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2010

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Summer Activity Pattern And Home Range Of Northern Pocket Gophers In An Alfalfa Field, Jon C. Pigage, Helen K. Pigage Dec 2010

Summer Activity Pattern And Home Range Of Northern Pocket Gophers In An Alfalfa Field, Jon C. Pigage, Helen K. Pigage

The Prairie Naturalist

AIlocation of time for feeding, resting and reproduction in subterranean animals is difficult to determine. Although pocket gophers (Thomomys spp.) are among the most widely studied subterranean rodents, there are conflicting reports on activity measurement in these animals. Activity studies have included opening gopher burrows (Tryon 1947), laboratory studies of activity (Vaughan and Hansen 1961), telemetry studies (Anderson and McMahon 1981, Bandoli 1987, and Cameron et al. 1988), and subcutaneously implanted radioactive gold wires (Gettinger 1984). The diversity of techniques reflects the difficulty of generalizing results from different species of pocket gophers in natural and artificial environments. Patton and …

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Bingroup: A Package For Group Testing, Christopher R. Bilder, Boan Zhang, Frank Schaarschmidt, Joshua M. Tebbs Dec 2010

Bingroup: A Package For Group Testing, Christopher R. Bilder, Boan Zhang, Frank Schaarschmidt, Joshua M. Tebbs

The R Journal

When the prevalence of a disease or of some other binary characteristic is small, group testing (also known as pooled testing) is frequently used to estimate the prevalence and/or to identify individuals as positive or negative. We have developed the binGroup package as the first package designed to address the estimation problem in group testing. We present functions to estimate an overall prevalence for a homogeneous population. Also, for this set ting, we have functions to aid in the very important choice of the group size. When individuals come from a heterogeneous population, our group testing regression functions can be …

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Dclone: Data Cloning In R, Péter Sólymos Dec 2010

Dclone: Data Cloning In R, Péter Sólymos

The R Journal

The dclone R package contains low level functions for implementing maximum likelihood estimating procedures for complex models using data cloning and Bayesian Markov Chain Monte Carlo methods with support for JAGS, WinBUGS and OpenBUGS.

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Hglm: A Package For Fitting Hierarchical Generalized Linear Models, Lars Rönnegård, Xia Shen, Moudud Alam Dec 2010

Hglm: A Package For Fitting Hierarchical Generalized Linear Models, Lars Rönnegård, Xia Shen, Moudud Alam

The R Journal

We present the hglm package for fit ting hierarchical generalized linear models. It can be used for linear mixed models and generalized linear mixed models with random effects for a variety of links and a variety of distributions for both the outcomes and the random effects. Fixed effects can also be fitted in the dispersion part of the model.

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Online Reproducible Research: An Application To Multivariate Analysis Of Bacterial Dna Fingerprint Data, Jean Thioulouse, Claire Valiente-Moro, Lionel Zenner Dec 2010

Online Reproducible Research: An Application To Multivariate Analysis Of Bacterial Dna Fingerprint Data, Jean Thioulouse, Claire Valiente-Moro, Lionel Zenner

The R Journal

This paper presents an example of online reproducible multivariate data analysis. This example is based on a web page providing an online computing facility on a server. HTML forms contain editable R code snippets that can be executed in any web browser thanks to the Rweb software. The example is based on the multivariate analysis of DNA fingerprints of the internal bacterial flora of the poultry red mite Dermanyssus gallinae. Several multivariate data analysis methods from the ade4 package are used to compare the fingerprints of mite pools coming from various poultry farms. All the computations and graphical displays …

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Review Of Grouse Of The Plains And Mountains - The South Dakota Story, By Lester D. Flake, John W. Connelly, Thomas R. Kirschenmann, And Andrew J. Lindbloom., Brent E. Jamison Dec 2010

Review Of Grouse Of The Plains And Mountains - The South Dakota Story, By Lester D. Flake, John W. Connelly, Thomas R. Kirschenmann, And Andrew J. Lindbloom., Brent E. Jamison

The Prairie Naturalist

Grouse are a fascinating group of birds that offer elaborate breeding displays for birders in the spring, provide sporting opportunities for hunters in the fall, and serve as indicators of grassland health. Though the authors claim that the book targets those who enjoy the outdoors, bird watching, and upland game bird hunting, there is ample reason for ecologists, ornithologists, and grouse researchers to reference this book as well. The book contains general information of interest to a broad audience, but often moves beyond the introductory information to greater detail. Many details are supported by peer-reviewed literature. This book strikes a …

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The Role And Importance Of Cave Microclimate In The Sustainable Use And Management Of Show Caves, Chris R. De Freitas Dec 2010

The Role And Importance Of Cave Microclimate In The Sustainable Use And Management Of Show Caves, Chris R. De Freitas

KIP Articles

Cave microclimate is important in the study of cave flora and fauna, certain karst processes underground and hydrogeologic aspects of speleothems; thus an understanding of microclimat­ic processes is especially important in the management of show caves. Here, examples are drawn from researchon New Zea­land caves and examined in the context of sustainable cave use management practices. The work considers that the cave man­ager is concerned, firstly, withdefining the desired or optimal level or range of environmental conditions that should prevail and, secondly, withmaintaining them. To do this requires an appropriate and reliable monitoring system. It involves select­ing key indicators to …

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Synthesis And Characterization Of Nitrogen Substituted Zeolites, Fulya Dogan Dec 2010

Synthesis And Characterization Of Nitrogen Substituted Zeolites, Fulya Dogan

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

The interest in basic solid materials, particularly for basic zeolites has considerably increased in the last two decades because of their potential use in catalysis and separation. Basic zeolites have most often been obtained by ion-exchange or impregnation with alkali metal cations or grafting of organic bases onto zeolite pore walls. Such materials often suffer from instability and/or pore blockage, because none of these approaches places basic sites directly into the zeolite framework. Recently zeolitic materials have been made with some of the bridging oxygen atoms in Si-O-Si and/or Si-O-Al linkages replaced by NH groups, i.e. by substitution of framework …

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Nucleocytoplasmic Transport Of The Transcription Factor Stat6, Hui-Chen Chen Dec 2010

Nucleocytoplasmic Transport Of The Transcription Factor Stat6, Hui-Chen Chen

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Signal Transducer and Activator of Transcription 6 (STAT6) is a member of the STAT family of transcription factors that regulate cytokine signaling pathways. STATs are activated by tyrosine phosphorylation by receptor-associated Janus kinases (JAKs) and gain the ability to bind DNA. In this manner they transmit signals from the cell membrane to the nucleus to induce expression of genes involved in many biological functions. STAT6 needs to enter the nucleus for its function as a transcription factor. Therefore, regulation of STAT6 nuclear trafficking provides a mechanism to control specific gene expression. STAT6 is primarily activated by interleukin-4 (IL-4) and interleukin-13 …

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Targeting And Roles Of Complexins In Zebrafish Ribbon-Containing Neurons, George Zanazzi Dec 2010

Targeting And Roles Of Complexins In Zebrafish Ribbon-Containing Neurons, George Zanazzi

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

The primary receptor cells of the visual, auditory, vestibular and lateral line systems encode a broad range of sensory information by modulating the tonic release of the neurotransmitter glutamate in response to graded changes in membrane potential. The output synapses of these neurons are marked by structures called synaptic ribbons, which tether a pool of releasable synaptic vesicles at the active zone. Despite the importance of the ribbon in synaptic transmission, the molecular mechanisms that govern the assembly and function of the exocytotic machinery in these terminals are poorly understood. We have identified a subfamily of SNARE complex regulators, composed …

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Statistical Modeling For Multiplex Rnai Screen Data Analysis, Jianping Zhang Dec 2010

Statistical Modeling For Multiplex Rnai Screen Data Analysis, Jianping Zhang

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Multiplex RNAi screen is an emerging tool for functional genomics. Most analysis methods presently available for Multiplex RNAi screen are based on single hairpin data. These approaches have serious limitations. They do not account for the redundancies in genome-scale libraries. Thus it is difficult to detect genes with modest but consistent effect. In addition, contradictory conclusions might be reached based on enriched and depleted hairpins for the same gene. Therefore, we propose the RNAi Set Enrichment Analysis (RSEA) framework based on the gene set enrichment analysis framework that will take multiple hairpins into consideration in accessing the gene effect on …

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Life Cycle And Population Dynamics Of The Marine Ectoparasite Dichelesthium Oblongum (Copepoda: Dichelesthiidae) On Atlantic Sturgeon (Acipenser Oxyrinchus Oxyrinchus), Alicia Brown Dec 2010

Life Cycle And Population Dynamics Of The Marine Ectoparasite Dichelesthium Oblongum (Copepoda: Dichelesthiidae) On Atlantic Sturgeon (Acipenser Oxyrinchus Oxyrinchus), Alicia Brown

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Dichelesthium oblongum belongs to the family Dichelesthiidae, within the Suborder Siphonostomatoida, subclass Copepoda (Kabata 1979; Huys and Boxshall 1991). A description of the life cycle and the morphology of its developmental stages is described and compared with that of other organisms within this family and suborder. As expected within the Dichelesthiidae, Dichelesthium oblongum, life cycle appears to consist of nine stages, from nauplius 1 to adult. Sexes are easily distinguished from the 1st copepodid stage on the host through adulthood. General trends include the development of the lateral process on the endopod of the second leg on the male, the …

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Local Adaptation Along A Latitudinal Gradient In Pacific Versus Atlantic-Coast Fishes, Elizabeth Ellen Brown Dec 2010

Local Adaptation Along A Latitudinal Gradient In Pacific Versus Atlantic-Coast Fishes, Elizabeth Ellen Brown

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Understanding how species adapt to spatial climate gradients can provide clues to potential evolutionary responses to climate change. Species distributed across broad environmental gradients, such as those that occur along latitudes or altitudes, often exhibit adaptive genetic variation. However, little attention has been given to how the type of environmental gradient shapes adaptive responses. To provide insight into this, local adaptation is compared in related fish species across two very different environmental gradients: the Atlantic and Pacific coasts of North America. Local adaptation is first examined in the California grunion (Leuresthes tenuis) and then results are compared to previous work …

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Life Cycle And Population Dynamics Of The Marine Ectoparasite Dichelesthium Oblongum (Copepoda: Dichelesthiidae) On Atlantic Sturgeon (Acipenser Oxyrinchus Oxyrinchus), Alicia Brown Dec 2010

Life Cycle And Population Dynamics Of The Marine Ectoparasite Dichelesthium Oblongum (Copepoda: Dichelesthiidae) On Atlantic Sturgeon (Acipenser Oxyrinchus Oxyrinchus), Alicia Brown

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Dichelesthium oblongum belongs to the family Dichelesthiidae, within the Suborder Siphonostomatoida, subclass Copepoda (Kabata 1979; Huys and Boxshall 1991). A description of the life cycle and the morphology of its developmental stages is described and compared with that of other organisms within this family and suborder. As expected within the Dichelesthiidae, Dichelesthium oblongum, life cycle appears to consist of nine stages, from nauplius 1 to adult. Sexes are easily distinguished from the 1st copepodid stage on the host through adulthood. General trends include the development of the lateral process on the endopod of the second leg on the male, the …

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Novel Nonparametric Approaches To Stock Assessment And Regime Shift Prediction, Charles Thomas Perretti Dec 2010

Novel Nonparametric Approaches To Stock Assessment And Regime Shift Prediction, Charles Thomas Perretti

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Ecosystem dynamics are often complex, nonlinear, and characterized by criticalthresholds or regime changes. Despite these difficulties, resource managers mustaccurately forecast species abundance and anticipate impending regime shifts in order toimplement sustainable management plans. In the first part of this thesis I explicitly describe a nonparametric method formultivariate forecasting which I call the MS-Map and evaluate its performance relative toa suite of parametric models. I found that, in the presence of noise, it is often possible toobtain more accurate forecasts from the MS-Map than from the model that was used togenerate the data. The inclusion of additional species yielded a large …

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Investigation Of Factors Involved In The Interaction Between Quahog Parasite Unknown (Qpx) And Its Host, The Hard Clam Mercenaria Mercenaria, Mickael Perrigault Dec 2010

Investigation Of Factors Involved In The Interaction Between Quahog Parasite Unknown (Qpx) And Its Host, The Hard Clam Mercenaria Mercenaria, Mickael Perrigault

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

QPX (Quahog parasite unknown) is a protistan parasite affecting the hard clam Mercenaria mercenaria along the Northeastern coast of the United States. The geographic distribution and occurrence of disease epizootics suggests the involvement of environmental parameters and host genotype in disease development. Field investigations and laboratory transmission studies revealed some variations in the susceptibility of different hard clam stocks to QPX infection. Histological observations demonstrated that clams mount marked inflammatory responses against the infection that can sometimes lead to the healing of infected individuals. This study investigated host-pathogen interactions in QPX disease by studying individual components of the tripartite interaction: …

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Exploring Fertility Expectations, Miranda Annette Moore Dec 2010

Exploring Fertility Expectations, Miranda Annette Moore

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

The past few decades have seen an incredible increase in the use of panel data to answer micro level questions in a variety of settings. This new longitudinal data has allowed economists to empirically explore many theoretical economic models. One area that has not been as extensively explored is the economics of fertility expectations. This paper uses data from the National Longitudinal Survey of Youth 1979 (NLSY79) to explore the fertility expectations of a cohort of women who were 14 to 21 years old in 1979.We begin by investigating the impact of changes in the woman's socioeconomic status on the …

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Interferon-Gamma Fosters A Shift From Acute To Chronic Inflammation In Lyme Disease, Gregory John Sabino Dec 2010

Interferon-Gamma Fosters A Shift From Acute To Chronic Inflammation In Lyme Disease, Gregory John Sabino

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Borrelia burgdorferi is an extracellular bacterium that causes Lyme disease, an inflammatory, multi-systemic ailment. Interferon-γ (IFNγ) is present in lesions of human Lyme disease and positively correlates with severity of illness. Endothelial cells, which line the vasculature, mediate recruitment of immune cells to sites of infection and inflammation. To determine whether IFNγ contributes to development of Lyme disease through its actions on endothelium, cultured human umbilical vein endothelial cells (HUVEC) were exposed to B. burgdorferi, IFNγ, or the two stimuli together. Treatment of HUVEC with both stimuli enhanced the transendothelial migration of monocytes and diminished that of natural killer cells, …

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Phosphorus Export From A Restored Wetland Ecosystem In Response To Natural And Experimental Hydrologic Fluctuations, Marcelo Ardón, Shaena Montanari, Jennifer L. Morse, Martin W. Doyle, Emily S. Bernhardt Dec 2010

Phosphorus Export From A Restored Wetland Ecosystem In Response To Natural And Experimental Hydrologic Fluctuations, Marcelo Ardón, Shaena Montanari, Jennifer L. Morse, Martin W. Doyle, Emily S. Bernhardt

Environmental Science and Management Faculty Publications and Presentations

Wetland restoration is a commonly used approach to reduce nutrient loading to freshwater and coastal ecosystems, with many wetland restoration efforts occurring in former agricultural fields. Restored wetlands are expected to be effective at retaining or removing both nitrogen and phosphorus (P), yet restoring wetland hydrology to former agricultural fields can lead to the release of legacy fertilizer P. Here, we examined P cycling and export following rewetting of the Timberlake Restoration Project, a 440 ha restored riverine wetland complex in the coastal plain of North Carolina. We also compared P cycling within the restored wetland to two minimally disturbed …

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And When I Die And Other Prose, Ralph Brandon Buckner Iii Dec 2010

And When I Die And Other Prose, Ralph Brandon Buckner Iii

Masters Theses and Doctoral Dissertations

This thesis consists of the first chapter of my novel, two short stories, and two nonfiction essays. These pieces explore the tensions of family, love, and sexual orientation. The most prominent theme that connects each work is the main character’s search for control in his life. In the introduction to this thesis, I critically analyze three novels that focus on characters trying to regain stability in their lives after the death of someone close to them, and then I have discussed how these novels shaped my thesis in terms of theme, mood, and conflict.

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Proceedings Of 3rd Asian Preventive Cardiology And Cardiac Rehabilitation Conference Cum 8th Certificate Course In Cardiac Rehabilitation Dec 2010

Proceedings Of 3rd Asian Preventive Cardiology And Cardiac Rehabilitation Conference Cum 8th Certificate Course In Cardiac Rehabilitation

Journal of the Hong Kong College of Cardiology

No abstract provided.

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Two-Phase Partitioning System Using Elvax 40w Polymer For The Biodegradation Of Aqueous Phenols, Amit Suresh Ghode Dec 2010

Two-Phase Partitioning System Using Elvax 40w Polymer For The Biodegradation Of Aqueous Phenols, Amit Suresh Ghode

Masters Theses & Specialist Projects

A solid-liquid two phase partitioning system (TPPS) is a new technology platform for destroying toxic organic compounds. TPPS have traditionally been operated by using an immiscible organic phase which partitions organic compounds into the aqueous phase. TPPS using an immiscible organic phase suffers from several limitations such as the organic phase could be biodegradable and hence only certain compatible microbial strains could be used. This therefore, eliminates the desired use of mixed microbial populations for efficient degradation. A solid-liquid two phase partitioning system, in which solid polymeric beads replace liquid organic phase, appears to have benefits over the traditional liquid-liquid …

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A Half-Century Of Changes In China's Lakes: Global Warming Or Human Influence?, Ronghua Ma, Hongtao Duan, Chuanmin Hu, Xuezhi Feng, Ainong Li, Weimin Ju, Jiahu Jiang, Guishan Yang Dec 2010

A Half-Century Of Changes In China's Lakes: Global Warming Or Human Influence?, Ronghua Ma, Hongtao Duan, Chuanmin Hu, Xuezhi Feng, Ainong Li, Weimin Ju, Jiahu Jiang, Guishan Yang

Marine Science Faculty Publications

Lake size is sensitive to both climate change and human activities, and therefore serves as an excellent indicator to assess environmental changes. Using a large volume of various datasets, we provide a first complete picture of changes in China's lakes between 1960s–1980s and 2005–2006. Dramatic changes are found in both lake number and lake size; of these, 243 lakes vanished mainly in the northern provinces (and autonomous regions) and also in some southern provinces while 60 new lakes appeared mainly on the Tibetan Plateau and neighboring provinces. Limited evidence suggested that these geographically unbalanced changes might be associated primarily with …

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Front Matter, The Texas Ornithological Society Dec 2010

Front Matter, The Texas Ornithological Society

Bulletin of the Texas Ornithological Society

No abstract provided.

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2009 Winter Texas Gulf Coast Aerial Shorebird Survey, Brent Ortego, Marc Ealy Dec 2010

2009 Winter Texas Gulf Coast Aerial Shorebird Survey, Brent Ortego, Marc Ealy

Bulletin of the Texas Ornithological Society

As part of a cooperative effort of southeastern states, we conducted an aerial survey from 9–17 February 2009 to determine major concentration areas for wintering shorebirds along the Texas Gulf Coast. Shorebirds were surveyed from a Partenavia P-68 based out of Victoria with two observers viewing on either side of the airplane while flying at an altitude of 30 m (100 ft.) and flight speed of 185 km/h (100 knots). Shorebirds were placed into size categories when counted because of difficulty of identifying birds to species under the conditions of the survey but were tallied to species where possible. All …

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Observations Of Seaside Sparrow (Ammodramus Maritimus) On Texas Gulf Coast, Mark B. Bartosik Dec 2010

Observations Of Seaside Sparrow (Ammodramus Maritimus) On Texas Gulf Coast, Mark B. Bartosik

Bulletin of the Texas Ornithological Society

I summarize observations on postures and displays used by juvenile and adult Seaside Sparrows (Ammodramus maritimus). Some displays, like carrying material, were only known to be practiced by adults during territorial disputes. I collected photographic documentation showing juveniles carrying material (debris, stems and feathers) during aggressive encounters. I also collected data on juvenile Seaside Sparrows manipulating natural and artificial objects and agonistic encounters. I describe a behavior in which juveniles carry materials such as debris or feathers, one of which was 16 cm long. I describe food items consumed by Seaside Sparrows during late summer/fall. These included a large quantity …

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Capture Rates Of Shorebirds At Managed And Riverine Freshwater Wetlands Near The Central Texas Coast, Brent Ortego Dec 2010

Capture Rates Of Shorebirds At Managed And Riverine Freshwater Wetlands Near The Central Texas Coast, Brent Ortego

Bulletin of the Texas Ornithological Society

Shorebirds were mist-netted at 500-ha of moist soil units ( Site A) and at a 400- ha riverine overflow basin (Site B) near the central Texas Coast from 1996-2001. A total of 3,745 shorebirds of 24 species were captured at the Site A at a rate of 76 birds per trip. A total of 1,543 shorebirds from 18 species were captured at the Site B at a rate of 106 birds per trip. Least Sandpiper (Calidris minutilla), Semipalmated Sandpiper (Calidris pusilla), Western Sandpiper (Calidris mauri), Dunlin (Calidris alpina), and Stilt Sandpiper (Calidris himantopus) were the most abundant species banded at …

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Polygyny In The Golden-Cheeked Warbler, Rebecca G. Peak, Daniel J. Lusk, Jessica. D. Peppers Dec 2010

Polygyny In The Golden-Cheeked Warbler, Rebecca G. Peak, Daniel J. Lusk, Jessica. D. Peppers

Bulletin of the Texas Ornithological Society

Cases of polygyny have been documented in eight of 21 species of the genus Dendroica. We document a case of polygyny in another member of this genus, the Golden cheeked Warbler (Dendroica chrysoparia). The first female mated with a polygynous male made two nesting attempts before successfully fledging young, while the second female made three attempts. It is unclear whether the polygynous male was the mate of the second female during her first two nesting attempts. The second nesting attempt of the first female and the third nesting attempt of the second female were 400 m apart. No other territories …

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Hutton’S Vireo Establishment As A Breeding Species In The Texas Hill Country, Zac G. Loman, Jill T. Loman Dec 2010

Hutton’S Vireo Establishment As A Breeding Species In The Texas Hill Country, Zac G. Loman, Jill T. Loman

Bulletin of the Texas Ornithological Society

Once thought to be a sporadic visitor to the Texas Hill Country, increasing evidence suggests Hutton’s Vireo (Vireo huttoni) is in fact a breeding resident. We documented several breeding events.

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Abandonment Of A Unique Breeding Colony Of Great-Tailed Grackles In North-Central Texas, Ray C. Telfair Ii Dec 2010

Abandonment Of A Unique Breeding Colony Of Great-Tailed Grackles In North-Central Texas, Ray C. Telfair Ii

Bulletin of the Texas Ornithological Society

No abstract provided.

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