent measurements …

Requirement Of Α And Β Subunit Transmembrane Helix Separation For Integrin Outside-In Signaling, Jieqing Zhu, Christopher V. Carman, Minsoo Kim, Motomu Shimaoka, Timothy A. Springer, Bing Hao Luo

Faculty Publications

Adhesion to extracellular ligands through integrins regulates cell shape, migration, growth, and survival. How integrins transmit signals in the outside-to-in direction remains unknown. Whereas in resting integrins the α and β subunit transmembrane domains are associated, ligand binding promotes dissociation and separation of these domains. Here we address whether such separation is required for outside-in signaling. By introduction of an intersubunit disulfide bond, we generated mutant integrin αIIbβ3 with blocked transmembrane separation that binds ligand, mediates adhesion, adopts an extended conformation after ligand binding, and forms antibody-induced macroclusters on the cell surface similarly to wild type. However, the mutant integrin …

Phylogenetic Conservatism And Antiquity Of A Tropical Specialization: Army-Ant-Following In The Typical Antbirds (Thamnophilidae), Robb T. Brumfield, Jose G. Tello, Z. A. Cheviron, Matthew D. Carling, Nanette Crochet, Kenneth V. Rosenberg

Faculty Publications

One of the most novel foraging strategies in Neotropical birds is army-ant-following, in which birds prey upon arthropods and small vertebrates flushed from the forest floor by swarm raids of the army-ant Eciton burchellii. This specialization is most developed in the typical antbirds (Thamnophilidae) which are divisible into three specialization categories: (1) those that forage at swarms opportunistically as army-ants move through their territories (occasional followers), (2) those that follow swarms beyond their territories but also forage independently of swarms (regular followers), and (3) those that appear incapable of foraging independently of swarms (obligate followers). Although army-ant-following is one of …

Split Luciferase Complementation Assay To Study Protein-Protein Interactions In Arabidopsis Protoplasts, Yukichi Fujikawa, Naohiro Kato

Faculty Publications

We developed a split luciferase complementation assay to study protein-protein interactions in Arabidopsis protoplasts. In this assay, the N- and C-terminal fragments of Renilla reniforms luciferase are translationally fused to bait and prey proteins, respectively. When the proteins interact, split luciferase becomes activated and emits luminescence that can be measured by a microplate luminometer. Split luciferase activity was measured by first transforming protoplasts with a DNA vector in a 96-well plate. DNA vector expressing both bait and prey genes was constructed through two independent in vitro DNA recombinant reactions, Gateway and Cre-loxP. As proof of concept, we detected the protein-protein …

Alu Recombination-Mediated Structural Deletions In The Chimpanzee Genome, Kyudong Han, Jungnam Lee, Thomas J. Meyer, Jianxin Wang, Shurjo K. Sen, Deepa Srikanta, Ping Liang, Mark A. Batzer

Faculty Publications

With more than 1.2 million copies, Alu elements are one of the most important sources of structural variation in primate genomes. Here, we compare the chimpanzee and human genomes to determine the extent of Alu recombination-mediated deletion (ARMD) in the chimpanzee genome since the divergence of the chimpanzee and human lineages (∼6 million y ago). Combining computational data analysis and experimental verification, we have identified 663 chimpanzee lineage-specific deletions (involving a total of ∼771 kb of genomic sequence) attributable to this process. The ARMD events essentially counteract the genomic expansion caused by chimpanzee-specific Alu inserts. The RefSeq databases indicate that …

Instrumentation And Metrology For Single Rna Counting In Biological Complexes Or Nanoparticles By A Single-Molecule Dual-View System, Hui Zhang, Dan Shu, Faqing Huang, Peixuan Guo

Faculty Publications

Limited by the spatial resolution of optical microscopy, direct detection or counting of single components in biological complexes or nanoparticles is challenging, especially for RNA, which is conformationally versatile and structurally flexible. We report here the assembly of a customized single-molecule dual-viewing total internal reflection fluorescence imaging system for direct counting of RNA building blocks. The RNA molecules were labeled with a single fluorophore by in vitro transcription in the presence of a fluorescent AMP. Precise calculation of identical or mixed pRNA building blocks of one, two, three, or six copies within the bacteriophage phi29 DNA packaging motor or other …

Psoda: Better Tasting And Less Filling Than Paup, Hyrum Carroll, Mark J. Clement, Mark Ebbert, Quinn O. Snell

Faculty Publications

PSODA is an open-source phylogenetic search application that implements traditional parsimony and likelihood search techniques as well as advanced search algorithms. PSODA is compatible with PAUP and the search algorithms are competitive with those in PAUP. PSODA also adds a basic scripting language to the PAUP block, making it possible to easily create advanced meta-searches. Additionally, PSODA provides a user-friendly GUI with real-time graphing visualizations and phylogeny viewer, and a multiple sequence alignment algorithm PSODA is freely available from the PSODA web site: http://csl.cs.byu.edu/psoda.

Religious V. Secular Ideologies And Sex Education: A Response To Professors Cahn And Carbone, Vivian E. Hamilton

Faculty Publications

No abstract provided.

Knowledge And Skills Required To Provide Health Information Related Virtual Reference Services: Evidence From A Survey, Feili Tu

Faculty Publications

http://www.ncbi.nlm.nih.gov/pmc/journals/72/ ©2007 Medical Library Association

Psodascript: Applying Advanced Language Constructs To Open-Source Phylogenetic Search, Hyrum Carroll, Mark J. Clement, Jonathan Krein, Quinn O. Snell, Adam R. Teichert

Faculty Publications

Due to the immensity of phylogenetic tree space for large data sets, researches must rely on heuristic searches to infer reasonable phylogenies. By designing meta-searches which appropriately combine a variety of heuristics and parameter settings, researchers can significantly improve the performance of heuristic searches. Advanced language constructs in the open-source PSODA project—including variables, mathematical and logical expressions, conditional statements, and user-defined commands—give researchers a better framework for the exploration and exploitation of phylogenetic meta-search algorithms. PSODA’s approach to scripting meta-search algorithms is unique among open-source packages and addresses several limitations of other phylogenetic applications.