Physical Sciences and Mathematics Commons^™

Lake Mead National Recreation Area Sensitive Wildlife Species Monitoring And Analysis: Quarterly Progress Report, Period Ending December 31, 2005, Margaret N. Rees

Wildlife Monitoring

• Topsoil replacement monitored at Willow Beach Wastewater Rehabilitation Project
• Desert tortoise surveys and monitoring conducted for Northshore Road reconstruction projects, and desert tortoise training provided to 9 construction contractors.
• Field work associated with the project to remove desert tortoise radio transmitters from animals on Mormon Mesa completed.
• Weekly data processing for Desert Bighorn Sheep monitoring associated with the Hoover Dam Bypass Project continued.
• Fall field surveys for relict leopard frogs completed (11 sites surveyed); last of this year’s head-started animals released; RLFCT meeting held.
• Work started on a digital database (GIS) of Peregrine falcon observations.
• Monthly shorebird surveys conducted (22 …

Lake Mead National Recreation Area Vegetation Monitoring And Management: Quarterly Progress Report, Period Ending December 31, 2005, Margaret N. Rees

Vegetation Monitoring

Executive Summary

• Required reports on sticky buckwheat (Eriogonum viscidulum) and threecorner milkvetch (Astragalus geyeri var. triquetrus) to be submitted through appropriate protocols by December 30, 2005
• Summary report on several other rare plants to be submitted through appropriate protocols by December 30, 2005
• Invasive perennial pepperweed (also called tall whitetop; Lepidium latifolium) documented and treated by Weed Sentry within Black Canyon, Lake Mojave

Distribution Of Foraging Shearwaters Relative To Inner Front Of Se Bering Sea, J. Jahncke, K. O. Coyle, Stephan I. Zeeman, N. B. Kachel, G. L. Hunt Jr.

Marine Sciences Faculty Publications

We examined the hypothesis that short-tailed shearwaters Puffinus tenuirostris aggregate to forage at the inner front of the SE Bering Sea because of enhanced production there. We tested this hypothesis by comparing primary production, the distribution of euphausiids and the distribution of shearwaters relative to the front during late spring and late summer/early fall of 1997, 1998 and 1999. We found enhanced primary production at the front and offshore of the front during summer but not during spring. Primary production varied between seasons and years. Major differences were related to anomalous conditions in 1997 and 1998. The density of euphausiids …

Measurements Of Trace Gas Emissions From Australian Forest Fires And Correlations With Coincident Measurements Of Aerosol Optical Depth, Clare Paton-Walsh, N. B. Jones, Stephen R. Wilson, V Haverd, A. Meier, D. W. Griffith

Faculty of Science - Papers (Archive)

We present vertically integrated measurements of C2H2, C2H4, C2H6, HCOOH, CO, H2CO, HCN and NH3 through smoke plumes from Australian forest fires measured by ground-based solar absorption spectroscopy. The column amounts of these gases are highly correlated with simultaneous, co-located measurements of aerosol optical depth, providing a potential method of mapping biomass-burning emissions using satellite measurements of aerosol optical depth. We have calculated emission ratios relative to CO for the trace gases using aerosol optical depth as a proxy for CO and converted to emission factors by using an average emission factor for CO from literature measurements of extra-tropical forest …

Bayesian Analysis Of Cell-Cycle Gene Expression Data, Chuan Zhou, Jon Wakefield, Linda Breeden

UW Biostatistics Working Paper Series

The study of the cell-cycle is important in order to aid in our understanding of the basic mechanisms of life, yet progress has been slow due to the complexity of the process and our lack of ability to study it at high resolution. Recent advances in microarray technology have enabled scientists to study the gene expression at the genome-scale with a manageable cost, and there has been an increasing effort to identify cell-cycle regulated genes. In this chapter, we discuss the analysis of cell-cycle gene expression data, focusing on a model-based Bayesian approaches. The majority of the models we describe …

Evaluation Of Striped Bass Stocks In Virginia : Monitoring And Tagging Studies, 2004-2008 Annual Report 1 September 2004 - 31 August 2005, Philip W. Sadler, John M. Hoenig, Robert E. Harris, B. Gail Holliman

Reports

This report presents the results of striped bass (Marone saxatilis) tagging and monitoring activities in Virginia during the period 1 September 2004 through 31 August 2005. It includes an assessment of the biological characteristics of striped bass taken from the 2005 spring spawning run, estimates of annual survival based on annual spring tagging, and the results of the fall 2004 directed mortality study that is a collaborative effort with the Maryland Department of Natural Resources. The information contained in this report is required by the Atlantic States Marine Fisheries Commission and is used to implement a coordinated management plan for …

Detecting Submarine Groundwater Discharge With Synoptic Surveys Of Sediment Resistivity, Radium, And Salinity, John A. Breier, Crystaline F. Breier, Henrietta Edmonds

School of Earth, Environmental, and Marine Sciences Faculty Publications and Presentations

A synoptic geophysical and geochemical survey was used to investigate the occurrence and spatial distribution of submarine discharges of water to upper Nueces Bay, Texas. The 17 km survey incorporated continuous resistivity profiling; measurements of surface water salinity, temperature, and dissolved oxygen; and point measurements of dissolved Ra isotopes. The survey revealed areas of interleaving, vertical fingers of high and low conductivity extending up through 7 m of bay bottom sediments into the surface water, located within 100 m of surface salinity and dissolved Ra maxima along with peaks in water temperature and lows in dissolved oxygen. These results indicate …

Estimation Of Iron Solubility From Observations And A Global Aerosol Model, Chao Luo, N. M. Mahowald, N. Meskhidze, Y. Chen, R. L. Siefert, A. R. Baker, Anne M. Johansen

All Faculty Scholarship for the College of the Sciences

Mineral aerosol deposition is the dominant source of iron to the open ocean. Soil iron is typically insoluble and understanding the atmospheric processes that convert insoluble iron to the more soluble forms observed over the oceans is crucial. In this paper, we model several proposed processes for the conversion of Fe(III) to Fe(II), and compare with cruise observations. The comparisons show that the model results in similar averaged magnitudes of iron solubility as measured during 8 cruises in 2001–2003. Comparisons show that results of cases including cloud, SO₂ and hematite processing are better than the other approaches used using …

Red Rock Desert Learning Center Core Group Meeting: December 6, 2005, Red Rock Desert Learning Center

Reports (RRLC)

1. Introductions & Announcements (5 min.)
2. Approval of Minutes from October 18, 2005 Meeting (5 min.)
3. Update on Project Schedule – Michael Reiland (10 min.)
   A. Utilities
   B. Water Line
   C. Parking
   D. Operator
4. Update on Design Development – Michael Reiland (10 min.)
5. Cultural Treatment Plan – Michael Reiland (10 min.)
6. Environmental Assessment Update – Otak Inc. (10 min.)
7. Curriculum Update – Jeanne Klockow (10 min.)
8. Standing Reports (10 min.)
   A. BLM Capital Improvements – Michael Reiland
   B. Community Outreach – LaNelda Rolley
9. Committee Reports (5 min.)
   A. Building Committee
   B. Design Oversight
   C. Educational Programs
   D. Fund-raising and Partnerships
   E. …

Living With Trees – Perspectives From The Suburbs, Lesley M. Head, Pat Muir

Faculty of Science - Papers (Archive)

A study of suburban backyards and backyarders in Sydney and Wollongong revealed evidence of attitudes and behaviours in relation to trees. Attitudes are characterised under themes that indicate conditions of tolerance and belonging. They include attachment/risk, order/freedom and nativeness/alienness. While love is common, high levels of suspicion and intolerance towards trees in the suburban context are more common. Our findings confirm and throw further light on previous work indicating that many Australians have very partitioned views of the world in relationto where humans and nonhuman lifeforms belong. This partitioning must be understood in conceptual as well as spatial terms.

The Prairie Naturalist, Volume 37, No.4 December 2005

The Prairie Naturalist

AVIAN COMMUNITY RESPONSE TO CONSTRUCTION OF A NATURALISTIC GOLF COURSE IN TALL GRASS PRAIRIE IN KANSAS ▪ R. J. Robel, S. L. Bye, K. E. Kemp, and S. J. Thien

SECOND REPORT OF THE NORTH DAKOTA BIRD RECORDS COMMITTEE: 2002-2003 ▪ D. Svingen, and R. E. Martin

RECENT RECORDS OF FORMERLY EXTIRPATED CARNIVORES IN NEBRASKA ▪ J. D. Hoffman, and H. H. Genoways

PLAINS HARVEST MOUSE IN NORTH DAKOTA ▪ R. W. Seabloom, and T. L. Shaffer

Book Reviews

A Primer on Prairie Ecology ▪ M. A. Cunningham

Range Wars: Have Prairie Dogs Lost the Battle for the West? ▪ …

Minerva 2005, The Honors College

Minerva

This issue of Minerva includes an article on the development of HON 170: Currents & Contexts; a discussion of the Honors College's "Last Lecture Series;" a reflection on the legacy of former Honors Program Director, Robert Thomson; and an article on the visual art found around the Honors College complex.

Openws-Transaction: Enabling Reliable Web Service Transactions, Ivan Vasquez, John A. Miller, Kunal Verma, Amit P. Sheth

Kno.e.sis Publications

OpenWS-Transaction is an open source middleware that enables Web services to participate in a distributed transaction as prescribed by the WS-Coordination and WS-Transaction set of specifications. Central to the framework are the Coordinator and Participant entities, which can be integrated into existing services by introducing minimal changes to application code. OpenWS-Transaction allows transaction members to recover their original state in case of operational failure by leveraging techniques in logical logging and recovery at the application level. Depending on transaction style, system recovery may involve restoring key application variables and replaying uncommitted database activity. Transactions are assumed to be defined in …

Monthly Variability In Florida Bay Benthic Foraminifera Community Structure, C. Featherstone, Patricia Blackwelder

Marine & Environmental Sciences Faculty Proceedings, Presentations, Speeches, Lectures

Florida Bay is a shallow subtropical estuary, which experiences highly variable environmental fluctuations due to natural forces (hurricanes, climatic variations and sea level rise) and anthropogenic influences (agricultural activity, water management and urbanization). Study of short time-scale variability in benthic community population structure and synchronous environmental change is essential to understanding forcing relationships between environment and its effects on population. Benthic foraminifera assemblage variability is an excellent indicator of environmental change in estuarine and coastal areas because populations may respond relatively quickly on spatial and temporal scales (Alve, 1995). Temporal resolution is enhanced because foraminifera may reproduce as often as …

Improved Peak Detection And Quantification Of Mass Spectrometry Data Acquired From Surface-Enhanced Laser Desorption And Ionization By Denoising Spectra With The Undecimated Discrete Wavelet Transform, Kevin R. Coombes, Spiros Tsavachidis, Jeffrey S. Morris, Keith A. Baggerly, Henry M. Kuerer

Jeffrey S. Morris

Background: Mass spectrometry, especially surface enhanced laser desorption and ionization (SELDI) is increasingly being used to find disease-related proteomic patterns in complex mixtures of proteins derived from tissue samples or from easily obtained biological fluids such as serum, urine, or nipple aspirate fluid. Questions have been raised about the reproducibility and reliability of peak quantifications using this technology. For example, Yasui and colleagues opted to replace continuous measures of the size of a peak by a simple binary indicator of its presence or absence in their analysis of a set of spectra from prostate cancer patients.

Methods: We collected nipple …

Pooling Information Across Different Studies And Oligonucleotide Microarray Chip Types To Identify Prognostic Genes For Lung Cancer., Jeffrey S. Morris, Guosheng Yin, Keith A. Baggerly, Chunlei Wu, Li Zhang

Jeffrey S. Morris

Our goal in this work is to pool information across microarray studies conducted at different institutions using two different versions of Affymetrix chips to identify genes whose expression levels offer information on lung cancer patients’ survival above and beyond the information provided by readily available clinical covariates. We combine information across chip types by identifying “matching probes” present on both chips, and then assembling them into new probesets based on Unigene clusters. This method yields comparable expression level quantifications across chips without sacrificing much precision or significantly altering the relative ordering of the samples. We fit a series of multivariable …

Regioselective Synthesis Of Novel E-Edge-[60]Fullerenylmethanodihydropyrroles And 1,2-Dihydromethano[60]Fullerenes, Leila Chaker, Graham E. Ball, James R. Williams, Glenn A. Burley, Bill C. Hawkins, Paul A. Keller, Stephen G. Pyne

Faculty of Science - Papers (Archive)

Treatment of a tethered N-(diphenylmethylene)glycinate-malonate derivative with [60]fullerene under Bingel conditions yielded an e-edge-[60]fullerenylmethanodihydropyrrole adduct in a regioselective manner. The regiochemical outcome was independent of the order of addition of either the N-(diphenylmethylene)glycinate or the malonate moieties. This new bis-adduct was also prepared in 13C enriched form allowing for its unequivocal structural characterization by 2D INADEQUATE NMR experiments. Ring-opening of the dihydropyrrole functionality of the bisadducts under reductive conditions gave exclusively novel dihydromethano[60]fullerene derivatives.

Culture As Concept And Influence In Environmental Research And Management, Lesley M. Head, D. Trigger, J. Mulcock

Faculty of Science - Papers (Archive)

Given that human activities have been implicated in the vast majority of contemporary environmental problems, it might be expected that research effort into those activities and the attitudes from which they stem would be both strongly supported by funding agencies, and of central interest to environmental scientists and land managers. In this paper we focus on an undervalued area of environmental humanities research—cultural analysis of the beliefs, practices and often unarticulated assumptions which underlie human–environmental relations. In discussing how cultural processes are central to environmental attitudes and behaviours, and how qualitative research methods can be used to understand them in …

Seasonal Forage Availability And Diet Of Reintroduced Elk In The Cumberland Mountains, Tennessee, Jason Lee Lupardus

Masters Theses

The Tennessee Wildlife Resources Agency (TWRA) reintroduced elk (Cervus elaphus manitobensis) into the Cumberland Mountains, Tennessee over a 3-year period beginning in December 2000. We radio-collared 160 elk and monitored them by aerial telemetry from February 2001 to June 2003. Locations (n = 1450) were used in a geographic information system (GIS) to develop a core herd home range (789-ha sampling area) to assess elk seasonal forage use and availability. We monitored diet and resource availability from November 2003 to October 2004 by vegetation sampling and microhistological analysis of feces. Tall fescue (Festuca arundinacea; 35.1%) dominated …

Demonstrating Dynamic Configuration And Execution Of Web Processes, Karthik Gomadam, Kunal Verma, Amit P. Sheth, John A. Miller

Kno.e.sis Publications

Web processes are next generation workflows on the web, created using Web services. In this paper we demonstrate the METEOR-S Configuration and Execution Environment (MCEE) system. It will illustrate the capabilities of the system to a) Discover partners b) Optimize partner selection using constraint analysis, c) Perform interaction protocol and data mediation. A graphical execution monitor to monitor the various phases of execution will be used to demonstrate various aspects of the system.

Discovering Informative Connection Subgraphs In Multi-Relational Graphs, Cartic Ramakrishnan, William Milnor, Matthew Perry, Amit P. Sheth

Kno.e.sis Publications

Discovering patterns in graphs has long been an area of interest. In most approaches to such pattern discovery either quantitative anomalies, frequency of substructure or maximum flow is used to measure the interestingness of a pattern. In this paper we introduce heuristics that guide a subgraph discovery algorithm away from banal paths towards more "informative" ones. Given an RDF graph a user might pose a question of the form: "What are the most relevant ways in which entity X is related to entity Y?" the response to which is a subgraph connecting X to Y. We use our heuristics to …

Degree Of Sedentarization Affects Risks And Conflicts For The Waso Boran In Northern Kenya, D. Layne Coppock, Abdullahi D. Jillo, Mark N. Mutinda, Abdilla A. Aboud

Environment and Society Faculty Publications

The Waso Borana have lived for over a century in northern Kenya. In the last few decades, however, their ability to maintain their traditions has been severely challenged. Here we report survey results from 540 households in Isiolo District, stratified among three groups differing in terms of lifestyle: sedentary, semi-sedentary, and mobile. In some cases these groups vary with respect to important perceived risks, causes of natural-resource related conflict, and possible solutions to conflict. For example, sedentary respondents often noted concerns over land tenure problems, human diseases, and political incitement. Mobile respondents, in contrast, often noted primary concerns over drought, …

Agro-Pastoralists’ Wrath For The Prosopis Tree: The Case Of The Il Chamus Of Baringo District, Kenya, D. Layne Coppock, Abdillahi A. Aboud, Phillip K. Kisoyan

Environment and Society Faculty Publications

Indigenous to Peru, Chile, and Argentina, the woody plant called Prosopis juliflora (also known by the American common name of “Honey Mesquite”) has spread world-wide in recent decades, including rangelands throughout Latin America, North America, south and central Asia, Australia, and sub-Saharan Africa. A species known for rapid establishment, high adaptability, and fast rates of growth, its dispersal has primarily been a consequence of intentional introduction by well- meaning “technical experts” who wanted to provide a new source of fodder, fuel wood, or a means to combat desertification in arid and semi-arid lands. One problem, however, is that unless Prosopis …

Linking Pastoralists And Exporters In A Livestock Marketing Chain: Recent Experiences From Ethiopia, D. Layne Coppock, Solomon Desta, Getachew Gebru, Seyoum Tezera

Environment and Society Faculty Publications

The Boran of southern Ethiopia have been traditionally viewed as unwilling or unable to engage in large scale, commercialized livestock trade. Here we report on the creation of a new livestock marketing chain from the Borana Plateau to export outlets largely serving the Gulf States. Since 2003 various meetings and exchange tours were organized by collaborating agencies and PARIMA to directly link pastoral producers with livestock exporters and policy makers. This occurred against a backdrop of growing export demand for small ruminants, rapid development of private export industry, formation of well-trained pastoral marketing groups (often dominated by women), and provision …

Collaborative Research: Toward Environmental Genomics: Can We Estimate Bacterial Diversity In The Ocean?, Daniel L. Distel

University of Maine Office of Research Administration: Grant Reports

Environmental genomics, wherein the total genomic diversity of a natural community may be sampled and analyzed in an ecological context, remains an elusive goal. This is due, at least in part, to (I) a lack of reliable estimates of total community diversity and (II) a lack of information regarding the exact phylogenetic, genomic and ecological units measured by commonly used diversity estimators. Although ribosomal RNA approaches have provided the first steps towards diversity estimation, and are widely used as a proxy for unique bacterial types in natural populations, the genomic unit a ribotype measures remains largely unexplored. It is generally …

Optimal Feature Selection For Nearest Centroid Classifiers, With Applications To Gene Expression Microarrays, Alan R. Dabney, John D. Storey

UW Biostatistics Working Paper Series

Nearest centroid classifiers have recently been successfully employed in high-dimensional applications. A necessary step when building a classifier for high-dimensional data is feature selection. Feature selection is typically carried out by computing univariate statistics for each feature individually, without consideration for how a subset of features performs as a whole. For subsets of a given size, we characterize the optimal choice of features, corresponding to those yielding the smallest misclassification rate. Furthermore, we propose an algorithm for estimating this optimal subset in practice. Finally, we investigate the applicability of shrinkage ideas to nearest centroid classifiers. We use gene-expression microarrays for …

A New Approach To Intensity-Dependent Normalization Of Two-Channel Microarrays, Alan R. Dabney, John D. Storey

UW Biostatistics Working Paper Series

A two-channel microarray measures the relative expression levels of thousands of genes from a pair of biological samples. In order to reliably compare gene expression levels between and within arrays, it is necessary to remove systematic errors that distort the biological signal of interest. The standard for accomplishing this is smoothing "MA-plots" to remove intensity-dependent dye bias and array-specific effects. However, MA methods require strong assumptions. We review these assumptions and derive several practical scenarios in which they fail. The "dye-swap" normalization method has been much less frequently used because it requires two arrays per pair of samples. We show …

Ontoqa: Metric-Based Ontology Quality Analysis, Samir Tartir, I. Budak Arpinar, Michael Moore, Amit P. Sheth, Boanerges Aleman-Meza

Kno.e.sis Publications

As the Semantic Web gains importance for sharing knowledge on the Internet this has lead to the development and publishing of many ontologies in different domains. When trying to reuse existing ontologies into their applications, users are faced with the problem of determining if an ontology is suitable for their needs. In this paper, we introduce OntoQA, an approach that analyzes ontology schemas and their populations (i.e. knowledgebases) and describes them through a well defined set of metrics. These metrics can highlight key characteristics of an ontology schema as well as its population and enable users to make an informed …

Process For The Preparation Of Citalopram Intermediate, Aslam A. Malik, Hasan Palandoken, Joy A. Stringer, Dershing Huang, Antonio Romero, Olivier Dapremont

Chemistry and Biochemistry

The present invention provides, inter alia, a novel process for the preparation of Citalopram, a known antidepressant.

Principal Component Analysis For Predicting Transcription-Factor Binding Motifs From Array-Derived Data, Yunlong Liu, Matthew P Vincenti, Hiroki Yokota

Dartmouth Scholarship

The responses to interleukin 1 (IL-1) in human chondrocytes constitute a complex regulatory mechanism, where multiple transcription factors interact combinatorially to transcription-factor binding motifs (TFBMs). In order to select a critical set of TFBMs from genomic DNA information and an array-derived data, an efficient algorithm to solve a combinatorial optimization problem is required. Although computational approaches based on evolutionary algorithms are commonly employed, an analytical algorithm would be useful to predict TFBMs at nearly no computational cost and evaluate varying modelling conditions. Singular value decomposition (SVD) is a powerful method to derive primary components of a given matrix. Applying SVD …