Digital Commons Network^™

Bioconductor: Open Software Development For Computational Biology And Bioinformatics, Robert C. Gentleman, Vincent J. Carey, Douglas J. Bates, Benjamin M. Bolstad, Marcel Dettling, Sandrine Dudoit, Byron Ellis, Laurent Gautier, Yongchao Ge, Jeff Gentry, Kurt Hornik, Torsten Hothorn, Wolfgang Huber, Stefano Iacus, Rafael Irizarry, Friedrich Leisch, Cheng Li, Martin Maechler, Anthony J. Rossini, Guenther Sawitzki, Colin Smith, Gordon K. Smyth, Luke Tierney, Yee Hwa Yang, Jianhua Zhang

Bioconductor Project Working Papers

The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. We detail some of the design decisions, software paradigms and operational strategies that have allowed a small number of researchers to provide a wide variety of innovative, extensible, software solutions in a relatively short time. The use of an object oriented programming paradigm, the adoption and development of a software package system, designing by contract, distributed development and collaboration with other projects are elements of this project's success. Individually, each of these concepts are useful and important but when combined they have …

Seeding The Universe With Life: Securing Our Cosmological Future, Michael Noah Mautner

Chemistry Publications

Life is unique in Nature, and for us, it is precious. Life is unique in its complex patterns, and in its purposeful self-continuation. We belong to life and share its drive for self-propagation. Belonging to life then implies a human purpose to secure, expand and propagate our family of gene/protein life.

This purpose is best achieved in space, where life has an immense future. We can start now to secure this future, by seeding with life new solar systems. New species can develop there into intelligent beings who will further expand life in the galaxy. Filling the universe with life …

An Inventory And Condition Survey Of The Pilbara Region, Western Australia, A M E Van Vreeswyk, K A. Leighton, A L. Payne, P Hennig

Technical Bulletins

The inventory and condition survey of the Pilbara region, undertaken by the Department of Agriculture, Western Australia between 1995 and 1999, describes and maps the natural resources of the region’s pastoral leasehold land. This survey report provides a baseline record of the existence and condition of the natural area’s resources, to assist with the planning and implementation of land management practices. The report identified and described the condition of soils, landforms, vegetation, habitat, ecosystems, and declared plants and animals. It also assessed the impact of pastoralism and made land management recommendations. The area surveyed covers about 181 723 km². Seven …

^{1}H, ^{13}C, ^{119}Sn Nmr, Mass, Mössbauer And Biological Studies Of Tri-,Di- And Chlorodiorganotin(Iv) Carboxylates, Hajra Masood, Saqib Ali, Mohummad Mazhar, Saira Shahzadi, Khadija Shahid

Turkish Journal of Chemistry

The reaction of 2-[(2,3-dimethylphenyl)amino]benzoic acid (HL) with tri- and diorganotin(IV) chlorides yielded complexes of the type R_{3}SnL and R_{2}SnL_{2} (R = n-C_{4}H_{9}, C_{6}H_{5}, C_{6}H_{5}CH_{2}, n-C_{8}H_{17}). The compounds R_{2}SnClL were obtained by a redistribution reaction between R_{2}SnL_{2} and R_{2}SnCl_{2}. All the compounds were characterized by CHN analysis, infrared, multinuclear NMR, mass and Mössbauer spectroscopy. The possible mode of carboxylate group bonding in solid as well as in solution is proposed on the basis of infrared, Mössbauer and NMR (^{1}H, ^{13}C, ^{119}Sn) spectroscopy.

Synthesis Of A Novel Family Of Amide Derivatives Of Podocarpic Acid, Dao Nguyen

Electronic Theses and Dissertations

As a class, amides are of great interest in biological studies and pharmaceutical application. In this work, podocarpic acid, a natural tricyclic diterpene, derived from Podocarpus species, has been employed to form a novel family of amide derivatives which will later be studied for their potential as new drug leads. Novel amide derivatives of podocarpic acid were synthesized from podocarpic acid in three steps. The first step involved methylation with dimethylsulfate to form methyl-O-methylpodocarpate. This step was followed by iodination with iodine to give iodomethyl-O-methylpodocarpate. Finally amidation with various aliphatic amides using a copper catalyst yielded four amide derivatives of …

Ecotoxicological Research At Dit, Maria Davoren, Colm O'Dowd, Sharon Ni Shuilleabhain

Articles

The term ecotoxicology first defined by Rene Truhart in 1969, essentially describes the study of the harmful effects of chemicals upon ecosystems.

A Probability-Based Similarity Measure For Saupe Alignment Tensors With Applications To Residual Dipolar Couplings In Nmr Structural Biology, Anthony K. Yan, Christopher J. Langmead, Bruce Randall Donald

Computer Science Technical Reports

High-throughput NMR structural biology and NMR structural genomics pose a fascinating set of geometric challenges. A key bottleneck in NMR structural biology is the resonance assignment problem. We seek to accelerate protein NMR resonance assignment and structure determination by exploiting a priori structural information. In particular, a method known as Nuclear Vector Replacement (NVR) has been proposed as a method for solving the assignment problem given a priori structural information [24,25]. Among several different kinds of input data, NVR uses a particular type of NMR data known as residual dipolar couplings (RDCs). The basic physics of residual dipolar couplings tells …

An Improved Nuclear Vector Replacement Algorithm For Nuclear Magnetic Resonance Assignment, Christopher James Langmead, Bruce Randall Donald

Computer Science Technical Reports

We report an improvement to the Nuclear Vector Replacement (NVR) algorithm for high-throughput Nuclear Magnetic Resonance (NMR) resonance assignment. The new algorithm improves upon our earlier result in terms of accuracy and computational complexity. In particular, the new NVR algorithm assigns backbone resonances without error (100% accuracy) on the same test suite examined in [Langmead and Donald J. Biomol. NMR 2004], and runs in $O(n^{5/2} \log {(cn)})$ time where $n$ is the number of amino acids in the primary sequence of the protein, and $c$ is the maximum edge weight in an integer-weighted bipartite graph.

Ranked Set Sampling Based On Binary Water Quality Data With Covariates, Paul Kvam

Department of Math & Statistics Faculty Publications

A ranked set sample (RSS) is composed of independent order statistics, formed by collecting and ordering independent subsamples, then measuring only one item from each subsample. If the cost of sampling is dominated by data measurement rather than collection or ranking, the RSS technique is known to be superior to ordinary sampling. Experiments based on binary data are not designed to exploit the advantages of ranked set sampling because categorical data typically are as easily measured as ranked, making RSS methods impractical. However, in some environmental and biological studies, the success probability of a bivariate outcome is related to one …

Flow Recommendations To Benefit Endangered Fishes In The Colorado And Gunnison Rivers, Charles W. Mcada

All U.S. Government Documents (Utah Regional Depository)

No abstract provided.

Functional Annotation And Dendrogram Representation Of Gene Expression Clustering Results, Antoneta Petkova Vladimirova

Theses

The advances in genomic sciences have created vast amounts of gene expression data. To make sense of the expression information, various techniques have been applied. Clustering is among the unsupervised methods used to group the results according to gene expression level. Dendrogram visualization allows graphical representation of the clustering. The aim of this thesis is to enhance these techniques by adding another layer of functionality, namely, annotating the dendrogram with gene functional information. Presented is an application which visualizes yeast clustering results as a dendrogram along with color-coded gene keyword annotations. Gene keyword information was extracted from a major biological …

Genome Analysis: Mutation Analysis Using Near Infrared Laser-Induced Fluorescence (Nir-Lif) And Single Molecule Detection In Microfluidic Devices, Musundi Ben Wabuyele

LSU Doctoral Dissertations

A number of genotyping methods have been developed for mutation analysis, each of which has its own unique advantage. DNA amplification via polymerase chain reaction (PCR) provides an unlimited supply of material for subsequent genetic analysis even in case where only a single copy of the DNA molecule is present in the sample. Research presented in this dissertation first examines the efficiency of in vitro amplification of single copy DNA with subsequent sequencing analysis of PCR product. The PCR products (amplicons) were investigated for possible alteration, distortions or mutations due to the amplification process. The sequencing data for single copy …

Developments In Relativistic Nonlinear Optics, Donald P. Umstadter, Sudeep Banerjee, Shouyuan Chen, E. Dodd, K. Flippo, Anatoly Maksimchuk, N. Saleh, A. Valenzuela, P. Zhang

Donald Umstadter Publications

We report recent results of experiments and simulations in the regime of peak laser intensities above 10¹⁹ W/cm², including the following topics: (1) electron and proton acceleration to energies in excess of 10 MeV in well collimated beams; (2) use of laser chirp to control the growth of plasma waves and acceleration of electrons by the Raman instability; (3) all optical injection and acceleration of electrons; (4) relativistic self-focusing by means of the mutual index of refraction of two overlapping laser pulses; (5) creation of a radioisotope by the reaction ¹⁰B(d,n)¹¹C; (6) …

Diets Of Baird’S Beaked Whales, Berardius Bairdii, In The Southern Sea Of Okhotsk And Off The Pacific Coast Of Honshu, Japan, William A. Walker, James G. Mead, Robert L. Brownell Jr.

United States Department of Commerce: Staff Publications

Stomach contents were analyzed from 127 Baird’s beaked whales, Berardizls bairdii, taken in coastal waters of Japan. During late July-August of 1985- 1987, 1989, and 1991, 107 samples were collected from off the Pacific coast of Honshu. An additional 20 samples were collected from whales taken in the southern Sea of Okhotsk during late August-September of 1988 and 1989. Prey identification using fish otoliths and cephalopod beaks revealed the whales fed primarily on deep-water gadiform fishes and cephalopods in both regions. Prey species diversity and the percentage of cephalopods and fish differed between the two regions. Off the Pacific …

The Mount Feather Diamicton Of The Sirius Group: An Accumulation Of Indicators Of Neogene Antarctic Glacial And Climatic History, G. A. Wilson, J. A. Barron, A. C. Ashworth, R. A. Askin, J. A. Carter, M. G. Curren, D. H. Dalhuisen, E. I. Friedmann, D. G. Fyodorov-Davidov, D. A. Gilichinsky, M. A. Harper, David M. Harwood, J. F. Hiemstra, T. R. Janecek, K. J. Licht, V. E. Ostroumov, R. D. Powell, E. M. Rivkina, S. A. Rose, A. P. Stroeven, P. Stroeven, J. J. M. Van Der Meer, M. C. Wizevich

Department of Earth and Atmospheric Sciences: Faculty Publications

A paucity of data from the Antarctic continent has resulted in conflicting interpretations of Neogene Antarctic glacial history. Much of the debate centres on interpretations of the glacigene Sirius Group strata that crop out as discrete deposits along the length of the Transantarctic Mountains and in particular on its age and the origin of the siliceous microfossils it encloses. Pliocene marine diatoms enclosed within Sirius Group strata are inferred to indicate a dynamic East Antarctic ice sheet that was much reduced, compared with today, in the early-middle Pliocene and then expanded again in the late Pliocene. However, the geomorphology of …

Fisheries Research Report No. 134, Volume 2 - Towards An Assessment Of The Natural And Human Use Impacts On The Marine Environment Of The Abrolhos Islands, C F. Chubb, F J. Webster, C J. Dibden

Fisheries Research Reports

These proceedings form the second of two public documents resulting from the project “Towards an assessment of the natural and human use impacts on the marine environment” funded by the Fisheries Research and Development Corporation (project no. 2000/166). Volume 1, a summary of existing information and assessment of current levels of human use, was presented at a Public Forum in Geraldton on July 11, 2001.

A two-day workshop was held immediately after the forum and was attended by invited representatives from professional fishing and recreational groups together with research and management experts. The issues identified in Volume 1, and those …

Assessment Of Elemental Concentrations In Streams Of The New Lead Belt In Southeastern Missouri, 2002–05, William G. Brumbaugh, Thomas W. May, John M. Besser, Ann L. Allert, Christopher J. Schmitt

United States Geological Survey: Publications

Concerns about possible effects of lead-mining activities on the water quality of federally protected streams located in southeastern Missouri prompted a suite of multidisciplinary studies to be conducted by the U.S. Geological Survey. As part of this investigation, a series of biological studies were initiated in 2001 for streams in the current mining region and the prospecting area. In this report, results are examined for trace elements and other selected chemical measurements in sediment, surface water, and sediment interstitial (pore) water sampled between 2002 and 2005 in association with these biological studies. Compared to reference sites, fine sediments collected downstream …

Artificial Peptides Containing Ca,A- Disubstituted Amino Acids: Synthesis, Conformational Studies, And Application As Β-Strand Mimics, Yanwen Fu

LSU Doctoral Dissertations

Short peptides containing C^α,α-dipropylglycine (Dpg) at alternating sequence positions were synthesized and examined for conformational behavior. Peptide assembly was performed using Fmoc-solid-phase chemistry where the coupling with PyAOP could be significantly enhanced at elevated temperature. Circular dichroism (CD) and NMR conformational studies revealed that incorporation of Dpg residues induced folded structures into peptides. It was observed that Dpg residues adopted helical conformation in a helix-promoting sequence. The resulting helical structure was comprised of consecutive β-turns whose structure was stabilized by salt bridge in aqueous solution. In this study, the preparation of sterically and polyfunctional C^α,α-disubstituted amino …

Structural And Functional Imaging With Carbon Nanotube Afm Probes, J. H. Hafner, Chin Li Cheung, A. T. Woolley, C. M. Lieber

Barry Chin Li Cheung Publications

Atomic force microscopy (AFM) has great potential as a tool for structural biology, a field in which there is increasing demand to characterize larger and more complex biomolecular systems. However, the poorly characterized silicon and silicon nitride probe tips currently employed in AFM limit its biological applications. Carbon nanotubes represent ideal AFM tip materials due to their small diameter, high aspect ratio, large Young’s modulus, mechanical robustness, well-defined structure, and unique chemical properties. Nanotube probes were first fabricated by manual assembly, but more recent methods based on chemical vapor deposition provide higher resolution probes and are geared towards mass production, …

Parallel 3d Reconstruction Of Assymmetric Virus Structure From Electron From Electron Micrographs: Algorithms And Experiments, Robert E. Lynch, Dan C. Marinescu, Yongchang Ji, Hong Lin

Department of Computer Science Technical Reports

No abstract provided.

High-Performance Liquid Chromatographic And Capillary Electrophoretic Enantioseparation Of Plant Growth Regulators And Related Indole Compounds Using Macrocyclic Antibiotics As Chiral Selectors, F. Hui, K. H. Ekborg-Ott, Daniel W. Armstrong

Chemistry Faculty Research & Creative Works

Enantioseparation of plant growth regulators, such as 3-(3-indolyl)-butyric acid, abscisic acid and structurally related molecules including a variety of substituted tryptophan compounds, has been achieved by HPLC and/or CE. The covalently bonded macrocyclic antibiotics, teicoplanin, ristocetin A and vancomycin, were used as chiral stationary phases (CSPs) in HPLC. Most of the racemates were baseline resolved in the reversed-phase mode (EtOH-H2O) using the teicoplanin CSP. The chiral recognition mechanism is discussed in regard to the structure of the analytes. In CE, the three aforementioned macrocyclic antibiotics were used as chiral additives in a phosphate run buffer. The effect of pH and …

Management Plan

National Invasive Species Council

Farmers, ranchers, scientists, State officials, and many others have urged the Federal Government to consider invasive species issues a priority and to develop a coordinated national effort to address the problem. In response, the President issued Executive Order 13112 on Invasive Species (Order) in February 1999. The Order established the National Invasive Species Council (Council), co-chaired by the Secretaries of Agriculture, Commerce, and the Interior; and includes the Secretaries of State, Treasury, Defense, and Transportation, and the Administrator of the Environmental Protection Agency. The Order directs the Council to form a non-Federal Invasive Species Advisory Committee (ISAC) to advise the …

Cruise Reveals History Of Holocene Larsen Ice Shelf, Eugene Domack, Amy Leventer, Robert Gilbert, Stefanie Brachfeld, Scott Ishman, Angelo Camerlenghi, Kathleen Gavahan, David Carlson, Athen Barkoukis

Department of Earth and Environmental Studies Faculty Scholarship and Creative Works

No abstract provided.

Red Imported Fire Ants: Impact On Biodiversity, Daniel P. Wojcik, Craig R. Allen, Richard J. Brenner, Elizabeth A. Forys, Donald P. Jouvenaz, R. Scott Lutz

Nebraska Cooperative Fish and Wildlife Research Unit: Staff Publications

The red imported fire ant, Solenopsis invicta Buren (hereafter referred to as imported fire ant), long considered a regional problem, is receiving renewed attention nationwide, with infestations found in Arizona, Maryland, Nevada, New Mexico, and Virginia (Mitchell 1996). Recently, infestations discovered in several regions of California caused great public concern (Brennan 1999, Schrader 1999). Initially, infestations appeared to be isolated in almond groves in Kern County; presumably these infestations originated from bee hives transported interstate for the purpose of pollinating crops. Separately, ornamental plants arriving in Las Vegas, NV, were infested with fire ants, and records showed that the point …

Development Of A Networked Interactive Information Environment Within A National Park, John Clifton

Theses

For the most part, the Killarney National Park (KNP) currently disseminates information to visitors in paper format and by word of mouth in a non-coherent fashion. Society as a whole is moving towards an Information Age delivered through an electronic medium. This project aims to facilitate the KNP in delivering a new electronically presented information experience to its global visitors.

Electronic media facilitate the delivery of in-depth multimedia as well as multilingual information. This information will be made available on demand to visitors and delivered through a variety of media including information points and handheld devices to facilitate the various …

The Endangered Species Act And Private Landowner Incentives, Jeffrey A. Michael

Human Conflicts with Wildlife: 2002 Symposium

While intended to increase the habitat available to endangered species, the restrictions of the Endangered Species Act (ESA) increase the costs of harboring an endangered species to private landowners and create incentives for private landowners to reduce habitat. This paper illustrates the incentive for habitat destruction with a simple model of private land use under the ESA, and uses it to predict the effects of changes in policy or biological conditions on private landowner incentives. Many anecdotal accounts and recent empirical research support the predictions of the model. Because of the ESA’s perverse incentives, many have proposed replacing the punitive …

Fisheries Research Report No. 121 - Synopsis Of The Biology And Exploitation Of The Blue Swimmer Crab, Portunus Pelagicus Linnaeus, In Western Australia, Mervi I. Kangas

Fisheries Research Reports

This report summarises the existing studies which have provided information on the biology, population characteristics and exploitation of the blue swimmer crab, Portunus pelagicus, in Western Australia. Gaps in the existing knowledge are also highlighted to assist in targeting new research initiatives. Portunus pelagicus matures at about one year and in temperate regions females mate only once a year. This is because mature crabs moult only once a year. It appears from studies to date that Western Australian crabs are one genetic population. This is being further investigated. Migration of the blue swimmer crab occurs between estuaries and the ocean …

Tws Wildlife Damage Management Working Group Newsletter: Winter 2000 – Volume 7(1) – Elections Issue!

TWS Wildlife Damage Management Working Group Newsletter

Forward - Scott Craven; Candidates for The Working Group Officers – March 2000 ;Stupid Pest Tricks (Or What Your Best Extension Call Was All About); Wildlife Damage Management Working Group Ballot – March 2000; Wisconsin DNR Won’t Bite On Compensating Muskie Victim; 3rd European Vertebrate Pest Management Conference; Symposia, Workshop, And Special Poster Sessions; Application For Membership / The Wildlife Society

Biologically-Controlled Mineralization Of Magnetic Iron Minerals By Magnetotactic Bacteria, D. A. Bazylinski, R. B. Frankel

Physics

No abstract provided.

An Algorithm For Parallel 3d Reconstruction Of Asymmetric Objects From Electron Micrographs, Robert E. Lynch, Hong Lin, Dan C. Marinescu

Department of Computer Science Technical Reports

No abstract provided.