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Riverside, CA, United States

The University of California, Riverside , is a public research university and one of the 10 general campuses of the University of California system. The main campus sits on 1,900 acres in a suburban district of Riverside, California, United States, with a branch campus of 20 acres in Palm Desert. Founded in 1907 as the UC Citrus Experiment Station, Riverside pioneered research in biological pest control and the use of growth regulators responsible for extending the citrus growing season in California from four to nine months. Some of the world's most important research collections on citrus diversity and entomology, as well as science fiction and photography, are located at Riverside.UCR's undergraduate College of Letters and Science opened in 1954. The Regents of the University of California declared UCR a general campus of the system in 1959, and graduate students were admitted in 1961. To accommodate an enrollment of 21,000 students by 2015, more than $730 million has been invested in new construction projects since 1999. Preliminary accreditation of the UCR School of Medicine was granted in October 2012 and the first class of 50 students was enrolled in August 2013. It is the first new research-based public medical school in 40 years.UCR is consistently ranked as one of the most ethnically and economically diverse universities in the United States. The 2014 U.S. News & World Report Best Colleges rankings places UCR 55th among top public universities, 112th nationwide and ranks 16+ graduate school programs including the Graduate School of Education and the Bourns College of Engineering based on peer assessment, student selectivity, financial resources, and other factors. Washington Monthly ranked UCR 5th in the United States in terms of social mobility, research and community service, while U.S. News ranks UCR as the fifth most ethnically diverse and, by the number of undergraduates receiving Pell Grants , the 15th most economically diverse student body in the nation. Nearly two-thirds of all UCR students graduate within six years without regard to economic disparity. UCR's extensive outreach and retention programs have contributed to its reputation as a "campus of choice" for minority students, including LGBT students. In 2005, UCR became the first public university campus in the nation to offer a gender-neutral housing option.UCR's sports teams are known as the Highlanders and play in the Big West Conference of the National Collegiate Athletic Association Division I. Their nickname was inspired by the high altitude of the campus, which lies on the foothills of Box Springs Mountain. The UCR women's basketball team won back to back Big West championships in 2006 and 2007. In 2007, the men's baseball team won its first conference championship and advanced to the regionals for the second time since the university moved to Division I in 2001. Wikipedia.


Henderson D.,Brigham Young University | Wu J.,University of California at Riverside
Journal of Physical Chemistry B | Year: 2012

Most theoretical studies of the properties of an electrolyte, including an ionic liquid, treat the electrolyte as a mixture of charged hard spheres in a solvent modeled as a dielectric continuum. However, ionic liquids generally consist of nonspherical ions that are not dissolved in a solvent. A simple extension of the primitivel model of electrolytes is to represent an ionic liquid as a mixture of charged hard spheres (negative monovalent ions in our case) and nonspherical ions consisting of a dimer of two touching hard spheres, one of which is charged (monovalent and positive in our case) and the other is neutral. This simple model has been used previously by Federov et al. and by ourselves. Here, we use the classical density functional theory to study the interfacial properties of the model ionic liquid over a range of electrode charges and two electrolyte concentrations. For simplicity, all of the spheres have the same diameter. In contrast to the simulations of Federov and Kornyshev, we find that a plot of the differential capacitance of the dimer electrolyte versus the surface potential typically exhibits only a single hump. Also, differing from the studies of Lamperski et al. for a spherical electrolyte, which showed a decline of the maximal differential capacitance as the ionic concentration decreases, the maximum of the differential capacitance of the dimer electrolyte increases slightly with decreasing ionic concentration. Our theoretical results show other unexpected effects of the geometry of ionic species on the electrochemical properties of the electric double layer of an ionic liquid. © 2012 American Chemical Society.


Zaera F.,University of California at Riverside
Chemical Society Reviews | Year: 2014

Infrared absorption spectroscopy has proven to be one of the most powerful spectroscopic techniques available for the characterization of catalytic systems. Although the history of IR absorption spectroscopy in catalysis is long, the technique continues to provide key fundamental information about a variety of catalysts and catalytic reactions, and to also offer novel options for the acquisition of new information on both reaction mechanisms and the nature of the solids used as catalysts. In this review, an overview is provided of the main contributions that have been derived from IR absorption spectroscopy studies of catalytic systems, and a discussion is included on new trends and new potential directions of research involving IR in catalysis. We start by briefly describing the power of Fourier-transform IR (FTIR) instruments and the main experimental IR setups available, namely, transmission (TIR), diffuse reflectance (DRIFTS), attenuated total reflection (ATR-IR), and reflection-absorption (RAIRS), for advancing research in catalysis. We then discuss the different environments under which IR characterization of catalysts is carried out, including in situ and operando studies of typical catalytic processes in gas-phase, research with model catalysts in ultrahigh vacuum (UHV) and so-called high-pressure cell instruments, and work involving liquid/solid interfaces. A presentation of the type of information extracted from IR data follows in terms of the identification of adsorbed intermediates, the characterization of the surfaces of the catalysts themselves, the quantitation of IR intensities to extract surface coverages, and the use of probe molecules to identify and titrate specific catalytic sites. Finally, the different options for carrying out kinetic studies with temporal resolution such as rapid-scan FTIR, step-scan FTIR, and the use of tunable lasers or synchrotron sources, and to obtain spatially resolved spectra, by sample rastering or by 2D imaging, are introduced. © the Partner Organisations 2014.


Amini-Bavil-Olyaee S.,University of Southern California | Choi Y.J.,University of Southern California | Lee J.H.,University of Southern California | Shi M.,University of Southern California | And 3 more authors.
Cell Host and Microbe | Year: 2013

Vesicle-membrane-protein-associated protein A (VAPA) and oxysterol-binding protein (OSBP) regulate intracellular cholesterol homeostasis, which is required for many virus infections. During entry, viruses or virus-containing vesicles can fuse with endosomal membranes to mediate the cytosolic release of virions, and alterations in endosomal cholesterol can inhibit this invasion step. We show that the antiviral effector protein interferon-inducible transmembrane protein 3 (IFITM3) interacts with VAPA and prevents its association with OSBP, thereby disrupting intracellular cholesterol homeostasis and inhibiting viral entry. By altering VAPA-OSBP function, IFITM3 induces a marked accumulation of cholesterol in multivesicular bodies and late endosomes, which inhibits the fusion of intraluminal virion-containing vesicles with endosomal membranes and thereby blocks virus release into the cytosol. Consequently, ectopic expression or depletion of the VAPA gene profoundly affects IFITM3-mediated inhibition of viral entry. Thus, IFITM3 disrupts intracellular cholesterol homeostasis to block viral entry, further underscoring the importance of cholesterol in virus infection. © 2013 Elsevier Inc.


Debus R.J.,University of California at Riverside
Biochimica et Biophysica Acta - Bioenergetics | Year: 2015

The photosynthetic conversion of water to molecular oxygen is catalyzed by the Mn4CaO5 cluster in Photosystem II and provides nearly our entire supply of atmospheric oxygen. The Mn4CaO5 cluster accumulates oxidizing equivalents in response to light-driven photochemical events within Photosystem II and then oxidizes two molecules of water to oxygen. The Mn4CaO5 cluster converts water to oxygen much more efficiently than any synthetic catalyst because its protein environment carefully controls the cluster's reactivity at each step in its catalytic cycle. This control is achieved by precise choreography of the proton and electron transfer reactions associated with water oxidation and by careful management of substrate (water) access and proton egress. This review describes the FTIR studies undertaken over the past two decades to identify the amino acid residues that are responsible for this control and to determine the role of each. In particular, this review describes the FTIR studies undertaken to characterize the influence of the cluster's metal ligands on its activity, to delineate the proton egress pathways that link the Mn4CaO5 cluster with the thylakoid lumen, and to characterize the influence of specific residues on the water molecules that serve as substrate or as participants in the networks of hydrogen bonds that make up the water access and proton egress pathways. This information will improve our understanding of water oxidation by the Mn4CaO5 catalyst in Photosystem II and will provide insight into the design of new generations of synthetic catalysts that convert sunlight into useful forms of storable energy. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems. © 2014 Elsevier B.V. All rights reserved.


Eastmond D.A.,University of California at Riverside
Mutation Research - Reviews in Mutation Research | Year: 2012

The determination of whether a chemical induces cancer through a mutagenic or genotoxic mechanism frequently plays an important role in evaluating the risks associated with low dose exposure. Although various approaches are employed for making mode of action decisions, a systematic investigation to identify the major factors that influence these determinations has not been performed. To accomplish this, over 40 chemical risk assessments conducted by U.S. or international regulatory agencies and organizations were reviewed to identify components that had played a significant role, either directly or indirectly, in the decision-making process. The major factors identified included the chemical properties of the agent, its metabolites and degradation products; its metabolism and toxicokinetics; genotoxic effects seen . in vivo, particularly in the target organ; structural or metabolic similarities to known mutagenic or nonmutagenic chemicals; characteristics of the tumors induced in the animal bioassays; and the origin of the observed effects. The quality of the data, the specific genotoxic endpoint and its sensitivity to assay conditions and toxicity were also important considerations. In all cases, the authoritative groups used a weight-of-evidence approach and, in most cases where evaluations were conducted by more than one authoritative body, similar conclusions were reached. In summary, a critical evaluation of the data as well as expert judgment is necessary in reaching mechanism of action conclusions. These determinations should be made within the broader context of evaluating the chemical's overall toxicity and carcinogenicity. © 2012 Elsevier B.V.


Harvey T.S.,University of California at Riverside
Medical Anthropology Quarterly | Year: 2011

Maya mobile medical providers in highland Guatemala and the goods and services that they offer from "soapboxes" on street corners, local markets, and on buses exemplify an important yet underinvestigated domain of localized health care, one that I refer to as the "other" public health. This medical and linguistic examination of traveling medical salespeople calls for a reconsideration (on a global scale) of what has come to be understood as "public health," arguing that "othered," local forms of public health that are often overlooked by anthropologists as "nontraditional" and delegitimized by bio-medicine as nonscientific merit serious consideration and investigation. This ethnography of marginalized forms of public health offers global insights into emerging heterodoxical forms of public health care that contest bio-medical authority and challenge our preexisting definitions of what counts as "access," wellness seeking, and even health care itself. © 2011 by the American Anthropological Association.


Medina M.,University of California at Merced | Sachs J.L.,University of California at Riverside
Genomics | Year: 2010

Microbial symbionts inhabit the soma and surfaces of most multicellular species and instigate both beneficial and harmful infections. Despite their ubiquity, we are only beginning to resolve major patterns of symbiont ecology and evolution. Here, we summarize the history, current progress, and projected future of the study of microbial symbiont evolution throughout the tree of life. We focus on the recent surge of data that whole-genome sequencing has introduced into the field, in particular the links that are now being made between symbiotic lifestyle and molecular evolution. Post-genomic and systems biology approaches are also emerging as powerful techniques to investigate host-microbe interactions, both at the molecular level of the species interface and at the global scale. In parallel, next-generation sequencing technologies are allowing new questions to be addressed by providing access to population genomic data, as well as the much larger genomes of microbial eukaryotic symbionts and hosts. Throughout we describe the questions that these techniques are tackling and we conclude by listing a series of unanswered questions in microbial symbiosis that can potentially be addressed with the new technologies. © 2010 Elsevier Inc. All rights reserved.


Miyawaki K.N.,Shanghai Center for Plant Stress Biology | Yang Z.,University of California at Riverside
Frontiers in Plant Science | Year: 2014

Rho-like GTPase from plants (ROPs) function as signaling switches that control a wide variety of cellular functions and behaviors including cell morphogenesis, cell division and cell differentiation. The Arabidopsis thaliana genome encodes 11 ROPs that form a distinct single subfamily contrarily to animal or fungal counterparts where multiple subfamilies of Rho GTPases exist. Since Rho proteins bind to their downstream effector proteins only in their GTP-bound “active” state, the activation of ROPs by upstream factor(s) is a critical step in the regulation of ROP signaling. Therefore, it is critical to examine the input signals that lead to the activation of ROPs. Recent findings showed that the plant hormone auxin is an important signal for the activation of ROPs during pavement cell morphogenesis as well as for other developmental processes. In contrast to auxin, another plant hormone, abscisic acid, negatively regulates ROP signaling. Calcium is another emerging signal in the regulation of ROP signaling. Several lines of evidence indicate that plasma membrane localized-receptor like kinases play a critical role in the transmission of the extracellular signals to intracellular ROP signaling pathways. This review focuses on how these signals impinge upon various direct regulators of ROPs to modulate various plant processes. © 2014 Miyawaki and Yang.


Maduro M.F.,University of California at Riverside
Developmental Dynamics | Year: 2010

Cell specification requires that particular subsets of cells adopt unique expression patterns that ultimately define the fates of their descendants. In C. elegans, cell fate specification involves the combinatorial action of multiple signals that produce activation of a small number of "blastomere specification" factors. These initiate expression of gene regulatory networks that drive development forward, leading to activation of "tissue specification" factors. In this review, the C. elegans embryo is considered as a model system for studies of cell specification. The techniques used to study cell fate in this species, and the themes that have emerged, are described. © 2010 Wiley-Liss, Inc.


Spindler S.R.,University of California at Riverside
Ageing Research Reviews | Year: 2010

Caloric restriction (CR), reduced protein, methionine, or tryptophan diets; and reduced insulin and/or IGFI intracellular signaling can extend mean and/or maximum lifespan and delay deleterious age-related physiological changes in animals. Mice and flies can shift readily between the control and CR physiological states, even at older ages. Many health benefits are induced by even brief periods of CR in flies, rodents, monkeys, and humans. In humans and nonhuman primates, CR produces most of the physiologic, hematologic, hormonal, and biochemical changes it produces in other animals. In primates, CR provides protection from type 2 diabetes, cardiovascular and cerebral vascular diseases, immunological decline, malignancy, hepatotoxicity, liver fibrosis and failure, sarcopenia, inflammation, and DNA damage. It also enhances muscle mitochondrial biogenesis, affords neuroprotection; and extends mean and maximum lifespan. CR rapidly induces antineoplastic effects in mice. Most claims of lifespan extension in rodents by drugs or nutrients are confounded by CR effects. Transcription factors and co-activators involved in the regulation of mitochondrial biogenesis and energy metabolism, including SirT1, PGC-1α, AMPK and TOR may be involved in the lifespan effects of CR. Paradoxically, low body weight in middle aged and elderly humans is associated with increased mortality. Thus, enhancement of human longevity may require pharmaceutical interventions. © 2009 Elsevier Ireland Ltd. All rights reserved.


Allen R.J.,University of California at Riverside
Journal of Geophysical Research: Atmospheres | Year: 2015

The tropical rain belt is a narrow band of clouds near the equator, where the most intense rainfall on the planet occurs. On seasonal timescales, the rain moves across the equator following the Sun, resulting in wet and dry seasons in the tropics. The position of the tropical rain belt also varies on longer timescales. Through the latter half of the twentieth century, for example, shifts in tropical rainfall have been associated with severe droughts, including the African Sahel and Amazon droughts. Here I show that climate models project a northward migration of the tropical rain belt through the 21st century, with future anthropogenic aerosol reductions driving the bulk of the shift. Models that include both aerosol indirect effects yield significantly larger northward shifts than models that lack aerosol indirect effects. Moreover, the rate of the shift corresponds to the rate of the decrease of anthropogenic aerosol emissions across different time periods and future emission scenarios. This response is consistent with relative warming of the Northern Hemisphere, a decrease in northward cross-equatorial moist static energy transport, and a northward shift of the Hadley circulation, including the tropical rain belt. The shift is relatively weak in the Atlantic sector, consistent with both a smaller decrease in aerosol emissions and a larger reduction in northward cross-equatorial ocean heat flux. Although aerosol effects remain uncertain, I conclude that future reductions in anthropogenic aerosol emissions may be the dominant driver of a 21st century northward shift of the tropical rain belt. Key Points Climate models project a northward shift of the tropical rain belt Future anthropogenic aerosol reductions drive the bulk of the shift The shift is largest in models that include both aerosol indirect effects. © 2015. American Geophysical Union. All Rights Reserved.


Diaz-Cruz J.L.,Autonomous University of Puebla | Ma E.,University of California at Riverside
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2011

If the standard model of particle interactions is extended to include a neutral SU(2)N gauge factor, with SU(3)C×SU(2)L×U(1)Y×SU(2)N embedded in E6 or [SU(3)]3, a conserved generalized R parity may appear. As a result, apart from the recent postulate of a separate non-Abelian gauge factor in the hidden sector, we have the first example of a possible dark-matter candidate X1 which is a non-Abelian vector boson coming from a known unified model. Using current data, its mass is predicted to be less than about 1 TeV. The associated Z' of this model, as well as some signatures of the Higgs sector, should then be observable at the LHC (Large Hadron Collider). © 2010 Elsevier B.V.


Choi M.K.,University of California at Riverside
Journal of Health Economics | Year: 2011

The new comprehensive health reform, beginning in 2014, will require Medicaid to expand all elements of coverage to individuals with incomes up to 133 percent of the federal poverty line. With millions more individuals gaining eligibility for adult Medicaid dental benefits, generating an unbiased estimate of the elasticity of demand for dental services is critical.The causal relationship between access to adult Medicaid dental benefits and usage of dental services for low-income adults is estimated, using difference-in-differences estimation procedures to exploit the state-level variation in adult Medicaid dental benefits.Results suggest that adult Medicaid dental benefits increase the probability of a dental visit within 12 months by 16.4-22 percent. A variety of robustness checks are invoked to confirm the finding. © 2011 Elsevier B.V.


Carter W.P.L.,University of California at Riverside
Atmospheric Environment | Year: 2010

An updated version of the SAPRC-99 gas-phase atmospheric chemical mechanism, designated SAPRC-07, is described. The rate constants and reactions have been updated based on current data and evaluations, the aromatics mechanisms have been reformulated and are less parameterized, chlorine chemistry has been added, the method used to represent peroxy reactions has been reformulated to be more appropriate for modeling gas-phase secondary organic aerosol precursors, and representations for many types of VOCs have been added or improved. This mechanism was evaluated against the result of ∼2400 environmental chamber experiments carried out in 11 different environmental chambers, including experiments to test mechanisms for over 110 types of VOCs. The performance in simulating the chamber data was generally satisfactory for most types of VOCs but some biases were seen in simulations of some types of experiments. The mechanism was used to derive updated MIR and other ozone reactivity scales for almost 1100 types of VOCs, though in most cases the changes in MIR values relative to SAPRC-99 were not large. This mechanism update results in somewhat lower predictions of ozone in one-day ambient model scenarios under low VOC/NO. x conditions. The files needed to implement the mechanism and additional documentation is available at the SAPRC mechanism web site at http://www.cert.ucr.edu/∼carter/SAPRC. © 2010 Elsevier Ltd.


Chen F.,Xiamen University | Cao Y.,Air Force Research Lab | Ren W.,University of California at Riverside
IEEE Transactions on Automatic Control | Year: 2012

We present a distributed discontinuous control algorithm for a team of agents to track the average of multiple time-varying reference signals with bounded derivatives. We use tools from nonsmooth analysis to analyze the stability of the system. For time-invariant undirected connected network topologies, we prove that the states of all agents will converge to the average of the time-varying reference signals with bounded derivatives in finite time provided that the control gain is properly chosen. The validity of this result is also established for scenarios with switching undirected connected network topologies. For time-invariant directed network topologies with a directed spanning tree, we show that all agents will still reach a consensus in finite time, but the convergent value is generally not the average of the time-varying reference signals with bounded derivatives. Simulation examples are presented to show the validity of the above results. © 1963-2012 IEEE.


Meng Z.,Shanghai JiaoTong University | Lin Z.,University of Virginia | Ren W.,University of California at Riverside
Systems and Control Letters | Year: 2012

In this paper, swarm tracking problems with group dispersion and cohesion behaviors are discussed for a group of Lagrange systems. The agent group is separated into two subgroups. One is called the leader group, whose members are encapsulated with the desired generalized coordinates and generalized coordinate derivatives. The other one, referred to as the follower group, is guided by the leader group. The objective is to guarantee distributed tracking of generalized coordinate derivatives for the followers and to drive the generalized coordinates of the followers close to the convex hull formed by those of the leaders. Both the case of constant leaders' generalized coordinate derivatives and the case of time-varying leaders' generalized coordinate derivatives are considered. The proposed control algorithms are shown to achieve velocity matching, connectivity maintenance and collision avoidance. In addition, the sum of the steady-state distances between the followers and the convex hull formed by the leaders is shown to be bounded and the bound is explicitly given. Simulation results are presented to validate the effectiveness of theoretical conclusions. © 2011 Elsevier B.V. All rights reserved.


Li J.,Nanjing University of Science and Technology | Li J.,Utah State University | Ren W.,University of California at Riverside | Xu S.,Nanjing University of Science and Technology
IEEE Transactions on Automatic Control | Year: 2012

This note studies the distributed containment control problem for a group of autonomous vehicles modeled by double-integrator dynamics with multiple dynamic leaders. The objective is to drive the followers into the convex hull spanned by the dynamic leaders under the constraints that the velocities and the accelerations of both the leaders and the followers are not available, the leaders are neighbors of only a subset of the followers, and the followers have only local interaction. Two containment control algorithms via only position measurements of the agents are proposed. Theoretical analysis shows that the followers will move into the convex hull spanned by the dynamic leaders if the network topology among the followers is undirected, for each follower there exists at least one leader that has a directed path to the follower, and the parameters in the algorithm are properly chosen. Numerical results are provided to illustrate the theoretical results. © 2011 IEEE.


Hirtmas D.R.,University of Kansas | Graham R.C.,University of California at Riverside
Soil Science Society of America Journal | Year: 2011

Mountains are impressive features of many desert landscapes because of their elevation, complex topography, and sheer extent. Soil genesis and landscape processes were studied in the southern Fry Mountains, Mojave Desert, California. Our aim was to better understand the processes responsible for the distribution of soil properties in this landscape. Measured properties in 65 soil pits across the study site show that dust, soluble salt, NO3--N, and carbonate distributions are correlated with the prevailing wind direction. This finding suggests that the mountain range effectively traps eolian sediment. Soils manding these mountains have accumulated, on average, 41 kg m -2 silicate dust, 172 g m-2 soluble salts, 3.3 g m -2 NO3--N, and 79 kg m-2 carbonate and reached maximum concentrations of 156 kg m-2,1800 g m -2,43 g m-2, and 398 kg m-2, respectively, on windward sides of the range. The basin floor encompassing Soggy Lake, an upwind playa, is the probable primary source of these materials. Soil morphology and land surface characteristics from four major mountain landforms were used to interpret the pedogenic and soil-geomorphic processes that have led to the distribution patterns of these accumulations. Our study demonstrates that arid mountains accumulate and store appreciable quantities of dust, soluble salts, NO3-, and carbonate and are therefore important to the overall geomorphic evolution and biogeochemical cycling of the region. The previously unaccounted storage of pedogenic carbonate in similar mountain ranges could increase the global soil inorganic C pool estimate by as much as 15 to 174 Pg C. © Soil Science Society of America, 5585 Guilford Rd., Madison WI 53711 USA All rights reserved.


Carter W.P.L.,University of California at Riverside
Atmospheric Environment | Year: 2010

The development of a condensed version of the SAPRC-07 mechanism, designated CS07A, is described. It is comparable in size to CB05 and was derived directly from detailed SAPRC-07, which serves as the basis for its predictive capability and evaluation against chamber data. It incorporates the more condensed and approximate peroxy radical lumped operator method employed in SAPRC-99, and condensations involving removing or lumping less reactive compounds, lumping some product species in isoprene or aromatic mechanisms with other species with similar mechanisms using reactivity weighting, removing some compounds and reactions that are rapidly reversed, and using fewer model species to represent emitted alkanes and similar species. It gives predictions of O3, total PANs and OH radicals that are very close to the standard SAPRC-07 mechanism for airshed models used as the starting point, but predicts about 15% more H2O2. Use of CS07A is suitable for models where the priority is O3 formation, while the less condensed version should be used if more accurate hydroperoxide predictions are a priority. © 2010 Elsevier Ltd.


Gaines R.R.,Pomona College | Droser M.L.,University of California at Riverside
Palaeogeography, Palaeoclimatology, Palaeoecology | Year: 2010

Burgess Shale-type (BST) biotas occur globally in Lower and Middle Cambrian shales, and were preserved under specific and exceptional circumstances. Among the circumstances surrounding fossilization, benthic redox conditions have been the subject of particular disagreement. While most authors have assumed that the sites of preservation were anoxic and therefore inhospitable to metazoans, several have recently argued that BST assemblages were preserved in situ under habitable benthic conditions. Here, we use field and laboratory intensive, fine-scale methods to investigate the paleoredox settings of fossil assemblages in two Burgess Shale-type deposits, the Wheeler and Marjum Formations of western Utah (Cambrian Series 3), and review recently published data for other principal Burgess Shale-type deposits. In the Wheeler and Marjum Formations, fossil assemblages and ichnofabrics were evaluated at the millimeter scale. An ichnological model was then applied to reconstruct relative paleo-oxygen content of bottom waters at a bed-to-bed scale through multiple intervals sampled continuously. This approach permits fine-scale evaluation of the relationships of discrete fossil assemblages to paleoredox conditions. Over 7800 individual beds were logged in this study. These data demonstrate that the Wheeler and Marjum Formations were deposited under dynamic benthic redox conditions. In both deposits, beds representing deposition under dysoxic conditions may be interbedded at the millimeter-centimeter scale with those representing deposition under anoxic conditions. Although the beds deposited under both types of redox conditions may be richly fossiliferous, the distribution of fossil assemblages within the Wheeler and Marjum Formations was regulated by dissolved oxygen content of bottom waters as a first-order control. BST preservation occurs within a microfacies inferred to represent deposition under anoxic conditions, and contains transported fossils along a recognizable proximal-distal gradient. Under dysoxic benthic conditions, assemblages of skeletonized body fossils dominated by trilobites occur in both formations. In the Wheeler Formation, the junction of these two benthic redox environments is characterized by dense monospecific associations of the opportunistic trilobite Elrathia kingii, but a comparable exaerobic taxon does not appear to be present in the Marjum Formation. These results demonstrate the control of near-bottom anoxia over preservation of BST assemblages in both formations and are consistent with the findings from the Burgess Shale and the Chengjiang. © 2010 Elsevier B.V.


Cooper R.A.,Institute of Geological & Nuclear Sciences | Sadler P.M.,University of California at Riverside
Paleobiology | Year: 2010

The most abundant and diverse graptolite assemblages are found in offshore, deep-water black shalesthe classical "graptolite facies" (deep-water or isograptid biofacies). The mean duration of Ordovician graptolite species confined to the deep-water facies (here referred to as "group 1" species) is 2.19 Myr, significantly shorter than the mean duration of species in the deep-water facies that are also known in sediments of the shallow-water shelf or platform ("group 2" species) -4.42 Myr, indicating a significantly higher extinction probability (p <0.001). These figures are based on the precise age ranges of species derived from the time-calibrated composite sequence of 1446 Ordovician to early Devonian graptolites, built by the constrained optimization procedure (CONOP) from 256 measured sections worldwide, and exclude the effects of the Hirnantian mass extinction. The difference between groups cuts across families, morphological types, and pandemic/endemic distributions. An environmental influence is strongly suggested, and although both groups were planktonic, they were unlikely to have shared the same habitat in the water column. The new duration measurements therefore are interpreted as favoring a depth-stratification of graptolite habitats in the water column. © 2010 The Paleontological Society. All rights reserved.


Quinton P.M.,University of California at San Diego | Quinton P.M.,University of California at Riverside
American Journal of Physiology - Cell Physiology | Year: 2010

The invitation to present the 2010 Hans Ussing lecture for the Epithelial Transport Group of the American Physiological Society offered me a unique, special, and very surprising opportunity to join in saluting a man whom I met only once, but whose work was the basis, not only for my career, but also for finding the molecular defect in the inherited disease cystic fibrosis (CF). In this context, I will venture to make the tribute with a new explanation of why a mutation in a single gene that codes for an anion channel can cause devastation of multiple epithelial systems with pathogenic mucus. In so doing, I hope to raise awareness of a new role for that peculiar anion around which so much physiology revolves, HCO3 -. I begin by introducing CF pathology as I question the name of the disease as well as the prevalent view of the basis of its pathology by considering: 1) mucus, 2) salt, and 3) HCO 3 -. I then present recent data showing that HCO 3 - is required for normal mucus discharge, and I will close with conjecture as to how HCO3 - may support mucus discharge and why the failure to transport this electrolyte is pathogenic in CF. Copyright © 2010 the American Physiological Society.


Weitz M.,TU Munich | Kim J.,California Institute of Technology | Kapsner K.,TU Munich | Winfree E.,California Institute of Technology | And 2 more authors.
Nature Chemistry | Year: 2014

In vitro compartmentalization of biochemical reaction networks is a crucial step towards engineering artificial cell-scale devices and systems. At this scale the dynamics of molecular systems becomes stochastic, which introduces several engineering challenges and opportunities. Here we study a programmable transcriptional oscillator system that is compartmentalized into microemulsion droplets with volumes between 33 fl and 16 pl. Simultaneous measurement of large populations of droplets reveals major variations in the amplitude, frequency and damping of the oscillations. Variability increases for smaller droplets and depends on the operating point of the oscillator. Rather than reflecting the stochastic kinetics of the chemical reaction network itself, the variability can be attributed to the statistical variation of reactant concentrations created during their partitioning into droplets. We anticipate that robustness to partitioning variability will be a critical challenge for engineering cell-scale systems, and that highly parallel time-series acquisition from microemulsion droplets will become a key tool for characterization of stochastic circuit function. © 2014 Macmillan Publishers Limited.


Nespolo R.F.,Austral University of Chile | Roff D.A.,University of California at Riverside
American Naturalist | Year: 2014

The evolution of endothermy is one of the most puzzling events in vertebrate evolution, for which several hypotheses have been proposed. The most accepted model is the aerobic model, which assumes the existence of a genetic correlation between resting metabolic rate (RMR) and maximum aerobic capacity (whose standard measure is maximum metabolic rate, MMR). This model posits that directional selection acted on maximum aerobic capacity and resting metabolic rate increased as a correlated response, in turn increasing body temperature. To test this hypothesis we implemented a simple two-trait quantitative genetic model in which RMR and MMR are initially independent of each other and subject to stabilizing selection to two separate optima. We show mutations that arise that affect both traits can lead to the evolution of a genetic correlation between the traits without any significant shifting of the two trait means. Thus, the presence of a genetic correlation between RMR and MMR in living animals provides no support in and of itself for the past elevation of metabolic rate via selection on aerobic capacity. This result calls into question the testability of the hypothesis that RMR increased as a correlated response to directional selection on MMR, in turn increasing body temperature, using quantitative genetics. Given the difficulty in studying ancient physiological processes, we suggest that approaches such as this model are a valuable alternative for analyzing possible mechanisms of endothermy evolution. © 2013 by The University of Chicago.


Vullev V.I.,University of California at Riverside
Journal of Physical Chemistry Letters | Year: 2011

Ever-growing global energy consumption, along with climate threats involving anthropogenic activities, places a premium on sustainable and environmentally safe energy sources. Solar radiation reaching the Earth?s surface delivers energy at a rate that considerably surpasses the current and projected rates of global energy consumption. Through the millennia of evolution, photosynthesis evolved to harvest solar energy and utilize it for the anabolism of caloric substances that are stored and used as biological fuels. Therefore, the photosynthetic systems are excellent paradigms for solar energy science and engineering. Mimicking photosynthesis provides a means not only to further the solar energy conversion science but also to test and elucidate key aspects of the biological light harvesting. Concurrently, inspiration from the biological and biomimetic advances is a key driving force in the development of solar energy conversion applications. This Perspective presents a view of the role of biomimesis and bioinspiration in meeting the demands for energy and sustainability. © 2011 American Chemical Society.


Ren W.,University of California at Riverside | Liu X.,Beijing Institute of Technology | Fu M.,Beijing Institute of Technology
IEEE Transactions on Automatic Control | Year: 2013

This technical brief considers the distributed consensus problems for multi-agent systems with general linear and Lipschitz nonlinear dynamics. Distributed relative-state consensus protocols with an adaptive law for adjusting the coupling weights between neighboring agents are designed for both the linear and nonlinear cases, under which consensus is reached for all undirected connected communication graphs. Extensions to the case with a leader-follower communication graph are further studied. In contrast to the existing results in the literature, the adaptive consensus protocols here can be implemented by each agent in a fully distributed fashion without using any global information. © 1963-2012 IEEE.


Lumba S.,University of Toronto | Cutler S.,University of California at Riverside | McCourt P.,University of Toronto
Annual Review of Cell and Developmental Biology | Year: 2010

Plant hormones are a group of chemically diverse small molecules that direct processes ranging from growth and development to biotic and abiotic stress responses. Surprisingly, genome analyses suggest that classic animal nuclear hormone receptor homologs do not exist in plants. It now appears that plants have co-opted several protein families to perceive hormones within the nucleus. In one solution to the problem, the hormones auxin and jasmonate ( JA) act as "molecular glue" that promotes protein-protein interactions between receptor F-boxes and downstream corepressor targets. In another solution, gibberellins (GAs) bind and elicit a conformational change in a novel soluble receptor family related to hormone-sensitive lipases. Abscisic acid (ABA), like GA, also acts through an allosteric mechanism involving a START-domain protein. The molecular identification of plant nuclear hormone receptors will allow comparisons with animal nuclear receptors and testing of fundamental questions about hormone function in plant development and evolution. Copyright © 2010 by Annual Reviews. All rights reserved.


Madani K.,University of Central Florida | Dinar A.,University of California at Riverside
Ecological Economics | Year: 2012

As demands for limited natural resources increase, developing management institutions that ensure the sustainability of such resources is essential. Many natural resources are Common Pool Resources (CPRs), managed under different non-cooperative, cooperative, and externally imposed management frameworks. While early studies of non-cooperative CPR management suggest inevitable "tragedy of the commons," here we discuss how users can avoid tragic outcomes by changing their decision making rationales and exploitation strategies even in a non-cooperative environment. This paper introduces and compares various types of non-cooperative institutions that are available to manage CPRs. These management institutions are then applied, using a numerical groundwater exploitation example, to determine how different planning variables are affected by the choice of management institution. Results indicate that CPR users can improve their gains by considering the externalities and developing long-term exploitation plans, as opposed to short-term plans with no consideration of externalities that result in rapid exhaustion of the resource and lead to the so-called "tragedy of the commons.". © 2011 Elsevier B.V.


Grafton-Cardwell E.E.,University of California at Riverside | Stelinski L.L.,University of Florida | Stansly P.A.,University of Florida
Annual Review of Entomology | Year: 2013

The Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Psyllidae), is the most important pest of citrus worldwide because it serves as a vector of Candidatus Liberibacter species (Alphaproteobacteria) that cause huanglongbing (citrus greening disease). All commercially cultivated citrus is susceptible and varieties tolerant to disease expression are not yet available. Onset of disease occurs following a long latent period after inoculation, and thus the pathogen can spread widely prior to detection. Detection of the pathogen in Brazil in 2004 and Florida in 2005 catalyzed a significant increase in research on D. citri biology. Chemical control is the primary management strategy currently employed, but recently documented decreases in susceptibility of D. citri to several insecticides illustrate the need for more sustainable tools. Herein, we discuss recent advances in the understanding of D. citri biology and behavior, pathogen transmission biology, biological control, and chemical control with respect to Candidatus Liberibacter asiaticus. Our goal is to point toward integrated and biologically relevant management of this pathosystem. © 2013 by Annual Reviews. All rights reserved.


Paine T.D.,University of California at Riverside | Steinbauer M.J.,La Trobe University | Lawson S.A.,Horticulture and Forestry Science
Annual Review of Entomology | Year: 2011

Eucalyptus species, native to Australia, Indonesia, the Philippines, and New Guinea, are the most widely planted hardwood timber species in the world. The trees, moved around the globe as seeds, escaped the diverse community of herbivores found in their native range. However, a number of herbivore species from the native range of eucalypts have invaded many Eucalyptus-growing regions in North America, Europe, Africa, Asia, and South America in the last 30 years. In addition, there have been shifts of native species, particularly in Africa, Asia, and South America, onto Eucalyptus. There are risks that these species as well as generalist herbivores from other parts of the world will invade Australia and threaten the trees in their native range. The risk to Eucalyptus plantations in Australia is further compounded by planting commercially important species outside their endemic range and shifting of local herbivore populations onto new host trees. Understanding the mechanisms underlying host specificity of Australian insects can provide insight into patterns of host range expansion of both native and exotic insects. © 2011 by Annual Reviews. All rights reserved.


Guan Y.,CAS Institute of Plant Physiology and Ecology | Guo J.,CAS Institute of Plant Physiology and Ecology | Li H.,CAS Institute of Plant Physiology and Ecology | Yang Z.,University of California at Riverside
Molecular Plant | Year: 2013

Pollen tubes elongate rapidly at their tips through highly polarized cell growth known as tip growth. Tip growth requires intensive exocytosis at the tip, which is supported by a dynamic cytoskeleton and vesicle trafficking. Several signaling pathways have been demonstrated to coordinate pollen tube growth by regulating cellular activities such as actin dynamics, exocytosis, and endocytosis. These signaling pathways crosstalk to form a signaling network that coordinates the cellular processes required for tip growth. The homeostasis of key signaling molecules is critical for the proper elongation of the pollen tube tip, and is commonly fine-tuned by positive and negative regulations. In addition to the major signaling pathways, emerging evidence implies the roles of other signals in the regulation of pollen tube growth. Here we review and discuss how these signaling networks modulate the rapid growth of pollen tubes. © 2013 The Author.


Carde R.T.,University of California at Riverside
Current Biology | Year: 2015

Summary To reproduce, the female yellow fever mosquito has to find a human host. There are many potential cues available to guide such navigation: exhaled carbon dioxide, a plethora of skin odors, the host's visual and heat signatures and, close by, moisture. Recent work is shedding now light on how these are integrated by the mosquito in targeting a human host. © 2015 Elsevier Ltd.


Joneson S.,University of Idaho | Stajich J.E.,University of California at Riverside | Shiu S.-H.,Michigan State University | Rosenblum E.B.,University of Idaho
PLoS Pathogens | Year: 2011

Understanding the molecular mechanisms of pathogen emergence is central to mitigating the impacts of novel infectious disease agents. The chytrid fungus Batrachochytrium dendrobatidis (Bd) is an emerging pathogen of amphibians that has been implicated in amphibian declines worldwide. Bd is the only member of its clade known to attack vertebrates. However, little is known about the molecular determinants of - or evolutionary transition to - pathogenicity in Bd. Here we sequence the genome of Bd's closest known relative - a non-pathogenic chytrid Homolaphlyctis polyrhiza (Hp). We first describe the genome of Hp, which is comparable to other chytrid genomes in size and number of predicted proteins. We then compare the genomes of Hp, Bd, and 19 additional fungal genomes to identify unique or recent evolutionary elements in the Bd genome. We identified 1,974 Bd-specific genes, a gene set that is enriched for protease, lipase, and microbial effector Gene Ontology terms. We describe significant lineage-specific expansions in three Bd protease families (metallo-, serine-type, and aspartyl proteases). We show that these protease gene family expansions occurred after the divergence of Bd and Hp from their common ancestor and thus are localized to the Bd branch. Finally, we demonstrate that the timing of the protease gene family expansions predates the emergence of Bd as a globally important amphibian pathogen. © 2011 Joneson et al.


Ellstrand N.C.,University of California at Riverside
American Journal of Botany | Year: 2014

Although theory has demonstrated rather low levels of gene flow are sufficient to counteract opposing mutation, drift, and selection, widespread recognition of the evolutionary importance of gene flow has come slowly. The perceived role of gene flow as an evolutionary force has vacillated over the last century. In the last few decades, new methods and analyses have demonstrated that plant gene flow rates vary tremendously-from nil to very high-depending on the species and specific populations involved, and sometimes over time for individual populations. In many cases, the measured gene flow rates are evolutionarily significant at distances of hundreds and sometimes thousands of meters, occurring at levels sufficient to counteract drift, spread advantageous alleles, or thwart moderate levels of opposing local selection. Gene flow in plants is likely to often act as a cohesive force, uniting individual plant species into real evolutionary units. Also, gene flow can evolve under natural selection, decreasing or increasing. The fact of frequent, but variable, plant gene flow has important consequences for applied issues in which the presence or absence of gene flow might influence the outcome of a policy, regulatory, or management decision. Examples include the unintended spread of engineered genes, the evolution of invasiveness, and conservation. New data-rich genomic techniques allow closer scrutiny of the role of gene flow in plant evolution. Most plant evolutionists now recognize the importance of gene flow, and it is receiving increased recognition from other areas of plant biology as well. © 2014 Botanical Society of America.


Fay D.A.,University of California at Riverside
Human Ecology | Year: 2012

In the early 1980s residents of Hobeni, in South Africa's Eastern Cape, were subjected to forced resettlement, under "betterment" policy ostensibly aimed at soil conservation. They were moved into a spatially contiguous but socially differentiated village. South Africa's political transition ended this policy, and in the early 1990s, some people, mainly from part of the resettlement area (Kunene) characterized by dense kinship networks who had faced pressure to leave, and began to return voluntarily to their former sites, opting to live in dispersed, flexible settlements. Few people resettled in Mhlanganisweni, a part of the village more diverse in its social composition, returned to their former sites. This research highlights the ways exclusion within "socially-embedded" land tenure systems, together with the layout of resettlement areas and other forms of social and economic differentiation, caused patterns of resettlement to diverge from planners' intentions. © 2012 Springer Science+Business Media, LLC.


Hille R.,University of California at Riverside
Dalton Transactions | Year: 2013

A perspective is provided of recent advances in our understanding of molybdenum-containing enzymes other than nitrogenase, a large and diverse group of enzymes that usually (but not always) catalyze oxygen atom transfer to or from a substrate, utilizing a MoO group as donor or acceptor. An emphasis is placed on the diversity of protein structure and reaction catalyzed by each of the three major families of these enzymes. © 2013 The Royal Society of Chemistry.


Triapitsyn S.V.,University of California at Riverside
Zootaxa | Year: 2013

The Palaearctic species of the common and speciose fairyfly genus Gonatocerus Nees ab Esenbeck (Hymenoptera: Mymaridae) are reviewed. Illustrated identification keys are provided to separate the three subgenera of Gonatocerus that occur in the region and to females of the species in each subgenus. Distribution ranges, including new records of extralimital specimens examined, and known host associations of the species are given. Forty-two valid taxa are recognized including 19 newly described ones: two in G. (Gonatocerus)-G. bukashka sp. n. (Denmark, Russia) and G. koz iavka sp. n. (Kyrgyzstan), 15 in G. (Lymaenon Wa l k e r) - G. berezovskiyi sp. n. (Turkmenistan), G. beshbarmak sp. n. (Kyrgyzstan), G. k a - lika sp. n. (Denmark), G. karakum sp. n. (Italy, Turkmenistan), G. karlik sp. n. (China, Republic of Korea, Russia), G. katraps sp. n. (Republic of Korea, Russia), G. kazak sp. n. (Russia, Spain), G. k omarik sp. n. (France), G. krasavchik sp. n. (Russia), G. kulik sp. n. (Russia), G. k um sp. n. (Russia), G. kusaka sp. n. (Russia), G. saulfrommeri sp. n. (Russia), G. svat sp. n. (China), G. ucri sp. n. (Russia), and two in G. (Cosmocomoidea Howard)-G. kikimora sp. n. (Russia) and G. woohoo sp. n. (Russia). New synonymies are proposed for the following names: G. (Gonatocerus) fuscicornis (Walker) [= G. sulphuripes (Foerster) syn. n., G. pictosimilis Soyka syn. n., Lymaenon synaptus Debauche syn. n., L. alecto Debauche syn. n., and L. crassipes D eba u che syn. n.]; G. (Gonatocerus) aegyptiacus Soyka [= G. saipanens is (Doutt) syn. n., G. a l a m i Shamim and Shafee syn. n., G. tarae Narayanan and Subba Rao syn. n., G. miurai Sahad syn. n., and G. minor Matthews syn. n.]; G. (Gonatocerus) pictus (Haliday) [= G. orthopenitus Guo, Lin and Hu syn. n.]; G. (Lymaenon) aureus Girault [= G. tenuipennis Girault syn. n., G. chrysis (Debauche) syn. n., G. vopros nom. n. pro G. flavus Soyka, 1950 (nec G. flavus Foerster, 1841) syn. n., G. pahlgamensis (Narayanan) syn. n., G. kanheriensis Mani and Saraswat syn. n., G. gracilentus Hellén syn. n., G. aligarhensis Shamim and Shafee syn. n., and G. fukuokensis Sahad syn. n.]; G. (Lymaenon) litoralis (Haliday) [= Alaptus fuscus Förster syn. n., G. exiguus Förster syn. n., G. americanus Brues syn. n., G. anthonomi Girault syn. n., G. brunneus Girault syn. n., G. illinoiensis Girault syn. n., G. maevius Girault syn. n., G. texanus Girault syn. n., and G. priesneri Soyka syn. n.]; G. (Lymaenon) longior Soyka [= G. conicus (Mathot) syn. n.]; G. (Cosmocomoidea) oxypygus Foerster [= G. ovicenatus Leonard and Crosby syn. n. and G. megalura (Mathot) syn. n.]. Lymaenon cunctator Mathot is reinstated as a valid species, G. (Lymaenon) cunctator (Mathot) stat. rev., based on study of its holotype. Lectotypes are designated for Alaptus fuscus, Gonatocerus anthonomi, G. ater Foerster, G. brunneus, G. exiguus, G. texanus, Lymaenon fuscicornis Walker, L. tremulae Bakkendorf, and Rachistus sulphuripes Foerster. Neotypes are designated for G. aureus and G. oxypygus. Copyright © 2013 Magnolia Press.


Bardeen C.J.,University of California at Riverside
Annual Review of Physical Chemistry | Year: 2014

The photophysical behavior of organic semiconductors is governed by their excitonic states. In this review, I classify the three different exciton types (Frenkel singlet, Frenkel triplet, and charge transfer) typically encountered in organic semiconductors. Experimental challenges that arise in the study of solid-state organic systems are discussed. The steady-state spectroscopy of intermolecular delocalized Frenkel excitons is described, using crystalline tetracene as an example. I consider the problem of a localized exciton diffusing in a disordered matrix in detail, and experimental results on conjugated polymers and model systems suggest that energetic disorder leads to subdiffusive motion. Multiexciton processes such as singlet fission and triplet fusion are described, emphasizing the role of spin state coherence and magnetic fields in studying singlet ↔ triplet pair interconversion. Singlet fission provides an example of how all three types of excitons (triplet, singlet, and charge transfer) may interact to produce useful phenomena for applications such as solar energy conversion. Copyright © 2014 by Annual Reviews.


Seitz A.R.,University of California at Riverside
Current Biology | Year: 2010

Recent studies show that humans can rapidly learn to differentiate originally meaningless sounds into long-lasting memories, illustrating the flexibility of sensory processes and raising important questions about how sensory memories are formed. © 2010 Elsevier Ltd All rights reserved.


Fatmi M.Q.,University of California at Riverside
PLoS computational biology | Year: 2010

The oligomerization/co-localization of protein complexes and their cooperative regulation in protein function is a key feature in many biological systems. The synergistic regulation in different subunits often enhances the functional properties of the multi-enzyme complex. The present study used molecular dynamics and Brownian dynamics simulations to study the effects of allostery, oligomerization and intermediate channeling on enhancing the protein function of tryptophan synthase (TRPS). TRPS uses a set of α/β-dimeric units to catalyze the last two steps of L-tryptophan biosynthesis, and the rate is remarkably slower in the isolated monomers. Our work shows that without their binding partner, the isolated monomers are stable and more rigid. The substrates can form fairly stable interactions with the protein in both forms when the protein reaches the final ligand-bound conformations. Our simulations also revealed that the α/β-dimeric unit stabilizes the substrate-protein conformation in the ligand binding process, which lowers the conformation transition barrier and helps the protein conformations shift from an open/inactive form to a closed/active form. Brownian dynamics simulations with a coarse-grained model illustrate how protein conformations affect substrate channeling. The results highlight the complex roles of protein oligomerization and the fine balance between rigidity and dynamics in protein function.


Lerner J.S.,Harvard University | Li Y.,University of California at Riverside | Valdesolo P.,Claremont McKenna College | Kassam K.S.,Carnegie Mellon University
Annual Review of Psychology | Year: 2015

A revolution in the science of emotion has emerged in recent decades, with the potential to create a paradigm shift in decision theories. The research reveals that emotions constitute potent, pervasive, predictable, sometimes harmful and sometimes beneficial drivers of decision making. Across different domains, important regularities appear in the mechanisms through which emotions influence judgments and choices. We organize and analyze what has been learned from the past 35 years of work on emotion and decision making. In so doing, we propose the emotion-imbued choice model, which accounts for inputs from traditional rational choice theory and from newer emotion research, synthesizing scientific models. © 2015 by Annual Reviews. All rights reserved.


Voesenek L.A.C.J.,University Utrecht | Bailey-Serres J.,University Utrecht | Bailey-Serres J.,University of California at Riverside
New Phytologist | Year: 2015

Unanticipated flooding challenges plant growth and fitness in natural and agricultural ecosystems. Here we describe mechanisms of developmental plasticity and metabolic modulation that underpin adaptive traits and acclimation responses to waterlogging of root systems and submergence of aerial tissues. This includes insights into processes that enhance ventilation of submerged organs. At the intersection between metabolism and growth, submergence survival strategies have evolved involving an ethylene-driven and gibberellin-enhanced module that regulates growth of submerged organs. Opposing regulation of this pathway is facilitated by a subgroup of ethylene-response transcription factors (ERFs), which include members that require low O2 or low nitric oxide (NO) conditions for their stabilization. These transcription factors control genes encoding enzymes required for anaerobic metabolism as well as proteins that fine-tune their function in transcription and turnover. Other mechanisms that control metabolism and growth at seed, seedling and mature stages under flooding conditions are reviewed, as well as findings demonstrating that true endurance of submergence includes an ability to restore growth following the deluge. Finally, we highlight molecular insights obtained from natural variation of domesticated and wild species that occupy different hydrological niches, emphasizing the value of understanding natural flooding survival strategies in efforts to stabilize crop yields in flood-prone environments. © 2015 New Phytologist Trust.


Santiago L.S.,University of California at Riverside
Biotropica | Year: 2010

This study investigates whether it is possible to simplify the complex influence of numerous species on leaf litter decomposition in a diverse tropical forest using functional classifications to predict litter quality, decomposition rate, and nutrient dynamics during decomposition, over a 2-yr period. Thirty-three lowland tropical forest plant species from contrasting growth forms (canopy trees, pioneer trees, lianas, palms, herbs) were studied. Twelve of 18 indices of litter quality varied significantly among growth forms, with canopy trees and palms showing lower litter quality than pioneer trees and herbs. Canopy leaves decomposed more slowly than understory leaves. Decomposition rate and mass loss trended greater (P<0.1) in herbs and pioneer trees compared with other growth forms. There were no significant differences between monocots and dicots, and no phylogenetic signal for decomposition was observed. Significant correlations between continuous litter quality variables and decomposition rate were observed with correlation coefficients up to 0.72. Litter lignin:Mg, P concentration, and lignin:K, were the litter quality variables most related to decomposition rate. All elements showed significant negative correlations between initial litter concentration and percent remaining, but many elements showed significant correlation between percent element remaining and initial concentrations of other elements, indicating a stoichiometric balance between these elements during decomposition. The results show that although classification by growth form and canopy position are helpful for considering the ecosystem implications of changing community composition, litter quality traits provide additional predictive power for estimating the effects of species change on decomposition. © 2009 by The Association for Tropical Biology and Conservation.


Balandin A.A.,University of California at Riverside
MRS Bulletin | Year: 2014

Phonons - quanta of crystal lattice vibrations - reveal themselves in electrical, thermal, optical, and mechanical phenomena in materials. Phonons carry heat, scatter electrons, and affect light-matter interactions. Nanostructures opened opportunities for tuning the phonon spectrum and related properties of materials for specific applications, thus realizing what was termed phonon engineering. Recent progress in graphene and two-dimensional van der Waals materials has led to a better understanding of phonon physics and created additional opportunities for controlling phonon interactions and phonon transport at room temperature. This article reviews the basics of phonon confinement effects in nanostructures, describes phonon thermal transport in graphene, discusses phonon properties of van der Waals materials, and outlines practical applications of low-dimensional materials that rely on phonon properties. © Materials Research Society 2014.


Madani K.,University of Central Florida | Dinar A.,University of California at Riverside
Water Resources Research | Year: 2012

Beneficiaries of common pool resources (CPRs) may select available noncooperative and regulatory exogenous institutions for managing the resource, as well as cooperative management institutions. All these institutions may increase the long-term gains, prolong the life of the resource, and help to escape the tragedy of the commons trap. Cooperative game theory approaches can serve as the backbone of cooperative CPR management institutions. This paper formulates and applies several commonly used cooperative game theoretic solution concepts, namely, the core, Nash-Harsanyi, Shapley, and nucleolus. Through a numerical groundwater example, we show how CPR users can share the gains obtained from cooperation in a fair and efficient manner based on these cooperative solution concepts (management institutions). Although, based on their fairness rationales, various cooperative management institutions may suggest different allocations that are potentially acceptable to the users, these allocation solutions may not be stable as some users may find them unfair. This paper discusses how different methods, such as application of the plurality rule and power index, stability index, and propensity to disrupt concepts, can help identify the most stable and likely solutions for enforcing cooperation among the CPR beneficiaries. Furthermore, how the noncooperative managerial characteristics of the CPR users can affect the stability and acceptability of the different cooperative CPR management institutions is discussed, providing valuable policy insights for cooperative CPR management at community levels. © 2012. American Geophysical Union. All Rights Reserved.


Wilson E.H.,University of California at Riverside | Weninger W.,Centenary Institute for Cancer Medicine and Cell Biology | Hunter C.A.,University of Pennsylvania
Journal of Clinical Investigation | Year: 2010

The CNS is an immune-privileged environment, yet the local control of multiple pathogens is dependent on the ability of immune cells to access and operate within this site. However, inflammation of the distinct anatomical sites (i.e., meninges, cerebrospinal fluid, and parenchyma) associated with the CNS can also be deleterious. Therefore, control of lymphocyte entry and migration within the brain is vital to regulate protective and pathological responses. In this review, several recent advances are highlighted that provide new insights into the processes that regulate leukocyte access to, and movement within, the brain.


Langergraber G.,University of Natural Resources and Life Sciences, Vienna | Simunek J.,University of California at Riverside
Vadose Zone Journal | Year: 2012

Constructed wetlands (CWs) are engineered water treatment systems designed to remove various types of contaminants. A large number of processes simultaneously contribute to water quality improvement in CWs. During the last decade, there has been a wide interest in the understanding of complex "constructed wetland" systems, including the development of numerical process-based models describing these systems. A number of process-based numerical models for subsurface flow (SSF) CWs have been developed during the last few years; however, most of them are either in an early stage of development or are available only in-house. The HYDRUS wetland module is the only implementation of a CW model that is currently publicly available. Version 2 of the HYDRUS wetland module includes two biokinetic model formulations simulating reactive transport in CWs: CW2D and CWM1. In CW2D, aerobic and anoxic transformation and degradation processes for organic matter, N, and P are considered, whereas in CWM1, aerobic, anoxic, and anaerobic processes for organic matter, N, and S are taken into account. We simulated horizontal flow CWs using both biokinetic models. Compared with the CWM1 implementation in the RETRASO code, the HYDRUS implementation was able to simulate fixed biomass, which is of high importance for obtaining realistic predictions for the treatment efficiency of CWs. We also compared simulation results for horizontal flow CWs obtained using both CW2D and CWM1 modules that showed that CWM1 produces more reasonable results because it also considers anaerobic degradation processes. The influence of wetland plants on the simulation results was also investigated. Simulated biomass profiles in the filter were completely different when considering O2 release from roots, thus indicating the importance of considering plant effects. © Soil Science Society of America.


Hua Y.,University of California at Riverside
IEEE Transactions on Signal Processing | Year: 2011

In this paper, we consider a channel estimation scheme for a two-hop nonregenerative MIMO relay system without the direct link between source and destination. This scheme has two phases. In the first phase, the source does not transmit while the relay transmits and the destination receives. In the second phase, the source transmits, the relay amplifies and forwards, and the destination receives. At the destination, the data received in the first phase are used to estimate the relay-to-destination channel, and the data received in the second phase are used to estimate the source-to-relay channel. The linear minimum mean-square error estimation (LMMSE) is used for channel estimation, which allows the use of prior knowledge of channel correlations. For phase 1, an algorithm is developed to compute the optimal source pilot matrix for use at the relay. For phase 2, an algorithm is developed to compute the optimal source pilot matrix for use at the source and the optimal relay pilot matrix for use at the relay. © 2011 IEEE.


Farley R.D.,University of California at Riverside
Arthropod Structure and Development | Year: 2010

The scanning electron microscope (SEM) was used to study the development of the opisthosomal appendages and book gills of the horseshoe crab, Limulus polyphemus. Later embryonic stages were examined as well as the first and second instars. The observations are compared with a much earlier light microscopic description of book gill development in the horseshoe crab and with book lung development in scorpion embryos and first and second instars in a recent study with SEM. After the third embryonic molt in the horseshoe crab, the opisthosomal appendages are of sufficient size so they could be fractured or dissected open so internal cells and other structures could be examined. The opisthosomal appendages and book gill lamellae of first and second instars were also opened. The observations support the earlier histological report that the gill lamellae are a hypodermal outgrowth from the posterior surface of the preceding branchial appendages. The genital operculum, branchial appendages and gill lamellae are very thin and consist of external cuticle, hypodermis and space holders. The latter help hold the cuticle walls in place so hemolymph can flow through the narrow channels. The space holders are formed from cell processes that extend into the lumen from the hypodermis just inside the external cuticle. In the recent SEM study in scorpion embryos and in some histological investigations in spider embryos, the book lung lamellae are formed by alignment of cells from an invaginated sac or mass of cells. This clearly differs from the mode of formation of gill lamellae as observed in this and earlier investigations. These reports of differences in embryology refine but do not preclude hypotheses about book gill/book lung homology since addition, deletion or modification of ancestral features often occur for the benefit of the embryos and larvae. © 2010 Elsevier Ltd.


Varma C.M.,University of California at Riverside
Reports on Progress in Physics | Year: 2012

An overview of the momentum and frequency dependence of effective electronelectron interactions which favor electronic instability to a superconducting state in the angular-momentum channel and the properties of the interactions which determine the magnitude of the temperature T c of the instability is provided. Interactions induced through exchange of electronic fluctuations of spin density, charge density or current density are considered. Special attention is paid to the role of quantum-critical fluctuations (QCFs) including pairing due to their virtual exchange as well as de-pairing due to inelastic scattering. Additional insight is gained by reviewing empirical data and theory specific to superfluidity in liquid He 3, superconductivity in some of the heavy-fermion compounds, in cuprates, in pncitides and the valence skipping compound. The physical basis for the following observation is provided: the ratio of the maximum T c to the typical phonon frequency in phonon induced s-wave superconductivity is O(10 1); the ratio of p-wave T c to the renormalized Fermi energy in liquid He 3, a very strongly correlated Fermi liquid near its melting pressure, is only O(10 3); in the cuprates and the heavy fermions where d-wave superconductivity occurs in a region governed by QCFs, this ratio rises to O(10 2). These discussions also suggest factors important for obtaining higher T c. Experiments and theoretical investigations are suggested to clarify the many unresolved issues. © 2012 IOP Publishing Ltd.


MacMillan S.N.,California Institute of Technology | Harman W.H.,University of California at Riverside | Peters J.C.,California Institute of Technology
Chemical Science | Year: 2014

Metal-borane complexes are emerging as promising systems for study in the context of bifunctional catalysis. Herein we describe diphosphineborane nickel complexes that activate Si-H bonds and catalyze the hydrosilylation of aldehydes. Treatment of [MesDPBPh]Ni (1) ([ MesDPBPh] = MesB(o-Ph2PC6H 4)2) with organosilanes affords the complexes [ MesDPBPh](μ-H)NiE (E = SiH2Ph (3), SiHPh2 (4)). Complex 4 is in solution equilibrium with 1 and the thermodynamic and kinetic parameters of their exchange have been characterized by NMR spectroscopy. Complex 1 is a catalyst for the hydrosilylation of a range of para-substituted benzaldehydes. Mechanistic studies on this reaction via multinuclear NMR spectroscopy are consistent with the intermediacy of a borohydrido-Ni-siloxyalkyl species. © 2014 The Royal Society of Chemistry.


When torpid animals arouse and warm up to restore normal body temperature (Tb), they produce heat at levels that can reach up to 10 times basal metabolic rate (BMR), close to the cold-induced summit metabolism (VO2-sum). Because torpor is an adaptation aimed at conserving energy over periods of low ambient temperature (Ta) and food availability, selective forces that have led to the evolution of torpor may have simultaneously favoured high thermogenic capacity (i.e. VO2-sum) relative to the maintenance costs (i.e. BMR), hence a higher factorial aerobic scope (FAS; the ratio of VO2-sum to BMR). My objective was to test this adaptive hypothesis using a phylogenetically informed comparative approach with data on BMR and VO 2-sum in rodents. I found a strong negative correlation between FAS and the average of the daily minimum Ta (Tmin) in species using torpor, which was due to differential effects of Ta on BMR (but not VO 2-sum) in species that use torpor compared with species that do not. In addition, FAS was negatively correlated with the lowest torpid Tb in a subset of nine species. These results suggest that in species using torpor, selective forces may have acted to maximize the efficiency of thermogenic capacity (VO2-sum) relative to maintenance costs (BMR), resulting in an increasing FAS with decreasing Ta. © 2013 The Author(s) Published by the Royal Society.


Gallie D.R.,University of California at Riverside
Plant Molecular Biology | Year: 2015

Ethylene is perceived following binding to endoplasmic reticulum-localized receptors, which in Arabidopsis thaliana, include ETR1, ERS1, EIN4, ETR2, and ERS2. These receptors fall into two subfamilies based on conservation of features within their histidine kinase domain. Subfamily 1 contains ETR1 and ERS1 whereas subfamily 2 contains EIN4, ETR2, and ERS2. Because ethylene receptors are found only in plants, this raises questions of when each receptor evolved. Here it is shown that subfamily 1 receptors encoded by a multigene family are present in all charophytes examined, these being most homologous to ETR1 based on their evolutionary relationship as well as containing histidine kinase and receiver domains. In charophytes and Physcomitrella patens, one or more gene family members contain the intron characteristic of subfamily 2 genes, indicating the first step in subfamily 2 receptor evolution. ERS1 homologs appear in basal angiosperm species after Amborella trichopoda and, in some early and basal angiosperm species and monocots in general, it is the only subfamily 1 receptor present. Distinct EIN4 and ETR2 homologs appear only in core eudicots and ERS2 homologs appear only in the Brassicaceae, suggesting it is the most recent receptor to evolve. These findings show that a subfamily 1 receptor had evolved and a subfamily 2 receptor had begun to evolve in plants prior to the colonization of land and only these two existed up to the appearance of the first basal angiosperm. The appearance of ERS2 in the Brassicaceae suggests ongoing evolution of the ethylene receptor family. © 2015, Springer Science+Business Media Dordrecht.


McGowen M.R.,University of California at Riverside
Molecular Phylogenetics and Evolution | Year: 2011

Oceanic dolphins (Delphinidae) are the product of a rapid radiation that yielded ∼36 extant species of small to medium-sized cetaceans that first emerged in the Late Miocene. Although they are a charismatic group of organisms that have become poster children for marine conservation, many phylogenetic relationships within Delphinidae remain elusive due to the slow molecular evolution of the group and the difficulty of resolving short branches from successive cladogenic events. Here I combine existing and newly generated sequences from four mitochondrial (mt) genes and 20 nuclear (nu) genes to reconstruct a well-supported phylogenetic hypothesis for Delphinidae. This study compares maximum-likelihood and Bayesian inference methods of several data sets including mtDNA, combined nuDNA, gene trees of individual nuDNA loci, and concatenated mtDNA. +. nuDNA. In addition, I contrast these standard phylogenetic analyses with the species tree reconstruction method of Bayesian concordance analysis (BCA). Despite finding discordance between mtDNA and individual nuDNA loci, the concatenated matrix recovers a completely resolved and robustly supported phylogeny that is also broadly congruent with BCA trees. This study strongly supports groupings such as Delphininae, Lissodelphininae, Globicephalinae, Sotalia+. Delphininae, Steno+. Orcaella+. Globicephalinae, and Leucopleurus acutus, Lagenorhynchus albirostris, and Orcinus orca as basal delphinid taxa. © 2011 Elsevier Inc.


Liu H.,University of California at Riverside
Journal of Biomedical Materials Research - Part A | Year: 2011

A novel class of biodegradable metals, magnesium (Mg) and Mg-based alloys, has recently attracted much attention because of unique biodegradation and mechanical properties for medical applications. Ideally, Mg-based devices should degrade no faster than the degradation products can be eliminated efficiently from the body. Additionally, for orthopedic and maxillofacial applications, the implant integration with the surrounding bone is critical for its clinical success. Therefore, it is necessary to thoroughly characterize Mg surface and degradation and investigate how these characteristics influence its interactions with essential cells, for example, bone marrow derived mesenchymal stem cells. The objectives of this study were to investigate (1) the effects of two surface conditions (the presence vs. absence of surface oxides) on Mg degradation and mesenchymal stem cell adhesion, and (2) the effects of two essential aqueous environments (the presence vs. absence of physiological ions and proteins) on Mg degradation. In an effort towards standardizing testing methods for Mg alloys, consistent and well-controlled experimental methods were designed to characterize the surface and degradation of Mg and its interactions with cells. The results demonstrated that original surface (oxidized vs. polished) conditions had a less pronounced effect on regulating initial cell adhesion, but did affect surface morphology and composition of the Mg samples after 24 h of cell culture. The presence versus absence of biological ions and proteins had a significant effect on Mg degradation mode and rate. In conclusion, the material surface and anatomical sites of implantation dependent on the intended applications must be carefully considered while assessing Mg alloys in vitro or in vivo for medical applications. Standardized testing procedures and methods are critically needed for developing more effective medical-grade Mg alloys. Copyright © 2011 Wiley Periodicals, Inc.


Barlas Y.,University of California at Riverside | Cote R.,Universite de Sherbrooke | Rondeau M.,Universite de Sherbrooke
Physical Review Letters | Year: 2012

ABC-stacked trilayer graphene's chiral band structure results in three (n=0, 1, 2) Landau level orbitals with zero kinetic energy. This unique feature has important consequences on the interaction-driven states of the 12-fold degenerate (including spin and valley) N=0 Landau level. In particular, at many filling factors ν T=±5, ±4, ±2, ±1 a quantum phase transition from a quantum Hall liquid state to a triangular charge-density wave occurs as a function of the single particle-induced Landau level orbital splitting Δ LL. Experimental signatures of this phase transition are also discussed. © 2012 American Physical Society.


Swanson H.L.,University of California at Riverside
Child Neuropsychology | Year: 2012

Adolescents (ages 14-17) with math disabilities (MD, n=12), reading disabilities (RD, n=19), math + reading disabilities (MD+RD, n=12), and average achievers (n=15) were compared on measures of visual-spatial processing, random generation (inhibition), writing speed, short-term memory (STM), and working memory (WM). Adolescents with MD performed significantly lower than adolescents with RD on measures of visual-spatial processing and visual WM. Adolescents with MD outperformed adolescents with RD +MD on measures of random generation and motor speed. Performance of all three low-achieving groups was inferior to average achievers on measures of random generation, motor speed, and verbal WM. The results were interpreted within a multicomponent model that attributed deficits related to MD in adolescents to deficits related the visual-spatial sketchpad of WM. © 2012 Psychology Press, an imprint of the Taylor & Francis Group, an Informa business.


Lee C.T.A.,Rice University | Morton D.M.,University of California at Riverside
Earth and Planetary Science Letters | Year: 2015

High silica (>70 wt.% SiO2) granites (HSGs) are important carriers of highly incompatible elements, thus, understanding their origin is relevant to understanding how the composition of the continental crust evolves. We examined a large-scale geochemical study of plutons in the Peninsular Ranges Batholith in southern California (USA) to better understand the petrogenetic relationships between HSGs and the batholith. Using highly incompatible and compatible elements, we show that HSGs represent residual liquids within a felsic (69-72 wt.% SiO2) magmatic crystal mush at crystal fractions of 50-60% and residual liquid fractions of 40-50%. Trace element systematics show that separation of the HSG liquid from the crystal mush is inefficient, such that no more than 70-80% of the HSG is fully extracted and the remaining greater than 20-30% remains trapped in cumulate mush. We find little evidence of more efficient liquid-crystal segregation, which suggests that compaction-induced segregation may be too slow to be important on a large scale. Instead, the terminal porosity of 20-30% coincides with theoretical maximum packing fraction of unimodal particles settled out of suspension (~0.74), which may indicate that crystal settling - perhaps in the form of hindered settling - drives segregation of viscous silicic melts and crystals. Unlike compaction, settling operates on timescales of 1-10 ky, fast enough to generate large volumes of HSG and complementary cumulates with trapped melt before magma chambers freeze. Many felsic plutons may thus be cumulates, but because of trapped melt, they are difficult to geochemically distinguish from plutons whose compositions fall along liquid lines of descent. The approach here, using a combination of highly incompatible and compatible elements, provides a way of identifying and quantifying trapped melt fractions. Finally, we show that HSGs appear to form only in the shallow crust (<10 km) and rarely in the middle to lower crust. Where HSGs are common, mafic magmas are common too, suggesting a genetic relationship between the two. If HSGs derive by crystal fractionation of basaltic parents, they represent at most 5% of the original mass of parental magma, but because they form almost exclusively at low pressures, they may be over-represented in shallowly exhumed batholiths. Why HSGs form primarily in the upper crust is unclear. © 2014 Elsevier B.V.


Aji V.,University of California at Riverside
Physical Review B - Condensed Matter and Materials Physics | Year: 2012

Weyl semimetals are three-dimensional analogs of graphene where the energy of the excitations is a linear function of their momentum. Pyrochlore iridates (A 2Ir 2O 7 with A yttrium or a lanthanide element) are conjectured to be examples of such a system, with the low-energy physics described by 24 Weyl nodes. An intriguing possibility is that these materials provide a physical realization of the Adler-Bell-Jackiw anomaly. In this Rapid Communication we investigate the properties of pyrochlore iridates in an applied magnetic field. We find that the dispersion of the lowest Landau level depends on the direction of the applied magnetic field. Consequently, the velocity at low energies can be manipulated by changing the direction of the applied field. The resulting anisotropy in longitudinal conductivity is investigated. © 2012 American Physical Society.


Miller T.A.,University of California at Riverside
Pest Management Science | Year: 2013

Enthusiasm greeted the development of synthetic organic insecticides in the mid-twentieth century, only to see this give way to dismay and eventually scepticism and outright opposition by some. Regardless of how anyone feels about this issue, insecticides and other pesticides have become indispensable, which creates something of a dilemma. Possibly as a result of the shift in public attitude towards insecticides, genetic engineering of microbes was first met with scepticism and caution among scientists. Later, the development of genetically modified crop plants was met with an attitude that hardened into both acceptance and hard-core resistance. Transgenic insects, which came along at the dawn of the twenty-first century, encountered an entrenched opposition. Those of us responsible for studying the protection of crops have been affected more or less by these protagonist and antagonistic positions, and the experiences have often left one thoughtfully mystified as decisions are made by non-participants. Most of the issues boil down to concerns over delivery mechanisms. © 2013 The Authors.


Van Norman J.M.,University of California at Riverside
Current Biology | Year: 2015

Summary Plasticity in plant form is achieved through differential elaboration of developmental pre-patterns during postembryonic organ development. A new report links the output of the root clock, an oscillatory transcriptional pre-patterning mechanism, with cell-type-specific production of the plant hormone auxin, and identifies a downstream component required for elaboration of the pre-pattern. © 2015 Elsevier Ltd All rights reserved.


Barlas Y.,University of California at Riverside | Yang K.,Florida State University
Physical Review B - Condensed Matter and Materials Physics | Year: 2012

Using the Onsager relation between electric and heat transport coefficients, and considering the very different roles played by the quantum Hall condensate and quasiparticles in transport, we argue that near the center of a quantum Hall plateau thermopower in a Corbino geometry measures entropy per quasiparticle per quasiparticle charge. This relation indicates that thermopower measurement in a Corbino setup is a more direct measure of quasiparticle entropy than in a Hall bar. Treating disorder within the self-consistent Born approximation, we show through an explicit microscopic calculation that this relation holds on an integer quantum Hall plateau at low temperatures. Applying this to non-Abelian quantum Hall states, we argue that Corbino thermopower at sufficiently low temperature becomes temperature independent and measures the quantum dimension of non-Abelian quasiparticles that determines the topological entropy they carry. © 2012 American Physical Society.


Lee H.-S.,Brookhaven National Laboratory | Ma E.,University of California at Riverside
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2010

Gauged B - L is a popular candidate for the origin of the conservation of R parity, i.e. R = (-)3 B + L + 2 j, in supersymmetry, but it fails to forbid the effective dimension-five terms arising from the superfield combinations Q Q Q L, uc uc dc ec, and uc dc dc Nc, which allow the proton to decay. Changing it to B - xi L, where xe + xμ + xτ = 3 (with xi ≠ 1) for the three families, would forbid these terms while still serving as a gauge origin of R parity. We show how this is achieved in two minimal models with realistic neutrino mass matrices, and discuss their phenomenological implications. © 2010 Elsevier B.V. All rights reserved.


Rossi A.M.,University of Maryland University College | Graham R.C.,University of California at Riverside
Soil Science Society of America Journal | Year: 2010

Porous weathered rock can play an important role in storing water and nutrients that are accessible to plants and microbes, especially in thin or skeletal soils. The objectives of this study were to measure the rate of porosity development in granitic rock fragments and determine how pore morphology changes with time. Total porosity and pore characteristics were measured on granodiorite clasts in soils of the Bishop Creek moraines, eastern Sierra Nevada, California. The soils formed a chronosequence; soil surface age represented the weathering time for the clasts. Clast porosity was estimated to form at a rate of 0.10% per thousand years. Pores were dominantly inter-and intramineral planar voids formed by stress fracturing induced through biotite expansion. Granodiorite clasts in the older moraines had greater total porosity, microporosity, and connectivity of pores, increasing potential for water movement and storage and ease of root and mycorrhizal penetration. Roots and clay films observed in pores inside the weathered clasts indicate water storage and movement from the soil into clasts. The most weathered clasts have significant porosity that contributes to the ecosystem functions of the regolith. © Soil Science Society of America.


Mills A.P.,University of California at Riverside
Canadian Journal of Physics | Year: 2013

The photoionization cross section for the positronium (Ps) negative ion, Ps-, at the lowest n = 2 Feshbach resonance, estimated by neglecting the influences of the weakly bound outer electron, is σF = 1.4 × 10-12 cm2, about 3 × 103 times the existing lower limit calculated by Igarashi and co-workers (New J. Phys. 2, 17 (2000)). Although the estimated cross section is 200 times smaller than the analogous cross section for photoexcitation of the Ps Lyman-α transition, including the effect of the broad line width of the resonance shows it will be feasible to observe this resonance to obtain precision information about the three body Ps- system. © 2013 Published by NRC Research Press.


Cummings F.,University of California at Riverside
Journal of Physics B: Atomic, Molecular and Optical Physics | Year: 2013

The Tavis-Cummings model of N two-level atoms interacting with a single resonant mode is extended to various cases of off-resonance, initial photon densities, and atom number N. © 2013 IOP Publishing Ltd.Printed in the UK & the USA.


Einhorn M.B.,University of California at Santa Barbara | Einhorn M.B.,University of Michigan | Wudka J.,University of California at Riverside
Nuclear Physics B | Year: 2013

With reference to the equivalence theorem, we discuss the selection of basis operators for effective field theories in general. The equivalence relation can be used to partition operators into equivalence classes, from which inequivalent basis operators are selected. These classes can also be identified as containing Potential-Tree-Generated (PTG) operators, Loop-Generated (LG) operators, or both, independently of the specific dynamics of the underlying extended models, so long as it is perturbatively decoupling. For an equivalence class containing both, we argue that the basis operator should be chosen from among the PTG operators, because they may have the largest coefficients. We apply this classification scheme to dimension-six operators in an illustrative Yukawa model as well in the Standard Model (SM). We show that the basis chosen by Grzadkowski et al. [5] for the SM satisfies this criterion. In this light, we also revisit and verify our earlier result [6] that the dimension-six corrections to the triple-gauge-boson couplings only arise from LG operators, so the magnitude of the coefficients should only be a few parts per thousand of the SM gauge coupling if BSM dynamics respects decoupling. The same is true of the quartic-gauge-boson couplings. © 2013 Elsevier B.V.


Dhahbi J.M.,University of California at Riverside | Dhahbi J.M.,Childrens Hospital Oakland Research Institute
Ageing Research Reviews | Year: 2014

Small noncoding RNAs (sncRNAs) mediate a variety of cellular functions in animals and plants. Deep sequencing has made it possible to obtain highly detailed information on the types and abundance of sncRNAs in biological specimens, leading to the discovery that sncRNAs circulate in the blood of humans and mammals. The most abundant types of circulating sncRNAs are microRNAs (miRNAs), 5' transfer RNA (tRNA) halves, and YRNA fragments, with minute amounts of other types that may nevertheless be significant. Of the more abundant circulating sncRNAs only miRNAs have well described functions, but characteristics of the others suggest specific processing and secretion as complexes that protect the RNA from degradation. The properties of circulating sncRNAs are consistent with their serving as signaling molecules, and investigations of circulating miRNAs support the view that they can enter cells and regulate cellular functions. The serum levels of specific sncRNAs change markedly with age, and these changes can be mitigated by calorie restriction (CR), indicating that levels are under physiologic control. The ability of circulating sncRNAs to transmit functions between cells and to regulate a broad spectrum of cellular functions, and the changes in their levels with age, implicate them in the manifestations of aging. Our understanding of the functions of circulating sncRNA, particularly in relation to aging, is currently at a very early stage; results to date suggest that more extensive investigation will yield important insights into mechanisms of aging. © 2014 Elsevier B.V.


Roper M.C.,University of California at Riverside
Molecular Plant Pathology | Year: 2011

Pantoea stewartii subsp. stewartii is a Gram-negative enteric bacterium that primarily infects sweet corn. Studies of this bacterium have provided useful insight into how xylem-dwelling bacteria establish themselves and incite disease in their hosts. Pantoea stewartii subsp. stewartii is a remarkable bacterial system for laboratory studies because of its relative ease of propagation and genetic manipulation, and the fact that it appears to employ a minimal number of pathogenicity mechanisms. In addition, P. stewartii subsp. stewartii produces copious amounts of its quorum sensing (QS) signal, acyl-homoserine lactone (AHL), making it an excellent organism for studying QS-controlled gene regulation in a plant-pathogenic bacterium. In fact, P. stewartii subsp. stewartii has become the microbial paradigm for QS control of gene expression by both repression and activation via a QS regulator that binds DNA in the absence and dissociates in the presence of the signal ligand. Moreover, P. stewartii subsp. stewartii is a member of the Enterobacteriaceae, and lessons learned from its interaction with plants may be extrapolated to other plant-associated enterics, such as Erwinia, Dickeya and Pectobacterium spp., or enteric human pathogens associated with plants, such as Escherichia coli and Salmonella spp. Taxonomy: Bacteria; Gammaproteobacteria; family Enterobacteriaceae; genus Pantoea; species stewartii (Mergaert, 1993). Microbiological properties: Gram-negative, motile, yellow pigmented, mucoid, facultative anaerobe. Host range: Pantoea stewartii subsp. stewartii (Smith, 1898) Dye causes Stewart's wilt of corn (Zea mays). Early-maturing sweet corn varieties and some elite inbred maize lines are particularly susceptible. Disease symptoms: There are two major phases of Stewart's wilt disease: (i) wilt and (ii) leaf blight. The wilt phase occurs when young seedlings are infected with P. stewartii subsp. stewartii (Fig.1A). Water-soaked lesions first appear on the young expanding leaves and, later, seedlings may become severely wilted (Fig.1B). The plants usually die when infected at the seedling stage. The leaf blight phase occurs when mature plants are infected (Fig.1C). The bacteria enter the xylem and cause long linear yellow-grey lesions with a wavy margin that run parallel to the leaf veins. These lesions later turn necrotic and dark in colour. The leaf blight phase is most apparent after tasselling and does not generally cause death of the plant. In addition, the bacteria can sometimes break out of the xylem and cause pith rot in mature sweet corn plants. In resistant varieties, lesions are usually limited to only a few centimetres depending on the level of resistance of the particular hybrid (Claflin, 2000; Pataky, 2003). 1 Disease symptoms associated with Stewart's wilt of sweet corn. (A) The seedling wilt phase of the disease which occurs when young plants are systemically infected. (B) Leaf lesions run parallel to the leaf veins. They begin as water-soaked areas that turn into long, pale-green to yellow gray streaks with wavy margins. (C) The leaf blight phase of the disease. This phase occurs when plants are infected after the seedling stage. Images used with permission from Pataky (2003, 2004). Useful websites: Molecular Plant Pathology © 2011 BSPP and Blackwell Publishing Ltd. No Claim tO Original US Government Works.


Khitun A.,University of California at Riverside
Journal of Applied Physics | Year: 2012

We describe and analyze magnonic logic circuits enabling parallel data processing on multiple frequencies. The circuits combine bi-stable (digital) input/output elements and an analog core. The data transmission and processing within the analog part is accomplished by the spin waves, where logic 0 and 1 are encoded into the phase of the propagating wave. The latter makes it possible to utilize a number of bit carrying waves on different frequencies for parallel data processing. The operation of the magnonic logic circuits is illustrated by numerical modeling. We also present the estimates on the potential functional throughput enhancement and compare it with scaled CMOS. The described multi-frequency approach offers a fundamental advantage over the transistor-based circuitry and may provide an extra dimension for the functional throughput enhancement. The shortcoming and potentials issues are also discussed. © 2012 American Institute of Physics.


Einhorn M.B.,University of California at Santa Barbara | Einhorn M.B.,University of Michigan | Wudka J.,University of California at Riverside
Nuclear Physics B | Year: 2013

The implications for Higgs decays of potential new physics beyond the Standard Model (BSM) are considered in the context of effective field theory, assuming perturbative decoupling. Using existing data to restrict which dimension-six operators can arise, it is shown that, given the existing experimental constraints, only a small number of operators can affect the decays of the Higgs: those that may be potentially-tree-generated (PTG) and modify the Higgs-fermion couplings, or those that may be loop-generated (LG) that modify the Higgs couplings to γγ, Zγ and GG. Implications for specific branching ratios are given in terms of the coefficients of various dimension-six operators. In such a scenario, the ratios Γ(H→WW*)/Γ(H→ZZ* ) and Γ(H→Wℓν)/Γ(H→Zℓℓ) equal to their Standard Model values to an accuracy of O(1%) or less. © 2013 Elsevier B.V.


Saltzman W.,University of California at Riverside | Ziegler T.E.,University of Wisconsin - Madison
Journal of Neuroendocrinology | Year: 2014

In the 5-10% of mammals in which both parents routinely provide infant care, fathers as well as mothers undergo systematic endocrine changes as they transition into parenthood. Although fatherhood-associated changes in such hormones and neuropeptides as prolactin, testosterone, glucocorticoids, vasopressin and oxytocin have been characterised in only a small number of biparental rodents and primates, they appear to be more variable than corresponding changes in mothers, and experimental studies typically have not provided strong or consistent evidence that these endocrine shifts play causal roles in the activation of paternal care. Consequently, their functional significance remains unclear. We propose that endocrine changes in mammalian fathers may enable males to meet the species-specific demands of fatherhood by influencing diverse aspects of their behaviour and physiology, similar to many effects of hormones and neuropeptides in mothers. We review the evidence for such effects, focusing on recent studies investigating whether mammalian fathers in biparental species undergo systematic changes in (i) energetics and body composition; (ii) neural plasticity, cognition and sensory physiology; and (iii) stress responsiveness and emotionality, all of which may be mediated by endocrine changes. The few published studies, based on a small number of rodent and primate species, suggest that hormonal and neuropeptide alterations in mammalian fathers might mediate shifts in paternal energy balance, body composition and neural plasticity, although they do not appear to have major effects on stress responsiveness or emotionality. Further research is needed on a wider variety of biparental mammals, under more naturalistic conditions, to more fully determine the functional significance of hormone and neuropeptide profiles of mammalian fatherhood and to clarify how fatherhood may trade off with (or perhaps enhance) aspects of organismal function in biparental mammals. © 2014 British Society for Neuroendocrinology.


Hughes N.C.,University of California at Riverside
Earth-Science Reviews | Year: 2016

The Indian subcontinent's biota and biostratigraphy is amongst the least well known internationally of any Cambrian succession worldwide. Recent revision of previously described type material and a substantial number of new finds reveal a typical Cambrian skeletonized fauna and an organic-walled biota, as well as various trace fossils. This biota, reviewed here synoptically, currently contains 51 non-agnostoid trilobite genera belonging to 50 species; 15 genera and species of agnostoids; one species of bradoriid arthropod; 18 brachiopod genera containing 20 species; echinoderm thecal and columnal plates; a soft-bodied eldoniid; representatives of three hyolith genera; other small shelly fossils some of which are identified to species level; acritarchs; and a variety of ichnotaxa. Regional biostratigraphic zonations for trilobites, brachiopods, small shelly fossils and organic-walled, and trace fossils are herein combined into an integrated Cambrian biostratigraphical scheme that permits correlation along and across the lithotectonic zones of the Himalayan margin and southward onto cratonic India. These consist of 13 named biostratigraphic units for trilobites, seven for brachiopods, three for small shelly and organic-walled fossils, and one for trace fossils. The basal boundary of the Cambrian (~ 541 Ma) is biostratigraphically localised in the Lesser Himalaya between Ediacaran carbonate-rich beds bearing the organic-walled tubular Shaanxilithes ningqiangensis, and dark, highly stratigraphically condensed, phosphate-rich shale bearing Fortunian (~ 535 Ma) and Cambrian Stage 2 age (~ 524 Ma) small shelly fossil assemblages. The oldest macrofossils presently known are somewhat younger, and represent early Cambrian Stage 4. The Redlichia noetlingi trilobite Zone/Botsfordia granulata brachiopod Zone (~ 512 Ma), is widely represented in siliciclastic rocks across and along the Himalaya, spanning the Tethyan, Lesser, and sub-Himalayan lithotectonic zones, and possibly also extending onto the craton. Stage 5 Cambrian fauna are the most diverse and best biostratigraphically characterised, much of which are relatively well preserved in limestone, but presently known only in the Tethyan Himalaya where species-level correlation between the Zanskar and Parahio valleys has been established. There, rates of sediment accumulation were notably high, with some 2000 m of rock when compacted deposited within approximately 13 Myr. During this interval, the ranges of some trilobite and brachiopod species (and their zones) were apparently less than one million years long. The indicus trilobite zone has recently been localized, shortly below the prachina zone. Furongian (late Cambrian, ~ 493 Ma) fossils are known only in the Bhutanese Himalaya. Except where faulted, the Cambrian succession is capped by an unconformity throughout the Himalaya. In the Salt Range and Lesser Himalaya this unconformity is sub-Permian, but in the Tethyan Himalaya it is sub-Ordovician. The regional Cambrian can now be correlated globally with reasonable precision, and all parts of the Himalayan margin south of the Yarlung-Tsangpo suture have an equatorial Gondwanan biota most similar to North China, and particularly, to South China. Links with Australia are suggested by non-cosmopolitan species but Indian biotas share less in common with Australia than with parts of China. Knowledge of the Himalayan Cambrian biota serves a critical role in constraining the Caenozoic uplift and erosional history of the orogen. © 2016 Elsevier B.V.


Funder D.C.,University of California at Riverside
Behavioral and Brain Sciences | Year: 2011

The target article tends to conflate self-deception and self-enhancement, but biased self-presentation can be negative as well as positive. Self-deceiving self-diminishers may be depressed and non-self-deceiving self-diminishers may project false modesty. The article's otherwise brilliant argument for the advantages of self-deceptive self-enhancement for deceiving others may underemphasize the risks it entails for poor decision making. © 2011 Cambridge University Press.


Gallie D.R.,University of California at Riverside
F1000Prime Reports | Year: 2015

Ethylene is a hormone involved in numerous aspects of growth, development, and responses to biotic and abiotic stresses in plants. Ethylene is perceived through its binding to endoplasmic reticulum-localized receptors that function as negative regulators of ethylene signaling in the absence of the hormone. In Arabidopsis thaliana, five structurally and functionally different ethylene receptors are present. These differ in their primary sequence, in the domains present, and in the type of kinase activity exhibited, which may suggest functional differences among the receptors. Whereas ethylene receptors functionally overlap to suppress ethylene signaling, certain other responses are controlled by specific receptors. In this review, I examine the nature of these receptor differences, how the evolution of the ethylene receptor gene family may provide insight into their differences, and how expression of receptors or their accessory proteins may underlie receptor-specific responses. © 2015 Faculty of 1000 Ltd.


McGowen M.R.,Wayne State University | Gatesy J.,University of California at Riverside | Wildman D.E.,Wayne State University
Trends in Ecology and Evolution | Year: 2014

Cetacea (whales, dolphins, and porpoises) is a model group for investigating the molecular signature of macroevolutionary transitions. Recent research has begun to reveal the molecular underpinnings of the remarkable anatomical and behavioral transformation in this clade. This shift from terrestrial to aquatic environments is arguably the best-understood major morphological transition in vertebrate evolution. The ancestral body plan and physiology were extensively modified and, in many cases, these crucial changes are recorded in cetacean genomes. Recent studies have highlighted cetaceans as central to understanding adaptive molecular convergence and pseudogene formation. Here, we review current research in cetacean molecular evolution and the potential of Cetacea as a model for the study of other macroevolutionary transitions from a genomic perspective. © 2014 Elsevier Ltd.


Sheikholeslami M.,Babol Noshirvani University of Technology | Domiri Ganji D.,Babol Noshirvani University of Technology | Younus Javed M.,National University of Sciences and Technology | Ellahi R.,University of California at Riverside
Journal of Magnetism and Magnetic Materials | Year: 2015

In this study, effect of thermal radiation on magnetohydrodynamics nanofluid flow between two horizontal rotating plates is studied. The significant effects of Brownian motion and thermophoresis have been included in the model of nanofluid. By using the appropriate transformation for the velocity, temperature and concentration, the basic equations governing the flow, heat and mass transfer are reduced to a set of ordinary differential equations. These equations, subjected to the associated boundary conditions are solved numerically using the fourth-order Runge-Kutta method. The effects of Reynolds number, magnetic parameter, rotation parameter, Schmidt number, thermophoretic parameter, Brownian parameter and radiation parameter on heat and mass characteristics are examined. Results show that Nusselt number has direct relationship with radiation parameter and Reynolds number while it has reverse relationship with other active parameters. It can also be found that concentration boundary layer thickness decreases with the increase of radiation parameter. © 2014 Elsevier B.V.


Kelliher J.P.,University of California at Riverside
Nonlinearity | Year: 2011

In part I, we construct a class of examples of initial velocities for which the unique solution to the Euler equations in the plane has an associated flow map that lies in no Hölder space of positive exponent for any positive time. In part II, we explore inverse problems that arise in attempting to construct an example of an initial velocity producing an arbitrarily poor modulus of continuity of the flow map. © 2011 IOP Publishing Ltd & London Mathematical Society.


Sun Q.,University of California at Riverside
Rapid communications in mass spectrometry : RCM | Year: 2011

Phosphorylation at histidine residues occurs frequently in biology, but is often overlooked in proteomics experiments due to extreme acid lability. A new method utilizing histidine labeling with iodine to record information about phosphorylation is described. Essentially, phosphorylated histidine residues are not labeled while unmodified histidine undergoes complete iodination. Iodination is stabile both under acidic conditions, and upon collisional activation in the gas phase. This enables site-specific information to be retained with standard liquid chromatography separations and tandem mass spectrometry by collisional activation. Semi-quantitative information about the relative amounts of phosphorylated versus unmodified states can also be easily obtained from the relative ion abundances. This new method should provide a pathway forward for analyzing histidine phosphorylation in complex systems. Copyright © 2011 John Wiley & Sons, Ltd.


Park G.,University of California at Riverside
Methods in molecular biology (Clifton, N.J.) | Year: 2011

The model filamentous fungus Neurospora crassa has been the focus of functional genomics studies for the past several years. A high-throughput gene knockout procedure has been developed and used to generate mutants for more than two-thirds of the ∼10,000 annotated N. crassa genes. Yeast recombinational cloning was incorporated as an efficient procedure to produce all knockout cassettes. N. crassa strains with the Δmus-51 or Δmus-52 deletion mutations were used as transformation recipients in order to reduce the incidence of ectopic integration and increase homologous recombination of knockout cassettes into the genome. A 96-well format was used for many steps of the procedure, including fungal transformation, isolation of homokaryons, and verification of mutants. In addition, development of software programs for primer design and restriction enzyme selection facilitated the high-throughput aspects of the overall protocol.


Andersen G.J.,University of California at Riverside
Journal of vision | Year: 2010

In the present study, we examined whether perceptual learning methods can be used to improve performance of older individuals. Subjects performed a texture discrimination task in the peripheral visual field and a letter discrimination task in central vision. The SOA threshold was derived by presenting a mask following the stimuli. Older subjects (age greater than 65 years) were either trained for 2 days using near threshold stimuli (experimental group) or were trained with the task with supra-threshold stimuli (older control group). The experimental group showed significant improvement in the task as a result of training whereas the older control group showed no significant improvement. The improved performance post-training equaled that of a younger control group and was maintained for at least 3 months. The results of two additional experiments indicate that the improved performance was not due to changes in divided attention, that the effect of perceptual learning was location specific, and that the pattern of learning was similar to that of younger subjects. These results indicate that perceptual learning with near threshold training can be used to improve visual performance among older individuals, that the improvements are not the result of practice with the visual task, and that the improvements do not transfer to nontrained locations.


Allen M.F.,University of California at Riverside
Journal of Arid Land | Year: 2011

Plant water availability, use, and management have largely focused on physical processes of infiltration and the role of roots in uptake and transpiration. However, roots and mycorrhizal fungi redistribute water in complex patterns. Here I describe some of our observations and experiments showing that mycorrhizal fungi play key roles in moving water for both transpiration and to facilitate nutrient acquisition under dry conditions. Mycorrhizal fungal hyphae grow from both surface and deep roots even into bedrock to help extract water under dry conditions. In both deep and surface roots, mycorrhizal fungi acquire water from pores too small for roots and root hairs to access, and at distances from roots and root hairs. Mycorrhizal fungi are also able to utilize hydraulic-lifted water from plants to obtain nutrients in extremely dry surface soils. The importance of these root symbionts in water and nutrient dynamics, and as integrators of surface and deeper water dynamics need further investigation.


Pang S.,University of Southern California | Dressel J.,University of California at Riverside | Brun T.A.,University of Southern California
Physical Review Letters | Year: 2014

Large weak values have been used to amplify the sensitivity of a linear response signal for detecting changes in a small parameter, which has also enabled a simple method for precise parameter estimation. However, producing a large weak value requires a low postselection probability for an ancilla degree of freedom, which limits the utility of the technique. We propose an improvement to this method that uses entanglement to increase the efficiency. We show that by entangling and postselecting n ancillas, the postselection probability can be increased by a factor of n while keeping the weak value fixed (compared to n uncorrelated attempts with one ancilla), which is the optimal scaling with n that is expected from quantum metrology. Furthermore, we show the surprising result that the quantum Fisher information about the detected parameter can be almost entirely preserved in the postselected state, which allows the sensitive estimation to approximately saturate the relevant quantum Cramér-Rao bound. To illustrate this protocol we provide simple quantum circuits that can be implemented using current experimental realizations of three entangled qubits. © 2014 American Physical Society.


Weber C.,Kings College London | Weber C.,University College London | Giamarchi T.,University of Geneva | Varma C.M.,University of California at Riverside
Physical Review Letters | Year: 2014

We study the phase diagram of an effective three-orbital model of the cuprates using variational Monte Carlo calculations on asymptotically large lattices and exact diagonalization on a 24-site cluster. States with ordered orbital current loops (LC), itinerant antiferromagnetism, d-wave superconductivity, and the Fermi liquid are investigated using appropriate Slater determinants refined by Jastrow functions for on-site and intersite correlations. We find an LC state stable in the thermodynamic limit for a range of parameters compatible with the Fermi surface of a typical hole doped superconductor provided the transfer integrals between the oxygen atoms have signs determined by the effects of indirect transfer through the Cu-4s orbitals as suggested by Andersen. The results of the calculations are that the LC phase gives way at lower dopings to an antiferromagnetism phase, and at larger dopings to superconductivity and Fermi liquid phases. © 2014 American Physical Society.


Uchoa B.,University of Oklahoma | Barlas Y.,University of California at Riverside
Physical Review Letters | Year: 2013

We describe the formation of superconducting states in graphene in the presence of pseudo-Landau-levels induced by strain, when time reversal symmetry is preserved. We show that superconductivity in strained graphene is quantum critical when the pseudo-Landau-levels are completely filled, whereas at partial fillings superconductivity survives at weak coupling. In the weak coupling limit, the critical temperature scales linearly with the coupling strength and shows a sequence of quantum critical points as a function of the filling factor that can be accessed experimentally. We argue that superconductivity can be induced by electron-phonon coupling and that the transition temperature can be controlled with the amount of strain and with the filling fraction of the Landau levels. © 2013 American Physical Society.


Ng J.C.K.,University of California at Riverside
Frontiers in Microbiology | Year: 2013

Successful vector-mediated plant virus transmission entails an intricate but poorly understood interplay of interactions among virus, vector, and plant. The complexity of interactions requires continually improving/evaluating tools and methods for investigating the determinants that are central to mediating virus transmission. A recent study using an organic fluorophore (Alexa Fluor)-based immunofluorescent localization assay demonstrated that specific retention of Lettuce infectious yellows virus (LIYV) virions in the anterior foregut or cibarium of its whitefly vector is required for virus transmission. Continuous exposure of organic fluorophore to high excitation light intensity can result in diminished or loss of signals, potentially confounding the identification of important interactions associated with virus transmission. This limitation can be circumvented by incorporation of photostable fluorescent nanocrystals, such as quantum dots (QDs), into the assay. We have developed and evaluated a QD-immunofluorescent labeling method for the in vitro and in situ localization of LIYV virions based on the recognition specificity of streptavidin-conjugated QD605 (S-QD605) for biotin-conjugated anti-LIYV IgG (B-αIgG). IgG biotinylation was verified in a blot overlay assay by probing SDS-PAGE separated B-αIgG with S-QD605. Immunoblot analyses of LIYV using B-αIgG and S-QD605 resulted in a virus detection limit comparable to that of DAS-ELISA. In membrane feeding experiments, QD signals were observed in the anterior foregut or cibarium of virion-fed whitefly vectors but absent in those of virion-fed whitefly non-vectors. Specific virion retention in whitefly vectors corresponded with successful virus transmission. A fluorescence photobleaching assay of viruliferous whiteflies fed B-αIgG and S-QD605 vs. those fed anti-LIYV IgG and Alexa Fluor 488-conjugated IgG revealed that QD signal was stable and deteriorated approx. seven- to eight-fold slower than that of Alexa Fluor. © 2013 Ng.


Mueller L.J.,University of California at Riverside
Concepts in Magnetic Resonance Part A: Bridging Education and Research | Year: 2011

The transformation of second-rank Cartesian tensors under rotation plays a fundamental role in the theoretical description of nuclear magnetic resonance experiments, providing the framework for describing anisotropic phenomena such as single crystal rotation patterns, tensor powder patterns, sideband intensities under magic-angle sample spinning, and as input for relaxation theory. Here, two equivalent procedures for effecting this transformation-direct rotation in Cartesian space and the decomposition of the Cartesian tensor into irreducible spherical tensors that rotate in subgroups of rank 0, 1, and 2-are reviewed. In a departure from the standard formulation, the explicit use of the spherical tensor basis for the decomposition of a spatial Cartesian tensor is introduced, helping to delineate the rotational properties of the basis states from those of the matrix elements. The result is a uniform approach to the rotation of a physical system and the corresponding transformation of the spatial components of the NMR Hamiltonian, expressed as either Cartesian or spherical tensors. This clears up an apparent inconsistency in the NMR literature, where the rotation of a spatial tensor in spherical tensor form has typically been partnered with the inverse rotation in Cartesian form to produce equivalent transformations. © 2011 Wiley Periodicals, Inc.


Ma E.,University of California at Riverside
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2013

The well-studied radiative model of neutrino mass through Z2 dark matter is shown to be naturally realizable in the context of SU(6) grand unification. A recent new proposal based on U(1)D dark matter is similarly accommodated in SU(7). Just as the proton is unstable at the scale of quark-lepton unification, dark matter is expected to be unstable at a similar scale. © 2013 American Physical Society.


Muchekehu R.W.,University of California at San Diego | Quinton P.M.,University of California at Riverside
Journal of Physiology | Year: 2010

Cervical mucus thinning and release during the female reproductive cycle is thought to rely mainly on fluid secretion. However, we now find that mucus released from the murine reproductive tract critically depends upon concurrent bicarbonate (HCO3 -) secretion. Prostaglandin E2 (PGE2)- and carbachol-stimulated mucus release was severely inhibited in the absence of serosal HCO3 -, HCO3 - transport, or functional cystic fibrosis transmembrane conductance regulator (CFTR). In contrast to mucus release, PGE2- and carbachol-stimulated fluid secretion was not dependent on bicarbonate or on CFTR, but was completely blocked by niflumic acid. We found stimulated mucus release was severely impaired in the cystic fibrosis ΔF508 reproductive tract, even though stimulated fluid secretion was preserved. Thus, CFTR mutations and/or poor bicarbonate secretion may be associated with reduced female fertility associated with abnormal mucus and specifically, may account for the increased viscosity and lack of cyclical changes in cervical mucus long noted in women with cystic fibrosis. © 2010 The Authors. Journal compilation © 2010 The Physiological Society.


Roff D.A.,University of California at Riverside
Annals of the New York Academy of Sciences | Year: 2015

Research on the evolution of mate choice has followed three avenues of investigation: (1) theoretical models of the evolution of preference and the preferred trait; (2) proposed models of mate choice; and (3) experiments and observations on mate choice, both in the laboratory and with free-ranging animals. However, there has been relatively little dialogue among these three areas. Most attempts to account for observations of mate choice using theoretical mate-choice models have focused only upon a subset of particular models and have generally failed to consider the difference between probabilistic and deterministic models. In this review, I outline the underlying reasoning of the commonly cited mate-choice models and review the conclusions of the empirical investigations. I present a brief outline of how one might go about testing these models. It remains uncertain if, in general, mate-choice models can be realistically analyzed. Although it is clear that females frequently discriminate among males, data also suggest that females may typically have a very limited number of males from which to choose. The extent to which female choice under natural conditions is relatively random because of limited opportunities remains an open question for the majority of species. © 2015 The New York Academy of Sciences.


Chen W.-H.,University of Akron | Xing Y.,University of California at Riverside | Pang Y.,University of Akron
Organic Letters | Year: 2011

Pyrophosphate (PPi) is a biologically important target. A binuclear system 3•2Zn is found to selectively recognize PPi, leading to a ratiometric fluorescent sensor at pH 7.4 in water. The binding event triggered a large fluorescence response (∼100 nm bathochromic shift) by turning on the excited state intramolecular proton transfer (ESIPT). Detection of PPi released from a PCR experiment indicated that this new probe could be a useful tool in bioanalytical applications. © 2011 American Chemical Society.


Maslov D.A.,University of California at Riverside
Molecular and Biochemical Parasitology | Year: 2010

Editing of mRNA transcribed from the mitochondrial cryptogenes ND8 (G1), ND9 (G2), G3, G4, ND3 (G5), RPS12 (G6) was investigated in Leishmania mexicana amazonensis, strain LV78, by amplification of the cDNA, cloning and sequencing. For each of these genes, extensively and partially edited transcripts were found to be relatively abundant compared to the respective pre-edited molecules. Moreover, the editing patterns observed in a majority of transcripts of each gene were consistent among themselves which allowed for inferring consensus editing sequences. The open reading frames contained in the consensus sequences were predicted to encode polypeptides that were highly similar to their counterparts in other species of Trypanosomatidae. Several kinetoplast DNA minicircles from this species available in the public domain were found to contain genes for guide RNAs which mediate editing of some of the mRNAs. The results indicate that the investigated strain of L. m. amazonensis has preserved its full editing capacity in spite of the long-term maintenance in culture. This property differs drastically from the other Leishmania species which lost some or all of the G1-G5 mRNA editing ability in culture. © 2010 Elsevier B.V.


Palacios-Laloy A.,CEA Saclay Nuclear Research Center | Mallet F.,CEA Saclay Nuclear Research Center | Nguyen F.,CEA Saclay Nuclear Research Center | Bertet P.,CEA Saclay Nuclear Research Center | And 3 more authors.
Nature Physics | Year: 2010

The violation of Bell inequalities with two entangled and spatially separated quantum two-level systems (TLSs) is often considered as the most prominent demonstration that nature does not obey local realism. Under different but related assumptions of macrorealism-which macroscopic systems plausibly fulfil-Leggett and Garg derived a similar inequality for a single degree of freedom undergoing coherent oscillations and being measured at successive times. Here, we test such a Bells inequality in time, which should be violated by a quantum TLS. Our TLS is a superconducting quantum circuit in which Rabi oscillations are continuously driven while it is continuously and weakly measured. The time correlations present at the detector output agree with quantum-mechanical predictions and violate the Leggett-Garg inequality by five standard deviations. © 2010 Macmillan Publishers Limited. All rights reserved.


Shamsuddin A.K.M.,University of California at San Diego | Quinton P.M.,University of California at San Diego | Quinton P.M.,University of California at Riverside
Journal of Physiology | Year: 2012

• Using a small glass capillary, an Ussing chamber was designed and used to measure electrical properties across very small pieces (<1 mm 2) of freshly dissected epithelia. • The system was applied to small airways of the lung to show that fluids on the airway surfaces are constantly being simultaneously secreted and absorbed. • A new model proposes that the accordion-like structure of folds and pleats in the epithelial lining of the airways serves to secrete fluid within the pleats and to absorb fluid along the folds so that fluid levels on the airway surfaces are maintained automatically and airways do not flood or become too dry. • These results help us understand the first line of lung defence against infections from bacteria and viruses and may be used to treat or prevent lung disease. Native small airways must remain wet enough to be pliable and support ciliary clearance, but dry enough to remain patent for gas flow. The airway epithelial lining must both absorb and secrete ions to maintain a critical level of fluid on its surface. Despite frequent involvement in lung diseases, the minuscule size has limited studies of peripheral airways. To meet this challenge, we used a capillary to construct an Ussing chamber (area <1 mm 2) to measure electrolyte transport across small native airways (∼1 mm ø) from pig lung. Transepithelial potentials (V t) were recorded in open circuit conditions while applying constant current pulses across the luminal surface of dissected airways to calculate transepithelial electrical conductance (G t) and equivalent short circuit current in the presence and absence of selected Na + and Cl - transport inhibitors (amiloride, GlyH-101, Niflumic acid) and agonists (Forskolin + IBMX, UTP). Considered together the responses suggest an organ composed of both secreting and absorbing epithelia that constitutively and concurrently transport fluids into and out of the airway, i.e. in opposite directions. Since the epithelial lining of small airways is arranged in long, accordion-like rows of pleats and folds that run axially down the lumen, we surmise that cells within the pleats are mainly secretory while the cells of the folds are principally absorptive. This structural arrangement could provide local fluid transport from within the pleats toward the luminal folds that may autonomously regulate the local surface fluid volume for homeostasis while permitting acute responses to maintain clearance. © 2012 The Authors. The Journal of Physiology © 2012 The Physiological Society.


Ives A.R.,University of Wisconsin - Madison | Garland T.,University of California at Riverside
Systematic Biology | Year: 2010

We develop statistical methods for phylogenetic logistic regression in which the dependent variable is binary (0 or 1) and values are nonindependent among species, with phylogenetically related species tending to have the same value of the dependent variable. The methods are based on an evolutionary model of binary traits in which trait values switch between 0 and 1 as species evolve up a phylogenetic tree. The more frequently the trait values switch (i.e., the higher the rate of evolution), the more rapidly correlations between trait values for phylogenetically related species break down. Therefore, the statistical methods also give a way to estimate the phylogenetic signal of binary traits. More generally, the methods can be applied with continuous-and/or discrete-valued independent variables. Using simulations, we assess the statistical properties of the methods, including bias in the estimates of the logistic regression coefficients and the parameter that estimates the strength of phylogenetic signal in the dependent variable. These analyses show that, as with the case for continuous-valued dependent variables, phylogenetic logistic regression should be used rather than standard logistic regression when there is the possibility of phylogenetic correlations among species. Standard logistic regression does not properly account for the loss of information caused by resemblance of relatives and as a result is likely to give inflated type I error rates, incorrectly identifying regression parameters as statistically significantly different from zero when they are not.


Lock J.,University of California at Riverside
International journal of nanomedicine | Year: 2011

Nanomaterials have unique advantages in controlling stem cell function due to their biomimetic characteristics and special biological and mechanical properties. Controlling adhesion and differentiation of stem cells is critical for tissue regeneration. This in vitro study investigated the effects of nano-hydroxyapatite, nano-hydroxyapatite-polylactide- co-glycolide (PLGA) composites, and a bone morphogenetic protein (BMP-7)- derived short peptide (DIF-7c) on osteogenic differentiation of human mesenchymal stem cells (MSC). The peptide was chemically functionalized onto nano-hydroxyapatite, incorporated into a nanophase hydroxyapatite-PLGA composite or PLGA control, or directly injected into culture media. Unlike the PLGA control, the nano-hydroxyapatite-PLGA composites promoted adhesion of human MSC. Importantly, nano-hydroxyapatite and nano-hydroxyapatite-PLGA composites promoted osteogenic differentiation of human MSCs, comparable with direct injection of the DIF-7c peptide into culture media. Nano-hydroxyapatite and nano-hydroxyapatite-PLGA composites provide a promising alternative in directing the adhesion and differentiation of human MSC. These nanocomposites should be studied further to clarify their effects on MSC functions and bone remodeling in vivo, eventually translating to clinical applications.


Ma E.,University of California at Riverside
Physical Review Letters | Year: 2014

The fundamental issue of the origin of mass for all quarks and leptons (including Majorana neutrinos) is linked to dark matter, odd under an exactly conserved Z2 symmetry which may or may not be derivable from an U(1)D gauge symmetry. The observable sector interacts with a proposed dark sector which consists of heavy neutral singlet Dirac fermions and suitably chosen new scalars. Flavor symmetry is implemented in a renormalizable context with just the one Higgs doublet (+,0) of the standard model in such a way that all observed fermions obtain their masses radiatively through dark matter. © 2014 American Physical Society.


Khitun A.,University of California at Riverside
Journal of Applied Physics | Year: 2013

In this work, we consider the possibility of building magnetic analog logic devices utilizing spin wave interference for special task data processing. As an example, we consider a multi-terminal magnonic matrix switch comprising multiferroic elements and a two-dimensional grid of magnetic waveguides connected via four-terminal cross-junctions. The multiferroic elements are placed on the periphery of the switch and used as input/output ports for signal conversion among the electric and magnetic domains. Data processing is accomplished via the use of spin wave interference within the magnonic matrix. We present the results of numerical modeling illustrating device operation for pattern matching, finding the period of the data string, and image processing. We also present the results of numerical modeling showing the device capabilities as a magnetic holographic memory. Magnonic holographic devices are of great potential to complement the conventional general-type processors in special task data processing and may provide a new direction for functional throughput enhancement. According to estimates, magnonic holographic devices can provide up to 1 Tb/cm2 data storage density and data processing rate exceeding 1018 bits/s/cm2. The physical limitations and practical challenges of the proposed approach are discussed. © 2013 AIP Publishing LLC.


Kposowa A.J.,University of California at Riverside
International Journal of Infectious Diseases | Year: 2013

Objectives: The purpose of the study was to examine associations between marital status groups and death from HIV/AIDS. The primary hypothesis was that divorced and single/never married individuals have a much higher risk of death than married persons. Methods: Data were derived from the third release of the US National Longitudinal Mortality Study. Cox proportional regression models were fitted to the data. Results: It was found that marital status is associated with mortality from HIV. Divorced and separated individuals were 4.3 times more likely to die of HIV/AIDS than married individuals (adjusted relative risk (aRR) 4.321, 95% confidence interval (CI) 2.978, 6.269). Single/never married persons were 13 times as likely to die of HIV/AIDS as their married counterparts (aRR 13.092, 95% CI 9.652, 17.757). When the sample was stratified by sex, however, it was observed that while marital status was associated with HIV/AIDS mortality among men, it had no significant association with death in women. However, African-American women (aRR 9.23, 95% CI 4.47, 19.03) and Hispanic women (aRR 7.06, 95% CI 3.03, 16.45) had a significantly higher risk of death than their non-Hispanic white female counterparts. Conclusions: Marital status is a significant risk factor for mortality from HIV/AIDS, but this association is only valid for men. The different gender mortality experiences suggest that for HIV/AIDS more population-based studies comprising marital status risk factor histories are needed, given the limited research on marital status and mortality from the disease. © 2013 International Society for Infectious Diseases.


Gehling J.G.,University of Adelaide | Droser M.L.,University of California at Riverside
Geology | Year: 2013

Patterns of origination, evolution, and extinction of early animal life on this planet are largely interpreted from the fossils of the Precambrian soft-bodied Ediacara Biota, spanning nearly 40 m.y. of the terminal Ediacaran period. Localities containing these fossils are loosely considered as part of either the Avalon, White Sea, or Nama Associations. These associations have been interpreted to have temporal, paleobiogeographic, preservational, and/or paleoenvironmental signifi -cance. Surprisingly, elements of all three associations occur within the Ediacara Member of the Rawnsley Quartzite of South Australia. An analysis of over 5000 specimens demonstrates that fossil distribution is strongly controlled by facies and taphonomy rather than time or biogeography and that individual taxa vary considerably in their environmental tolerance and taphonomic integrity. The recognition that these taxa represent organisms living in various distinct environments, both juxtaposed and shared, holds strong implications for our interpretation of the record of early animal life on this planet and questions the biostratigraphic utility of the three associations. Furthermore, although in situ soft-bodied preservation provides a unique perspective on composition of benthic fossil assemblages, the record should not be interpreted as a simple "snapshot". Fossil beds represent a range of preservational modifi cations varying from current winnowed census samples of benthic communities at different depths and ecological maturity, to entirely transported assemblages. Unless the appropriate environments and taphonomic conditions are present for certain taxa, the absence of a particular taxon may or may not indicate its extinction in space or time. © 2013 Geological Society of America.


Wang Q.,Xinjiang Institute of Ecology and Geography | Wang Q.,University of California at Riverside | Chen X.,Xinjiang Institute of Ecology and Geography | Jha A.N.,University of Plymouth | Rogers H.,University of Oxford
Renewable and Sustainable Energy Reviews | Year: 2014

Extraction of natural gas from shale rock in the United States (US) is one of the landmark events in the 21st century. The combination of horizontal drilling and hydraulic fracturing can extract huge quantities of natural gas from impermeable shale formations, which were previously thought to be either impossible or uneconomic to produce. This review offers a comprehensive insight into US shale gas opportunities, appraising the evolution, evidence and the challenges of shale gas production in the US. The history of US shale gas in this article is divided into three periods and based on the change of oil price (i.e., the period before the 1970s oil crisis, the period from 1970s to 2000, and the period since 2000), the US has moved from being one of the world's biggest importers of gas to being self-sufficient in less than a decade, with the shale gas production increasing 12-fold (from 2000 to 2010). The US domestic natural gas price hit a 10-year low in 2012. The US domestic natural gas price in the first half of 2012 was about $2 per million British Thermal Unit (BTU), compared with Brent crude, the world benchmark price for oil, now about $ 80-100/barrel, or $14-17 per million BTU. Partly due to an increase in gas-fired power generation in response to low gas prices, US carbon emissions from fossil-fuel combustion fell by 430 million ton CO2 - more than any other country - between 2006 and 2011. Shale gas also stimulated economic growth, creating 600,000 new jobs in the US by 2010. However, the US shale gas revolution would be curbed, if the environmental risks posed by hydraulic fracturing are not managed effectively. The hydraulic fracturing is water intensive, and can cause pollution in the marine environment, with implications for long-term environmental sustainability in several ways. Also, large amounts of methane, a powerful greenhouse gas, can be emitted during the shale gas exploration and production. Hydraulic fracturing also may induce earthquakes. These environmental risks need to be managed by good practices which is not being applied by all the producers in all the locations. Enforcing stronger regulations are necessary to minimize risk to the environment and on human health. Robust regulatory oversight can however increase the cost of extraction, but stringent regulations can foster an historic opportunity to provide cheaper and cleaner gas to meet the consumer demand, as well as to usher in the future growth of the industry. © 2013 Elsevier Ltd.


Sete E.A.,University of California at Riverside | Eleuch H.,McGill University
Physical Review A - Atomic, Molecular, and Optical Physics | Year: 2014

We investigate nonlinear effects in an electromechanical system consisting of a superconducting charge qubit coupled to a transmission line resonator and a nanomechanical oscillator, which in turn is coupled to another transmission line resonator. The nonlinearities induced by the superconducting qubit and the optomechanical coupling play an important role in creating optomechanical entanglement as well as the squeezing of the transmitted microwave field. We show that strong squeezing of the microwave field and robust optomechanical entanglement can be achieved in the presence of moderate thermal decoherence of the mechanical mode. We also discuss the effect of the coupling of the superconducting qubit to the nanomechanical oscillator on the bistability behavior of the mean photon number. © 2014 American Physical Society.


Alarcon R.,University of California at Riverside | Alarcon R.,California State University, Channel Islands
Oikos | Year: 2010

Most recent studies describing pollination networks are based on observed flower visits, and few have explicitly tested if the floral visitors actually carry pollen. Since floral visitors can vary in their ability to remove and transfer pollen, it is important to show that visitation patterns reflect effective pollination. Given the difficulty of measuring per-visit pollen deposition at the community scale, a first step is to examine the amount of conspecific pollen carried by insect visitors. Here I compared the plant-animal visitation network with the pollen-transport network, estimated from insect pollen loads, for a montane meadow community from southern California, USA. Visitation and pollen-transport networks were positively associated with each other in both 2001 and 2002. However, the exclusion of visitors that do not carry any conspecific pollen reveals that pollen-transport networks are more specialized from the plants' perspective and that species are involved in fewer mutualistic interactions compared with estimates derived from visitation frequencies. Although conspecific pollen loads were smaller in 2002, bees tended to carry the largest conspecific loads in both years and were responsible for transporting the most pollen. These results suggest that, although visitation networks are suitable first-order approximations of pollination networks, information on which visitors carry conspecific pollen, and in what amounts, is crucial for distinguishing between antagonistic and mutualistic interactions. © 2009 Oikos.


Hua Y.,University of California at Riverside
Proceedings - IEEE Military Communications Conference MILCOM | Year: 2010

This paper provides an overview of the design of transmit and receive beamformers and transmit power allocation for MIMO relays. Soft and hard methods for interference cancelation are presented, which play a critical role for all MIMO relays whether they are full-duplex or half-duplex, regenerative or non-regenerative, one-way relay or two-way relay. A perspective of MIMO relays in a network of many hops is illustrated. A distinction is made between feedback loop of energy and feedback loop of noise. Subspace computation and a generalized water-filling (GWF) algorithm are shown as important building blocks for the design. ©2010 IEEE.


Olds G.R.,University of California at Riverside
Transactions of the American Clinical and Climatological Association | Year: 2013

Worms or helminths have historically infected more than half the world's population, but were largely neglected by medical science and public health interventions because they were considered non-fatal and of minimal clinical significance. During the 1980s, several oral drugs that were originally developed for veterinary use were discovered to cure, in a single dose, most human helminth infections. This allowed the first systematic population-based studies of the morbid sequelae of chronic worm infection and their potential reversibility after treatment. Based on these studies, we now know that almost all infected children and many adults, particularly pregnant and lactating women, suffer adverse effects from worms, including growth stunting, anemia, decreased cognitive development, and poor birth outcomes as well as poor school and work performance. Worm-infected people also respond less well to vaccinations and are more susceptible to several co-conditions such as HIV and cirrhosis. Based on these findings, several vertically organized national control programs were initiated in developing countries against schistosomiasis and the soil-transmitted helminths (hookworm, ascariasis, and whipworm). In 2005, the impact of helminth infections was redefined in terms of disability-adjusted life years (DALYs). All worm infections amenable to population-based mass chemotherapy are thought today to cause 30 million DALYs worldwide or very close to the worldwide impact of tuberculosis (TB) or malaria. In addition, almost all worm-induced DALYs are potentially reversible or preventable with periodic treatment. In 2001, the World Health Assembly advocated for mass deworming to reach 75% of the at-risk school-aged children of the world, but by 2011 only 13% had been reached. The recent large donations of anti-helminth drugs by major pharmaceutical companies linked to the inclusion of the "neglected tropical diseases" into current priorities for AIDS/TB and malaria now represent the best hope for closing this gap.


Balandin A.A.,University of California at Riverside
Nature Materials | Year: 2011

Recent years have seen a rapid growth of interest by the scientific and engineering communities in the thermal properties of materials. Heat removal has become a crucial issue for continuing progress in the electronic industry, and thermal conduction in low-dimensional structures has revealed truly intriguing features. Carbon allotropes and their derivatives occupy a unique place in terms of their ability to conduct heat. The room-temperature thermal conductivity of carbon materials span an extraordinary large range-of over five orders of magnitude-from the lowest in amorphous carbons to the highest in graphene and carbon nanotubes. Here, I review the thermal properties of carbon materials focusing on recent results for graphene, carbon nanotubes and nanostructured carbon materials with different degrees of disorder. Special attention is given to the unusual size dependence of heat conduction in two-dimensional crystals and, specifically, in graphene. I also describe the prospects of applications of graphene and carbon materials for thermal management of electronics. © 2011 Macmillan Publishers Limited. All rights reserved.


Garay J.E.,University of California at Riverside
Annual Review of Materials Research | Year: 2010

This review of current-activated, pressure-assisted densification (CAPAD) focuses on both fundamental and practical issues. We provide some useful background for researchers interested in the process and critically assess the state of the technique. © 2010 by Annual Reviews. All rights reserved.


Katiyar-Agarwal S.,University of Delhi | Jin H.,University of California at Riverside
Annual Review of Phytopathology | Year: 2010

Plant defense responses against pathogens are mediated by activation and repression of a large array of genes. Host endogenous small RNAs are essential in this gene expression reprogramming process. Here, we discuss recent findings on pathogen-regulated host microRNAs (miRNAs) and small interfering RNAs (siRNAs) and their roles in plant-microbe interaction. We further introduce small RNA pathway components, including Dicer-like proteins (DCLs), double-stranded RNA (dsRNA) binding protein, RNA-dependent RNA polymerases (RDRs), small RNA methyltransferase HEN1, and Argonaute (AGO) proteins, that contribute to plant immune responses. The strategies that pathogens have evolved to suppress host small RNA pathways are also discussed. Collectively, host small RNAs and RNA silencing machinery constitute a critical layer of defense in regulating the interaction of pathogens with plants. © 2010 by Annual Reviews. All rights reserved.


Baharlouei Z.,Isfahan University of Technology | Hashemi M.,Isfahan University of Technology | Narimani H.,Isfahan University of Technology | Mohsenian-Rad H.,University of California at Riverside
IEEE Transactions on Smart Grid | Year: 2013

Autonomous demand response (DR) programs are scalable and result in a minimal control overhead on utilities. The idea is to equip each user with an energy consumption scheduling (ECS) device to automatically control the user's flexible load to minimize his energy expenditure, based on the updated electricity pricing information. While most prior works on autonomous DR have focused on coordinating the operation of ECS devices in order to achieve various system-wide goals, such as minimizing the total cost of generation or minimizing the peak-to-average ratio in the load demand, they fall short addressing the important issue of fairness. That is, while they usually guarantee optimality, they do not assure that the participating users are rewarded according to their contributions in achieving the overall system's design objectives. Similarly, they do not address the important problem of co-existence when only a sub-set of users participate in a deployed autonomous DR program. In this paper, we seek to tackle these shortcomings and design new autonomous DR systems that can achieve both optimality and fairness. In this regard, we first develop a centralized DR system to serve as a benchmark. Then, we develop a smart electricity billing mechanism that can enforce both optimality and fairness in autonomous DR systems in a decentralized fashion. © 2010-2012 IEEE.


The charge-density-wave (CDW) phase is a macroscopic quantum state consisting of a periodic modulation of the electronic charge density accompanied by a periodic distortion of the atomic lattice in quasi-1D or layered 2D metallic crystals. Several layered transition metal dichalcogenides, including 1T-TaSe2, 1T-TaS2 and 1T-TiSe2 exhibit unusually high transition temperatures to different CDW symmetry-reducing phases. These transitions can be affected by the environmental conditions, film thickness and applied electric bias. However, device applications of these intriguing systems at room temperature or their integration with other 2D materials have not been explored. Here, we demonstrate room-temperature current switching driven by a voltage-controlled phase transition between CDW states in films of 1T-TaS2 less than 10 nm thick. We exploit the transition between the nearly commensurate and the incommensurate CDW phases, which has a transition temperature of 350 K and gives an abrupt change in current accompanied by hysteresis. An integrated graphene transistor provides a voltage-tunable, matched, low-resistance load enabling precise voltage control of the circuit. The 1T-TaS2 film is capped with hexagonal boron nitride to provide protection from oxidation. The integration of these three disparate 2D materials in a way that exploits the unique properties of each yields a simple, miniaturized, voltage-controlled oscillator suitable for a variety of practical applications. © 2016 Nature Publishing Group


Friedman H.S.,University of California at Riverside | Kern M.L.,University of Pennsylvania | Hampson S.E.,Oregon Research Institute | Duckworth A.L.,University of Pennsylvania
Developmental Psychology | Year: 2014

Conscientiousness has been shown to predict healthy behaviors, healthy social relationships, and physical health and longevity. The causal links, however, are complex and not well elaborated. Many extant studies have used comparable measures for conscientiousness, and a systematic endeavor to build cross-study analyses for conscientiousness and health now seems feasible. Of particular interest are efforts to construct new, more comprehensive causal models by linking findings and combining data from existing studies of different cohorts. Although methodological perils can threaten such integration, such efforts offer an early opportunity to enliven a life course perspective on conscientiousness, to see whether component facets of conscientiousness remain related to each other and to relevant mediators across broad spans of time, and to bolster the findings of the few long-term longitudinal studies of the dynamics of personality and health. A promising approach to testing new models involves pooling data from extant studies as an efficient and heuristic prelude to large-scale testing of interventions. © 2012 American Psychological Association.


Aphasizheva I.,University of California at Irvine | Maslov D.,University of California at Riverside | Wang X.,University of California at Irvine | Huang L.,University of California at Irvine | Aphasizhev R.,University of California at Irvine
Molecular Cell | Year: 2011

The majority of trypanosomal mitochondrial pre-mRNAs undergo massive uridine insertion/deletion editing, which creates open reading frames. Although the pre-editing addition of short 3′ A tails is known to stabilize transcripts during and after the editing, the processing event committing the fully edited mRNAs to translation remained unknown. Here, we show that a heterodimer of pentatricopeptide repeat-containing (PPR) proteins, termed kinetoplast poly. adenylation/uridylation factors (KPAFs) 1 and 2, induces the postediting addition of A/U heteropolymers by KPAP1 poly(A) polymerase and RET1 terminal uridyltransferase. Edited transcripts bearing 200- to 300-nucleotide-long A/U tails, but not short A tails, were enriched in translating ribosomal complexes and affinity-purified ribosomal particles. KPAF1 repression led to a selective loss of A/U-tailed mRNAs and concomitant inhibition of protein synthesis. These results establish A/U extensions as the defining cis-elements of translation-competent mRNAs. Furthermore, we demonstrate that A/U-tailed mRNA preferentially interacts with the small ribosomal subunit, whereas edited substrates and complexes bind to the large subunit. © 2011 Elsevier Inc.


Ma E.,University of California at Riverside | Srivastava R.,Chennai Mathematical Institute
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2015

Many studies have been made on extensions of the standard model with B-L gauge symmetry. The addition of three singlet (right-handed) neutrinos renders it anomaly-free. It has always been assumed that the spontaneous breaking of B-L is accomplished by a singlet scalar field carrying two units of B-L charge. This results in a very natural implementation of the Majorana seesaw mechanism for neutrinos. However, there exists in fact another simple anomaly-free solution which allows Dirac or inverse seesaw neutrino masses. We show for the first time these new possibilities and discuss an application to neutrino mixing with S3 flavor symmetry. © 2015 The Authors.


Whitney K.D.,Rice University | Garland Jr. T.,University of California at Riverside
PLoS Genetics | Year: 2010

Mechanisms underlying the dramatic patterns of genome size variation across the tree of life remain mysterious. Effective population size (Ne) has been proposed as a major driver of genome size: selection is expected to efficiently weed out deleterious mutations increasing genome size in lineages with large (but not small) Ne. Strong support for this model was claimed from a comparative analysis of Neu and genome size for ≈30 phylogenetically diverse species ranging from bacteria to vertebrates, but analyses at that scale have so far failed to account for phylogenetic nonindependence of species. In our reanalysis, accounting for phylogenetic history substantially altered the perceived strength of the relationship between Neu and genomic attributes: there were no statistically significant associations between Neu and gene number, intron size, intron number, the half-life of gene duplicates, transposon number, transposons as a fraction of the genome, or overall genome size. We conclude that current datasets do not support the hypothesis of a mechanistic connection between Ne and these genomic attributes, and we suggest that further progress requires larger datasets, phylogenetic comparative methods, more robust estimators of genetic drift, and a multivariate approach that accounts for correlations between putative explanatory variables. © 2010 Whitney, Garland.


Oikawa P.Y.,University of California at Riverside | Lerdau M.T.,University of Virginia
Trends in Plant Science | Year: 2013

Plants emit a diverse array of phytogenic volatile organic compounds (VOCs). The production and emission of VOCs has been an important area of research for decades. However, recent research has revealed the importance of VOC catabolism by plants and VOC degradation in the atmosphere for plant growth and survival. Specifically, VOC catabolism and degradation have implications for plant C balance, tolerance to environmental stress, plant signaling, and plant-atmosphere interactions. Here we review recent advances in our understanding of VOC catabolism and degradation, propose experiments for investigating VOC catabolism, and suggest ways to incorporate catabolism into VOC emission models. Improving our knowledge of VOC catabolism and degradation is crucial for understanding plant metabolism and predicting plant survival in polluted environments. © 2013 Elsevier Ltd.


Norman A.W.,University of California at Riverside
Annals of Nutrition and Metabolism | Year: 2012

It is largely through historical accident in the interval of 1920-1940 that vitamin D3 became classified as a vitamin rather than as a steroid hormone. The formal definition of a vitamin is that it is a trace dietary constituent required to produce the normal function of a physiological process or processes. The emphasis here is on trace and the fact that the vitamin must be supplied regularly in the diet; this implies that the body is unable to metabolically synthesize the vitamin in question. However, the ultraviolet exposure of 7-dehydrocholesterol present in the skin results in the photochemical production of vitamin D3. Thus, vitamin D3 becomes a true vitamin only when the animal or human does not have regular access to sunlight or ultraviolet light. Under normal physiological circumstances, all mammals, including humans, can generate, via ultraviolet exposure of 7-dehydrocholesterol present in the skin, adequate quantities of vitamin D3 to meet their nutritionally defined requirements. There is a vibrant historical record beginning in 1650 and culminating in 1963 concerned with the determination of the chemical structures of vitamin D3 and vitamin D2. A surprising aspect concerning vitamin D3 is that it is itself biologically inert. There are no known essential biological actions or contributions that rely specifically on the molecule vitamin D 3. While chemists had certainly appreciated the strong structural similarity between the vitamins D and other steroids, this correlation was never widely acknowledged in the biological, clinical, or nutritional sciences until 1965-1970. The biological role of vitamin D3 is to serve as a substrate for the liver 25-hydroxylase which produces 25-hydroxyvitamin D 3 [25(OH)D3]. 25(OH)D3 in turn serves as the substrate for the kidney proximal tubule 25(OH)D3-1α- hydroxylase enzyme which produces the steroid hormone 1α,25(OH) 2-vitamin D3 [1α,25(OH)2D3]. Copyright © 2012 S. Karger AG, Basel.


Dunn M.F.,University of California at Riverside
Archives of Biochemistry and Biophysics | Year: 2012

The tryptophan synthase α 2β 2 bi-enzyme complex catalyzes the last two steps in the synthesis of L-tryptophan (L-Trp). The α-subunit catalyzes cleavage of 3-indole-D-glycerol 3′-phosphate (IGP) to give indole and D-glyceraldehyde 3′-phosphate (G3P). Indole is then transferred (channeled) via an interconnecting 25 -long tunnel, from the α-subunit to the β-subunit where it reacts with L-Ser in a pyridoxal 5′-phosphate-dependent reaction to give L-Trp and a water molecule. The efficient utilization of IGP and L-Ser by tryptophan synthase to synthesize L-Trp utilizes a system of allosteric interactions that (1) function to switch the α-site on and off at different stages of the β-subunit catalytic cycle, and (2) prevent the escape of the channeled intermediate, indole, from the confines of the α- and β-catalytic sites and the interconnecting tunnel. This review discusses in detail the chemical origins of the allosteric interactions responsible both for switching the α-site on and off, and for triggering the conformational changes between open and closed states which prevent the escape of indole from the bienzyme complex. © 2011 Elsevier Inc. All rights reserved.


Qin X.,University of California at Riverside
Planta | Year: 2014

Jatropha curcas, a biodiesel plant with a short life cycle, has great potentials to be a new model woody plant. In this study, we found a plant-specific transcription factor JcNAC1, an intriguing regulator modulating plant responses to abiotic stresses and pathogen infection. Expression of JcNAC1 was strongly increased when plants were treated with abscisic acid, salt and polyethylene glycol, and was decreased with salicylic acid, ethylene, and pathogens. Overexpressing JcNAC1 plants showed enhanced tolerance to drought and increased susceptibility to pathogens. Furthermore, over-expression of JcNAC1 in plants also resulted in the expression changes of some stress-related maker genes including curcin-L, which is a special stress-inducible ribosome-inactivating protein gene in J. curcas. These results indicate that JcNAC1 is responsible for stress responses in J. curcas.


Farley R.D.,University of California at Riverside
Frontiers in Zoology | Year: 2011

Background: Near the end of the nineteenth century the hypothesis was presented for the homology of book lungs in arachnids and book gills in the horseshoe crab. Early studies with the light microscope showed that book gill lamellae are formed by outgrowth and possibly some invagination (infolding) of hypodermis (epithelium) from the posterior surface of opisthosomal limb buds. Scorpion book lungs are formed near the bilateral sites of earlier limb buds. Hypodermal invaginations in the ventral opisthosoma result in spiracles and sac-like cavities (atria). In early histological sections of embryo book lungs, widening of the atrial entrance of some lamellae (air channels, air sacs, saccules) was interpreted as an indication of invagination as hypothesized for book gill lamellae. The hypodermal infolding was thought to produce the many rows of lamellar precursor cells anterior to the atrium. The ultrastructure of scorpion book lung development is compared herein with earlier investigations of book gill formation.Results: In scorpion embryos, there is ingression (inward migration) of atrial hypodermal cells rather than invagination or infolding of the atrial hypodermal layer. The ingressing cells proliferate and align in rows anterior to the atrium. Their apical-basal polarity results in primordial air channels among double rows of cells. The cuticular walls of the air channels are produced by secretion from the apical surfaces of the aligned cells. Since the precursor cells are in rows, their secreted product is also in rows (i.e., primordial air channels, saccules). For each double row of cells, their opposed basal surfaces are gradually separated by a hemolymph channel of increasing width.Conclusions: The results from this and earlier studies show there are differences and similarities in the formation of book lung and book gill lamellae. The homology hypothesis for these respiratory organs is thus supported or not supported depending on which developmental features are emphasized. For both organs, when the epithelial cells are in position, their apical-basal polarity results in alternate page-like channels of hemolymph and air or water with outward directed hemolymph saccules for book gills and inward directed air saccules for book lungs. © 2011 Farley; licensee BioMed Central Ltd.


Huang Y.,Qualcomm | Hua Y.,University of California at Riverside
IEEE Transactions on Signal Processing | Year: 2011

This paper addresses a transmission energy problem for distributed (or decentralized) estimation in multihop wireless sensor networks (WSN). A primary advantage of distributed estimation is its energy efficiency when compared to centralized estimation. Two distributed estimation schemes are considered in this paper: progressive estimation and consensus estimation. We develop a generalized energy planning algorithm for a progressive estimation method which exploits routing tree and channel state information. We also analyze the energy cost for a consensus estimation method used in broadcast multihop WSN. We demonstrate by analysis and simulation that, subject to an equivalent performance, the total energy cost for consensus estimation is typically much higher than that for progressive estimation, but the peak energy for the former can be less than that for the latter. © 2011 IEEE.


Samadi P.,University of British Columbia | Mohsenian-Rad H.,University of California at Riverside | Wong V.W.S.,University of British Columbia | Schober R.,University of British Columbia
IEEE Transactions on Smart Grid | Year: 2013

In this paper, we propose a novel optimization-based real-time residential load management algorithm that takes into account load uncertainty in order to minimize the energy payment for each user. Unlike most existing demand side management algorithms that assume perfect knowledge of users' energy needs, our design only requires knowing some statistical estimates of the future load demand. Moreover, we consider real-time pricing combined with inclining block rate tariffs. In our problem formulation, we take into account different types of constraints on the operation of different appliances such as must-run appliances, controllable appliances that are interruptible, and controllable appliances that are not interruptible. Our design is multi-stage. As the demand information of the appliances is gradually revealed over time, the operation schedule of controllable appliances is updated accordingly. Simulation results confirm that the proposed energy consumption scheduling algorithm can benefit both users, by reducing their energy expenses, and utility companies, by improving the peak-to-average ratio of the aggregate load demand. © 2010-2012 IEEE.


Turecek F.,University of Washington | Julian R.R.,University of California at Riverside
Chemical Reviews | Year: 2013

The salient aspect of cation radical reactions is that they are mostly radical driven. They involve omolytic bond cleavages and hydrogen atom migrations. Mass spectrometry of small free radicals has been reviewed. Dissociations of even-electron ions under slow heating conditions are dominated by heterolytic bond cleavages accompanied by proton or larger group migrations that often result in quite complicated reaction pathways. In the particular case of peptide even-electron ions, the main dissociations are eliminations of small molecules (water, ammonia) and proton-driven cleavages of amide bonds. The latter are essential for peptide sequencing by mass spectrometry. A different approach to peptide cation radicals relied on transition metal complexes produced by electrospray that showed radical-driven dissociations such as homolytic bond dissociations upon collisional activation in the slow heating regime. With a proper choice of the metal ion and organic ligands, peptide ternary complexes have been shown to undergo intramolecular electron transfer upon collisional activation, producing metal-free peptide ions.


Bartels L.,University of California at Riverside
Nature Chemistry | Year: 2010

The design of networks of organic molecules at metal surfaces, highly attractive for a variety of applications ranging from molecular electronics to gas sensors to protective coatings, has matured to a degree that patterns with multinanometre unit cells and almost any arbitrary geometry can be fabricated. This Review provides an overview of vacuum-deposited organic networks at metal surfaces, using intermolecular hydrogen bonding, metal-atom coordination and in situ polymerization. Recent progress in these areas highlights how the design of surface patterns can benefit from the wealth of information available from solution- and bulk-phase chemistry, while at the same time providing novel insights into the nature of such bonds through the applicability of direct scanning probe imaging at metal surfaces. © 2010 Macmillan Publishers Limited. All rights reserved.


Daane K.M.,University of California at Berkeley | Johnson M.W.,University of California at Riverside
Annual Review of Entomology | Year: 2010

Olive fruit fly, Bactrocera oleae (Rossi) (Diptera: Tephritidae), is the major pest of commercial olives worldwide. Various aspects of its biology, ecology, management, and impact on olive production are highlighted. With the discovery of insecticidal resistance in some populations frequently treated with organophosphates, old and new control options are being investigated. The potential of biological control is examined. Surveys suggest that a small group of braconids in the Opiinae subfamily best represent the primary parasitoids attacking olive fruit fly in its native range. These species include Psyttalia lounsburyi, P. dacicida, P. concolor, P. ponerophaga, and Utetes africanus. Bracon celer, another braconid but in the Braconinae subfamily, is also reared from the fruit fly in its native range. The potential of these and other natural enemies is discussed with respect to olive fruit fly biology, commercial olive production, and biological constraints that may limit their success. We suggest that numerous species exist that should be further investigated as control agents for olive fruit fly in the many climatic regimes where the pest is found. © 2010 by Annual Reviews All rights reserved.


Vafai K.,University of California at Riverside | Yang K.,Huazhong University of Science and Technology
Transport in Porous Media | Year: 2013

This work address a number of fundamental issues and concepts related to local thermal non-equilibrium and the heat flux bifurcation phenomenon in porous media. Different types of heat flux bifurcation phenomenon are discussed in relation to previous works by the authors. © 2012 Springer Science+Business Media Dordrecht.


Lin K.,Zhejiang University of Technology | Gan J.,University of California at Riverside
Chemosphere | Year: 2011

Presence of pharmaceuticals at trace levels in recycled water is an emerging issue impacting the beneficial reuse of treated wastewater, including practices such as irrigation and groundwater recharge in arid and semi-arid regions. To assess the environmental risks of irrigation with recycled water containing such micropollutants, in this study we evaluated sorption and degradation of five pharmaceuticals that are antibiotic and anti-inflammatory drugs in two soils collected from arid regions. Naproxen and trimethoprim showed moderate to strong sorption, while the sorption of diclofenac, ibuprofen and sulfamethoxazole was negligible in both soils. Under aerobic conditions, the studied compounds were susceptible to microbial degradation with half-lives varying from 4.8 to 69.3. d. Apart from sulfamethoxazole, the other compounds were relatively persistent under anaerobic conditions as indicated by a negligible loss over 84. d of incubation or half-lives >50. d. The degradation of the selected pharmaceuticals was influenced by microbial activities, oxygen status in the soil, soil type and compound characteristics. The poor sorption and relative persistence of diclofenac and ibuprofen under anaerobic conditions suggest that the two chemicals may pose a high leaching risk when using recycled for irrigation or groundwater replenishment. © 2010 Elsevier Ltd.


Jenerette G.D.,University of California at Riverside | Shen W.,CAS South China Botanical Garden
Landscape Ecology | Year: 2012

Experimentation in landscape ecology is widely conducted using diverse approaches to answer a broad range of questions. By assessing the response to controlled manipulations alternate hypotheses can be clearly refuted, model parameters quantified, and conditions are often ripe for unexpected insights. Results from landscape experiments complement the many well developed observational and modeling approaches more commonly used in landscape ecology. To better understand how landscape experimentation has been conducted and to identify future research directions, we reviewed and organized the diversity of experiments. We identified fifteen distinct landscape experiment types, which we categorized into four broad groups including (I) identifying landscape structure, (II) identifying how ecological processes vary within existing landscapes, (III) identifying how landscape structure influences ecological processes, and (IV) identifying landscape pattern formation factors. Experiment types vary along axes of scalable to real landscapes and generalizability, suitability for analysis through traditional experimental design and flexibility of experimental setup, and complexity of implementation and resource requirements. The next generation of experiments are benefiting from more explicit inclusion of scaling theories and tighter coupling between experiments and cyberinfrastructure. Future experimental opportunities for landscape ecologists include expanded collaborations among experiments, better representations of microbial-soil structure relationships at microscales, and direct evaluations of landscape interactions with global changes. The history, current practice, and future needs of landscape ecological research strongly support an expanded role of experimental approaches that complements the rich observational and modeling strengths of the field. © 2012 Springer Science+Business Media B.V.


Baerenklau K.A.,University of California at Riverside
Land Economics | Year: 2010

A method for incorporating unobserved heterogeneity into aggregate count data frameworks is presented and used to control for endogenous spatial sorting in zonal recreation models. The method is based on latent class analysis, which has become a popular tool for analyzing heterogeneous preferences with individual data but has not yet been applied to aggregate count data. The method is tested using data on backcountry hikers for a southern California study site and performs well for relatively small numbers of classes. The latent class model produces substantially smaller welfare estimates compared to a constrained version that assumes homogeneity throughout the population. © 2010 by the Board of Regents of the University of Wisconsin System.


Razak K.A.,University of California at Riverside
Frontiers in Physiology | Year: 2013

Auditory neurons in bats that use frequency modulated (FM) sweeps for echolocation are selective for the behaviorally-relevant rates and direction of frequency change. Such selectivity arises through spectrotemporal interactions between excitatory and inhibitory components of the receptive field. In the pallid bat auditory system, the relationship between FM sweep direction/rate selectivity and spectral and temporal properties of sideband inhibition have been characterized. Of note is the temporal asymmetry in sideband inhibition, with low-frequency inhibition (LFI) exhibiting faster arrival times compared to high-frequency inhibition (HFI). Using the two-tone inhibition over time (TTI) stimulus paradigm, this study investigated the interactions between two sound parameters in shaping sideband inhibition: intensity and time. Specifically, the impact of changing relative intensities of the excitatory and inhibitory tones on arrival time of inhibition was studied. Using this stimulation paradigm, single unit data from the auditory cortex of pentobarbital-anesthetized cortex show that the threshold for LFI is on average ~8 dB lower than HFI. For equal intensity tones near threshold, LFI is stronger than HFI. When the inhibitory tone intensity is increased further from threshold, the strength asymmetry decreased. The temporal asymmetry in LFI vs. HFI arrival time is strongest when the excitatory and inhibitory tones are of equal intensities or if excitatory tone is louder. As inhibitory tone intensity is increased, temporal asymmetry decreased suggesting that the relative magnitude of excitatory and inhibitory inputs shape arrival time of inhibition and FM sweep rate and direction selectivity. Given that most FM bats use downward sweeps as echolocation calls, a similar asymmetry in threshold and strength of LFI vs. HFI may be a general adaptation to enhance direction selectivity while maintaining sweep-rate selective responses to downward sweeps. © 2013 Razak.


Ma E.,University of California at Riverside
International Journal of Modern Physics A | Year: 2014

Three families of quarks and leptons, one Higgs to rule them all, and in the darkness bind them. © 2014 World Scientific Publishing Company.


Reed C.A.,University of California at Riverside
Accounts of Chemical Research | Year: 2013

Recent research has taught us that most protonated species are decidedly not well represented by a simple proton addition. What is the actual nature of the hydrogen ion (the "proton") when H+, HA, H 2A+, and so forth are written in formulas, chemical equations, and acid catalyzed reactions? In condensed media, H+ must be solvated and is nearly always dicoordinate, as illustrated by isolable bisdiethyletherate salts having H(OEt2)2 + cations and weakly coordinating anions. Even carbocations such as protonated alkenes have significant C-H···anion hydrogen bonding that gives the active protons two-coordinate character.Hydrogen bonding is everywhere, particularly when acids are involved. In contrast to the normal, asymmetric O-H···O hydrogen bonding found in water, ice, and proteins, short, strong, low-barrier (SSLB) H-bonding commonly appears when strong acids are present. Unusually low frequency IR νOHO bands are a good indicator of SSLB H-bonds, and curiously, bands associated with group vibrations near H+ in low-barrier H-bonding often disappear from the IR spectrum.Writing H3O+ (the Eigen ion), as often appears in textbooks, might seem more realistic than H+ for an ionized acid in water. However, this, too, is an unrealistic description of H (aq) +. The dihydrated H+ in the H 5O2 + cation (the Zundel ion) gets somewhat closer but still fails to rationalize all the experimental and computational data on H(aq) +. Researchers do not understand the broad swath of IR absorption from H(aq) +, known as the "continuous broad absorption" (cba). Theory has not reproduced the cba, but it appears to be the signature of delocalized protons whose motion is faster than the IR time scale. What does this mean for reaction mechanisms involving H(aq) +?For the past decade, the carborane acid H(CHB11Cl11) has been the strongest known Brønsted acid. (It is now surpassed by the fluorinated analogue H(CHB11F 11).) Carborane acids are strong enough to protonate alkanes at room temperature, giving H2 and carbocations. They protonate chloroalkanes to give dialkylchloronium ions, which decay to carbocations. By partially protonating an oxonium cation, they get as close to the fabled H 4O2+ ion as can be achieved outside of a computer. © 2013 American Chemical Society.


Meredith R.W.,University of California at Riverside
Proceedings. Biological sciences / The Royal Society | Year: 2011

Whales in the suborder Mysticeti are filter feeders that use baleen to sift zooplankton and small fish from ocean waters. Adult mysticetes lack teeth, although tooth buds are present in foetal stages. Cladistic analyses suggest that functional teeth were lost in the common ancestor of crown-group Mysticeti. DNA sequences for the tooth-specific genes, ameloblastin (AMBN), enamelin (ENAM) and amelogenin (AMEL), have frameshift mutations and/or stop codons in this taxon, but none of these molecular cavities are shared by all extant mysticetes. Here, we provide the first evidence for pseudogenization of a tooth gene, enamelysin (MMP20), in the common ancestor of living baleen whales. Specifically, pseudogenization resulted from the insertion of a CHR-2 SINE retroposon in exon 2 of MMP20. Genomic and palaeontological data now provide congruent support for the loss of enamel-capped teeth on the common ancestral branch of crown-group mysticetes. The new data for MMP20 also document a polymorphic stop codon in exon 2 of the pygmy sperm whale (Kogia breviceps), which has enamel-less teeth. These results, in conjunction with the evidence for pseudogenization of MMP20 in Hoffmann's two-toed sloth (Choloepus hoffmanni), another enamel-less species, support the hypothesis that the only unique, non-overlapping function of the MMP20 gene is in enamel formation.


Schwitzgebel E.,University of California at Riverside
Neuroethics | Year: 2012

"Mad belief" (in analogy with Lewisian "mad pain") would be a belief state with none of the causal role characteristic of belief-a state not caused or apt to have been caused by any of the sorts of events that usually cause belief and involving no disposition toward the usual behavioral or other manifestations of belief. On token-functionalist views of belief, mad belief in this sense is conceptually impossible. Cases of delusion-or at least some cases of delusion-might be cases of belief gone half-mad, cases in which enough of the functional role characteristic of belief is absent that the subject is in an "in-between" state regarding the delusive content, such that it is neither quite right to say the subject determinately believes the delusive content nor quite right to say that she determinately fails to believe that content. Although Bortolotti (2010) briefly mentions such "sliding scale" approaches to the relationship of delusion and belief, she dismisses such approaches on rather thin grounds and then later makes some remarks that seem consonant with sliding scale approaches. © 2011 Springer Science+Business Media B.V.


Bailey-Serres J.,University of California at Riverside | Voesenek L.A.C.J.,University Utrecht | Voesenek L.A.C.J.,Center for Biosystems Genomics
Current Opinion in Plant Biology | Year: 2010

Recent reports on responses to flooding, submergence, and low-oxygen stress have connected components in an essential regulatory network that underlies plasticity in growth and metabolism essential for the survival of distinct flooding regimes. Here, we discuss growth under severe oxygen-limited conditions (anaerobic growth) and less oxygen-deficient underwater conditions (ethylene-driven underwater growth). Low-oxygen stress causes an energy and carbohydrate crisis that must be controlled through regulated consumption of carbohydrates and energy reserves. In rice (Oryza sativa L.), low-oxygen stress, energy homeostasis and growth are connected by a calcineurin B-like interacting binding kinase (CIPK) in seeds germinated under water. In shoots, two opposing adaptive strategies to submergence, elongation (escape) and inhibition of elongation (quiescence), are controlled by related ethylene response factor (ERF) DNA binding proteins that act downstream of ethylene and modulate gibberellin-mediated shoot growth. Increased resolution of the flooding signaling network will require more precise investigation of the interactions between oxygen tension and cellular energy status in regulation of anaerobic metabolism and ethylene-driven growth, both essential to survival in variable flooding environments. © 2010 Elsevier Ltd.


Essenberg C.J.,University of California at Riverside
Oecologia | Year: 2013

Responses of flower-visiting animals to floral density can alter interactions between plants, influencing a variety of biological processes, including plant population dynamics and the evolution of flowering phenology. Many studies have found effects of floral or plant density on pollinator visitation rates at patch scales, but little is known about responses of flower visitors to floral densities at larger scales. Here, I present data from an observational field study in which I measured the effects of floral density on visitation to the annual composite Holocarpha virgata at both patch (4 m2) and site (12. 6 ha) spatial scales. The species composition of flower visitors changed with floral density, and did so in different ways at the two scales. At the site scale, average floral density within patches of H. virgata or within patches of all summer-flowering species combined had a significant positive effect on per-flowerhead visitation by the long-horned bee Melissodes lupina and no significant effects on visitation by any other taxa. At the patch scale, per-flowerhead visitation by honeybees significantly increased whereas visitation by M. lupina often decreased with increasing floral density. For both species, responses to patch-scale floral density were strongest when site-scale floral density was high. The scale-dependence of flower visitor responses to floral density and the interactions between site- and patch-scale effects of floral density observed in this study underscore the importance of improving our understanding of pollinators' responses to floral density at population scales. © 2012 Springer-Verlag.


Martinez E.,University of California at Riverside
Transcription | Year: 2012

The core promoter of eukaryotic genes is structurally and functionally diverse and contributes to the combinatorial control of gene-specific transcription. Recent findings identifying specific coactivators and architectural proteins as core promoter-specific basal cofactors for RNA polymerase II suggest possible mechanisms for the core promoter selectivity of certain regulators and enhancers.


Biamonte M.A.,Drug Discovery for Tropical Diseases | Wanner J.,Hoffmann-La Roche | Le Roch K.G.,University of California at Riverside
Bioorganic and Medicinal Chemistry Letters | Year: 2013

This digest covers some of the most relevant progress in malaria drug discovery published between 2010 and 2012. There is an urgent need to develop new antimalarial drugs. Such drugs can target the blood stage of the disease to alleviate the symptoms, the liver stage to prevent relapses, and the transmission stage to protect other humans. The pipeline for the blood stage is becoming robust, but this should not be a source of complacency, as the current therapies set a high standard. Drug discovery efforts directed towards the liver and transmission stages are in their infancy but are receiving increasing attention as targeting these stages could be instrumental in eradicating malaria. © 2013 Elsevier Ltd. All rights reserved.


Kposowa A.J.,University of California at Riverside
Social Psychiatry and Psychiatric Epidemiology | Year: 2013

Objectives: The purpose of the study was to examine the association of suicide rates, firearm ownership, political conservatism, religious integration at the state level, and individual suicide risk. Social structural and social learning and social integration theories were theoretical frameworks employed. It was hypothesized that higher suicide rates, higher state firearm availability, and state conservatism elevate individual suicide risk. Method: Data were pooled from the Multiple Cause of Death Files. Multilevel logistic regression models were fitted to all deaths occurring in 2000 through 2004 by suicide. Results: The state suicide rate significantly elevated individual suicide risk (AOR = 1.042, CI = 1.037, 1.046). Firearm availability at the state level was associated with significantly higher odds of individual suicide (AOR = 1.004, CI = 1.003, 1.006). State political conservatism elevated the odds of individual suicides (AOR = 1.005, CI = 1.003, 1.007), while church membership at the state level reduced individual odds of suicide (AOR = 0.995, CI = 0.993, 0.996). The results held even after controlling for socioeconomic and demographic variables at the individual level. Conclusion: It was concluded that the observed association between individual suicide odds and national suicide rates, and firearm ownership cannot be discounted. Future research ought to focus on integrating individual level data and contextual variables when testing for the impact of firearm ownership. Support was found for social learning and social integration theories. © 2013 Springer-Verlag Berlin Heidelberg.


Dochtermann N.A.,University of Nevada, Reno | Roff D.A.,University of California at Riverside
Philosophical Transactions of the Royal Society B: Biological Sciences | Year: 2010

Current interest in behavioural syndromes, or 'animal personalities', reinforces a need for behavioural ecologists to adopt a multivariate view of phenotypes. Fortunately, many of the methodological and theoretical issues currently being dealt with by behavioural ecologists within the context of behavioural syndromes have previously been investigated by researchers in other areas of evolutionary ecology. As a result of these previous efforts, behavioural syndrome researchers have considerable theory and a wide range of tools already available to them. Here, we discuss aspects of quantitative genetics useful for understanding the multivariate phenotype as well as the relevance of quantitative genetics to behavioural syndrome research. These methods not only allow the proper characterization of the multivariate behavioural phenotype and genotype-including behaviours within, among and independent of behavioural syndrome structures-but also allow predictions as to how populations may respond to selection on behaviours within syndromes. An application of a quantitative genetics framework to behavioural syndrome research also clarifies and refines the questions that should be asked. © 2010 The Royal Society.


Talbot C.,California State University, San Bernardino | Lytle C.,University of California at Riverside
American Journal of Physiology - Gastrointestinal and Liver Physiology | Year: 2010

The colon is believed to absorb NaCl via the coupled operation of apical Na/H exchanger-3 (NHE3) and Cl/HCO3 exchanger SLC26A3 (DRA). Efficient coupling requires that NHE3 and DRA operate in close proximity within common luminal and cytosolic microenvironments. Thus we examined whether these proteins coexist along the apical margin of surface enterocytes by quantitative immunofluorescence microscopy in consecutive colon segments from nonfasted mice and rats. The cecocolonic profiles of NHE3 and DRA expression were roughly inverse; NHE3 was highest in proximal colon (PC) and negligible in distal colon, whereas DRA was absent in early PC and highest in the late midcolon, and DRA was prominent in the cecum whereas NHE3 was not. NHE3 and DRA coexisted only in the middle third of the colon. The consequences of unpaired NHE3/DRA expression on mucosal surface (subscript MS) pH and Na+ concentration ([Na +]) were assessed in nonfasted rats in situ using miniature electrodes. In the cecum, where only DRA is expressed, pHMS was ∼7.5, markedly higher than underlaying stool (6.3), consistent with net HCO3 - secretion. In the early PC, where NHE3 is not expressed with DRA, pHMS was acidic (6.2), consistent with unopposed H+ secretion. [Na+]MS was ∼60 mM in the cecum, decreased along the PC to ∼20 mM, and declined further to ∼10 mM distally. Cl- was secreted into the PC, then reabsorbed distally. Our results suggest a model in which 1) unpaired DRA activity in the cecum maintains an alkaline mucosal surface that could neutralize fermentative H +; 2) unpaired NHE3 activity in the early PC preserves an acidic mucosal surface that could energize short-chain fatty acid absorption; and 3) coupled NHE3/DRA activities in the midcolon allow for vigorous NaCl absorption at a neutral pHMS. Copyright © 2010 the American Physiological Society.


Oglesby D.D.,University of California at Riverside | Mai P.M.,King Abdullah University of Science and Technology
Geophysical Journal International | Year: 2012

Using the 3-D finite-element method, we develop dynamic spontaneous rupture models of earthquakes on the North Anatolian Fault system in the Sea of Marmara, Turkey, considering the geometrical complexity of the fault system in this region. We find that the earthquake size, rupture propagation pattern and ground motion all strongly depend on the interplay between the initial (static) regional pre-stress field and the dynamic stress field radiated by the propagating rupture. By testing several nucleation locations, we observe that those far from an oblique normal fault stepover segment (near Istanbul) lead to large through-going rupture on the entire fault system, whereas nucleation locations closer to the stepover segment tend to produce ruptures that die out in the stepover. However, this pattern can change drastically with only a 10° rotation of the regional stress field. Our simulations also reveal that while dynamic unclamping near fault bends can produce a new mode of supershear rupture propagation, this unclamping has a much smaller effect on the speed of the peak in slip velocity along the fault. Finally, we find that the complex fault geometry leads to a very complex and asymmetric pattern of near-fault ground motion, including greatly amplified ground motion on the insides of fault bends. The ground-motion pattern can change significantly with different hypocentres, even beyond the typical effects of directivity. The results of this study may have implications for seismic hazard in this region, for the dynamics and ground motion of geometrically complex faults, and for the interpretation of kinematic inverse rupture models. © 2012 The Authors Geophysical Journal International © 2012 RAS.


Ma E.,University of California at Riverside | Maniatis M.,University of Heidelberg
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2010

The new phenomenon of symbiotic symmetries is described in the context of the Two-Higgs-Doublet Model (THDM). The quartic potential has two or more separate sectors with unequal symmetries, but these unequal symmetries persist even though the different sectors are renormalized by one another. We discuss all such symmetries of the THDM, consistent with the SU (2) × U (1) gauge interactions, using the Pauli formalism. © 2009 Elsevier B.V.


Cutler S.R.,University of California at Riverside | Rodriguez P.L.,Institute Biologia Molecular Y Celular Of Plantas | Finkelstein R.R.,University of California at Santa Barbara | Abrams S.R.,National Research Council Canada
Annual Review of Plant Biology | Year: 2010

Abscisic acid (ABA) regulates numerous developmental processes and adaptive stress responses in plants. Many ABA signaling components have been identified, but their interconnections and a consensus on the structure of the ABA signaling network have eluded researchers. Recently, several advances have led to the identification of ABA receptors and their three-dimensional structures, and an understanding of how key regulatory phosphatase and kinase activities are controlled by ABA. A new model for ABA action has been proposed and validated, in which the soluble PYR/PYL/RCAR receptors function at the apex of a negative regulatory pathway to directly regulate PP2C phosphatases, which in turn directly regulate SnRK2 kinases. This model unifies many previously defined signaling components and highlights the importance of future work focused on defining the direct targets of SnRK2s and PP2Cs, dissecting the mechanisms of hormone interactions (i.e., cross talk) and defining connections between this new negative regulatory pathway and other factors implicated in ABA signaling. Copyright © 2010 by Annual Reviews. All rights reserved.


Judelson H.S.,University of California at Riverside
Eukaryotic Cell | Year: 2012

The eukaryotic microbes known as oomycetes are common inhabitants of terrestrial and aquatic environments and include saprophytes and pathogens. Lifestyles of the pathogens extend from biotrophy to necrotrophy, obligate to facultative pathogenesis, and narrow to broad host ranges on plants or animals. Sequencing of several pathogens has revealed striking variation in genome size and content, a plastic set of genes related to pathogenesis, and adaptations associated with obligate biotrophy. Features of genome evolution include repeat-driven expansions, deletions, gene fusions, and horizontal gene transfer in a landscape organized into gene-dense and gene-sparse sectors and influenced by transposable elements. Gene expression profiles are also highly dynamic throughout oomycete life cycles, with transcriptional polymorphisms as well as differences in protein sequence contributing to variation. The genome projects have set the foundation for functional studies and should spur the sequencing of additional species, including more diverse pathogens and nonpathogens. © 2012, American Society for Microbiology. All Rights Reserved.


Ma E.,University of California at Riverside
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2015

The standard model of quarks and leptons is extended to connect three outstanding issues in particle physics and astrophysics: (1) the absence of strong CP nonconservation, (2) the existence of dark matter, and (3) the mechanism of nonzero neutrino masses, and that of the first family of quarks and leptons, all in the context of having only one Higgs boson in a renormalizable theory. Some phenomenological implications are discussed. © 2014 The Author.


Hollis R.S.,University of California at Riverside
Nuclear Physics A | Year: 2013

Cu + Au collisions provide a test for theories trying to describe heavy-ion data by changing the initial conditions and introducing distinct asymmetries into the initial geometry of the collision system. We present the first results from the PHENIX collaboration from these asymmetric collisions. The measured hadron v1 is found to be large at midrapidity, whilst v3 is found to be small when the reaction plane is determined from the spectators. In the forward region, the J/ψ is found to be more suppressed in the Cu-going direction compared to the Au-going direction. © 2013 Elsevier B.V.


Jung H.,University of California at Riverside
SAE Technical Papers | Year: 2013

Passengers are exposed to roadway pollutants due to entrainment of outside air into the vehicle cabin. Previous works found cabin air-recirculation can reduce pollutant particle concentrations significantly. However simultaneous increase of CO2 concentrations in the cabin prevented wide use of recirculation mode for such purpose. A mathematical model was developed to predict CO2 concentrations in vehicle cabin air during air-recirculation mode. The model predicts temporal CO2 concentration changes as a function of cabin volume, vehicle body leakage, and number of passengers. This model can be used to design and control air-recirculation mode for a variety of vehicle conditions. Copyright © 2013 SAE International.


Ma E.,University of California at Riverside | Picek I.,University of Zagreb | Radovcic B.,University of Zagreb
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2013

We propose a new realization of the one-loop radiative model of neutrino mass generated by dark matter (scotogenic), where the particles in the loop have an additional U(1)D gauge symmetry, which may be exact or broken to Z2. This model is relevant to a number of astrophysical observations, including AMS-02 and the dark-matter distribution in dwarf galactic halos. © 2013 Elsevier B.V.


Understanding the mechanism of photosynthetic water oxidation requires characterizing the reactions of the water molecules that serve as substrate or that otherwise interact with the oxygen-evolving Mn4CaO5 cluster. FTIR difference spectroscopy is a powerful tool for studying the structural changes of hydrogen bonded water molecules. For example, the O-H stretching mode of water molecules having relatively weak hydrogen bonds can be monitored near 3600 cm-1, the D-O-D bending mode can be monitored near 1210 cm-1, and highly polarizable networks of hydrogen bonds can be monitored as broad features between 3000 and 2000 cm-1. The two former regions are practically devoid of overlapping vibrational modes from the protein. In Photosystem II, water oxidation requires a precisely choreographed sequence of proton and electron transfer steps in which proton release is required to prevent the redox potential of the Mn4CaO5 cluster from rising to levels that would prevent its subsequent oxidation. Proton release takes place via one or more proton egress pathways leading from the Mn4CaO5 cluster to the thylakoid lumen. There is growing evidence that D1-D61 is the initial residue of one dominant proton egress pathway. This residue interacts directly with water molecules in the first and second coordination spheres of the Mn4CaO5 cluster. In this study, we explore the influence of D1-D61 on the water reactions accompanying oxygen production by characterizing the FTIR properties of the D1-D61A mutant of the cyanobacterium, Synechocystis sp. PCC 6803. On the basis of mutation-induced changes to the carbonyl stretching region near 1747 cm-1, we conclude that D1-D61 participates in the same extensive networks of hydrogen bonds that have been identified previously by FTIR studies. On the basis of mutation-induced changes to the weakly hydrogen-bonded O-H stretching region, we conclude that D1-D61 interacts with water molecules that are located near the Cl-(1) ion and that deprotonate or participate in stronger hydrogen bonds as a result of the S1 to S2 and S2 to S3 transitions. On the basis of the elimination of a broad feature between 3100 and 2600 cm-1, we conclude that the highly polarizable network of hydrogen bonds whose polarizability or protonation state increases during the S1 to S2 transition involves D1-D61. On the basis of the elimination of features in the D-O-D bending region, we conclude that D1-D61 forms a hydrogen bond to one of the H2O molecules whose H-O-H bending mode changes in response to the S1 to S2 transition. The elimination of this H2O molecule in the D1-D61A mutant provides one rationale for the decreased efficiency of water oxidation in this mutant. Finally, we discuss reasons why the recent conclusion that a substrate-containing cluster of five water molecules accepts a proton from the Mn4CaO5 cluster during the S1 to S2 transition and deprotonates during subsequent S state transitions should be reassessed. © 2014 American Chemical Society.


Ma E.,University of California at Riverside
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2013

Predictive spontaneous CP violation is possible if it is obtained geometrically through a non-Abelian discrete symmetry. I propose such a model of neutrino mass and mixing based on δ(27). © 2013 .


Zhao F.,University of California at Riverside
G3 (Bethesda, Md.) | Year: 2012

Genotype by environment interaction is a phenomenon that a better genotype in one environment may perform poorly in another environment. When the genotype refers to a quantitative trait locus (QTL), this phenomenon is called QTL by environment interaction, denoted by Q×E. Using a recently developed new Bayesian method and genome-wide marker information, we estimated and tested QTL main effects and Q×E interactions for a well-known barley dataset produced by the North American Barley Genome Mapping Project. This dataset contained seven quantitative traits collected from 145 doubled-haploid (DH) lines evaluated in multiple environments, which derived from a cross between two Canadian two-row barley lines, Harrington and TR306. Numerous main effects and Q×E interaction effects have been detected for all seven quantitative traits. However, main effects seem to be more important than the Q×E interaction effects for all seven traits examined. The number of main effects detected varied from 26 for the maturity trait to 75 for the heading trait, with an average of 61.86. The heading trait has the most detected effects, with a total of 98 (75 main, 29 Q×E). Among the 98 effects, 6 loci had both the main and Q×E effects. Among the total number of detected loci, on average, 78.5% of the loci show the main effects whereas 34.9% of the loci show Q×E interactions. Overall, we detected many loci with either the main or the Q×E effects, and the main effects appear to be more important than the Q×E interaction effects for all the seven traits. This means that most detected loci have a constant effect across environments. Another discovery from this analysis is that Q×E interaction occurs independently, regardless whether the locus has main effects.


Xu S.,University of California at Riverside
Genetics | Year: 2013

The correct models for quantitative trait locus mapping are the ones that simultaneously include all significant genetic effects. Such models are difficult to handle for high marker density. Improving statistical methods for high-dimensional data appears to have reached a plateau. Alternative approaches must be explored to break the bottleneck of genomic data analysis. The fact that all markers are located in a few chromosomes of the genome leads to linkage disequilibrium among markers. This suggests that dimension reduction can also be achieved through data manipulation. High-density markers are used to infer recombination breakpoints, which then facilitate construction of bins. The bins are treated as new synthetic markers. The number of bins is always a manageable number, on the order of a few thousand. Using the bin data of a recombinant inbred line population of rice, we demonstrated genetic mapping, using all bins in a simultaneous manner. To facilitate genomic selection, we developed a method to create user-defined (artificial) bins, in which breakpoints are allowed within bins. Using eight traits of rice, we showed that artificial bin data analysis often improves the predictability compared with natural bin data analysis. Of the eight traits, three showed high predictability, two had intermediate predictability, and two had low predictability. A binary trait with a known gene had predictability near perfect. Genetic mapping using bin data points to a new direction of genomic data analysis. © 2013 by the Genetics Society of America.


Xu S.,University of California at Riverside
Genetics | Year: 2013

A new mixed-model method was developed for mapping quantitative trait loci (QTL) by incorporating multiple polygenic covariance structures. First, we used genome-wide markers to calculate six different kinship matrices. We then partitioned the total genetic variance into six variance components, one corresponding to each kinship matrix, including the additive, dominance, additive × additive, dominance × dominance, additive × dominance, and dominance × additive variances. The six different kinship matrices along with the six estimated polygenic variances were used to control the genetic background of a QTL mapping model. Simulation studies showed that incorporating epistatic polygenic covariance structure can improve QTL mapping resolution. The method was applied to yield component traits of rice. We analyzed four traits (yield, tiller number, grain number, and grain weight) using 278 immortal F2 crosses (crosses between recombinant inbred lines) and 1619 markers. We found that the relative importance of each type of genetic variance varies across different traits. The total genetic variance of yield is contributed by additive × additive (18%), dominance × dominance (14%), additive × dominance (48%), and dominance × additive (15%) variances. Tiller number is contributed by additive (17%), additive × additive (22%), and dominance × additive (43%) variances. Grain number is mainly contributed by additive (42%), additive × additive (19%), and additive × dominance (31%) variances. Grain weight is almost exclusively contributed by the additive (73%) variance plus a small contribution from the additive × additive (10%) variance. Using the estimated genetic variance components to capture the polygenic covariance structure, we detected 39 effects for yield, 39 effects for tiller number, 24 for grain number, and 15 for grain weight. The new method can be directly applied to polygenic-effect-adjusted genome-wide association studies (GWAS) in human and other species. © 2013 by the Genetics Society of America.


This commentary on Kim and Harris (2014) addresses the authors' interpretation of the halo effect, in which 5- to 6-year-old children preferentially agreed with an informant who could read other people's minds, regardless of domain of knowledge. © 2014 The British Psychological Society.


Vlahou E.L.,Institute for Language and Speech Processing | Protopapas A.,Institute for Language and Speech Processing | Seitz A.R.,University of California at Riverside
Journal of Experimental Psychology: General | Year: 2012

Learning nonnative speech contrasts in adulthood has proven difficult. Standard training methods have achieved moderate effects using explicit instructions and performance feedback. In this study, the authors question preexisting assumptions by demonstrating a superiority of implicit training procedures. They trained 3 groups of Greek adults on a difficult Hindi contrast (a) explicitly, with feedback (Experiment 1), or (b) implicitly, unaware of the phoneme distinctions, with (Experiment 2) or without (Experiment 3) feedback. Stimuli were natural recordings of consonant-vowel syllables with retroflex and dental unvoiced stops by a native Hindi speaker. On each trial, participants heard pairs of tokens from both categories and had to identify the retroflex sounds (explicit condition) or the sounds differing in intensity (implicit condition). Unbeknownst to participants, in the implicit conditions, target sounds were always retroflex, and distractor sounds were always dental. Post-training identification and discrimination tests showed improved performance of all groups, compared with a baseline of untrained Greek listeners. Learning was most robust for implicit training without feedback. It remains to be investigated whether implicitly trained skills can generalize to linguistically relevant phonetic categories when appropriate variability is introduced. These findings challenge traditional accounts on the role of feedback in phonetic training and highlight the importance of implicit, reward-based mechanisms. © 2011 American Psychological Association.


Ma E.,University of California at Riverside
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2015

A new theoretical insight into the pattern of neutrino mixing and leptonic CP violation is presented. It leads naturally and uniquely to a specific dark sector of three real neutral scalar singlets, with the radiative implementation of the inverse seesaw mechanism for neutrino mass. The new simple but crucial enabling idea is that a familiar A4 transformation turns any orthogonal 3×3 matrix into one which predicts θ23=π/4 and δCP=±π/2 for the neutrino mixing matrix, in good agreement with present data. © 2015 American Physical Society. © 2015 American Physical Society.


Ma E.,University of California at Riverside
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2012

There are two simple ways that the Higgs boson H of the Standard Model (SM) may be more difficult to observe than expected at the Large Hadron Collider (LHC) or the Tevatron. One is well known, i.e. H decays invisibly, into dark-matter scalar particles for example. The other is that H mixes with a heavy singlet scalar S which couples to new colored fermions and scalars. Of the two mass eigenstates, the light one could (accidentally) have a suppressed effective coupling to two gluons, and the heavy one could be kinematically beyond the reach of the LHC. © 2011 Elsevier B.V.


Ma E.,University of California at Riverside
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2012

A new and radical scenario of the simple 2006 model of radiative neutrino mass is proposed, where there is no seesaw mechanism, i.e. neutrino masses are not inversely proportional to some large mass scale, contrary to the prevalent theoretical thinking. The neutral singlet fermions in the loop have masses of order 10 keV, the lightest of which is absolutely stable and the others are very long-lived. All are components of warm dark matter, which is a possible new paradigm for explaining the structure of the Universe at all scales. © 2012.


Dressel J.,University of Rochester | Malik M.,University of California at Riverside | Miatto F.M.,University of Rochester | Jordan A.N.,Austrian Academy of Sciences | Boyd R.W.,University of Ottawa
Reviews of Modern Physics | Year: 2014

Since its introduction 25 years ago, the quantum weak value has gradually transitioned from a theoretical curiosity to a practical laboratory tool. While its utility is apparent in the recent explosion of weak value experiments, its interpretation has historically been a subject of confusion. Here a pragmatic introduction to the weak value in terms of measurable quantities is presented, along with an explanation for how it can be determined in the laboratory. Further, its application to three distinct experimental techniques is reviewed. First, as a large interaction parameter it can amplify small signals above technical background noise. Second, as a measurable complex value it enables novel techniques for direct quantum state and geometric phase determination. Third, as a conditioned average of generalized observable eigenvalues it provides a measurable window into nonclassical features of quantum mechanics. In this selective review, a single experimental configuration to discuss and clarify each of these applications is used. © 2014 American Physical Society.


Defea K.A.,University of California at Riverside
Progress in Molecular Biology and Translational Science | Year: 2013

Arrestins have emerged as important regulators of actin reorganization and cell migration. Both in their classical roles as mediators of receptor desensitization and internalization, and in their newer role as signaling scaffolds, β-arrestins help orchestrate the cellular response to chemotactic signals. However, there is still a considerable amount to be learned about the precise molecular mechanisms underlying these processes. This review discusses how, by regulating receptor internalization and by scaffolding of signaling molecules in discrete cellular locations, arrestins facilitate gradient sensing and cytoskeletal reorganization, ultimately resulting in cell migration. In addition, putative new targets of β-arrestin regulation that may play important roles in cell migration are discussed, as continued research on these targets may provide important details to fill in the current gaps in our understanding of these processes. © 2013 Elsevier Inc.


Haddon R.C.,University of California at Riverside | Haddon R.C.,King Abdulaziz University
ChemPhysChem | Year: 2012

One for the half: Recent work on atomic hydrogen and neutral radical heterocyclic molecules has moved the field of spin S=1/2 solids closer to the realization of synthetic intrinsic metals and superconductors. High-pressure experiments on hydrogen and chalcogenide-nitrogen molecules (see picture) show evidence of metallic character. The molecular radicals exhibit a positive temperature coefficient of resistance under pressure-the classic signature of a metal. © 2012 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.


Andersen G.J.,University of California at Riverside
Current Biology | Year: 2011

A new behavioral training approach has been found significantly to improve visual function; the results further attest to the high degree of plasticity in sensory systems. © 2011 Elsevier Ltd.


Pekker D.,University of Pittsburgh | Varma C.M.,University of California at Riverside
Annual Review of Condensed Matter Physics | Year: 2015

The order parameter and its variations in space and time in many different states in condensed matter physics at low temperatures are described by the complex function ?(r, t). These states include erfluids, erconductors, and a subclass of antiferromagnets and charge density waves. The collective fluctuations in the ordered state may then be categorized as oscillations of phase and amplitude of ?(r, t). The phase oscillations are the Goldstone modes of the broken continuous symmetry. The amplitude modes, even at long wavelengths, are well defined and are decoupled from the phase oscillations only near particle-hole symmetry, where the equations of motion have an effective Lorentz symmetry, as in particle physics and if there are no significant avenues for decay into other excitations. They bear close correspondence with the so-called Higgs modes in particle physics, whose prediction and discovery are very important for the standard model of particle physics. In this review, we discuss the theory and the possible observation of the amplitude or Higgs modes in condensed matter physics - in erconductors, cold atoms in periodic lattices, and uniaxial antiferromagnets. We discuss the necessity for at least approximate particle-hole symmetry as well as the special conditions required to couple to such modes because, being scalars, they do not couple linearly to the usual condensed matter probes. © 2015 by Annual Reviews.


Sladek F.M.,University of California at Riverside
Molecular and Cellular Endocrinology | Year: 2011

Nuclear receptors (NRs) are a family of highly conserved transcription factors that regulate transcription in response to small lipophilic compounds. They play a role in every aspect of development, physiology and disease in humans. They are also ubiquitous in and unique to the animal kingdom suggesting that they may have played an important role in their evolution. In contrast to the classical endocrine receptors that originally defined the family, recent studies suggest that the first NRs might have been sensors of their environment, binding ligands that were external to the host organism. The purpose of this review is to provide a broad perspective on NR ligands and address the issue of exactly what constitutes a NR ligand from historical, biological and evolutionary perspectives. This discussion will lay the foundation for subsequent reviews in this issue as well as pose new questions for future investigation. © 2010 Elsevier Ireland Ltd.


DeFea K.A.,University of California at Riverside
Cellular Signalling | Year: 2011

Over the last decade β-arrestins have emerged as pleiotropic scaffold proteins, capable of mediating numerous diverse responses to multiple agonists. Most well characterized are the G-protein-coupled receptor (GPCR) stimulated β-arrestin signals, which are sometimes synergistic with, and sometimes independent of, heterotrimeric G-protein signals. β-arrestin signaling involves the recruitment of downstream signaling moieties to β-arrestins; in many cases specific sites of interaction between β-arrestins and the downstream target have been identified. As more information unfolds about the nature of β-arrestin scaffolding interactions, it is evident that these proteins are capable of adopting multiple conformations which in turn reveal a specific set of interacting domains. Recruitment of β-arrestin to a specific GPCR can promote formation of a specific subset of available β-arrestin scaffolds, allowing for a higher level of specificity to given agonists. This review discusses recent advances in β-arrestin signaling, discussing the molecular details of a subset of known β-arrestin scaffolds and the significance of specific binding interactions on the ultimate cellular response. © 2010 Elsevier Inc.


Orosco M.J.,University of California at Riverside | Klingner J.,University of Colorado at Boulder
Journal of Learning Disabilities | Year: 2010

The purpose of this study was to determine how a response-to-intervention (RTI) model was implemented with a large percentage of Latino English language learners who were having reading difficulties in an urban elementary school at the primary level (K-2). The authors sought to describe school personnel's perceptions of RTI, what the model looked like in their school, and the challenges they faced. The authors focused on how teachers' understandings, beliefs, judgments, professional development, and training affected the RTI decision-making process by investigating classroom-based literacy instruction and problem-solving meetings. This study contributes to the literature by presenting a qualitative, in-depth description of how teachers implemented an RTI model for English language learners. These themes were intertwined and functioned as a negative cycle that created a deficits-based RTI literacy model. © Hammill Institute on Disabilities 2010.


McCole D.F.,University of California at Riverside
Inflammatory Bowel Diseases | Year: 2014

Technological advances in the large scale analysis of human genetics have generated profound insights into possible genetic contributions to chronic diseases including the inflammatory bowel diseases (IBDs), Crohn's disease and ulcerative colitis. To date, 163 distinct genetic risk loci have been associated with either Crohn's disease or ulcerative colitis, with a substantial degree of genetic overlap between these 2 conditions. Although many risk variants show a reproducible correlation with disease, individual gene associations only affect a subset of patients, and the functional contribution(s) of these risk variants to the onset of IBD is largely undetermined. Although studies in twins have demonstrated that the development of IBD is not mediated solely by genetic risk, it is nevertheless important to elucidate the functional consequences of risk variants for gene function in relevant cell types known to regulate key physiological processes that are compromised in IBD. This article will discuss IBD candidate genes that are known to be, or are suspected of being, involved in regulating the intestinal epithelial barrier and several of the physiological processes presided over by this dynamic and versatile layer of cells. This will include assembly and regulation of tight junctions, cell adhesion and polarity, mucus and glycoprotein regulation, bacterial sensing, membrane transport, epithelial differentiation, and restitution. Copyright © 2014 Crohn's & Colitis Foundation of America, Inc.


Ishimori H.,Kyoto University | Ma E.,University of California at Riverside | Ma E.,University of Tokyo
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2012

In a new simple application of the non-Abelian discrete symmetry A 4 to charged-lepton and neutrino mass matrices, we show that for the current experimental central value of sin22θ 130.1, leptonic CP violation is necessarily large, i.e., |tanδ CP>1. 3. This result is of broad interest because CP violation in the leptonic sector is closely connected to the origin of the observed matter-antimatter asymmetry of the Universe through leptogenesis. © 2012 American Physical Society.


Zaera F.,University of California at Riverside
Surface Science | Year: 2011

In this Prospective, a critical overview is provided on the status and future of the analytical techniques available for the study of chemistry at liquid/solid interfaces. A number of spectroscopies already available are identified, including infrared absorption, surface-enhanced Raman (SERS) and sum frequency generation (SFG) to obtain vibrational information, and second harmonic generation (SHG) and X-ray absorption (XAS) to provide electronic details of surfaces and adsorbates. X-ray scattering and X-ray diffraction techniques are also used for structural characterization, and surface plasmon resonance (SPR) and quartz crystal microbalance (QCM) to follow adsorption uptakes and kinetics. Finally, optical and scanning microscopies add a spatial dimension to these studies. Overall, a number of surface-sensitive techniques do already exist to address chemical issues at liquid/solid interfaces, but those are still limited, and have perhaps not been exploited to their fullest yet. There is also a need for more cross collaboration among different research communities, and for new and clever developments to augment the toolbox of liquid/solid interface characterization. © 2011 Elsevier B.V.


Beran G.J.O.,University of California at Riverside
Angewandte Chemie - International Edition | Year: 2015

(Chemical Equation Presented). From first principles: In recent studies the lattice energy of crystalline benzene was predicted with sub-kilojoule per mole accuracy. Fundamental to this success was the combination of a fragment approach with state-of-the-art electronic structure methods. © 2015 Wiley-VCH Verlag GmbH & Co. KGaA.


Arendt J.D.,University of California at Riverside
Evolution | Year: 2011

Many ectotherms show crossing growth trajectories as a plastic response to rearing temperature. As a result, individuals growing up in cool conditions grow slower, mature later, but are larger at maturation than those growing up in warm conditions. To date, no entirely satisfactory explanation has been found for why this pattern, often called the temperature-size rule, should exist. Previous theoretical models have assumed that size-specific mortality rates were most likely to drive the pattern. Here, I extend one theoretical model to show that variation in size-fecundity relationships may also be important. Plasticity in the size-fecundity relationship has rarely been considered, but a number of studies show that fecundity increases more quickly with size in cold environments than it does in warm environments. The greater increase in fecundity offsets costs of delayed maturation in cold environments, favoring a larger size at maturation. This can explain many cases of crossing growth trajectories, not just in relation to temperature. © 2010 The Author(s). Evolution © 2010 The Society for the Study of Evolution.


Essenberg C.J.,University of California at Riverside
American Naturalist | Year: 2012

Pollinator responses to floral density have important implications for plant biology. In particular, a decline in pollinator visitation at low density can cause an Allee effect (a positive relation of fitness to density) in the plant population, which heightens that population's vulnerability to extinction. Empiricists have reported a variety of relations between flower or plant density and pollinator visitation rates. Here I develop and test a model that provides explanations for this diversity. The model assumes that pollinators distribute themselves between a focal patch of flowers and the surrounding environment so as to maximize foraging success. The resulting relation of per-flower visitation rate to focal-patch floral density is nonlinear, with positive effects at low floral densities and weaker or negative effects at higher densities. The relation is influenced by floral density in the surrounding environment and traits of both the plants and their pollinators. In a field experiment, floral density of Holocarpha virgata ssp. virgata had a nonlinear effect on per-flower visitation that was largely consistent with the model's predictions. By producing testable hypotheses based on biologically reasonable assumptions, this model serves as a starting point for explaining an important facet of plant-pollinator mutualisms. © 2012 by The University of Chicago.


Rust M.K.,University of California at Riverside | Su N.-Y.,University of Florida
Annual Review of Entomology | Year: 2012

Social insects have a tremendous economic and social impact on urban communities. The rapid urbanization of the world has dramatically increased the incidence of urban pests. Human commerce has resulted in the spread of urban invasive species worldwide such that various species are now common to many major urban centers. We aim to highlight those social behaviors that can be exploited to control these pests with the minimal use of pesticides. Their cryptic behavior often prohibits the direct treatment of colonies. However, foraging and recruitment are essential aspects of their social behavior and expose workers to traps, baits, and pesticide applications. The advent of new chemistries has revolutionized the pest management strategies used to control them. In recent years, there has been an increased environmental awareness, especially in the urban community. Advances in molecular and microbial agents promise additional tools in developing integrated pest management programs against social insects. © 2012 by Annual Reviews. All rights reserved.


Cardullo R.A.,University of California at Riverside
Methods in Cell Biology | Year: 2013

Typically, light microscopic methodologies using conventional optics are limited by the diffraction limit yielding resolutions that cannot be reached lower than approximately 200. nm. However, using appropriate donor-acceptor pairs, nonradiative fluorescence resonance energy transfer (FRET) allows the microscopist to detect, and in some cases quantify, molecular interactions on the order of Angstroms. In this chapter, the basic principles of FRET are introduced using both steady state and lifetime modes to detect the close association of fluorescent donor and acceptor molecules. The basic design of experiments and optical and imaging components is discussed to create a microscope that is capable of monitoring dynamic molecular associations in living cells. © 2007 Elsevier Inc.


Iordanova A.,University of California at Riverside
Journal of Physics: Conference Series | Year: 2013

The flexibility of RHIC to collide different nuclei provides experiments with a rich set of data to systematically test models and scaling behaviors in various collision systems. The latest RHIC run collided U+U and Cu+Au nuclei. These collisions promise an array of unique initial geometrical configurations. For example, in U+U collisions the slightly elongated nuclei overlap in a variety of different ways such that, even at zero impact parameter, distinct configurations exist. In central Cu+Au collisions the Cu nucleus is completely embedded within the Au. Such geometries present an opportunity to measure the wide range of initial energy densities of these systems. They also allow the study of some unique features arising from these configurations. In particular, the odd harmonics from the Cu+Au system offer sensitivity to v3 generated from the collision geometry as opposed to fluctuations in a symmetric system. In these proceedings the analysis status of the recently taken U+U and Cu+Au data in PHENIX is presented. The results from the global particle production and the challenges in analyzing these asymmetric systems is discussed. © Published under licence by IOP Publishing Ltd.


Farzan Y.,Institute for Research in Fundamental Sciences | Ma E.,University of California at Riverside | Ma E.,University of Tokyo
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2012

In 2006, a simple extension of the standard model was proposed in which neutrinos obtain radiative Majorana masses at one-loop level from their couplings with dark matter, hence the term "scotogenic," from the Greek "scotos" meaning darkness. Here an analogous mechanism for Dirac neutrino masses is discussed in a minimal model. In different ranges of the parameter space, various candidates for dark matter are possible. In particular, the lightest Dirac fermion which appears in the loop diagram generating neutrino mass can be a viable dark-matter candidate. Such a possibility does not exist for the Majorana case. Realistic neutrino mixing in the context of A 4 is discussed. A possible supersymmetric extension is also briefly discussed. © 2012 American Physical Society.


Seitz A.R.,University of California at Riverside
Current Biology | Year: 2011

A new study has found that changes in visual cortical processing account for behavioral perceptual learning, supporting the idea that stimulus-specific learning can result from low-level visual plasticity. © 2011 Elsevier Ltd. All rights reserved.


Zaera F.,University of California at Riverside
Physical Chemistry Chemical Physics | Year: 2013

A personal perspective is offered on the state of the art of our current understanding of the mechanism of olefin hydrogenations promoted by transition-metal catalysts. Much is known about these reactions, but many key issues remain poorly understood. It is acknowledged that these reactions take place on surfaces covered with strongly adsorbed carbonaceous layers, but the role that those play in the catalysis is still in question. The active adsorption state of olefins that converts to the alkanes has been identified as a pi-bonded external precursor, that is, as an olefin weakly adsorbed on top of a first layer of strongly adsorbed organic fragments, but the specific details of the interaction of those pi-bonded intermediates with the metal and the way they incorporate hydrogen atoms to produce surface alkyl intermediates need to be worked out still. Molecular hydrogen is known to dissociate on the metal to yield the surface atomic hydrogens that participate in the hydrogenation steps, but its adsorption kinetics is affected by the carbonaceous layers in ways not well characterized to date, and the possible the participation of sub-surface or bulk hydrogen species has been advanced but not generally proven. Knowledge of the energetics and dynamics of the formation of the alkyl intermediates, key in these hydrogenations, is still by and large undeveloped, and the competition between the beta-hydride and reductive elimination steps from that species that define reaction selectivities has been barely quantified. Bridging the pressure and materials gap between studies with single-crystals under vacuum and more realistic catalytic conditions has offered additional challenges. Some experiments that may answer these questions are proposed. © 2013 the Owner Societies.


Liew C.G.,University of California at Riverside
The review of diabetic studies : RDS | Year: 2010

The pancreas arises from Pdx1-expressing progenitors in developing foregut endoderm in early embryo. Expression of Ngn3 and NeuroD1 commits the cells to form endocrine pancreas, and to differentiate into subsets of cells that constitute islets of Langerhans. β-cells in the islets transcribe gene-encoding insulin, and subsequently process and secrete insulin, in response to circulating glucose. Dysfunction of β-cells has profound metabolic consequences leading to hyperglycemia and diabetes mellitus. β-cells are destroyed via autoimmune reaction in type 1 diabetes (T1D). Type 2 diabetes (T2D), characterized by impaired β-cell functions and reduced insulin sensitivity, accounts for 90% of all diabetic patients. Islet transplantation is a promising treatment for T1D. Pluripotent stem cells provide an unlimited cell source to generate new β-cells for patients with T1D. Furthermore, derivation of induced pluripotent stem cells (iPSCs) from patients captures "disease-in-a-dish" for autologous cell replacement therapy, disease modeling, and drug screening for both types of diabetes. This review highlights essential steps in pancreas development, and potential stem cell applications in cell regeneration therapy for diabetes mellitus.


Bonebrake T.C.,University of California at Los Angeles | Bonebrake T.C.,University of California at Riverside | Deutsch C.A.,University of California at Los Angeles
Ecology | Year: 2012

Evolutionary history and physiology mediate species responses to climate change. Tropical species that do not naturally experience high temperature variability have a narrow thermal tolerance compared to similar taxa at temperate latitudes and could therefore be most vulnerable to warming. However, the thermal adaptation of a species may also be influenced by spatial temperature variations over its geographical range. Spatial climate gradients, especially from topography, may also broaden thermal tolerance and therefore act to buffer warming impacts. Here we show that for low-seasonality environments, high spatial heterogeneity in temperature correlates significantly with greater warming tolerance in insects globally. Based on this relationship, we find that climate change projections of direct physiological impacts on insect fitness highlight the vulnerability of tropical lowland areas to future warming. Thus, in addition to seasonality, spatial heterogeneity may play a critical role in thermal adaptation and climate change impacts particularly in the tropics. © 2012 by the Ecological Society of America.


Ma E.,University of California at Riverside | Ma E.,University of Lisbon
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2012

A new and novel idea for a predictive neutrino mass matrix is presented, using the non-Abelian discrete symmetry A4 and the seesaw mechanism with only two heavy neutral fermion singlets. Given the components of the one necessarily massless neutrino eigenstate, the other two massive states are automatically generated. A realistic example is discussed with predictions of a normal hierarchy of neutrino masses and maximal CP violation. © 2012 American Physical Society.


Hua M.,University of California at Riverside
Journal of medical Internet research | Year: 2013

The health effects caused by electronic cigarette (e-cigarette) use are not well understood. Our purpose was to document the positive and negative short-term health effects produced by e-cigarette use through an analysis of original posts from three online e-cigarettes forums. Data were collected into Microsoft Access databases and analyzed using Cytoscape association graphics, frequency distributions, and interactomes to determine the number and type of health effects reported, the organ systems affected the frequency of specific effects, and systems interactions. A total of 405 different symptoms due to e-cigarette use were reported from three forums. Of these, 78 were positive, 326 were negative, and one was neutral. While the reported health effects were similar in all three forums, the forum with the most posts was analyzed in detail. Effects, which were reported for 12 organ systems/anatomical regions, occurred most often in the mouth and throat and in the respiratory, neurological, sensory, and digestive systems. Users with negative symptoms often reported more than one symptom, and in these cases interactions were often seen between systems, such as the circulatory and neurological systems. Positive effects usually occurred singly and most frequently affected the respiratory system. This is the first compilation and analysis of the health effects reported by e-cigarette users in online forums. These data show that e-cigarette use can have wide ranging positive and negative effects and that online forums provide a useful resource for examining how e-cigarette use affects health.


Cooper Jr. W.E.,Indiana University - Purdue University Fort Wayne | Pyron R.A.,George Washington University | Garland Jr. T.,University of California at Riverside
Proceedings of the Royal Society B: Biological Sciences | Year: 2014

OneofDarwin's most widelyknown conjecturesisthat preyare tameonremote islands, wheremammalianpredators are absent. Manyspecies appeartopermit close approach on such islands, but no comparative studies have demonstrated reducedwariness quantifiedasflight initiationdistance (FID; i.e.predator-prey distance when the prey begins to flee) in comparison with mainland relatives. We used the phylogenetic comparative method to assess influence of distance from the mainland and island area on FID of 66 lizard species. Because body size and predator approach speed affect predation risk, we included these as independent variables. Multiple regression showed that FID decreases as distance from mainland increases and is shorter in island than mainland populations. Although FID increased as area increased in some models, collinearity made it difficult to separate effects of area from distance and island occupancy. FID increases as SVL increases and approach speed increases; these effects are statistically independent of effects of distance to mainland and island occupancy. Ordinary least-squares models fit the data better than phylogenetic regressions, indicating little or no phylogenetic signal in residual FID after accounting for the independent variables. Our results demonstrate that island tameness is a real phenomenon in lizards. © 2014 The Author(s) Published by the Royal Society. All rights reserved.


Walker A.,University of California at Riverside
Nature communications | Year: 2010

Human pluripotent stem (hPS) cells such as human embryonic stem (hES) and induced pluripotent stem (hiPS) cells are vulnerable under single cell conditions, which hampers practical applications; yet, the mechanisms underlying this cell death remain elusive. In this paper, we demonstrate that treatment with a specific inhibitor of non-muscle myosin II (NMII), blebbistatin, enhances the survival of hPS cells under clonal density and suspension conditions, and, in combination with a synthetic matrix, supports a fully defined environment for self-renewal. Consistent with this, genetically engineered mouse embryonic stem cells lacking an isoform of NMII heavy chain (NMHCII), or hES cells expressing a short hairpin RNA to knock down NMHCII, show greater viability than controls. Moreover, NMII inhibition increases the expression of self-renewal regulators Oct3/4 and Nanog, suggesting a mechanistic connection between NMII and self-renewal. These results underscore the importance of the molecular motor, NMII, as a novel target for chemically engineering the survival and self-renewal of hPS cells.


Kaplinghat M.,University of California at Irvine | Linden T.,University of Chicago | Yu H.-B.,University of California at Riverside
Physical Review Letters | Year: 2015

Observations by the Fermi Large-Area Telescope have uncovered a significant γ-ray excess directed toward the Milky Way Galactic Center. There has been no detection of a similar signal in the stacked population of Milky Way dwarf spheroidal galaxies. Additionally, astronomical observations indicate that dwarf galaxies and other faint galaxies are less dense than predicted by the simplest cold dark matter models. We show that a self-interacting dark matter model with a particle mass of roughly 50 GeV annihilating to the mediator responsible for the strong self-interaction can simultaneously explain all three observations. The mediator is necessarily unstable, and its mass must be below about 100 MeV in order to decrease the dark matter density of faint galaxies. If the mediator decays to electron-positron pairs with a cross section on the order of the thermal relic value, then we find that these pairs can up-scatter the interstellar radiation field in the Galactic center and produce the observed γ-ray excess. © 2015 American Physical Society.


Varma C.M.,University of California at Riverside
Physical Review Letters | Year: 2015

Quasi-two-dimensional itinerant fermions in the antiferromagnetic (AFM) quantum-critical region of their phase diagram, such as in the Fe-based superconductors or in some of the heavy-fermion compounds, exhibit a resistivity varying linearly with temperature and a contribution to specific heat or thermopower proportional to TlnT. It is shown, here, that a generic model of itinerant anti-ferromagnet can be canonically transformed so that its critical fluctuations around the AFM-vector Q can be obtained from the fluctuations in the long wavelength limit of a dissipative quantum XY model. The fluctuations of the dissipative quantum XY model in 2D have been evaluated recently, and in a large regime of parameters, they are determined, not by renormalized spin fluctuations, but by topological excitations. In this regime, the fluctuations are separable in their spatial and temporal dependence and have a spatial correlation length which is proportional to the logarithm of the temporal correlation length, i.e., for some purposes, the effective dynamic exponent z=. The time dependence gives ω/T scaling at criticality. The observed resistivity and entropy then follow. Several predictions to test the theory are also given. © 2015 American Physical Society. © 2015 American Physical Society.


Alam K.,East West University of Bangladesh | Lake R.K.,University of California at Riverside
IEEE Transactions on Electron Devices | Year: 2012

The performance of a 5-nm gate length monolayer MoS2 transistor is benchmarked against an ultrathin body Si transistor of similar dimensions and the ITRS requirements for 2026 low operating power (LOP) technology. The MoS2 transistor has a subthreshold slope of 70 mV/dec, an on-/off-current ratio of 4.8 × 104, a drive current of 238 μA/μM, a peak transconductance of 2.65 mS/μm, a total capacitance of 0.164 fF/μm , and an intrinsic switching delay of 0.276 ps. These numbers for the silicon competitor are 79 mV/dec, 1.8 × 104, 89 μA/μm, 1.22 mS/μm, 0.0733 fF/μm, and 0.331 ps, respectively. The heavier effective mass of the MoS2 significantly reduces the direct source-drain leakage current, and it increases the drive current and the transconductance. The performance metrics of MoS2 transistor are comparable to the ITRS 2026 LOP technology requirements. © 1963-2012 IEEE.


Cohen S.R.,University of California at Riverside
Journal of Policy and Practice in Intellectual Disabilities | Year: 2013

Community services and supports for children with intellectual disabilities (ID) can ameliorate the negative effects of caregiving and enhance child outcomes. For example, in Central and South America, many children with disabilities are institutionalized with inadequate sanitation and medical care. In the United States, certain demographic factors (e.g., poverty, limited access to healthcare, language barriers, and immigrant status) contribute to the underdiagnosis and poor-quality treatment of Latino families and their children with ID, thus limiting their access to effective community and family supports. This paper utilizes a cultural lens to target advocacy as a mechanism for improving access to local community services and social supports for children with ID. The author examines specific cultural beliefs regarding family support and child development among Latino families, and provides policy recommendations derived from these cultural beliefs that aim to enhance advocacy efforts among Latino caregivers. The author notes that effective advocacy, at the family and at the policy level, can be a useful tool to access crucial community and social supports that enhance child and family outcomes. © 2013 International Association for the Scientific Study of Intellectual Disabilities and Wiley Periodicals, Inc.


The fairyfly genus Ooctonus Haliday (Hymenoptera: Mymaridae) from the Palaearctic region is revised. Twelve speces are recognized, including the newly described O. lokomotiv Triapitsyn sp. n. (Far East of Russia), O. saturn Triapitsyn sp. n. (Far East of Russia, and Japan), O. spartak Triapitsyn sp. n. (Kyrgyzstan), O. tretiakovi Triapitsyn sp. n. (Far East of Russia), and O. us Triapitsyn sp. n. (Japan, and Republic of Korea). All the species are redescribed, illustrated, and diagnosed, as is the Oriental species O. himalayus Subba Rao, based mainly on non-type specimens from Nepal (its male is newly described). Taxonomic notes are provided on the other three previously described Oriental species of Ooctonus and one new Oriental species, O. lapen Triapitsyn sp. n., is described from Nepal. Extralimital records are included for the species with Holarctic distribution. Twenty-five new synonymies are proposed: O. major Foerster syn. n., O. elegantissimus Soyka syn. n., O. austriacus Soyka syn. n., O. silvestris Soyka syn. n., and O. isotomus Mathot syn. n. under O. insignis Haliday; O. acutiventris Soyka syn. n., O. askhamensis Hincks syn. n., O. collinus Soyka syn. n., O. stammeri Soyka syn. n., O. viennensis Soyka syn. n., O. niger Soyka syn. n., and O. americanus Girault syn. n. under O. vulgatus Haliday; O. amoenus (Foerster) syn. n., O. hemipterus igneus Debauche syn. n., O. foersteri Soyka syn. n., O. wagneri Soyka syn. n., and O. pechlaneri Soyka syn. n. under O. hemipterus Haliday; O. atroflavus Soyka syn. n., O. diversicornis Soyka syn. n., and O. auripes Whittaker syn. n. under O. notatus Walker; O. polonicus Soyka syn. n., O. montanus Soyka syn. n., O. remonti Mathot syn. n., and O. dovrensis Solem & Sveum syn. n. under O. sublaevis Foerster; and O. flaviventris Donev syn. n. under O. novickyi Soyka. Ooctonus sevae Risbec (from Madagascar) is transferred to Gonatocerus Nees ab Esenbeck as Gonotocerus (Lymaenon) sevae (Risbec), comb. n. Lectotypes are designated for O. austriacus Soyka, O. elegantissimus Soyka, O. foersteri Soyka, O. heterotomus Foerster, O. major Foerster, and O. sublaevis Foerster. Separate keys are provided to females of Ooctonus from the Palaearctic region, to both sexes of the European species, and also to females of the known Oriental species of Ooctonus. A brief diagnosis of the genus is given based on its world fauna, and information on the distribution and known host associations of Ooctonus species is provided. A historical account of the Walter Soyka collection of microhymenoptera is presented, with references to the Arnold Foerster collection of Mymaridae. Copyright © 2010 Magnolia Press.


Heinson A.,University of California at Riverside | Junk T.R.,Fermi National Accelerator Laboratory
Annual Review of Nuclear and Particle Science | Year: 2011

The field of experimental particle physics has become more sophisticated over time, as fewer, larger experimental collaborations search for small signals in samples with large components of background. The search for and the observation of electroweak single top quark production by the CDF and DØ Collaborations at Fermilab's Tevatron collider are an example of an elaborate effort to measure the rate of a very rare process in the presence of large backgrounds and to learn about the properties of the top quark's weak interaction. We present the techniques used to make this groundbreaking measurement and the interpretation of the results in the context of the Standard Model. © 2011 by Annual Reviews. All rights reserved.


Xu S.,University of California at Riverside
Heredity | Year: 2010

The least absolute shrinkage and selection operator (Lasso) estimation of regression coefficients can be expressed as Bayesian posterior mode estimation of the regression coefficients under various hierarchical modeling schemes. A Bayesian hierarchical model requires hyper prior distributions. The regression coefficients are parameters of interest. The normal distribution assigned to each regression coefficient is a prior distribution. The variance parameter in the normal prior distribution is further assigned a hyper prior distribution so that the variance parameter can be estimated from the data. We developed an expectation-maximization (EM) algorithm to estimate the variance parameter of the prior distribution for each regression coefficient. Performance of the EM algorithm was evaluated through simulation study and real data analysis. We found that the Jeffreys hyper prior for the variance component usually performs well with regard to generating the desired sparseness of the regression model. The EM algorithm can handle not only the usual regression models but it also conveniently deals with linear models in which predictors are defined as classification variables. In the context of quantitative trait loci (QTL) mapping, this new EM algorithm can estimate both genotypic values and QTL effects expressed as linear contrasts of the genotypic values. © 2010 Macmillan Publishers Limited All rights reserved.


Sheikholeslami M.,Babol Noshirvani University of Technology | Ellahi R.,FBAS | Ellahi R.,University of California at Riverside
International Journal of Heat and Mass Transfer | Year: 2015

In this paper magnetohydrodynamics nanofluid hydrothermal treatment in a cubic cavity heated from below is presented. The mathematical model consists of continuity and the momentum equations, while a new model is proposed to see the effects Brownian motion on the effective viscosity and thermal conductivity of nanofluid. The Lattice Boltzmann method is utilized to simulate three dimensional problems. The Koo-Kleinstreuer-Li correlation is also taken into account. Numerical calculation is made for different values of Hartmann number, nanoparticle volume fraction and Rayleigh number. The results are presented graphically in terms of streamlines, isotherms and isokinetic energy as well as Nusselt number. It is observed that the applying magnetic field results in a force opposite to the flow direction that leads to drag the flow and then reduces the convection currents by reducing the velocities. Also it can be concluded that Nusselt number is an increasing function of Rayleigh number and nanofluid volume fraction while it is a decreasing function of Hartmann number. © 2015 Elsevier Ltd.


Mills Jr. A.P.,University of California at Riverside
Rivista del Nuovo Cimento | Year: 2011

These notes contain speculations about interesting situations that might occur when two or more low-energy positrons interact with each other and/or with various forms of ordinary matter. Topics include many positrons compressed to high density at a field emission tip, a long-lived metastable cold neutral electron positron plasma in a box, dipositronium and other multipositron molecules, the positronium Bose-Einstein condensate, precision measurements on positronium cooled by a pulsed laser method, stimulated emission of annihilation radiation, headon collisions of two positronium annihilation gamma-ray laser pulses, and possible uses for gamma-ray lasers. © Società Italiana di Fisica.


Rao A.L.N.,University of California at Riverside | Kalantidis K.,University of Crete
Virology | Year: 2015

Since the discovery of non-coding, small, highly structured, satellite RNAs (satRNAs) and viroids as subviral pathogens of plants , have been of great interest to molecular biologists as possible living fossils of pre-cellular evolution in an RNA world. Despite extensive studies performed in the last four decades, there is still mystery surrounding the origin and evolutionary relationship between these subviral pathogens. Recent technical advances revealed some commonly shared replication features between these two subviral pathogens. In this review, we discuss our current perception of replication and evolutionary origin of these petite RNA pathogens. © 2015 Elsevier Inc.


Chinnusamy V.,University of California at Riverside
Methods in molecular biology (Clifton, N.J.) | Year: 2010

Cold stress adversely affects plant growth and development and thus limits crop productivity. Diverse plant species tolerate cold stress to a varying degree, which depends on reprogramming gene expression to modify their physiology, metabolism, and growth. Cold signal in plants is transmitted to activate CBF-dependent (C-repeat/drought-responsive element binding factor-dependent) and CBF-independent transcriptional pathway, of which CBF-dependent pathway activates CBF regulon. CBF transcription factor genes are induced by the constitutively expressed ICE1 (inducer of CBF expression 1) by binding to the CBF promoter. ICE1-CBF cold response pathway is conserved in diverse plant species. Transgenic analysis in different plant species revealed that cold tolerance can be significantly enhanced by genetic engineering CBF pathway. Posttranscriptional regulation at pre-mRNA processing and export from nucleus plays a role in cold acclimation. Small noncoding RNAs, namely micro-RNAs (miRNAs) and small interfering RNAs (siRNAs), are emerging as key players of posttranscriptional gene silencing. Cold stress-regulated miRNAs have been identified in Arabidopsis and rice. In this chapter, recent advances on cold stress signaling and tolerance are highlighted.


Seto K.C.,Yale University | Sanchez-Rodriguez R.,University of California at Riverside | Fragkias M.,Arizona State University
Annual Review of Environment and Resources | Year: 2010

Contemporary urbanization differs from historical patterns of urban growth in terms of scale, rate, location, form, and function. This review discusses the characteristics of contemporary urbanization and the roles of urban planning, governance, agglomeration, and globalization forces in driving and shaping the relationship between urbanization and the environment. We highlight recent research on urbanization and global change in the context of sustainability as well as opportunities for bundling urban development efforts, climate mitigation, and adaptation strategies to create synergies to transition to sustainability. We conclude with an analysis of global greenhouse gas emissions under different scenarios of future urbanization growth and discuss their implications. Copyright © 2010 by Annual Reviews. All rights reserved.


Walton W.E.,University of California at Riverside
Wetlands Ecology and Management | Year: 2012

Constructed wetland technology has broad applications for the treatment of many types of wastewaters and provides an ecological approach to mitigate the release of nutrients and toxic materials into the environment. However, design features, maintenance activities and the characteristics of the wastewater undergoing treatment contribute differentially to potential levels of mosquito production and, consequently, to threats to human and animal health from mosquito-borne pathogens. Of the variables typically considered when designing free-water surface constructed wetlands for the improvement of water quality of municipal and agricultural wastewaters, organic loading (i. e., biochemical oxygen demand, total suspended solids), nutrients (nitrogen and phosphorus), and the configuration and maintenance of emergent vegetation can have strong effects on mosquito production. The production of Culex vectors of encephalitides and filarial worms is directly related to loading rates of organic matter and bottom-up enrichment of larval mosquito resources and their interaction with design features and management practices that reduce the physical and biological factors causing mortality of immature mosquitoes. As loading rates of organic matter and nutrients decline, the diversity of mosquitoes produced by treatment wetlands tends to increase and the relative abundance of Anopheles species, which are capable of vectoring the causative agents of malaria, increases in temperate man-made wetlands. Habitat features and management practices that create intermittently inundated substrate can lead to the production of other mosquitoes (i. e., Aedes, Psorophora) with floodwater life histories. Constructed wetland technology is expected to play an increasing role in water treatment and reclamation in tropical and subtropical countries where virulent mosquito-borne pathogens already cause significant levels of morbidity and mortality. © 2011 Springer Science+Business Media B.V.


Esteban E.,CITA Government of Aragon | Albiac J.,University of California at Riverside
Ecological Economics | Year: 2011

Gisser and Sánchez (1980a) state the conditions under which welfare gains from policy intervention are negligible in aquifer management, when compared with non-regulation or "free market" outcomes. This is the so-called Gisser-Sánchez effect (GSE), which has been supported by the ensuing literature during recent decades. The GSE requires a number of assumptions, among which is the disregard for aquatic ecosystems linked and dependent on aquifer systems. The depletion of aquifer systems in arid and semiarid regions worldwide is causing acute water scarcity and quality degradation, and leading to extensive ecosystem damages. This study shows that by including environmental damages into the analytical model, results can change substantially. The analysis highlights both theoretically and empirically the importance of policies in groundwater management, as well as the potential role for stakeholders' cooperation. The empirical application deals with two large aquifers in Spain, the Western La Mancha aquifer which is grossly mismanaged, and the Eastern La Mancha aquifer, which is moving towards sustainable management. Western and Eastern La Mancha aquifers illustrate that policies and institutions are essential to avoid the current global aquifer mismanagement. © 2011 Elsevier B.V.


Furness A.I.,University of California at Riverside
Biological Reviews | Year: 2016

An annual life cycle is characterized by growth, maturity, and reproduction condensed into a single, short season favourable to development, with production of embryos (seeds, cysts, or eggs) capable of surviving harsh conditions which juveniles or adults cannot tolerate. More typically associated with plants in desert environments, or temperate-zone insects exposed to freezing winters, the evolution of an annual life cycle in vertebrates is fairly novel. Killifish, small sexually dimorphic fishes in the Order Cyprinodontiformes, have adapted to seasonally ephemeral water bodies across much of Africa and South America through the independent evolution of an annual life history. These annual killifish produce hardy desiccation-resistant eggs that undergo diapause (developmental arrest) and remain buried in the soil for long periods when fish have perished due to the drying of their habitat. Killifish are found in aquatic habitats that span a continuum from permanent and stable to seasonal and variable, thus providing a useful system in which to piece together the evolutionary history of this life cycle using natural comparative variation. I first review adaptations for life in ephemeral aquatic environments in killifish, with particular emphasis on the evolution of embryonic diapause. I then bring together available evidence from a variety of approaches and provide a scenario for how this annual life cycle evolved. There are a number of features within Aplocheiloidei killifish including their inhabitation of marginal or edge aquatic habitat, their small size and rapid attainment of maturity, and egg properties that make them particularly well suited to the colonization of ephemeral waters. © 2015 Cambridge Philosophical Society


Wilke P.J.,University of California at Riverside
Quaternary International | Year: 2013

A big-game wing-trap complex in Mineral County, Nevada, seen standing and in apparently usable condition in 1845, is described, with interpretations on the manner in which it likely was used to capture Pronghorn (Antilocapra americana). The complex occurs at an elevation of 2000 m in a valley narrows, and was built mostly of juniper posts set in the ground, with bracing rocks as needed. When first seen, sagebrush also was used in its construction. It consists of several features, including a drift fence more than a kilometer long; a large oval-shaped corral with flagstones across the entrance, and containing stone blinds or shooting stations; an adjoining small corral; various other structures; and a nearby campsite. Faunal remains from the looted campsite are mostly those of large mammals, and all of the identified elements are of pronghorn. Interpretation of the manner in which the trap probably functioned conflicts in many ways with descriptions of communal pronghorn trapping provided by Great Basin ethnographers. But there is good reason to believe that descriptions of pronghorn trapping in regional ethnographies are seriously flawed. Study of this and other nearby wing-traps suggests that by late prehistoric and historic times the Indians of the southwestern Great Basin relied heavily on a set of similar communal strategies for mass entrapment of large game animals, especially pronghorn, but including also deer. They employed a built environment consisting of large wing-traps, perhaps using several such traps annually while pursuing a seasonally nomadic foraging cycle. If pronghorn trapping was paired with pine-nut gathering, exploitation of pronghorn may of necessity have occurred in different localities in successive years, allowing local populations to restore themselves. This pattern apparently prevailed in southwestern Nevada and eastern California for at least several thousand years. © 2013 Elsevier Ltd and INQUA.


Roff D.A.,University of California at Riverside
Current Biology | Year: 2011

The evolution of conditional, alternative strategies is a major factor in adaptation. In animals, the frequency of alternative morphs, characterized by different morphologies and mating tactics, can be both condition-dependent and subject to rapid evolutionary change. © 2011 Elsevier Ltd.


Cao Y.,Air Force Research Lab | Yu W.,Nanjing Southeast University | Yu W.,RMIT University | Ren W.,University of California at Riverside | Chen G.,City University of Hong Kong
IEEE Transactions on Industrial Informatics | Year: 2013

This paper reviews some main results and progress in distributed multi-agent coordination, focusing on papers published in major control systems and robotics journals since 2006. Distributed coordination of multiple vehicles, including unmanned aerial vehicles, unmanned ground vehicles, and unmanned underwater vehicles, has been a very active research subject studied extensively by the systems and control community. The recent results in this area are categorized into several directions, such as consensus, formation control, optimization, and estimation. After the review, a short discussion section is included to summarize the existing research and to propose several promising research directions along with some open problems that are deemed important for further investigations. © 2005-2012 IEEE.


Alexander J.M.,ETH Zurich | Diez J.M.,University of California at Riverside | Levine J.M.,ETH Zurich
Nature | Year: 2015

Understanding how species respond to climate change is critical for forecasting the future dynamics and distribution of pests, diseases and biological diversity. Although ecologists have long acknowledged species' direct physiological and demographic responses to climate, more recent work suggests that these direct responses can be overwhelmed by indirect effects mediated via other interacting community members. Theory suggests that some of the most dramatic impacts of community change will probably arise through the assembly of novel species combinations after asynchronous migrations with climate. Empirical tests of this prediction are rare, as existing work focuses on the effects of changing interactions between competitors that co-occur today. To explore how species' responses to climate warming depend on how their competitors migrate to track climate, we transplanted alpine plant species and intact plant communities along a climate gradient in the Swiss Alps. Here we show that when alpine plants were transplanted to warmer climates to simulate a migration failure, their performance was strongly reduced by novel competitors that could migrate upwards from lower elevation; these effects generally exceeded the impact of warming on competition with current competitors. In contrast, when we grew the focal plants under their current climate to simulate climate tracking, a shift in the competitive environment to novel high-elevation competitors had little to no effect. This asymmetry in the importance of changing competitor identity at the leading versus trailing range edges is best explained by the degree of functional similarity between current and novel competitors. We conclude that accounting for novel competitive interactions may be essential to predict species' responses to climate change accurately. © 2015 Macmillan Publishers Limited.


Heidt C.,University of California at Riverside
Nuclear and Particle Physics Proceedings | Year: 2016

The Muon Ionization Cooling Experiment (MICE) is progressing towards a demonstration of the cooling technology required for the Neutrino Factory and the Muon Collider. MICE Step IV will allow the cooling properties of liquid hydrogen and lithium hydride to be studied in detail and provide the first opportunity to observe the reduction of normalized transverse emittance using ionization cooling. Absorbers sited within a superconducting focus-coil magnet will cause the muon beam to lose energy. The muon-beam phase space upstream and downstream of the absorber/focus-coil module will be measured using two solenoidal spectrometers. After a brief summary of the status of the experiment, the physics program of Step IV is described. © 2015 Elsevier B.V.


Ma E.,University of California at Riverside | Ma E.,Hong Kong University of Science and Technology
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2016

I propose a model of radiative charged-lepton and neutrino masses with A4 symmetry. The soft breaking of A4 to Z3 lepton triality is accomplished by dimension-three terms. The breaking of Z3 by dimension-two terms allows cobimaximal neutrino mixing (θ13≠0, θ23=π/4, δCP=±π/2) to be realized with only very small finite calculable deviations from the residual Z3 lepton triality. This construction solves a long-standing technical problem inherent in renormalizable A4 models since their inception. © 2016 The Author.


Ma E.,University of California at Riverside
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2016

In the context of the non-Abelian discrete symmetry A4, the neutrino mass matrix has been studied extensively. A brief update is presented to focus on the conceptual shift from tribimaximal mixing (θ13=0, θ23=π/4, tan2θ12=1/2) to cobimaximal mixing (θ13≠0, θ23=π/4, δCP=±π/2) which agrees well with present data. Three specific realistic examples are proposed, two with three and the third with just two parameters. © 2015 The Author.


Hollis R.S.,University of California at Riverside
Nuclear and Particle Physics Proceedings | Year: 2016

The PHENIX experiment at the Relativistic Heavy Ion Collider has measured a suite of observables for open and closed heavy flavor in a variety of collision systems, p+p, d+Au, Cu+Cu, Au+Au, U+U, and at different beam energies. These results indicate substantial modification in the yields of quarkonia, including J/ψ, ψ', and Υ states, and a substantial redistribution in momentum space of open heavy flavor quarks. We discuss the latest results and comparisons to theoretical interpretations. © 2015.


Chen X.,University of California at Riverside
Plant Journal | Year: 2010

Summary Small RNAs associated with post-transcriptional gene silencing were first discovered in plants in 1999. Although this study marked the beginning of small RNA biology in plants, the sequence of the Arabidopsis genome and related genomic resources that were soon to become available to the Arabidopsis community launched the research on small RNAs at a remarkable pace. In 2000, when the genetic blueprint of the first plant species was revealed, the tens of thousands of endogenous small RNA species as we know today remained hidden features of the genome. However, the subsequent 10 years have witnessed an explosion of our knowledge of endogenous small RNAs: their widespread existence, diversity, biogenesis, mode of action and biological functions. As key sequence-specific regulators of gene expression in the nucleus and the cytoplasm, small RNAs influence almost all aspects of plant biology. Because of the extensive conservation of mechanisms concerning the biogenesis and molecular actions of small RNAs, research in the model plant Arabidopsis has contributed vital knowledge to the small RNA field in general. Our knowledge of small RNAs gained primarily from Arabidopsis has also led to the invention of effective gene knock-down technologies that are applicable to diverse plant species, including crop plants. Here, I attempt to recount the developments of the small RNA field in the pre- and post-genomic era, in celebration of the 10th anniversary of the completion of the first plant genome. © 2010 Blackwell Publishing Ltd.


Ma E.,University of California at Riverside | Ma E.,Hong Kong University of Science and Technology
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2016

In all scalar extensions of the standard model of particle interactions, the one Higgs boson responsible for electroweak symmetry breaking always mixes with other neutral scalars at tree level unless a symmetry prevents it. An unexplored important option is that the mixing may be radiative, and thus guaranteed to be small. Two first such examples are discussed. One is based on the soft breaking of the discrete symmetry Z3. The other starts with the non-Abelian discrete symmetry A4 which is then softly broken to Z3, and results in the emergence of an interesting dark-matter candidate together with a light mediator for the dark matter to have its own long-range interaction. © 2016 The Author.


Das S.,Argonne National Laboratory | Das S.,Purdue University | Gulotty R.,Argonne National Laboratory | Gulotty R.,University of California at Riverside | And 2 more authors.
Nano Letters | Year: 2014

In this article, we report only 10 atomic layer thick, high mobility, transparent thin film transistors (TFTs) with ambipolar device characteristics fabricated on both a conventional silicon platform as well as on a flexible substrate. Monolayer graphene was used as metal electrodes, 3-4 atomic layers of h-BN were used as the gate dielectric, and finally bilayers of WSe2 were used as the semiconducting channel material for the TFTs. The field effect carrier mobility was extracted to be 45 cm2/(V s), which exceeds the mobility values of state of the art amorphous silicon based TFTs by ∼100 times. The active device stack of WSe2-hBN-graphene was found to be more than 88% transparent over the entire visible spectrum and the device characteristics were unaltered for in-plane mechanical strain of up to 2%. The device demonstrated remarkable temperature stability over 77-400 K. Low contact resistance value of 1.4 kω-μm, subthreshold slope of 90 mv/decade, current ON-OFF ratio of 107, and presence of both electron and hole conduction were observed in our all two-dimensional (2D) TFTs, which are extremely desirable but rarely reported characteristics of most of the organic and inorganic TFTs. To the best of our knowledge, this is the first report of all 2D transparent TFT fabricated on flexible substrate along with the highest mobility and current ON-OFF ratio. © 2014 American Chemical Society.


Lapidus M.L.,University of California at Riverside
Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences | Year: 2015

This research expository article not only contains a survey of earlier work but also contains a main new result, which we first describe. Given c ≥ 0, the spectral operator a = ac can be thought of intuitively as the operator which sends the geometry onto the spectrum of a fractal string of dimension not exceeding c. Rigorously, it turns out to coincide with a suitable quantization of the Riemann zeta function ζ = ∂ (s): a = ζ (∂), where ∂ = ∂c is the infinitesimal shift of the real line acting on the weighted Hilbert space L2(ℝ, e-2ct dt). In this paper, we establish a new asymmetric criterion for the Riemann hypothesis (RH), expressed in terms of the invertibility of the spectral operator for all values of the dimension parameter c ∈ (0, 1/2) (i.e. for all c in the left half of the critical interval (0, 1)). This corresponds (conditionally) to a mathematical (and perhaps also, physical) 'phase transition' occurring in the midfractal case when c =1/2. Both the universality and the non-universality of ζ = ζ (s) in the right (resp., left) critical strip {1/2 < Re(s) < 1} (resp.,{0 < Re(s) < 1/2}) play a key role in this context. These new results are presented here. We also briefly discuss earlier joint work on the complex dimensions of fractal strings, and we survey earlier related work of the author with Maier and with Herichi, respectively, in which were established symmetric criteria for the RH, expressed, respectively, in terms of a family of natural inverse spectral problems for fractal strings of Minkowski dimension D ∈ (0, 1), with D ≠ 1/2, and of the quasi-invertibility of the family of spectral operators ac (with c ∈ (0, 1), c ≠ 1/2). © 2015 The Author(s) Published by the Royal Society. All rights reserved.


Ma E.,University of California at Riverside
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2014

It is shown that the inherent one-loop quadratic divergence of the Higgs mass renormalization of the standard model may be avoided in the well-studied scotogenic model of radiative neutrino mass as well as other analogous extensions. © 2014 The Author.


Gallie D.R.,University of California at Riverside
Nutrients | Year: 2013

Vitamin C serves as a cofactor in the synthesis of collagen needed to support cardiovascular function, maintenance of cartilage, bones, and teeth, as well as being required in wound healing. Although vitamin C is essential, humans are one of the few mammalian species unable to synthesize the vitamin and must obtain it through dietary sources. Only low levels of the vitamin are required to prevent scurvy but subclinical vitamin C deficiency can cause less obvious symptoms such as cardiovascular impairment. Up to a third of the adult population in the U.S. obtains less than the recommended amount of vitamin C from dietary sources of which plant-based foods constitute the major source. Consequently, strategies to increase vitamin C content in plants have been developed over the last decade and include increasing its synthesis as well as its recycling, i.e., the reduction of the oxidized form of ascorbic acid that is produced in reactions back into its reduced form. Increasing vitamin C levels in plants, however, is not without consequences. This review provides an overview of the approaches used to increase vitamin C content in plants and the successes achieved. Also discussed are some of the potential limitations of increasing vitamin C and how these may be overcome. © 2013 by the authors.


Ding D.,Xian University of Science and Technology | Liu K.,Xian University of Science and Technology | He S.,Xian University of Science and Technology | Gao C.,Xian University of Science and Technology | Yin Y.,University of California at Riverside
Nano Letters | Year: 2014

Plasmonic noble metal nanoparticles have emerged as a promising material in sensitizing wide-bandgap semiconductors for visible-light photocatalysis. Conventional methods in constructing such heterocatalysts suffer from either poor control over the size of the metal nanoparticles or inefficient charge transfer through the metal/semiconductor interface, which limit their photocatalytic activity. To solve this problem, in this work we construct Au/TiO2 photocatalysts by depositing presynthesized colloidal Au nanoparticles with well-controlled sizes to TiO2 nanocrystals and then removing capping ligands on the Au surface through a delicately designed ligand-exchange method, which leads to close Au/TiO2 Schottky contact after a mild annealing process. Benefiting from this unique synthesis strategy, the obtained photocatalysts show superior activity to conventionally prepared photocatalysts in dye decomposition and water-reduction hydrogen production under visible-light illumination. This study not only opens up new opportunities in designing photoactive materials with high stability and enhanced performance for solar energy conversion but also provides a potential solution for the well-recognized challenge in cleaning capping ligands from the surface of colloidal catalyst nanoparticles. © 2014 American Chemical Society.


Lin P.,Chongqing University | Lin P.,Beijing University of Posts and Telecommunications | Ren W.,University of California at Riverside
IEEE Transactions on Automatic Control | Year: 2014

In this note, a constrained consensus problem is studied for multi-agent systems in unbalanced networks in the presence of communication delays. Here each agent needs to lie in a closed convex constraint set while reaching a consensus. The communication graphs are directed, dynamically changing, and not necessarily balanced and only the union of the graphs is assumed to be strongly connected among each time interval of a certain bounded length. The analysis is performed based on an undelayed equivalent system that is composed of a linear main body and an error auxiliary. To tackle the loss of symmetry caused by unbalanced graphs and communication delays, a novel approach is proposed. The idea is to estimate the distance from each agent to the intersection set of all agents' constraint sets based on the properties of the projection on convex sets so as to show consensus convergence by contradiction. It is shown that the error auxiliary vanishes as time evolves and the linear main body converges to a vector with an exponential rate as a separate system. It is also shown that the communication delays do not affect the consensus stability and constrained consensus is reached even if the communication delays are arbitrarily bounded. Finally, a numerical example is included to illustrate the obtained theoretical results. © 2013 IEEE.


Ziemann P.J.,University of California at Riverside
International Reviews in Physical Chemistry | Year: 2011

Aerosol particles have significant effects on a number of important atmospheric processes and phenomena including atmospheric chemistry, visibility, cloud formation, precipitation, climate and human health. A large fraction of this particulate matter is secondary organic aerosol (SOA), which is formed by gas-toparticle conversion of volatile organic compounds (VOC) emitted to the atmosphere from biogenic and anthropogenic sources. The physical and chemical processes by which SOA is formed are complex and are not sufficiently wellunderstood to provide adequate understanding and predictions regarding the role of this material in the atmospheric system. This review describes and illustrates the fundamental components of the SOA formation process using results from systematic experimental and modelling studies of the reactions of two major classes of VOC emissions, alkanes and alkenes, with the dominant atmospheric oxidant, OH radicals, under conditions representative of a polluted atmosphere. In particular, the presentation draws from studies aimed at elucidating the effects of molecular structure including carbon number, chain branching and C=C double bonds on the reaction kinetics, products and mechanisms and their subsequent impact on SOA formation. The simple concepts drawn from the presented results provide a useful framework for understanding the chemistry of SOA formation from more complex reactions and for identifying critical areas for future research. © 2011 Taylor & Francis.


Xu F.,University of California at Riverside
Communications in Mathematical Physics | Year: 2013

Motivated by our subfactor generalization of Wall's conjecture, in this paper we determine all intermediate subfactors for conformal subnets corresponding to four infinite series of conformal inclusions, and as a consequence we verify that these series of subfactors verify our conjecture. Our results can be stated in the framework of Vertex Operator Algebras. We also verify our conjecture for Jones-Wassermann subfactors from representations of Loop groups extending our earlier results. © 2012 Springer-Verlag Berlin Heidelberg.


Dasgupta B.,International Center for Theoretical Physics | Ma E.,University of California at Riverside | Tsumura K.,Nagoya University
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2014

The Peccei-Quinn anomalous global U(1)PQ symmetry is important for solving the strong CP problem with a cosmologically relevant axion. We add to this the simple (but hitherto unexplored) observation that it also has a residual Z2 symmetry which may be responsible for a second component of dark matter, i.e., an absolutely stable weakly interacting singlet scalar. This new insight provides a theoretical justification for this simplest of all possible dark-matter models. It also connects with the notion of generating radiative neutrino mass through dark matter. Two such specific realizations are proposed. In our general scenario, dark-matter detection is guaranteed at existing direct-detection experiments and/or axion searches. Observable signals at the Large Hadron Collider are discussed. © 2014 American Physical Society.


Madani K.,University of California at Riverside
Journal of Hydrology | Year: 2010

Managing water resources systems usually involves conflicts. Behaviors of stakeholders, who might be willing to contribute to improvements and reach a win-win situation, sometimes result in worse conditions for all parties. Game theory can identify and interpret the behaviors of parties to water resource problems and describe how interactions of different parties who give priority to their own objectives, rather than system's objective, result in a system's evolution. Outcomes predicted by game theory often differ from results suggested by optimization methods which assume all parties are willing to act towards the best system-wide outcome. This study reviews applicability of game theory to water resources management and conflict resolution through a series of non-cooperative water resource games. The paper illustrates the dynamic structure of water resource problems and the importance of considering the game's evolution path while studying such problems. © 2009 Elsevier B.V. All rights reserved.


Ma E.,University of California at Riverside | Ma E.,Hong Kong University of Science and Technology
Physical Review Letters | Year: 2015

It is shown that in extensions of the standard model of quarks and leptons where the additive lepton number L is broken by two units, so that Z2 lepton parity, i.e., (-1)L which is either even or odd, remains exactly conserved, there is the possibility of stable dark matter without additional symmetry. This applies to many existing simple models of Majorana neutrino mass with dark matter, including some radiative models. Several well-known examples are discussed. This new insight leads to the construction of a radiative type II seesaw model of neutrino mass with dark matter where the dominant decay of the doubly charged Higgs boson ξ++ is into W+W+ instead of the expected li+lj+ lepton pairs for the well-known tree-level model. © 2015 American Physical Society. © 2015 American Physical Society.


Larsen P.B.,University of California at Riverside
Essays in Biochemistry | Year: 2015

Ethylene is the simplest unsaturated hydrocarbon, yet it has profound effects on plant growth and development, including many agriculturally important phenomena. Analysis of the mechanisms underlying ethylene biosynthesis and signalling have resulted in the elucidation of multistep mechanisms which at first glance appear simple, but in fact represent several levels of control to tightly regulate the level of production and response. Ethylene biosynthesis represents a two-step process that is regulated at both the transcriptional and post-translational levels, thus enabling plants to control the amount of ethylene produced with regard to promotion of responses such as climacteric flower senescence and fruit ripening. Ethylene production subsequently results in activation of the ethylene response, as ethylene accumulation will trigger the ethylene signalling pathway to activate ethylene-dependent transcription for promotion of the response and for resetting the pathway. A more detailed knowledge of the mechanisms underlying biosynthesis and the ethylene response will ultimately enable new approaches to be developed for control of the initiation and progression of ethylene-dependent developmental processes, many of which are of horticultural significance. © 2015 Authors.


Tuncel E.,University of California at Riverside | Gunduz D.,Imperial College London
IEEE Transactions on Information Theory | Year: 2014

A high-dimensional database system is studied where the noisy versions of the underlying feature vectors are observed in both the enrollment and query phases. The noisy observations are compressed before being stored in the database, and the user wishes to both identify the correct entry corresponding to the noisy query vector and reconstruct the original feature vector within a desired distortion level. A fundamental capacity-storage-distortion tradeoff is identified for this system in the form of single-letter information theoretic expressions. The relation of this problem to the classical Wyner-Ziv rate-distortion problem is shown, where the noisy query vector acts as the correlated side information available only in the lossy reconstruction of the feature vector. © 1963-2012 IEEE.


Murray E.A.,University of California at Riverside
Proceedings. Biological sciences / The Royal Society | Year: 2013

While ant colonies serve as host to a diverse array of myrmecophiles, few parasitoids are able to exploit this vast resource. A notable exception is the wasp family Eucharitidae, which is the only family of insects known to exclusively parasitize ants. Worldwide, approximately 700 Eucharitidae species attack five subfamilies across the ant phylogeny. Our goal is to uncover the pattern of eucharitid diversification, including timing of key evolutionary events, biogeographic patterns and potential cophylogeny with ant hosts. We present the most comprehensive molecular phylogeny of Eucharitidae to date, including 44 of the 53 genera and fossil-calibrated estimates of divergence dates. Eucharitidae arose approximately 50 Ma after their hosts, during the time when the major ant lineages were already established and diversifying. We incorporate host association data to test for congruence between eucharitid and ant phylogenies and find that their evolutionary histories are more similar than expected at random. After a series of initial host shifts, clades within Eucharitidae maintained their host affinity. Even after multiple dispersal events to the New World and extensive speciation within biogeographic regions, eucharitids remain parasitic on the same ant subfamilies as their Old World relatives, suggesting host conservatism despite access to a diverse novel ant fauna.


Ma E.,University of California at Riverside
Modern Physics Letters A | Year: 2010

Neutrino tribimaximal mixing is obtained from the breaking of A4 to Z3 in the charged-lepton sector and to Z2 in the neutrino sector. To enforce this conflicting pattern, extra particles and symmetries are usually invoked, often accompanied by nonrenormalizable interactions and even extra dimensions. It is shown here in a specific renormalizable model how A4 alone will accomplish this, with only the help of lepton number. © 2010 World Scientific Publishing Company.


Dekker T.,University of California at Riverside | Carde R.T.,Swedish University of Agricultural Sciences
Journal of Experimental Biology | Year: 2011

Odours are crucial cues enabling female mosquitoes to orient to prospective hosts. However, their in-flight manoeuvres to host odours are virtually unknown. Here we analyzed in 3-D the video records of female Aedes aegypti mosquitoes flying in a wind tunnel in response to host odour plumes that differed in spatial structure and composition. Following a brief (∼0.03s) encounter with CO 2, mosquitoes surged upwind and, in the absence of further encounters, counterturned without displacing upwind. These patterns resemble moth responses to encounter and loss of a filament of pheromone. Moreover, CO 2 encounters induced a highly regular pattern of counterturning across the windline in the horizontal (crosswind) and vertical planes, causing the mosquito to transect repeatedly the area where CO 2 was previously detected. However, despite the rapid changes across all three axes following an encounter with CO 2, the angular velocities remained remarkably constant. This suggests that during these CO 2- induced surges mosquitoes stabilize flight through sensors, such as the halteres and Johnston organs, sensitive to Coriolis forces. In contrast to the instantaneous responses of the mosquito CO 2, a brief encounter with a filament of human skin odour did not induce a consistent change in mosquito flight. These differential responses were reflected in further experiments with broad plumes. A broad homogeneous plume of skin odour induced rapid upwind flight and source finding, whereas a broad filamentous plume of skin odour lowered activation rates, kinetic responses and source finding compared with homogeneous plumes. Apparently, yellow fever mosquitoes need longer continuous exposure to complex skin-odour blends to induce activation and source finding. © 2011. Published by The Company of Biologists Ltd.


Hare J.D.,University of California at Riverside
Annual Review of Entomology | Year: 2011

Plants often release a blend of volatile organic compounds in response to damage by herbivorous insects that may serve as cues to locate those herbivores by natural enemies. The blend of compounds emitted by plants may be more variable than is generally assumed. The quantity and the composition of the blends may vary with the species of the herbivore, the plant species and genotype within species, the environmental conditions under which plants are grown, and the number of herbivore species attacking the plant. Although it is often assumed that induced emission of these compounds is an adaptive tactic on the part of plants, the evidence that such responses minimize fitness losses of plants remains sparse because the necessary data on plant fitness rarely have been collected. The application of techniques of evolutionary quantitative genetics may facilitate the testing of widely held hypotheses about the evolution of induced production of volatile compounds under natural conditions. © 2011 by Annual Reviews. All rights reserved.


Gao L.,University of California at Riverside
Nature Genetics | Year: 2016

SWI/SNF-type chromatin remodelers, such as BRAHMA (BRM), and H3K27 demethylases both have active roles in regulating gene expression at the chromatin level, but how they are recruited to specific genomic sites remains largely unknown. Here we show that RELATIVE OF EARLY FLOWERING 6 (REF6), a plant-unique H3K27 demethylase, targets genomic loci containing a CTCTGYTY motif via its zinc-finger (ZnF) domains and facilitates the recruitment of BRM. Genome-wide analyses showed that REF6 colocalizes with BRM at many genomic sites with the CTCTGYTY motif. Loss of REF6 results in decreased BRM occupancy at BRM–REF6 co-targets. Furthermore, REF6 directly binds to the CTCTGYTY motif in vitro, and deletion of the motif from a target gene renders it inaccessible to REF6 in vivo. Finally, we show that, when its ZnF domains are deleted, REF6 loses its genomic targeting ability. Thus, our work identifies a new genomic targeting mechanism for an H3K27 demethylase and demonstrates its key role in recruiting the BRM chromatin remodeler. © 2016 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.


Jordan A.N.,University of Rochester | Korotkov A.N.,University of California at Riverside
Contemporary Physics | Year: 2010

We review and expand on recent advances in theory and experiments concerning the problem of wavefunction uncollapse: given an unknown state that has been disturbed by a generalised measurement, restore the state to its initial configuration. We describe how this is probabilistically possible with a subsequent measurement that involves erasing the information extracted about the state in the first measurement. The general theory of abstract measurements is discussed, focusing on quantum information aspects of the problem, in addition to investigating a variety of specific physical situations and explicit measurement strategies. Several systems are considered in detail: the quantum double dot charge qubit measured by a quantum point contact (with and without Hamiltonian dynamics), the superconducting phase qubit monitored by a SQUID detector, and an arbitrary number of entangled charge qubits. Furthermore, uncollapse strategies for the quantum dot electron spin qubit, and the optical polarisation qubit are also reviewed. For each of these systems the physics of the continuous measurement process, the strategy required to ideally uncollapse the wavefunction, as well as the statistical features associated with the measurement are discussed. We also summarise the recent experimental realisation of two of these systems, the phase qubit and the polarisation qubit. © 2010 Taylor & Francis.


Mei J.,Harbin Institute of Technology | Ren W.,University of California at Riverside | Ma G.,Harbin Institute of Technology
Automatica | Year: 2012

In this paper, we study the distributed containment control problem for networked Lagrangian systems with multiple dynamic leaders in the presence of parametric uncertainties under a directed graph that characterizes the interaction among the leaders and the followers. We propose a distributed adaptive control algorithm combined with distributed sliding-mode estimators. A necessary and sufficient condition on the directed graph is presented such that all followers converge to the dynamic convex hull spanned by the dynamic leaders asymptotically. As a byproduct, we show a necessary and sufficient condition on leaderless consensus for networked Lagrangian systems under a directed graph. Numerical simulation results are given to show the effectiveness of the proposed control algorithms. © 2012 Elsevier Ltd. All rights reserved.


Lyubomirsky I.,University of California at Riverside
Journal of Lightwave Technology | Year: 2010

This paper proposes and analyzes a quadrature duobinary modulation format with coherent detection for high-spectral efficiency wavelength-division- multiplexing transmission systems at 112 Gb/s per channel. A practical system design of a dual polarization quadrature duobinary (DP-QDB) format with coherent heterodyne detection is analyzed and compared with the DP-differential quadrature phase-shift keying format for feasibility of 112 Gb/s transmission. Using simulation analysis, we show that the relatively narrow spectrum of quadrature duobinary modulation provides an effective practical means for realizing high-spectral efficiency transmission, approaching the theoretical limit of 4 bits/s/Hz, while also providing excellent tolerance to optical filter cascades for a robust optical networking functionality. © 2009 IEEE.


Bailey-Serres J.,University of California at Riverside
Annual Review of Plant Biology | Year: 2013

The expression of nuclear protein-coding genes is controlled by dynamic mechanisms ranging from DNA methylation, chromatin modification, and gene transcription to mRNA maturation, turnover, and translation and the posttranslational control of protein function. A genome-scale assessment of the spatiotemporal regulation of gene expression is essential for a comprehensive understanding of gene regulatory networks. However, there are major obstacles to the precise evaluation of gene regulation in multicellular plant organs; these include the monitoring of regulatory processes at levels other than steady-state transcript abundance, resolution of gene regulation in individual cells or cell types, and effective assessment of transient gene activity manifested during development or in response to external cues. This review surveys the advantages and applications of microgenomics technologies that enable panoramic quantitation of cell-type-specific expression in plants, focusing on the importance of querying gene activity at multiple steps in the continuum, from histone modification to selective translation. © Copyright ©2013 by Annual Reviews. All rights reserved.


Ellahi R.,University of California at Riverside | Hameed M.,University of South Carolina
International Journal of Numerical Methods for Heat and Fluid Flow | Year: 2012

Purpose - The purpose of this paper is to study the effects of nonlinear partial slip on the walls for steady flow and heat transfer of an incompressible, thermodynamically compatible third grade fluid in a channel. The principal question the authors address in this paper is in regard to the applicability of the no-slip condition at a solid-liquid boundary. The authors present the effects of slip, magnetohydrodynamics (MHD) and heat transfer for the plane Couette, plane Poiseuille and plane Couette-Poiseuille flows in a homogeneous and thermodynamically compatible third grade fluid. The problem of a non-Newtonian plane Couette flow, fully developed plane Poiseuille flow and Couette-Poiseuille flow are investigated. Design/methodology/approach - The present investigation is an attempt to study the effects of nonlinear partial slip on the walls for steady flow and heat transfer of an incompressible, thermodynamically compatible third grade fluid in a channel. A very effective and higher order numerical scheme is used to solve the resulting system of nonlinear differential equations with nonlinear boundary conditions. Numerical solutions are obtained by solving nonlinear ordinary differential equations using Chebyshev spectral method. Findings - Due to the nonlinear and highly complicated nature of the governing equations and boundary conditions, finding an analytical or numerical solution is not easy. The authors obtained numerical solutions of the coupled nonlinear ordinary differential equations with nonlinear boundary conditions using higher order Chebyshev spectral collocation method. Spectral methods are proven to offer a superior intrinsic accuracy for derivative calculations. Originality/value - To the best of the authors' knowledge, no such analysis is available in the literature which can describe the heat transfer, MHD and slip effects simultaneously on the flows of the non-Newtonian fluids. © Emerald Group Publishing Limited.


Sadler P.M.,University of California at Riverside
Bulletin of Geosciences | Year