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Nebraska Bird Review (December 2013) 81(4), Whole Issue

Nebraska Bird Review

Fall Field Report, August–November 2013 … 134

First Documented Record of Hooded Oriole (Icterus cucullatus) in Nebraska … 161

Hayden, Tristram, and a Pigeon from “Nebraska” … 165

Bridgeport Fall Field Days, September 20–22, 2013 ... 169

Index to Volume 81 ... 175

Subscription and Organization Information ... 187

Dual Capture Of A Piñon Deer Mouse And A Silky Pocket Mouse Resulting In Consumption Of The Smaller Animal, Jon C. Pigage, Roger D. Peyton

The Prairie Naturalist

Intraspecific dual captures of rodents are uncommon, but not rare. There are several reports of brown rats (Rattus norvegicus), white-footed deer mice (Peromyscus leucopus), North American deer mice (P. maniculatus), western harvest mice (Reithrodontomys megalotis) and meadow voles (Microtus pennsylvanicus) caught simultaneously in the same trap (i.e. a door-closing live-trap; Davis 1955, Getz 1961, Blaustein and Rothstein 1978, Jenkins and Llewellyn 1981, Novak 1983). Some reports are incidental whereas others are interpreted as social associations or bonding between conspecifics. Interspecific dual captures are rarely reported in the literature. The earliest report of …

Whooping Cranes Consume Plains Leopard Frogs At Migratory Stopover Sites In Nebraska, Keith Geluso, Brad T. Krohn, Mary J. Harner, Michael J. Assenmacher

The Prairie Naturalist

Whooping cranes (Grus americana) currently consist of a single, wild population that migrates annually from breeding grounds at Wood Buffalo National Park, Canada, to wintering grounds on and around the Aransas National Wildlife Refuge along the Texas coast, USA (NRC 2005). This population reached a low of less than 20 individuals in 1941 (Allen 1952) but has rebounded to over 250 individuals (Chavez-Ramirez and Wehtje 2012, Gil-Weir et al. 2012). Whooping cranes migrate approximately 4,000 km each spring and autumn, traversing much of the North American Great Plains (Lewis 1995) and periodically landing along rivers, wetlands, and other …

Changes On Cran, Kurt Hornik, Achim Zeileis

The R Journal

New CRAN task views

New packages in CRAN task views

New contributed packages

Other changes

Hayden, Tristram, And A Pigeon From “Nebraska”, Rick Wright

Nebraska Bird Review

A passenger pigeon skin in the World Museum in Liverpool, England, was collected during an expedition to Nebraska and Dakota led by Gouverneur K. Warren between 1855 and 1857 and later cataloged by geologist and naturalist Ferdinand V. Hayden. For a time it was in the collection of Henry Baker Tristram, a famous naturalist and a founder of the British Ornithologists’ Union. Passenger pigeons were once “quite abundant” along the Missouri River.

Fall Field Report, August–November 2013, W. Ross Silcock

Nebraska Bird Review

In most ways, this was a routine fall season. Most interesting from an ongoing point of view were quite a large number of sightings of passerines at rather late dates, notably Empidonax flycatchers, wood warblers, native sparrows, tanagers, towhees, grosbeaks, and buntings. A similar phenomenon was noted among a few cold-sensitive non-passerines, such as Black and Common Terns.

One of the more significant ongoing trends is the proliferation of western and southern hummingbirds and the alteration of traditional migration and summer ranges; no fewer than 6 species were found. Calliope and Rufous Hummingbirds were seemingly more numerous in the east …

The Effects Of Isolation On Endemic Cozumel Island Rodents: A Test Of The Island Rule, Brittany Marie Nuttall

Theses and Dissertations

Island isolation can cause changes in body size, cranial characteristics, and genetic variation in mammals. We use geometric morphometrics to test skull and mandible shape and size change across three species of endemic Cozumel Island rodents in order to test the “island rule” of larger size in isolated rodents. We also sequenced the D-Loop and cytochrome b region of the mitochondrial genome and tested for differences in genetic variation between island and mainland groups, as well as population structure and gene flow in order to assess the effect of island isolation on these three rodents. We found that the three …

Application Of Next-Generation Transcriptomic Tools For Non-Model Organisms: Gene Discovery And Marker Developmentwithin Plecoptera (Insecta), Nicholas Gregory Davis

Theses and Dissertations

Phylogenetic research on non-model organisms has been hindered by limited marker availability. Next generation sequencing techniques are eliminating that barrier. Using Illumina sequencing technology, Trinity assembly software, custom Perl reciprocal BLAST scripts, and Primer3 primer prediction software, we produced and analyzed 7 Plecopteran transcriptomes, representing 7 of the 16 total families, in an attempt to identify and develop conserved orthologous genetic markers. The transcriptomes were used to reconstruct a gene content phylogeny using a simple distance matrix generated from reciprocal blastn data. By producing and filtering a reciprocal blast network we identified and aligned over 450 putative orthologs. Out of …

Population Genetic Structure Of Bromus Tectorum In The American Desert Southwest, Desiree Rochelle Eldon

Theses and Dissertations

Following its introduction to North America in the late nineteenth century, Bromus tectorum L., an inbreeding invasive winter annual grass, has become dominant on millions of hectares of sagebrush steppe habitat throughout Intermountain Western North America. It appears that within the last 30-40 years, B. tectorum has expanded its range southward into the Mojave Desert and also into more climatically extreme salt desert environments. Previous research using microsatellite markers and experimental studies has suggested that lineages found in desert habitats are genetically distinct from those found in the sagebrush-steppe habitat and possess suites of traits that pre-adapt them to these …

Habitat Selection By Two K-Selected Species: An Application To Bison And Sage Grouse, Joshua Taft Kaze

Theses and Dissertations

Population growth for species with long lifespans and low reproductive rates (i.e., K-selected species) is influenced primarily by both survival of adult females and survival of young. Because survival of adults and young is influenced by habitat quality and resource availability, it is important for managers to understand factors that influence habitat selection during the period of reproduction. My thesis contains two chapters addressing this issue for K-selected species in Utah. Chapter one evaluates habitat selection of greater sage-grouse (Centrocercusurophasianus) on Diamond Mountain during the critical nesting and brood-rearing period. Chapter two address selection of birth sites by bison (Bison …

Exploring Post-Fire Recovery Of Biocrusts And Desert Ecosystem Services, Jason R. Bahr

Theses and Dissertations

Biocrusts and the ecosystem services they provide are becoming more susceptible to fire as exotic annual grass invasions facilitate the spread of desert wildfires. Further, precipitation patterns across the western United States are predicted to change over the next century, and have the potential to dramatically influence fire regimes and the recovery of burned biocrusts. Despite these changes to desert fire and precipitation cycles, our understanding of post-fire biocrust recovery is limited, especially regarding the first two years after fire. To investigate biocrust recovery, we created burn manipulations (i.e., unburned and burned) and tracked crust form and function over two …

Importance Of Placement Depth In Evaluating Soil Nitrogen, Phosphorus, And Sulfur Using Ion Exchange Resin Capsules In Semi-Arid, Low Fertility Soils, Rachel Lynn Buck

Theses and Dissertations

Ion exchange resin capsules provide a possible alternative to conventional soil testing procedures. Previous studies with semi-arid, low fertility soils observed poor relationships with poorly mobile nutrients such as phosphorus (P). We propose that placement depth may improve those relationships. Our objective was to (1) determine if placement depth could improve resin capsule estimation of the bioavailability of nitrogen (N), P, and sulfur (S) and (2) to determine if resin capsules can effectively estimate S availability in semi-arid, low fertility soils. Field sites were established in Rush and Skull Valleys, Utah on loam and sandy loam soils, respectively. Fertilizer was …

Involvement Of Ampk And Ap-1 Biochemical Pathways In Il-6 Regulation Of Steroidogenic Enzymes In The Adrenal Cortex, Matharage Shenali De Silva

Theses and Dissertations

The adrenal cortex is a crucial endocrine gland in the mammalian stress response. In chronic inflammatory stress, cortisol is elevated whereas adrenal androgens are decreased. Furthermore, ACTH levels have poor correlation with the plasma cortisol in these conditions, thus suggesting that other factors are driving the stress response during chronic inflammatory stress. Interleukin-6 (IL-6), a cytokine which is released during chronic inflammatory stress, is assumed to be one such factor. Thus the biochemical pathways by which IL-6 increases cortisol release from the zona fasciculata (ZF), and decreases adrenal androgen release from the zona reticularis (ZR) were investigated. Since IL-6 activates …

Ferritin-Based Photo-Oxidation Of Biomass For Nanoparticle Synthesis, Bioremediation, And Hydrogen Evolution, Oscar Petrucci

Theses and Dissertations

The cell is the basic unit of all living organisms. It is an amazing machine capable of self-replicating, growing, and synthesizing and shuttling thousands of compounds. To perform all of these activities the cell needs energy. The original source of energy for all living beings is the Sun. The energy of the sun is collected by the autotrophs (mostly plants) through photosynthesis and stored in the chemical bonds of carbohydrates and lipids through carboxylic acid intermediates; animals use these compounds to obtain the energy for their cells. Most of the energy extracted by the cell comes from the citric acid …

Raman Spectroscopic Investigation Of Chondroitinase Abc Treatment After Spinal Cord Injury In An Organotypic Model, Shane Ruberto

Theses - ALL

This study investigated (1) the ability of an organotypic model of spinal cord injury (SCI) to recapitulate significant pathobiological events of in vivo SCI from a Raman spectroscopic perspective, and (2) the Raman spectroscopic effects of chondroitinase ABC (cABC) treatment on said model of SCI. Tissue from mouse spinal cords was excised, sectioned, and placed into culture, before being systematically injured to induce trauma. Cultures with and without cABC treatment were assessed using Raman spectroscopy at varying times post-injury. We demonstrate that Raman spectral phenomena characteristic of SCI can be observed using an organotypic model. By comparing these phenomena with …

Influence Of Hydrogel Substrate On Cell Growth And Virus Infection, Fan Yang

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

The interaction of cells with their extracellular matrix is of great importance when cells adapt to their environment. The purpose of this thesis is to design substrates with controllable properties and to study cellular interaction on these substrates. Firstly, enzymatically cross-linked gelatin hydrogels with different elastic modulus were prepared. Then, we studied the condition of cell growth and virus infection on these hydrogels as a followed-up. In the first part of the study, we made enzymatically cross-linked gelatin hydrogels with five different elastic modulus. As a parameter of stiffness, elastic modulus varies from 2.4 KPa to 7.5 KPa based on …

Computer Aided Design Of Planar Four-Bar Linkages On Ios Using A Novel Svd Algorithm, Xin Ge

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

Motion synthesis has been a practical topic existing for a long time. Various methods have been tried and put into practice. It is well done by the scientists and engineers to solve large equations of matrix. Although it can be done and get the good result, the efficiency is low and labor is very much consuming. Comparatively, our methods are much more easier and efficient, it is more suitable for the software to realize the calculation by itself. It is mature in PCs to have a motion synthesis software, but since the mobile system is going into everyday life and …

Lack Of Csk-Mediated Negative Regulation In A Unicellular Src Kinase, Kira Schultheiss

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

Tyrosine kinases play important roles in cellular communication in animals. c-Src is a nonreceptor tyrosine kinase that is involved in survival, angiogenesis, proliferation, and invasion pathways. There are 9 Src family kinases, and they have a conserved domain arrangement (SH3-SH2-kinase) that is necessary for regulation. The basal activity of c-Src is normally kept low due to phosphorylation by C-terminal Src kinase (Csk). This regulatory relationship has been conserved throughout the evolution of animals. Until recently, it was thought that complex signaling molecules, such as the tyrosine kinases, did not exist outside of multicellular animals. Newly discovered unicellular precursors to mammalian …

Reproduction, Sexual Swellings And Mating Behavior In Sanje Mangabeys (Cercocebus Sanjei), David Fernandez Sobrado

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

Inter-sexual conflict, or the opposing reproductive strategies of males and females, has become a primary structural factor in current models of social organization as it drives an evolutionary arms-race between the sexes. In many primates living in polygynandrous groups, the mating strategy of dominant males is to guard fertile females, while females develop sexual swellings that provide males with information regarding the approximate, but not exact, timing of ovulation. This allows females to mate promiscuously, confusing paternity, while concentrating paternity on males with the best competitive ability, i.e. | those that are able to mate guard during the peak swelling …

Regulatory Mechanism Of Hematopoietic Stem Cell Self-Renewal By Stem Cell Factor Sall4, Jing Yang

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

All types of blood cells in the human body are derived from Hematopoietic Stem Cells (HSCs).The self-renewal ability of HSCs ensure that blood cells replenish and sustain life. The regulatory mechanism of HSCs self-renewal, however, remains an unsolved problem. Recent studies found that the stem cell gene SALL4 has the ability to stimulate HSCs expansion and maintain their pluripotent tendencies. In this article we summarize the current research on SALL4 and its isoforms, and how they affect HSCs self-renewal capacity. To further understand the regulatory mechanism underlying this activity, researchers explored the connection between SALL4 and other regulatory molecules. They …

Molecular Movie Magic: Real-Time Picosecond To Microsecond Structural Dynamics Of Photoactive Flavoproteins, Richard James Brust

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

Femtosecond (fs) excitation of photoreceptors results in protein structural changes that occur on the microsecond to millisecond timescale or longer. It is thus of fundamental interest to understand how these fast timescale events dictate large scale protein dynamics that occur on much longer (106 orders of magnitude) timescales. AppA is a blue light using FAD (BLUF) protein which acts as a transcriptional antirepressor in Rhodobacter sphaeroides. The ultrafast photocycle and IR spectra are well characterized and involve a near instantaneous (<100 fs) response of the protein matrix that surrounds the chromophore. While there has been extensive study on the ultrafast time scales there has never been an observation of the kinetics of the light induced structural changes in the protein. Here we investigated the ultrafast (ps) to ms structural dynamics through transient IR. The data show that significant structural changes occur on the sub microsecond timescale following photoactivation. In addition our work has expanded to other BLUF proteins. BlsA is a BLUF protein found in the pathogenic bacterium Acinetobacter baumannii. Vibrational data together with homology modeling identify significant differences in β 5 strand caused by photoactivation, a region of BLUF photoreceptors proposed to be essential for signal modulation, that are unique for BlsA. In addition, the BLUF protein PixD, from Synechocystis, was characterized by transient IR, where photoexcitation results in radical pair formation, an event not observed in AppA. Transient IR also revealed that light state formation is complete within nanoseconds for PixD, suggesting a unique mechanism for single and multidomain BLUF systems. | 254 pages

Drug Discovery Through Combination Of Computational Screening And Design, Chemical Synthesis And Biological Evaluations, William Theodore Berger

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

A long-standing problem with the use of conventional cancer chemotherapy is the inherent lack of tumor specificity. Tumor-targeting drug-delivery systems (TTDS) have since been explored to overcome this deficiency. These drug conjugates can deliver potent cytotoxic drugs specifically to tumors and tumor cells with minimal systemic toxicity. Among various tumor-targeting molecules discussed, Designed Ankyrin Repeat Proteins (DARPins) represent a new approach to tumor targeting. In particular, DARPins targeting CD326 Epithelial Cell Adhesion Molecule (EpCAM) receptors provide an effective cancer target, as EpCAM is critical to the regulation of cellular matrix composition and overall cancer aggressiveness. Botulism is a human illness …

The Genetic Diversity Of Endangered Fishes In The Northwest Atlantic, Shannon Joy O'Leary

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

Genetic diversity is the fundamental building block of biodiversity, harboring the adaptive potential of populations. The magnitude of the two main factors eroding genetic diversity, inbreeding and genetic drift, increases as the effective population size (Ne) decreases. Ne describes the number of reproductively mature adults effectively contributing to the next generation. In populations with overlapping generations, the effective number of breeders (Nb). Loss of genetic diversity has long been a concern for terrestrial and freshwater organisms, but traditionally less so for fisheries management due to the paradigm that marine fish populations are large, panmictic and thus resistant to the erosion …

Blood Of The Earth: Natural Resources, Economic Visions, And Revolution In La Paz, Bolivia, 1927-1971, Kevin Young

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

Natural resource extraction and resource nationalism are central to understanding recent protests around the world. These mobilizations have important precedents in mid-twentieth-century Bolivia. The quest for national control over natural resources--particularly tin and oil--was the central factor uniting urban sectors in the years before and after the 1952 Bolivian Revolution, which brought to power the Movimiento Nacionalista Revolucionario (MNR) party. Focusing on La Paz, this dissertation examines the contours of popular economic thought and the conflicts among urban popular sectors, the MNR regime, and the United States to define economic policy. Natural resources were the key locus of contention in …

An Ex Vivo Femoral Artery Model To Demonstrate Inflammatory Response And Monocyte Response Following Increased Vascular Wall Shear Stress, Aparna Kadam Baldwin

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

Background Vascular remodeling reestablishes blood flow in the case of occlusions and can save tissue that would otherwise become hypoxic and necrotic. Vascular growth in an adult can occur in two ways: angiogenesis and/or arteriogenesis. While some pathways that govern the two are similar, the triggers have been found to be distinct. This study focuses on arteriogenesis- believed to be triggered by increases in wall shear stress (WSS) due to arterial occlusion. Hypothesis Inflammatory response will be initiated in an ex vivo femoral artery model in response to an increase in WSS. The inflammatory response will be detected by increases …

A Ranavirus-Related Mortality Event And The First Report Of Ranavirus In New Jersey, Kirsten Monsen-Collar, Lisa Hazard, Paola Dolcemascolo

Department of Biology Faculty Scholarship and Creative Works

No abstract provided.

Loss Of Vascular Endothelial Growth Factor A (Vegfa) Isoforms In The Testes Of Male Mice Causes Subfertility, Reduces Sperm Numbers, And Alters Expression Of Genes That Regulate Undifferentiated Spermatogonia, Ningxia Lu, Kevin M. De Avila, Debra T. Clopton, William E. Pohlmeier, Vanessa M. Brauer, Renee M. Mcfee, John S. Weber, Napoleone Ferrara, David W. Silversides, Andrea S. Cupp

Department of Animal Science: Faculty Publications

Vascular endothelial growth factor A (VEGFA) isoform treatment has been demonstrated to alter spermatogonial stem cell homeostasis. Therefore, we generated pDmrt1-Cre;Vegfa^−/− (knockout, KO) mice by crossing pDmrt1-Cre mice to floxed Vegfa mice to test whether loss of all VEGFA isoforms in Sertoli and germ cells would impair spermatogenesis. When first mated, KO males took 14 days longer to get control females pregnant (P < .02) and tended to take longer for all subsequent parturition intervals (9 days; P < .07). Heterozygous males sired fewer pups per litter (P < .03) and after the first litter took 10 days longer (P < .05) to impregnate females, suggesting a more progressive loss of fertility. Reproductive organs were collected from 6-month-old male mice. There were fewer sperm per tubule in the corpus epididymides (P < .001) and fewer ZBTB16-stained undifferentiated spermatogonia (P < .003) in the testes of KO males. Testicular mRNA abundance for Bcl2 (P < .02), Bcl2:Bax (P < .02), Neurog3 (P < .007), and Ret was greater (P = .0005), tended to be greater for Sin3a and tended to be reduced for total Foxo1 (P < .07) in KO males. Immunofluorescence for CD31 and VE-Cadherin showed no differences in testis vasculature; however, CD31-positive staining was evident in undifferentiated spermatogonia only in KO testes. Therefore, loss of VEGFA isoforms in Sertoli and germ cells alters genes necessary for long-term maintenance of undifferentiated spermatogonia, ultimately reducing sperm numbers and resulting in subfertility.

Tilting Toward Millennials: Updating Online Information Literacy Instruction For Post-Modern Learners, Rebecca Befus, Joshua Neds-Fox

LOEX Conference Proceedings 2011

This session will describe the challenge of reinventing a graphically outdated and content heavy online information literacy tutorial and tilting it toward a millennial audience. You will learn how we reinvented substantive content from an instructional design perspective and be provided general suggestions for creating quality content. In addition, you will learn specific design strategies, focusing on innovative web design trends, collaboration with public services librarians, and using cost-effective resources to create successful virtual learning environments. You will also view results from a study performed on the tutorial and learn how the results have influenced updates.

Using Mashups And Multimedia To Provide Online User Independence For All Learning Styles, Lori S. Mestre

LOEX Conference Proceedings 2011

In the globalized e-learning environment, students coming from different cultures have different characteristics and require different support designed for their approaches to study and learning styles. Learn effective strategies of how to revolutionize your web pages and online instructional efforts to create engaging online learning tools and mashups that appeal to diverse learning styles. Improve your ability to move from passive presentation methods to more effective online instruction that focuses on independent student active learning.

After a discussion of a usability study to assess learning style preferences as they pertain to library tutorials, the audience will help to redesign a …

Information Visualization And Keyword Searching, Matt Conner, Melissa Browne

LOEX Conference Proceedings 2011

The session will provide an overview of advances in visual literacy and their relevance to library instruction and focus on the sub-field of information visualization as an emerging area that synthesizes trends in computer science, education, and psychology. Information visualization will then be related to the search behaviors of users which appear to be deteriorating under the influence of the internet. Three graphical pedagogies (based on information visualization) for teaching the generation of keywords will be discussed. The session will end with an update on research underway to test the effectiveness of the three pedagogies.