Digital Commons Network^™

Deporting Grandma: Why Grandparent Deportation May Be The Next Big Immigration Crisis And How To Solve It, Marcia A. Yablon-Zug

Faculty Publications

This Article explores the issue of grandparent caregiver deportation. The phenomenon of grandparents raising grandchildren is not new, but the number of children being raised by grandparents is at an all-time high and growing. Numerous circumstances can lead to a grandparent's assumption of caregiving responsibilities, but in most cases, grandparents assume this role because there is no one else. For thousands of children, grandparents are the only family they have, and without them these children would be placed in foster care and subject to the serious problems that plague children in foster care. The importance of grandparent caregivers cannot be …

Sensitivity Of The Carbon Cycle In The Arctic To Climate Change, A. David Mcguire, Leif G. Anderson, Torben R. Christensen, Scott Dallimore, Laodong Guo, Daniel J. Hayes, Martin Heimann, Robie W. Macdonald, Nigel Roulet

Faculty Publications

The recent warming in the Arctic is affecting a broad spectrum of physical, ecological, and human/cultural systems that may be irreversible on century time scales and have the potential to cause rapid changes in the earth system. The response of the carbon cycle of the Arctic to changes in climate is a major issue of global concern, yet there has not been a comprehensive review of the status of the contemporary carbon cycle of the Arctic and its response to climate change. This review is designed to clarify key uncertainties and vulnerabilities in the response of the carbon cycle of …

Chemalign: Biologically Relevant Multiple Sequence Alignment Using Physicochemical Properties, Hyrum Carroll, Mark J. Clement, Quinn O. Snell, David Mcclellan

Faculty Publications

We present a new algorithm, ChemAlign, that uses physicochemical properties and secondary structure elements to create biologically relevant multiple sequence alignments (MSAs). Additionally, we introduce the Physicochemical Property Difference (PPD) score for the evaluation of MSAs. This score is the normalized difference of physicochemical property values between a calculated and a reference alignment. It takes a step beyond sequence similarity and measures characteristics of the amino acids to provide a more biologically relevant metric. ChemAlign is able to produce more biologically correct alignments and can help to identify potential drug docking sites.

Predicting Gull/Human Conflicts With Mathematical Models: A Tool For Management, James L. Hayward, Shandelle M. Henson, Richard D. Tkachuck, Cynthia M. Tkachuck, Brianna G. Payne, Cassaundra K. Boothby

Faculty Publications

Gulls are highly adaptable animals that thrive in proximity to humans. Although gulls enjoy legal protection in North America, England, and Europe, they often conflict with human interests by spreading disease, transporting contaminants, fouling public areas with droppings, and colliding with aircraft. Of particular concern are aggregates of " loafing" gulls that gather on parking lots, rooftops, and airport runways. Loafing in birds is a general state of immobility that involves behaviors such as sleeping, sitting, standing, resting, preening, and defecating. The ability to predict the incidence of aggregated loafing provides a first step toward the amelioration of bird/human conflicts. …

Comparative Transcriptional Profiling Established The Awn As The Major Photosynthetic Organ Of The Barley Spike While The Lemma And The Palea Primarily Protect The Seed, Tilahun Abebe, Roger P. Wise, Ronald W. Skadsen

Faculty Publications

The lemma, palea, and awn of a barley (Hordeum vulgare L.) spike are photosynthetic organs that supply the developing seed with carbohydrates. The lemma and palea also enclose the seed and protect it from pathogens and insects. Despite the important roles they play, little information exists on gene expression in these organs that identifies their function. In this study, we compared gene expression among the lemma, palea, awn, and developing seed of barley during grain filling using the Barley1 Genome Array to identify highly expressed genes involved in the primary function of these organs. Hierarchical clustering and mixed model analysis …

Openness, Dynamic Specialization, And The Disaggregated Future Of Higher Education, John L. Hilton Iii, David Wiley

Faculty Publications

Openness is a fundamental value underlying significant changes in society and is a prerequisite to changes institutions of higher education need to make in order to remain relevant to the society in which they exist. There are a number of ways institutions can be more open, including programs of open sharing of educational materials. Individual faculty can also choose to be more open without waiting for institutional programs. Increasing degrees of openness in society coupled with innovations in business strategy like dynamic specialization are enabling radical experiments in higher education and exerting increasing competitive pressure on conventional higher education institutions. …

Openness, Dynamic Specialization, And The Disaggregated Future Of Higher Education, John Hilton Iii, David Wiley

Faculty Publications

Openness is a fundamental value underlying significant changes in society and is a prerequisite to changes institutions of higher education need to make in order to remain relevant to the society in which they exist. There are a number of ways institutions can be more open, including programs of open sharing of educational materials. Individual faculty can also choose to be more open without waiting for institutional programs. Increasing degrees of openness in society coupled with innovations in business strategy like dynamic specialization are enabling radical experiments in higher education and exerting increasing competitive pressure on conventional higher education institutions. …

Synthetic Science: A Response To Rainbow, David S. Caudill

Faculty Publications

Rabinow’s description of the unique collaborative goal of synthetic biology at Berkeley, to foster a coproduction among multiple disciplines and perspectives from the outset (as opposed to downstream reflection upon ethical, legal, and social implications), is somewhat misleading. While that particular assemblage is represented as coproductive, the inevitability of science as a coproduction is eclipsed. That shortcoming may well be a strategic compromise to ensure effective collaboration, but it could backfire. Idealized images of science, which might be termed synthetic or artificial, have had adverse consequences in legal and administrative assessments of reliable science.

Magnetic And Nonmagnetic Nanoparticles From A Group Of Uniform Materials Based On Organic Salts, Aaron Tesfai, Bilal El-Zahab, Algernon T. Kelley, Min Li, Jayne C. Garno, Gary A. Baker, Isiah M. Warner

Faculty Publications

The size and uniformity of magnetic nanoparticles developed from a group of uniform materials based on organic salts (GUMBOS) were controlled using an in situ ion exchange, water-in-oil (w/o) microemulsion preparation. Most of these nanoGUMBOS are in fact ionic liquids (i.e., melting points less than 100 °C), while others have melting points above the conventional 100 °C demarcation. Simple variations in the reagent concentrations following a w/o approach allowed us to smoothly and predictably vary nanoparticle dimensions across a significant size regime with excellent uniformity. Average sizesofGUMBOS particles ranging from 14 to 198 nm were achieved by manipulation of the …

In-Plane All-Photonic Transduction With Differential Splitter Using Double-Step Rib Waveguide For Photonic Microcantilever Arrays, Ryan Anderson, Seunghyun Kim, Gregory P. Nordin, Jong Wook Noh, Weisheng Hu

Faculty Publications

We report a differential splitter consisting of an asymmetric double-step multimode rib waveguide and a Y-branch splitter for in-plane photonic transduction of photonic microcantilever deflection. Arrays of photonic microcantilevers are integrated with differential splitters and an optical waveguide network to demonstrate uniformity and sensitivity of transduction. Measurement results from multiple arrays indicate a sensitivity of 0.32 x 10-3 nm-1 and minimum detectable deflection of 141 pm for a 3.5 Hz measurement bandwidth.

Cyanochromes Are Blue/Green Light Photoreversible Photoreceptors Defined By A Stable Double Cysteine Linkage To A Phycoviolobilin-Type Chromophore, Andrew T. Ulijasz, Gabriel Cornilescu, David Von Stetten, Claudia Cornilescu, Francisco Velazquez Escobar, Junrui Zhang, Robert J. Stankey, Mario Rivera, Peter Hildebrandt, Richard D. Vierstra

Faculty Publications

Phytochromes are a collection of bilin-containing photoreceptors that regulate a diverse array of processes in microorganisms and plants through photoconversion between two stable states, a red light-absorbing Pr form, and a far red light-absorbing Pfr form. Recently, a novel set of phytochrome-like chromoproteins was discovered in cyanobacteria, designated here as cyanochromes, that instead photoconvert between stable blue and green light-absorbing forms Pb and Pg, respectively. Here, we show that the distinctive absorption properties of cyanochromes are facilitated through the binding of phycocyanobilin via two stable cysteine-based thioether linkages within the cGMP phosphodiesterase/ adenyl cyclase/FhlA domain. Absorption, resonance Raman and infrared …

The Pentameric Vertex Proteins Are Necessary For The Icosahedral Carboxysome Shell To Function As A Co2 Leakage Barrier, Fei Cai, Balaraj B. Menon, Gordon C. Cannon, Kenneth J. Curry, Jessup M. Shively, Sabine Heinhorst

Faculty Publications

Background

Carboxysomes are polyhedral protein microcompartments found in many autotrophic bacteria; they encapsulate the CO₂ fixing enzyme, ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) within a thin protein shell and provide an environment that enhances the catalytic capabilities of the enzyme. Two types of shell protein constituents are common to carboxysomes and related microcompartments of heterotrophic bacteria, and the genes for these proteins are found in a large variety of bacteria.

Methodology/Principal Findings

We have created a Halothiobacillus neapolitanus knockout mutant that does not produce the two paralogous CsoS4 proteins thought to occupy the vertices of the icosahedral carboxysomes and related microcompartments. Biochemical …

Why We Don't Understand The Rule Of Law, Noel B. Reynolds

Faculty Publications

This paper presents an assessment of current theories of law and their continuing failure to account in a convincing way for the rule of law as an ideal that guides and reassures modern democratic societies. It then explores the possibility that emerging understandings of human evolution and brain function may help us understand the process of convention making in a way that could reveal the underlying moral and epistemological context of law and allow us to identify a complete set of standards for the rule of law in human societies.

Knockdown Of The Drosophila Gtpase Nucleostemin 1 Impairs Large Ribosomal Subunit Biogenesis, Cell Growth, And Midgut Precursor Cell Maintenance, Raphyel Rosby, Cui Zhengfang, Emily Rogers, Megan A. Delivron, Victoria L. Robinson, Patrick J. Dimario

Faculty Publications

Mammalian nucleostemin (NS) is a nucleolar guanosine triphosphate-binding protein implicated in cell cycle progression, stem cell proliferation, and ribosome assembly. Drosophila melanogaster contains a four-member nucleostemin family (NS1-4). NS1 is the closest orthologue to human NS; it shares 33% identity and 67% similarity with human NS. We show that NS1 has intrinsic GTPase and ATPase activity and that it is present within nucleoli of most larval and adult cells. Endogenous NS1 and lightly expressed green fluorescent protein (GFP)-NS1 enrich within the nucleolar granular regions as expected, whereas overexpressed GFP-NS1 localized throughout the nucleolus and nucleoplasm, and to several transcriptionally active …

An Intertidal Sea Star Adjusts Thermal Inertia To Avoid Extreme Body Temperatures, Sylvain Pincebourde, Eric Sanford, Brian Helmuth

Faculty Publications

The body temperature of ectotherms is influenced by the interaction of abiotic conditions, morphology, and behavior. Although organisms living in different thermal habitats may exhibit morphological plasticity or move from unfavorable locations, there are few examples of animals adjusting their thermal properties in response to short-term changes in local conditions. Here, we show that the intertidal sea star Pisaster ochraceus modulates its thermal inertia in response to prior thermal exposure. After exposure to high body temperature at low tide, sea stars increase the amount of colder than-air fluid in their coelomic cavity when submerged during high tide, resulting in a …

St. John's Wort Inhibits Adipocyte Differentiation And Induces Insulin Resistance In Adipocytes, Zhaleh Amini, Bryant Boyd, Julie Doucet, David M. Ribnicky, Jacqueline M. Stephens

Faculty Publications

Adipocytes are insulin sensitive cells that play a major role in energy homeostasis. Obesity is the primary disease of fat cells and a major risk factor for the development of Type II diabetes, cardiovascular disease, and metabolic syndrome. Obesity and its related disorders result in dysregulation of the mechanisms that control adipocyte gene expression and function. To identify potential novel therapeutic modulators of adipocytes, we screened 425 botanical extracts for their ability to modulate adipogenesis and insulin sensitivity. We observed that less than 2% of the extracts had substantial effects on adipocyte differentiation of 3T3-L1 cells. Two of the botanical …

Sharing Landmark Information Using Mixture Of Gaussian Terrain Spatiograms, Damian M. Lyons

Faculty Publications

In this paper we evaluate the use of a novel spatial histogram called the terrain spatiogram as a common representation for exchanging landmark information between robots working as a team to map an area. Individual robots use range sensors to provide the spatial dimension of the spatiogram and video for the image dimension. We have previously shown that terrain spatiograms can be shared between robots in a heterogeneous team to recognize landmarks and to fuse observations from multiple sensors or multiple platforms. A terrain spatiogram using a mixture of Gaussians (MOG) model is introduced and a corresponding normalized spatiogram similarity …

It's Time To Check The Nets: Research And Conservation Of Rafinesque Big-Eared Bats In East Texas, Christopher E. Comer

Faculty Publications

No abstract provided.

Nil: The Value Of Patents In A Major Crisis Such As An Influenza Pandemic, Dennis D. Crouch

Faculty Publications

This essay focuses on the role of patents in relation to a potential global crisis such as an influenza pandemic or other public health crisis. I argue that patent rights will be largely ignored during an epidemic and that any post-crisis compensation would likely be low when compared to traditional patent rewards or settlements entered under threat of injunctive relief. In some situations, such as use of a patented invention by a state or local government, a patentee may have no recourse. Part III of the essay raises a separate issue that stems from the relatively long time frame for …

Integrating Elf4 Into The Circadian System Through Combined Structural And Functional Studies, Elsebeth Kolmos, Monika Nowak, Maria Werner, Katrin Fischer, Guenter Schwarz, Sarah Mathews, Heiko Schoof, Ferenc Nagy, Janusz M. Bujnicki, Seth J. Davis

Faculty Publications

The circadian clock is a timekeeping mechanism that enables anticipation of daily environmental changes. In the plant Arabidopsis thaliana, the circadian system is a multiloop series of interlocked transcription-translation feedbacks. Several genes have been arranged in these oscillation loops, but the position of the core-clock gene ELF4 in this network was previously undetermined. ELF4 lacks sequence similarity to known domains, and functional homologs have not yet been identified. Here we show that ELF4 is functionally conserved within a subclade of related sequences, and forms an alpha-helical homodimer with a likely electrostatic interface that could be structurally modeled. We support this …

The Impact Of Retrotransposons On Human Genome Evolution, Richard Cordaux, Mark A. Batzer

Faculty Publications

Their ability to move within genomes gives transposable elements an intrinsic propensity to affect genome evolution. Non-long terminal repeat (LTR) retrotransposons including LINE-1, Alu and SVA elements have proliferated over the past 80 million years of primate evolution and now account for approximately one-third of the human genome. In this Review, we focus on this major class of elements and discuss the many ways that they affect the human genome: from generating insertion mutations and genomic instability to altering gene expression and contributing to genetic innovation. Increasingly detailed analyses of human and other primate genomes are revealing the scale and …

Encoding Properties Of Auditory Neurons In The Brain Of A Soniferous Damselfish: Response To Simple Tones And Complex Conspecific Signals, Karen P. Maruska, Timothy C. Tricas

Faculty Publications

The fish auditory system encodes important acoustic stimuli used in social communication, but few studies have examined response properties of central auditory neurons to natural signals. We determined the features and responses of single hindbrain and midbrain auditory neurons to tone bursts and playbacks of conspecific sounds in the soniferous damselfish, Abudefduf abdominalis. Most auditory neurons were either silent or had slow irregular resting discharge rates ~130 Hz but ranged from 80 to 400 Hz with strong phase-locking. This low-frequency sensitivity matches the frequency band of natural sounds. Auditory neurons were also modulated by playbacks of conspecific sounds with thresholds …

Copper Oxide Nanoparticles Induce Oxidative Stress And Cytotoxicity In Airway Epithelial Cells, Baher Fahmy, Stephania A. Cormier

Faculty Publications

Metal oxide nanoparticles are often used as industrial catalysts and elevated levels of these particles have been clearly demonstrated at sites surrounding factories. To date, limited toxicity data on metal oxide nanoparticles are available. To understand the impact of these airborne pollutants on the respiratory system, airway epithelial (HEp-2) cells were exposed to increasing doses of silicon oxide (SiO2), ferric oxide (Fe2O3) and copper oxide (CuO) nanoparticles, the leading metal oxides found in ambient air surrounding factories. CuO induced the greatest amount of cytotoxicity in a dose-dependent manner; while even high doses (400 μg/cm2) of SiO2 and Fe2O3 were non-toxic …

Tarnished Plant Bug (Hemiptera: Miridae) Thresholds And Sampling Comparisons For Flowering Cotton In The Midsouthern United States, Fred R. Musser, Angus L. Catchot, Scott D. Stewart, Ralph D. Bagwell, Gus M. Lorenz, Kelly V. Tindall, Glenn E. Studebaker, B. Rogers Leonard, D. Scott Akin, Donald R. Cook, Chris A. Daves

Faculty Publications

The tarnished plant bug, Lygus lineolaris (Palisot de Beauvois) (Hemiptera: Miridae), has become the primary target of foliar insecticides in cotton, Gossypium hirsutum L., throughout the Midsouth over the past several years. This prompted a reevaluation of existing action thresholds for flowering cotton under current production practices and economics. A trial was conducted at 19 locations throughout the Midsouth during 2006 and 2007. Threshold treatments ranged from a weekly automatic insecticide application to a very high threshold of 10 tarnished plant bugs per 1.5 row-m on a black drop cloth. Individually, all locations reached the lowest threshold, and eight locations …

On Neolepisorus Emeiensis And N. Dengii (Polypodiaceae) From China, Xiao Si Guo, Bin Li

Faculty Publications

Neolepisorus dengii, N. dengii f. hastatus and N. emeiensis f. dissectus should be considered synonyms of N. emeiensis. This treatment is justified on the basis of complete intergradation of the frond forms that supposedly separate these taxa. The intergradation can be found on the same individual. © 2009, Americian Fern Society.

Extreme Weathering/Erosion During The Miocene Climatic Optimum: Evidence From Sediment Record In The South China Sea, Shiming Wan, Wolfram M. Kürschner, Peter D. Clift, Anchun Li, Tiegang Li

Faculty Publications

Investigating the interplay between continental weathering and erosion, climate, and atmospheric CO2 concentrations is significant in understanding the mechanisms that force the Cenozoic global cooling and predicting the future climatic and environmental response to increasing temperature and CO2 levels. The Miocene represents an ideal test case as it encompasses two distinct extreme climate periods, the Miocene Climatic Optimum (MCO) with the warmest time since 35 Ma in Earth's history and the transition to the Late Cenozoic icehouse mode with the establishment of the east Antarctic ice sheet. However the precise role of continental weathering during this period of major climate …

Revolutionary Decision, Meredith Jones-Gray

Faculty Publications

No abstract provided.

A Framework For Detecting Glaucomatous Progression In The Optic Nerve Head Of An Eye Using Proper Orthogonal Decomposition, Madhusudhanan Balasubramanian, Stanislav Žabić, Christopher Bowd, Hilary W. Thompson, Peter Wolenski, S. Sitharama Iyengar, Bijaya B. Karki, Linda M. Zangwill

Faculty Publications

Glaucoma is the second leading cause of blindness worldwide. Often, the optic nerve head (ONH) glaucomatous damage and ONH changes occur prior to visual field loss and are observable in vivo. Thus, digital image analysis is a promising choice for detecting the onset and/or progression of glaucoma. In this paper, we present a new framework for detecting glaucomatous changes in the ONH of an eye using the method of proper orthogonal decomposition (POD). A baseline topograph subspace was constructed for each eye to describe the structure of the ONH of the eye at a reference/baseline condition using POD. Any glaucomatous …

Ojs At Byu, C. Jeffrey Belliston

Faculty Publications

A number of years ago, the library began hosting the digitized back files of several campus-based journal publications in CONTENTdm. A little over two years ago, Mark Belk, the editor of the Western North American Naturalist whose backfile we were hosting, approached Randy Olsen, our University Librarian with a problem. Mark explained that in his role as editor he was drowning in e-mails and things were falling through the cracks. Randy tasked me to investigate options. This investigation was made considerably easier by work done by Mark Czyzk from Johns Hopkins. The investigation led to the selection of OJS as …

A Method Of Successive Corrections Of The Control Subspace In The Reduced-Order Variational Data Assimilation, Max Yaremchuk, Dmitri A. Nechaev, Gleb Panteleev

Faculty Publications

A version of the reduced control space four-dimensional variational method (R4DVAR) of data assimilation into numerical models is proposed. In contrast to the conventional 4DVAR schemes, the method does not require development of the tangent linear and adjoint codes for implementation. The proposed R4DVAR technique is based on minimization of the cost function in a sequence of low-dimensional subspaces of the control space. Performance of the method is demonstrated in a series of twin-data assimilation experiments into a nonlinear quasigeostrophic model utilized as a strong constraint. When the adjoint code is stable, R4DVAR's convergence rate is comparable to that of …