Riverside, CA, United States
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.


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Penilla E.H.,University of California at Riverside | Kodera Y.,University of California at Riverside | Garay J.E.,University of California at Riverside
Advanced Functional Materials | Year: 2013

Alumina (Al2O3) is one of the most versatile ceramics, utilized in an amazing range of structural and optical applications. In fact, chromium-doped single crystal Al2O3 was the basis for the first laser. Today, most photoluminescent (PL) materials rely on rare earth (RE) rather than transition-metal dopants because RE doping produces greater efficiencies and lower lasing thresholds. RE-doped alumina could provide an extremely versatile PL ceramic, opening the door for a host of new applications and devices. However, producing a transparent RE:Al 2O3 suitable for PL applications is a major challenge due to the very low equilibrium solubility of RE (∼10-3%) in Al 2O3 in addition to alumina's optical anisotropy. A method is presented here to successfully incorporate Tb3+ ions up to a concentration of 0.5 at% into a dense alumina matrix, achieving a transparent light-emitting ceramic. Sub-micrometer alumina and nanometric RE oxide powders are simultaneously densified and reacted using current-activated, pressure-assisted densification (CAPAD), often called spark plasma sintering (SPS). These doped ceramics have a high transmission (∼75% at 800 nm) and display PL peaks centered at 485 nm and 543 nm, characteristic of Tb 3+ emission. Additionally, the luminescent lifetimes are long and compare favorably with lifetimes of other laser ceramics. The high transparencies and PL properties of these ceramics have exciting prospects for high energy laser technology. Tb3+ ions at concentration of 0.5 at% are incorporated into a dense alumina matrix, achieving a transparent light-emitting ceramic. These doped ceramics have a high transmission (∼75% at 800 nm) and display photoluminescence (PL) peaks centered at 485 nm and 543 nm, characteristic of Tb3+ emission. The high transparencies and PL properties of these ceramics have exciting prospects for high-energy laser technologies. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


El Shawa H.,University of California at Riverside | Abbott III C.W.,University of California at Riverside | Huffman K.J.,University of California at Riverside
Journal of Neuroscience | Year: 2013

In utero ethanol exposure from a mother's consumption of alcoholic beverages impacts brain and cognitive development, creating a range of deficits in the child (Levitt, 1998; Lebel et al., 2012). Children diagnosed with fetal alcohol spectrum disorders (FASD) are often born with facial dysmorphology and may exhibit cognitive, behavioral, and motor deficits from ethanol-related neurobiological damage in early development. Prenatal ethanol exposure (PrEE) is the number one cause of preventable mental and intellectual dysfunction globally, therefore the neurobiological underpinnings warrant systematic research.Wedocument novel anatomical and gene expression abnormalities in the neocortex of newborn mice exposed to ethanol in utero. This is the first study to demonstrate large-scale changes in intraneocortical connections and disruption of normal patterns of neocortical gene expression in any prenatal ethanol exposure animal model. Neuroanatomical defects and abnormal neocortical RZRβ, Id2, and Cadherin8 expression patterns are observed in PrEE newborns, and abnormal behavior is present in 20-d-old PrEE mice. The vast network of neocortical connections is responsible for high-level sensory and motor processing as well as complex cognitive thought and behavior in humans. Disruptions to this network from PrEErelated changes in gene expression may underlie some of the cognitive-behavioral phenotypes observed in children with FASD. © 2013 the authors.


Zhang Q.,University of California at Riverside | Wang Y.,University of California at Riverside
Biochimica et Biophysica Acta - Gene Regulatory Mechanisms | Year: 2010

High mobility group (HMG) proteins assume important roles in regulating chromatin dynamics, transcriptional activities of genes and other cellular processes. Post-translational modifications of HMG proteins can alter their interactions with DNA and proteins, and consequently, affect their biological activities. Although the mechanisms through which these modifications are involved in regulating biological processes in different cellular contexts are not fully understood, new insights into these modification "codes" have emerged from the increasing appreciation of the functions of these proteins. In this review, we focus on the chemical modifications of mammalian HMG proteins and highlight their roles in nuclear functions. © 2009 Elsevier B.V. All rights reserved.


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.


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.


Yu Y.,University of California at Riverside | Hua Y.,University of California at Riverside
IEEE Transactions on Signal Processing | Year: 2010

A power allocation or scheduling problem is studied for a multiuser multiple-input multiple-output (MIMO) wireless relay system where there is a non-regenerative relay between one access point and multiple users. Each node in the system is equipped with multiple antennas. The purpose of this study is to develop fast algorithms to compute the source covariance matrix (or matrices) and the relay transformation matrix to optimize a system performance. We consider the minimization of power consumption subject to rate constraint and also the maximization of system throughput subject to power constraint. These problems are nonconvex and apparently have no simple solutions. In this paper, a number of computational strategies are presented and their performances are investigated. Both uplink and downlink cases are considered. The use of multiple carriers is also discussed. Moreover, a generalized water-filling (GWF) algorithm is developed to solve a special class of convex optimization problems. The GWF algorithm is used for two of the strategies shown in this paper. © 2006 IEEE.


Qin Z.,University of California at Riverside | Shelton C.R.,University of California at Riverside
Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition | Year: 2012

We address the problem of multi-person data-association-based tracking (DAT) in semi-crowded environments from a single camera. Existing tracklet-association-based methods using purely visual cues (like appearance and motion information) show impressive results but rely on heavy training, a number of tuned parameters, and sophisticated detectors to cope with visual ambiguities within the video and low-level processing errors. In this work, we consider clustering dynamics to mitigate such ambiguities. This leads to a general optimization framework that adds social grouping behavior (SGB) to any basic affinity model. We formulate this as a nonlinear global optimization problem to maximize the consistency of visual and grouping cues for trajectories in both tracklet-tracklet linking space and tracklet-grouping assignment space. We formulate the Lagrange dual and solve it using a two-stage iterative algorithm, employing the Hungarian algorithm and K-means clustering. We build SGB upon a simple affinity model and show very promising performance on two publicly available real-world datasets with different tracklet extraction methods. © 2012 IEEE.


Duprez K.,University of California at Riverside | Scranton M.A.,University of California at Riverside | Walling L.L.,University of California at Riverside | Fan L.,University of California at Riverside
Acta Crystallographica Section D: Biological Crystallography | Year: 2014

The acidic leucine aminopeptidase (LAP-A) from tomato is induced in response to wounding and insect feeding. Although LAP-A shows in vitro peptidase activity towards peptides and peptide analogs, it is not clear what kind of substrates LAP-A hydrolyzes in vivo. In the current study, the crystal structure of LAP-A was determined to 2.20Å resolution. Like other LAPs in the M17 peptidase family, LAP-A is a dimer of trimers containing six monomers of bilobal structure. Each monomer contains two metal ions bridged by a water or a hydroxyl ion at the active site. Modeling of different peptides or peptide analogs in the active site of LAP-A reveals a spacious substrate-binding channel that can bind peptides of five or fewer residues with few geometric restrictions. The sequence specificity of the bound peptide is likely to be selected by the structural and chemical restrictions on the amino acid at the P1 and P1' positions because these two amino acids have to bind perfectly at the active site for hydrolysis of the first peptide bond to occur. The hexameric assembly results in the merger of the open ends of the six substrate-binding channels from the LAP-A monomers to form a spacious central cavity allowing the hexameric LAP-A enzyme to simultaneously hydrolyze six peptides containing up to six amino acids each. The hexameric LAP-A enzyme may also hydrolyze long peptides or proteins if only one such substrate is bound to the hexamer because the substrate can extend through the central cavity and the two major solvent channels between the two LAP-A trimers. © 2014 International Union of Crystallography.


Zhu Y.,University of California at Riverside | Nayak N.M.,University of California at Riverside | Roy-Chowdhury A.K.,University of California at Riverside
IEEE Journal on Selected Topics in Signal Processing | Year: 2013

In this paper, we propose a mathematical framework to jointly model related activities with both motion and context information for activity recognition and anomaly detection. This is motivated from observations that activities related in space and time rarely occur independently and can serve as context for each other. The spatial and temporal distribution of different activities provides useful cues for the understanding of these activities. We denote the activities occurring with high frequencies in the database as normal activities. Given training data which contains labeled normal activities, our model aims to automatically capture frequent motion and context patterns for each activity class, as well as each pair of classes, from sets of predefined patterns during the learning process. Then, the learned model is used to generate globally optimum labels for activities in the testing videos. We show how to learn the model parameters via an unconstrained convex optimization problem and how to predict the correct labels for a testing instance consisting of multiple activities. The learned model and generated labels are used to detect anomalies whose motion and context patterns deviate from the learned patterns. We show promising results on the VIRAT Ground Dataset that demonstrates the benefit of joint modeling and recognition of activities in a wide-area scene and the effectiveness of the proposed method in anomaly detection. © 2007-2012 IEEE.


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.


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.


Much of the literature describing the search for agents that increase the life span of rodents was found to suffer from confounds. One-hundred-six studies, absent 20 contradictory melatonin studies, of compounds or combinations of compounds were reviewed. Only six studies reported both life span extension and food consumption data, thereby excluding the potential effects of caloric restriction. Six other studies reported life span extension without a change in body weight. However, weight can be an unreliable surrogate measure of caloric consumption. Twenty studies reported that food consumption or weight was unchanged, but it was unclear whether these data were anecdotal or systematic. Twenty-nine reported extended life span likely due to induced caloric restriction. Thirty-six studies reported no effect on life span, and three a decrease. The remaining studies suffer from more serious confounds. Though still widely cited, studies showing life span extension using short-lived or "enfeebled" rodents have not been shown to predict longevity effects in long-lived animals. We suggest improvements in experimental design that will enhance the reliability of the rodent life span literature. First, animals should receive measured quantities of food and its consumption monitored, preferably daily, and reported. Weights should be measured regularly and reported. Second, a genetically heterogeneous, long-lived rodent should be utilized. Third, chemically defined diets should be used. Fourth, a positive control (e.g., a calorically restricted group) is highly desirable. Fifth, drug dosages should be chosen based on surrogate endpoints or accepted cross-species scaling factors. These procedures should improve the reliability of the scientific literature and accelerate the identification of longevity and health span-enhancing agents. © 2011 The Author(s).


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.


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.


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.


Cao Y.,Utah State University | Cao Y.,University of California at Riverside | Ren W.,Utah State University | Ren W.,University of California at Riverside
IEEE Transactions on Automatic Control | Year: 2012

A distributed coordinated tracking problem is solved via a variable structure approach when there exists a dynamic virtual leader who is a neighbor of only a subset of a group of followers, all followers have only local interaction, and only partial measurements of the states of the virtual leader and the followers are available. In the context of coordinated tracking, we focus on both consensus tracking and swarm tracking algorithms. In the case of first-order kinematics, we propose a distributed consensus tracking algorithm without velocity measurements under both fixed and switching network topologies. In particular, we show that distributed consensus tracking can be achieved in finite time. The algorithm is then extended to achieve distributed swarm tracking without velocity measurements. In the case of second-order dynamics, we first propose two distributed consensus tracking algorithms without acceleration measurements when the velocity of the virtual leader is varying under, respectively, a fixed and switching network topology. In particular, we show that the proposed algorithms guarantee at least global exponential tracking. We then propose a distributed consensus tracking algorithm and a distributed swarm tracking algorithm when the velocity of the virtual leader is constant. When the velocity of the virtual leader is varying, distributed swarm tracking is solved by using a distributed estimator. For distributed consensus tracking, a mild connectivity requirement is proposed by adopting an adaptive connectivity maintenance mechanism in which the adjacency matrix is defined in a proper way. Similarly, a mild connectivity requirement is proposed for distributed swarm tracking by adopting a connectivity maintenance mechanism in which the potential function is defined in a proper way. Several simulation examples are presented as a proof of concept. © 2006 IEEE.


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.


Yang S.,University of California at Riverside | Bhanu B.,University of California at Riverside
IEEE Transactions on Systems, Man, and Cybernetics, Part B: Cybernetics | Year: 2012

Existing video-based facial expression recognition techniques analyze the geometry-based and appearance-based information in every frame as well as explore the temporal relation among frames. On the contrary, we present a new image-based representation and an associated reference image called the emotion avatar image (EAI), and the avatar reference, respectively. This representation leverages the out-of-plane head rotation. It is not only robust to outliers but also provides a method to aggregate dynamic information from expressions with various lengths. The approach to facial expression analysis consists of the following steps: 1) face detection; 2) face registration of video frames with the avatar reference to form the EAI representation; 3) computation of features from EAIs using both local binary patterns and local phase quantization; and 4) the classification of the feature as one of the emotion type by using a linear support vector machine classifier. Our system is tested on the Facial Expression Recognition and Analysis Challenge (FERA2011) data, i.e., the Geneva Multimodal Emotion Portrayal-Facial Expression Recognition and Analysis Challenge (GEMEP-FERA) data set. The experimental results demonstrate that the information captured in an EAI for a facial expression is a very strong cue for emotion inference. Moreover, our method suppresses the person-specific information for emotion and performs well on unseen data. © 2012 IEEE.


Kafai M.,University of California at Riverside | Bhanu B.,University of California at Riverside
IEEE Transactions on Industrial Informatics | Year: 2012

Vehicle classification has evolved into a significant subject of study due to its importance in autonomous navigation, traffic analysis, surveillance and security systems, and transportation management. While numerous approaches have been introduced for this purpose, no specific study has been conducted to provide a robust and complete video-based vehicle classification system based on the rear-side view where the camera's field of view is directly behind the vehicle. In this paper, we present a stochastic multiclass vehicle classification system which classifies a vehicle (given its direct rear-side view) into one of four classes: sedan, pickup truck, SUV/minivan, and unknown. A feature set of tail light and vehicle dimensions is extracted which feeds a feature selection algorithm to define a low-dimensional feature vector. The feature vector is then processed by a hybrid dynamic Bayesian network to classify each vehicle. Results are shown on a database of 169 videos for four classes. © 2006 IEEE.


Han W.,Peking University | Han W.,IBM | Kawakami R.K.,Ohio State University | Kawakami R.K.,University of California at Riverside | And 2 more authors.
Nature Nanotechnology | Year: 2014

The isolation of graphene has triggered an avalanche of studies into the spin-dependent physical properties of this material and of graphene-based spintronic devices. Here, we review the experimental and theoretical state-of-art concerning spin injection and transport, defect-induced magnetic moments, spin-orbit coupling and spin relaxation in graphene. Future research in graphene spintronics will need to address the development of applications such as spin transistors and spin logic devices, as well as exotic physical properties including topological states and proximity-induced phenomena in graphene and other two-dimensional materials. © 2014 Macmillan Publishers Limited.


Lopez T.,University of California at Riverside | Mangolini L.,University of California at Riverside
Nanoscale | Year: 2014

We have experimentally determined the crystallization rate of plasma-produced amorphous silicon powder undergoing in-flight thermal annealing, and have found a significant reduction in the activation energy for crystallization compared to amorphous silicon thin films. This finding allows us to shed light onto the mechanism leading to the formation of high quality nanocrystals in non-thermal plasmas. © 2013 The Royal Society of Chemistry.


Sloniowski S.,University of California at Riverside | Ethell I.M.,University of California at Riverside
Seminars in Cell and Developmental Biology | Year: 2012

Eph receptors and their ligands ephrins comprise a complex signaling system with diverse functions that span a wide range of tissues and developmental stages. The variety of Eph receptor functions stems from their ability to mediate bidirectional signaling through trans-cellular Eph/ephrin interactions. Initially thought to act by directing repulsion between cells, Ephs have also been demonstrated to induce and maintain cell adhesive responses at excitatory synapses in the central nervous system. EphB receptors are essential to the development and maintenance of dendritic spines, which accommodate the postsynaptic sites of most glutamatergic excitatory synapses in the brain. Functions of EphB receptors are not limited to control of the actin cytoskeleton in dendritic spines, as EphB receptors are also involved in the formation of functional synaptic specializations through the regulation of glutamate receptor trafficking and functions. In addition, EphB receptors have recently been linked to the pathophysiology of Alzheimer's disease and neuropathic pain, thus becoming promising targets for therapeutic interventions. In this review, we discuss recent findings on EphB receptor functions in synapses, as well as the mechanisms of bidirectional trans-synaptic ephrin-B/EphB receptor signaling that shape dendritic spines and influence post-synaptic differentiation. © 2011 Elsevier Ltd.


Hong J.,University of California at Riverside | Zaera F.,University of California at Riverside
Journal of the American Chemical Society | Year: 2012

The catalytic performance of cinchonidine in the promotion of thiol additions to conjugated ketones was used as a probe to assess the tethering of molecular functionality onto solid surfaces using well-known "click" chemistry involving easy-to-react linkers. It has been assumed in many applications that the tethered molecules retain their chemical properties and dominate the chemistry of the resulting solid systems, but it is shown here that this is not always the case. Indeed, a loss of enantioselectivity was observed upon tethering, which could be accounted for by a combination of at least three effects: (1) the nonselective catalytic activity of the surface of the solid itself; (2) the activity of the OH species generated by hydrolysis of some of the Si-alkoxy groups in the trialkoxy moieties used to bind many linkers to oxide surfaces; and (3) the bonding of the molecule to be tethered directly to the surface. Several ideas were also tested to minimize these problems, including the silylation of the active OH groups within the surface of the oxide support, the selection of solvents to optimize silane polymerization and minimize their breaking up via hydrolysis or alcoholysis reactions, and the linking at defined positions in the molecule to be tethered in order to minimize its ability to interact with the surface. © 2012 American Chemical Society.


Fudali S.L.,University of California at Riverside | Wang C.,University of California at Riverside | Williamson V.M.,University of California at Riverside
Molecular Plant-Microbe Interactions | Year: 2013

Infective juveniles of the root-knot nematode Meloidogyne hapla are attracted to the zone of elongation of roots where they invade the host but little is known about what directs the nematode to this region of the root. We found that Arabidopsis roots exposed to an ethylene (ET)-synthesis inhibitor attracted significantly more nematodes than control roots and that ET-overproducing mutants were less attractive. Arabidopsis seedlings with ET-insensitive mutations were generally more attractive whereas mutations resulting in constitutive signaling were less attractive. Roots of the ET-insensitive tomato mutant Never ripe (Nr) were also more attractive, indicating that ET signaling also modulated attraction of root-knot nematodes to this host. ET-insensitive mutants have longer roots due to reduced basipetal auxin transport. However, assessments of Arabidopsis mutants that differ in various aspects of the ET response suggest that components of the ET-signaling pathway directly affecting root length are not responsible for modulating root attractiveness and that other components of downstream signaling result in changes in levels of attractants or repellents for M. hapla. These signals may aid in directing this pathogen to an appropriate host and invasion site for completing its life cycle. © 2013 The American Phytopathological Society.


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.


Gao C.,University of California at Riverside | Zhang Q.,University of California at Riverside | Lu Z.,University of California at Riverside | Yin Y.,University of California at Riverside
Journal of the American Chemical Society | Year: 2011

We report a general method for the synthesis of noble metal nanorods, including Au, Ag, Pt, and Pd, based on their seeded growth in silica nanotube templates. The controlled growth of the metals occurs exclusively on the seeds inside the silica nanotubes, which act as hard templates to confine the one-dimensional growth of the metal nanorods and define their aspect ratios. This method affords large quantities of noble metal nanorods with well-controlled aspect ratios and high yield, which may find wide use in the fields of nanophotonics, catalysis, sensing, imaging, and biomedicine. © 2011 American Chemical Society.


Gu S.,University of California at Riverside | Cai R.,University of California at Riverside | Yan Y.,University of California at Riverside
Chemical Communications | Year: 2011

A simple self-crosslinking strategy, without the needs of a separate crosslinker or a catalyst, is reported here. The crosslinking drastically lowers the water swelling ratio (e.g., 5-10 folds reduction) and provides excellent solvent-resistance. The self-crosslinked membrane (DCL: 5.3%) shows the highest IEC-normalized hydroxide conductivity among all crosslinked HEMs reported. © The Royal Society of Chemistry.


Moore B.N.,University of California at Riverside | Ly T.,University of California at Riverside | Julian R.R.,University of California at Riverside
Journal of the American Chemical Society | Year: 2011

Electron capture dissociation (ECD) is an important analytical technique which is used frequently in proteomics experiments to reveal information about both primary sequence and posttranslational modifications. Although the utility of ECD is unquestioned, the underlying chemistry which leads to the observed fragmentation is still under debate. Backbone dissociation is frequently the exclusive focus when mechanistic questions about ECD are posed, despite the fact that numerous other abundant dissociation channels exist. Herein, the focus is shifted to side chain loss and other dissociation channels which offer clues about the underlying mechanism(s). It is found that the initially formed hydrogen abundant radicals in ECD can convert quickly to hydrogen deficient radicals via a variety of pathways. Dissociation which occurs subsequent to this conversion is mediated by hydrogen deficient radical chemistry, which has been the subject of extensive study in experiments which are independent from ECD. Statistical analysis of fragments observed in ECD is in excellent agreement with predictions made by an understanding of hydrogen deficient radical chemistry. Furthermore, hydrogen deficient radical mediated dissociation likely contributes to observed ECD fragmentation patterns in unexpected ways, such as the selective dissociation observed at disulfide bonds. Many aspects of dissociation observed in ECD are easily reproduced in well-controlled experiments examining hydrogen deficient radicals generated by non-ECD methods. All of these observations indicate that when considering the means by which electron capture leads to dissociation, hydrogen deficient radical chemistry must be given careful consideration. © 2011 American Chemical Society.


Xu S.,University of California at Riverside | Hua Y.,University of California at Riverside
IEEE Transactions on Wireless Communications | Year: 2011

This paper considers a system where two users exchange information via a non-regenerative half-duplex two-way MIMO relay and each of the two users and the relay is equipped with multiple antennas. We study the design of the spatial source covariance matrices (or source matrices) at the two users and the spatial transformation matrix (or relay matrix) at the relay to maximize the achievable weighted sum rate of the system. The source matrices and the relay matrix are optimized alternately until convergence. If the relay matrix is given, we show that the optimal design of the source matrices (for uniformly weighted sum rate) follows a generalized water filling (GWF) algorithm. If the source matrices are given, we show two search algorithms to optimize the relay matrix. The first algorithm is a hybrid gradient method which adaptively switches between the (steepest) gradient descent and the Newton's search. The second is an iterative weighted minimum mean square error (WMMSE) method which alternately refines the MMSE equalizers at the users and the relay matrix. We compare the convergence behaviors of the two algorithms and demonstrate their advantage over prior algorithms. We also show an optimal structure of the relay matrix, which is useful to reduce the search complexity. © 2011 IEEE.


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.


Zhu Y.,University of California at Riverside | Zaera F.,University of California at Riverside
Catalysis Science and Technology | Year: 2014

The structure sensitivity of the catalytic hydrogenation of cinnamaldehyde was studied by carrying out comparative studies with Pt/SiO2 catalysts of various metal loadings, between 0.5 and 5.0 Pt wt%. Transmission electron microscopy (TEM) characterization was complemented with carbon monoxide adsorption experiments using infrared absorption spectroscopy and with kinetic studies under high (10 bar) pressures of H2. Specific total turnover frequencies, normalized by the number of exposed Pt atoms, were found to correlate with both the average diameter of the metal nanoparticles and the average number of CO molecules adsorbed on flat terraces. It was concluded that cinnamaldehyde conversion is likely to take place on close-packed (111) planes. The selectivity between the hydrogenation of CC versus CO bonds, on the other hand, appears to be independent of either the particle size or the extent of the conversion, at least within the Pt particle size range explored in this study. This journal is © the Partner Organisations 2014.


Simonovis J.,University of California at Riverside | Zaera F.,University of California at Riverside
Chemical Science | Year: 2016

A sharp increase in the rate of hydrogen isotope scrambling was identified during the hydrogenation of olefins with H2 + D2 mixtures on Pt(111) catalysts, which spectroscopic data suggest is due to a sudden increase in atomic hydrogen surface mobility because of a decrease in the size of the islands of the adsorbed hydrocarbons. © The Royal Society of Chemistry 2016.


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.


Wen S.,University of California at Riverside | Beran G.J.O.,University of California at Riverside
Journal of Chemical Theory and Computation | Year: 2011

We combine quantum and classical mechanics in a fragment-based many-body interaction model to predict organic molecular crystal lattice energies. Individual molecules in the central unit cell and their short-range pairwise interactions are modeled quantum mechanically, while long-range pairwise and many-body interactions are approximated classically. The classical contributions are evaluated using an accurate ab initio force field that is constructed on-the-fly from quantum mechanical calculations on the individual molecules in the unit cell. The force field parameters include ab initio distributed multipole moments, distributed polarizabilities, and isotropic two- and three-body atomic dispersion coefficients. This QM/MM fragment model reproduces full periodic MP2 lattice energies to within a couple kJ/mol at substantially reduced cost. When high-level electronic structure methods are coupled with the ab initio force field, molecular crystal lattice energies are predicted to within 2 kJ/mol of their experimental values for six of the seven crystals examined here. Finally, Axilrod-Teller-Muto three-body dispersion energy plays a nontrivial role in several of the molecular crystals studied here. © 2011 American Chemical Society.


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.


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.


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.


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.


Hou Y.,University of California at Riverside | Zuo F.,University of California at Riverside | Dagg A.P.,University of California at Riverside | Liu J.,University of California at Riverside | Feng P.,University of California at Riverside
Advanced Materials | Year: 2014

A hybrid WO3/C3N4/CoOx system exhibits excellent photoelectrochemical activity for water oxidation. The system comprises a novel three-dimensionally branched WO3 nanosheet array coated with a layer of C3N4 heterojunctions that are further decorated with CoOx nanoparticles. The photoelectrochemical activity arises from the effective light harvesting due to the 3D structure and "window effect," the excellent charge separation and transport in the heterojunction, and the fast interfacial charge collection and surface reactions due to the large surface area. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


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.


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.


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.


Jung B.,University of California at Riverside | Rao A.L.N.,University of California at Riverside | Anvari B.,University of California at Riverside
ACS Nano | Year: 2011

We have engineered an optical nanoconstruct composed of genome-depleted brome mosaic virus doped with indocyanine green (ICG), an FDA-approved near-infrared (NIR) chromophore. Constructs are highly monodispersed with standard deviation of ±3.8 nm from a mean diameter of 24.3 nm. They are physically stable and exhibit a high degree of optical stability at physiological temperature (37 °C). Using human bronchial epithelial cells, we demonstrate the effectiveness of the constructs for intracellular optical imaging in vitro, with greater than 90% cell viability after 3 h of incubation. These constructs may serve as a potentially nontoxic and multifunctional nanoplatform for site-specific deep-tissue optical imaging, and therapy of disease. © 2011 American Chemical Society.


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.


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.


Williams M.,University of California at Riverside | Talbot P.,University of California at Riverside
Nicotine and Tobacco Research | Year: 2011

Introduction: This study investigated the performance of electronic cigarettes (e-cigarettes), compared different models within a brand, compared identical copies of the same model within a brand, and examined performance using different protocols. Methods: Airflow rate required to generate aerosol, pressure drop across e-cigarettes, and aerosol density were examined using three different protocols. Results: First 10 puff protocol: The airflow rate required to produce aerosol and aerosol density varied among brands, while pressure drop varied among brands and between the same model within a brand. Total air hole area correlated with pressure drop for some brands. Smoke-out protocol: E-cigarettes within a brand generally performed similarly when puffed to exhaustion; however, there was considerable variation between brands in pressure drop, airflow rate required to produce aerosol, and the total number of puffs produced. With this protocol, aerosol density varied significantly between puffs and gradually declined. Consecutive trial protocol: Two copies of one model were subjected to 11 puffs in three consecutive trials with breaks between trials. One copy performed similarly in each trial, while the second copy of the same model produced little aerosol during the third trial. The different performance properties of the two units were attributed to the atomizers. Conclusion: There was significant variability between and within brands in the airflow rate required to produce aerosol, pressure drop, length of time cartridges lasted, and production of aerosol. Variation in performance properties within brands suggests a need for better quality control during e-cigarette manufacture. © The Author 2011. Published by Oxford University Press on behalf of the Society for Research on Nicotine and Tobacco. All rights reserved.


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.


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.


Marschner P.,University of Adelaide | Crowley D.,University of California at Riverside | Rengel Z.,University of Western Australia
Soil Biology and Biochemistry | Year: 2011

Iron and phosphorus availability is low in many soils; hence, microorganisms and plants have evolved mechanisms to acquire these nutrients by altering the chemical conditions that affect their solubility. In plants, this includes exudation of organic acid anions and acidification of the rhizosphere by release of protons in response to iron and phosphorus deficiency. Grasses (family Poaceae) and microorganisms further respond to Fe deficiency by production and release of specific chelators (phytosiderophores and siderophores, respectively) that complex Fe to enhance its diffusion to the cell surface. In the rhizosphere, the mutual demand for Fe and P results in competition between plants and microorganisms with the latter being more competitive due to their ability to decompose plant-derived chelators and their proximity to the root surface; however microbial competitiveness is strongly affected by carbon availability. On the other hand, plants are able to avoid direct competition with microorganisms due to the spatial and temporal variability in the amount and composition of exudates they release into the rhizosphere. In this review, we present a model of the interactions that occur between microorganisms and roots along the root axis, and discuss advantages and limitations of methods that can be used to study these interactions at nanometre to centimetre scales. Our analysis suggests mechanisms such as increasing turnover of microbial biomass or enhanced nutrient uptake capacity of mature root zones that may enhance plant competitiveness could be used to develop plant genotypes with enhanced efficiency in nutrient acquisition. Our model of interactions between plants and microorganisms in the rhizosphere will be useful for understanding the biogeochemistry of P and Fe and for enhancing the effectiveness of fertilization. © 2011 Elsevier Ltd.


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.


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.


Hall A.E.,University of California at Riverside
Frontiers in Physiology | Year: 2012

Methods for phenotyping cowpeas for adaptation to drought are reviewed. Key factors involve achieving optimal time of flowering and cycle length, and appropriate morphology for different types of cultivars as they relate to their utilization for dry grain, hay, and fresh pea production. Strong resistance to vegetative-stage drought is available and should be incorporated. The extreme ability of extra-early erect cowpea cultivars to escape terminal drought should be exploited in zones with very short rainfall seasons. In zones with the possibility of limited rainfall in the middle of the growing season, resistance to mid-season drought, and the delayed-leaf-senescence trait can be valuable. Breeding for water-use efficiency, deeper rooting, and heat tolerance are discussed. Diseases and pests that influence adaptation to drought are considered. Resistance to the organism causing ashy stem blight disease should be incorporated because this disease can destroy cowpea seedlings under hot, dry soil conditions. The value of varietal intercrops with contrasting types of cowpea cultivars in enhancing adaptation to drought is described. Implications of cowpea/cereal rotations for cowpea breeding are discussed. Breeding strategies for enhancing cowpea adaptation to drought are described. © 2012 Hall.


Moore B.N.,University of California at Riverside | Julian R.R.,University of California at Riverside
Physical Chemistry Chemical Physics | Year: 2012

In biochemistry, free radicals are versatile species which can perform diverse functions including: signaling, synthesis, and destructive modification. It is of interest to understand how radicals behave within all biomolecules and specifically within peptides and proteins. The 20 standard amino acids contain a wide range of chemical structures, which give proteins their complexity and ultimately their functionality. Many factors influence how radicals interact with these complex molecules, including the bond dissociation energies (BDEs) for homolytically cleaving any X-H bonds. The BDEs provide a simple measure for comparing the thermodynamic favorability of abstracting hydrogen atoms from various sites within a protein. BDEs for abstractable hydrogen atoms have been calculated for each amino acid, the peptide backbone, and peptide termini in order to compile a roadmap of the relative thermodynamics which influence protein radical chemistry. With this information it is possible to gain insight into what contributions both kinetics and thermodynamics will make to various radical mediated reaction pathways. © 2012 The Owner Societies.


Huffman K.,University of California at Riverside
Frontiers in Genetics | Year: 2012

A hallmark of mammalian development is the generation of functional subdivisions within the nervous system. In humans, this regionalization creates a complex system that regulates behavior, cognition, memory, and emotion. During development, specification of neocortical tissue that leads to functional sensory and motor regions results from an interplay between cortically intrinsic, molecular processes, such as gene expression, and extrinsic processes regulated by sensory input. Cortical specification in mice occurs pre-and perinatally, when gene expression is robust and various anatomical distinctions are observed alongside an emergence of physiological function. After patterning, gene expression continues to shift and axonal connections mature into an adult form. The function of adult cortical gene expression may be to maintain neocortical subdivisions that were established during early patterning. As some changes in neocortical gene expression have been observed past early development into late adulthood, gene expression may also play a role in the altered neocortical function observed in age-related cognitive decline and brain dysfunction.This review provides a discussion of how neocortical gene expression and specific patterns of neocortical sensori-motor axonal connections develop and change throughout the lifespan of the animal. We posit that a role of neocortical gene expression in neocortex is to regulate plasticity mechanisms that impact critical periods for sensory and motor plasticity in aging. We describe results from several studies in aging brain that detail changes in gene expression that may relate to microstructural changes observed in brain anatomy. We discuss the role of altered glucocorticoid signaling in age-related cognitive and functional decline, as well as how aging in the brain may result from immune system activation. We describe how caloric restriction or reduction of oxidative stress may ameliorate effects of aging on the brain. © 2012 Huffman.


Kain P.,University of California at Riverside | Dahanukar A.,University of California at Riverside
Neuron | Year: 2015

The gustatory system provides vital sensory information to determine feeding and appetitive learning behaviors. Very little is known, however, about higher-order gustatory circuits in the highly tractable model for neurobiology, Drosophila melanogaster. Here we report second-order sweet gustatory projection neurons (sGPNs) in the Drosophila brain using a powerful behavioral screen. Silencing neuronal activity reduces appetitive behaviors, whereas inducible activation results in food acceptance via proboscis extensions. sGPNs show functional connectivity with Gr5a+ sweet taste neurons and are activated upon sucrose application to the labellum. By tracing sGPN axons, we identify the antennal mechanosensory and motor center (AMMC) as an immediate higher-order processing center for sweet taste. Interestingly, starvation increases sucrose sensitivity of the sGPNs in the AMMC, suggesting that hunger modulates the responsiveness of the secondary sweet taste relay. Together, our results provide a foundation for studying gustatory processing and its modulation by the internal nutrient state. © 2015 Elsevier Inc.


Gatesy J.,University of California at Riverside | Springer M.S.,University of California at Riverside
Molecular Phylogenetics and Evolution | Year: 2014

Large datasets are required to solve difficult phylogenetic problems that are deep in the Tree of Life. Currently, two divergent systematic methods are commonly applied to such datasets: the traditional supermatrix approach (= concatenation) and "shortcut" coalescence (= coalescence methods wherein gene trees and the species tree are not co-estimated). When applied to ancient clades, these contrasting frameworks often produce congruent results, but in recent phylogenetic analyses of Placentalia (placental mammals), this is not the case. A recent series of papers has alternatively disputed and defended the utility of shortcut coalescence methods at deep phylogenetic scales. Here, we examine this exchange in the context of published phylogenomic data from Mammalia; in particular we explore two critical issues - the delimitation of data partitions ("genes") in coalescence analysis and hidden support that emerges with the combination of such partitions in phylogenetic studies. Hidden support - increased support for a clade in combined analysis of all data partitions relative to the support evident in separate analyses of the various data partitions, is a hallmark of the supermatrix approach and a primary rationale for concatenating all characters into a single matrix. In the most extreme cases of hidden support, relationships that are contradicted by all gene trees are supported when all of the genes are analyzed together. A valid fear is that shortcut coalescence methods might bypass or distort character support that is hidden in individual loci because small gene fragments are analyzed in isolation. Given the extensive systematic database for Mammalia, the assumptions and applicability of shortcut coalescence methods can be assessed with rigor to complement a small but growing body of simulation work that has directly compared these methods to concatenation. We document several remarkable cases of hidden support in both supermatrix and coalescence paradigms and argue that in most instances, the emergent support in the shortcut coalescence analyses is an artifact. By referencing rigorous molecular clock studies of Mammalia, we suggest that inaccurate gene trees that imply unrealistically deep coalescences debilitate shortcut coalescence analyses of the placental dataset. We document contradictory coalescence results for Placentalia, and outline a critical conundrum that challenges the general utility of shortcut coalescence methods at deep phylogenetic scales. In particular, the basic unit of analysis in coalescence analysis, the coalescence-gene, is expected to shrink in size as more taxa are analyzed, but as the amount of data for reconstruction of a gene tree ratchets downward, the number of nodes in the gene tree that need to be resolved ratchets upward. Some advocates of shortcut coalescence methods have attempted to address problems with inaccurate gene trees by concatenating multiple coalescence-genes to yield "gene trees" that better match the species tree. However, this hybrid concatenation/coalescence approach, "concatalescence," contradicts the most basic biological rationale for performing a coalescence analysis in the first place. We discuss this reality in the context of recent simulation work that also suggests inaccurate reconstruction of gene trees is more problematic for shortcut coalescence methods than deep coalescence of independently segregating loci is for concatenation methods. © 2014 Elsevier Inc.


Hedin M.,San Diego State University | Starrett J.,University of California at Riverside | Hayashi C.,University of California at Riverside
Molecular Ecology | Year: 2013

Antrodiaetus riversi is a dispersal-limited, habitat-specialized mygalomorph spider species endemic to mesic woodlands of northern and central California. Here, we build upon prior phylogeographic research using a much larger geographic sample and include additional nuclear genes, providing more detailed biogeographic insights throughout the range of this complex. Of particular interest is the uncovering of unexpected and replicated trans-valley biogeographic patterns, where in two separate genetic clades western haplotypes in the California south Coast Ranges are phylogenetically closely related to eastern haplotypes from central and northern Sierran foothills. In both instances, these trans-valley phylogenetic patterns are strongly supported by multiple genes. These western and eastern populations are currently separated by the Central Valley, a well-recognized modern-day and historical biogeographic barrier in California. For one clade, the directionality is clearly northeast to southwest, and all available evidence is consistent with a jump dispersal event estimated at 1.2-1.3 Ma. During this time period, paleogeographic data indicate that northern Sierran rivers emptied to the ocean in the south Coast Ranges, rather than at the San Francisco Bay. For the other trans-valley clade genetic evidence is less conclusive regarding the mechanism and directionality of biogeographic exchange, although the estimated timeframe is similar (approximately 1.8 Ma). Despite the large number of biogeographic studies previously conducted in central California, to the best of our knowledge no prior studies have discussed or revealed a northern Sierran to south Coast Range biogeographic connection. This uniqueness may reflect the low-dispersal biology of mygalomorph spiders, where 'post-event' gene exchange rarely erases historical biogeographic signal. © 2012 Blackwell Publishing Ltd.


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.


Jin H.,University of California at Riverside | Zhu J.-K.,University of California at Riverside | Zhu J.-K.,King Abdullah University of Science and Technology
Genes and Development | Year: 2010

RNA viruses are particularly vulnerable to RNAi-based defenses in the host, and thus have evolved specific proteins, known as viral suppressors of RNA silencing (VSRs), as a counterdefense. In this issue of Genes & Development, Azevedo and colleagues (pp. 904-915) discovered that P38, the VSR of Turnip crinkle virus, uses its glycine/tryptophane (GW) motifs as an ARGONAUTE (AGO) hook to attract and disarm the host's essential effector of RNA silencing. Several GW motif-containing cellular proteins are known to be important partners of AGOs in RNA silencing effector complexes in yeast, plants, and animals. The GW motif appears to be a versatile and effective tool for regulating the activities of RNA silencing pathways, and the use of GW mimicry to compete for and inhibit host AGOs may be a strategy used by many pathogens to counteract host RNAi-based defenses. © 2010 by Cold Spring Harbor Laboratory Press.


Li Z.,Peking University | Ren W.,University of California at Riverside | Liu X.,Beijing Institute of Technology | Xie L.,Nanyang Technological University
Automatica | Year: 2013

This paper considers the distributed consensus problem of multi-agent systems with general continuous-time linear dynamics for both the cases without and with a leader whose control input might be nonzero and time varying. For the case without a leader, based on the relative output information of neighboring agents, two types of distributed adaptive dynamic consensus protocols are proposed, namely, the edge-based adaptive protocol which assigns a time-varying coupling weight to each edge in the communication graph and the node-based adaptive protocol which uses a time-varying coupling weight for each node. These two adaptive protocols are designed to ensure that consensus is reached in a fully distributed fashion for all undirected connected communication graphs. It is shown that the edge-based adaptive consensus protocol is applicable to arbitrary switching connected graphs. For the case where there exists a leader whose control input is possibly nonzero and bounded, a distributed continuous adaptive protocol is designed to guarantee the ultimate boundedness of the consensus error with respect to any communication graph which contains a directed spanning tree with the leader as the root and whose subgraph associated with the followers is undirected, requiring neither global information of the communication graph nor the upper bound of the leader's control input. A distributed discontinuous protocol is also discussed as a special case. Simulation examples are finally given to illustrate the theoretical results. © 2013 Published by Elsevier Ltd.


Wu Q.,University of California at Riverside | Wang X.,University of California at Riverside | Ding S.-W.,University of California at Riverside
Cell Host and Microbe | Year: 2010

RNA-based viral immunity (RVI) operates in fungi, plants, and invertebrates to specifically destroy viral RNAs using the cellular RNA interference machinery. Discovery of diverse viral proteins as suppressors of RNA silencing provides strong validation for the effectiveness of RVI. Here we review recent studies that have revealed new mechanistic insights into plant and insect viral suppressors of RVI or suggested a role for RNA silencing suppression during mammalian viral infection. © 2010 Elsevier Inc.


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.


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.


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.


Sun Y.,University of California at Riverside | Bhanu B.,University of California at Riverside
IEEE Transactions on Pattern Analysis and Machine Intelligence | Year: 2012

This paper presents a new symmetry-integrated region-based image segmentation method. The method is developed to obtain improved image segmentation by exploiting image symmetry. It is realized by constructing a symmetry token that can be flexibly embedded into segmentation cues. Interesting points are initially extracted from an image by the SIFT operator and they are further refined for detecting the global bilateral symmetry. A symmetry affinity matrix is then computed using the symmetry axis and it is used explicitly as a constraint in a region growing algorithm in order to refine the symmetry of the segmented regions. A multi-objective genetic search finds the segmentation result with the highest performance for both segmentation and symmetry, which is close to the global optimum. The method has been investigated experimentally in challenging natural images and images containing man-made objects. It is shown that the proposed method outperforms current segmentation methods both with and without exploiting symmetry. A thorough experimental analysis indicates that symmetry plays an important role as a segmentation cue, in conjunction with other attributes like color and texture. © 2012 IEEE.


Juntawong P.,University of California at Riverside | Bailey-Serres J.,University of California at Riverside
Frontiers in Plant Science | Year: 2012

Light, a dynamic environmental parameter, is an essential regulator of plant growth and development. Light-regulated transcriptional networks are well documented, whereas light-regulated post-transcriptional regulation has received limited attention. In this study, dynamics in translation of cytosolic mRNAs were evaluated at the genome-level in Arabidopsis thaliana seedlings grown under a typical light/dark diurnal regime, shifted to darkness at midday, and then re-illuminated. One-hour of unanticipated darkness reduced levels of polysomes by 17% in a manner consistent with inhibition of initiation of translation. This down-regulation of translation was reversed within 10 min of re-illumination. Quantitative comparison of the total cellular population of transcripts (the transcriptome) to those associated with one or more 80S ribosome (the translatome) identified over 1600 mRNAs that were differentially translated in response to light availability. Unanticipated darkness limited both transcription and translation of mRNAs encoding components of the photosynthetic machinery. Many mRNAs encoding proteins associated with the energy demanding process of protein synthesis were stable but sequestered in the dark, in a rapidly reversible manner. A meta-analysis determined these same transcripts were similarly and coordinately regulated in response to changes in oxygen availability. The dark and hypoxia translationally repressed mRNAs lack highly supported candidate RNA-regulatory elements but are characterized by G + C-rich 5′-untranslated regions. We propose that modulation of translation of a subset of cellular mRNAs functions as an energy conservation mechanism. © 2012 Juntawong and Bailey-Serres.


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.


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.


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.


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.


Roff D.A.,University of California at Riverside | Fairbairn D.J.,University of California at Riverside
Journal of Evolutionary Biology | Year: 2013

Melanism is an important component of insect cuticle and serves numerous functions that enhance fitness. Despite its importance, there is little information on its genetic basis or its phenotypic and genetic correlation with fitness-related traits. Here, we examine the heritability of melanism in the wing dimorphic sand cricket and determine its phenotypic and genetic correlation with wing morphology, gonad mass and size of the dorso-longitudinal muscles (the principle flight muscles). Previously demonstrated trade-offs among these traits are significant factors in the evolution of life history variation. Using path analysis, we show that melanization is causally related to gonad mass, but not flight muscle mass. Averaged over the sexes, the heritability of melanism was 0.61, the genetic correlation with gonad mass was -0.36 and with wing morph was 0.51. The path model correctly predicted the ranking of melanization score in lines selected for increased ovary mass, increased flight muscle mass, an index that increased both traits and an unselected control. Our results support the general hypothesis that melanization is costly for insects and negatively impacts investment in early reproduction. © 2013 European Society For Evolutionary Biology.


He L.,University of California at Riverside | Wang M.,University of California at Riverside | Ge J.,University of California at Riverside | Ge J.,Tongji University | Yin Y.,University of California at Riverside
Accounts of Chemical Research | Year: 2012

Responsive photonic structures can respond to external stimuli by transmitting optical signals. Because of their important technological applications such as color signage and displays, biological and chemical sensors, security devices, ink and paints, military camouflage, and various optoelectronic devices, researchers have focused on developing these functional materials. Conventionally, self-assembled colloidal crystals containing periodically arranged dielectric materials have served as the predominant starting frameworks. Stimulus-responsive materials are incorporated into the periodic structures either as the initial building blocks or as the surrounding matrix so that the photonic properties can be tuned. Although researchers have proposed various versions of responsive photonic structures, the low efficiency of fabrication through self-assembly, narrow tunability, slow responses to the external stimuli, incomplete reversibility, and the challenge of integrating them into existing photonic devices have limited their practical application.In this Account, we describe how magnetic fields can guide the assembly of superparamagnetic colloidal building blocks into periodically arranged particle arrays and how the photonic properties of the resulting structures can be reversibly tuned by manipulating the external magnetic fields. The application of the external magnetic field instantly induces a strong magnetic dipole-dipole interparticle attraction within the dispersion of superparamagnetic particles, which creates one-dimensional chains that each contains a string of particles. The balance between the magnetic attraction and the interparticle repulsions, such as the electrostatic force, defines the interparticle separation. By employing uniform superparamagnetic particles of appropriate sizes and surface charges, we can create one-dimensional periodicity, which leads to strong optical diffraction. Acting remotely over a large distance, magnetic forces drove the rapid formation of colloidal photonic arrays with a wide range of interparticle spacing. They also allowed instant tuning of the photonic properties because they manipulated the interparticle force balance, which changed the orientation of the colloidal assemblies or their periodicity.This magnetically responsive photonic system provides a new platform for chromatic applications: these colloidal particles assemble instantly into ordered arrays with widely, rapidly, and reversibly tunable structural colors, which can be easily and rapidly fixed in a curable polymer matrix. Based on these unique features, we demonstrated many applications of this system, such as structural color printing, the fabrication of anticounterfeiting devices, switchable signage, and field-responsive color displays. We also extended this idea to rapidly organize uniform nonmagnetic building blocks into photonic structures. Using a stable ferrofluid of highly charged magnetic nanoparticles, we created virtual magnetic moments inside the nonmagnetic particles. This "magnetic hole" strategy greatly broadens the scope of the magnetic assembly approach to the fabrication of tunable photonic structures from various dielectric materials. © 2012 American Chemical Society.


He Y.,University of California at Riverside | Varma C.M.,University of California at Riverside
Physical Review B - Condensed Matter and Materials Physics | Year: 2012

The collective modes observed in the loop-current ordered state in underdoped cuprates by polarized neutron scattering require that the ground state is a linear combination in each unit cell of the four basis states that are the possible classical magnetic moment configurations in each unit cell. The direction of such moments is in the c axis of the crystals. The basis states are connected by both time reversal as well as spatial rotations about the center of the unit cells. Several new features arise in the theory of polarized neutron scattering cross section in this situation that appear not to have been encountered before. An important consequence of these is that a finite component transverse to the classical magnetic moment directions is detected in the experiments. We show that this transverse component is of purely quantum-mechanical origin and that its direction in the plane normal to the c axis is not detectable, even in principle, in experiments, at least in the quantum-mechanical model we have adopted. We estimate the direction of the "tilt" in the moment, i.e., the ratio of the transverse component to the c-axis component, using parameters of the ground state obtained by fitting to the observed dispersion of the collective modes in the ordered state. We can obtain reasonable agreement with experiments but only by introducing a parameter for which only an approximate magnitude can be estimated. Approximate calculations of the form factors are also provided. © 2012 American Physical Society.


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.


Habib K.M.M.,University of California at Riverside | Lake R.K.,University of California at Riverside
Physical Review B - Condensed Matter and Materials Physics | Year: 2012

A relative rotation of 90 - between two graphene nanoribbons (GNRs) creates a crossbar with a nanoscale overlap region. Calculations, based on the first principles density functional theory (DFT) and the nonequilibrium Green's function (NEGF) formalism, show that the electronic states of the individual GNRs of an unbiased crossbar are decoupled from each other similar to the decoupling that occurs in twisted bilayer graphene. Analytical calculations, based on Fermi's golden rule, reveal that the decoupling is a consequence of the cancellation of quantum phases of the electronic wave functions of the individual GNRs. As a result, the inter-GNR transmission is strongly suppressed over a large energy window. An external bias applied between the GNRs changes the relative phases of the wave functions resulting in modulation of the transmission and current by several orders of magnitude. A built-in potential between the two GNRs can lead to a large peak-to-valley current ratio (1000) resulting from the strong electronic decoupling of the two GNRs that occurs when they are driven to the same potential. Current switching by voltage control of the quantum phase in a graphene crossbar structure is a novel switching mechanism. It is robust even with an overlap of ∼1.8nm×1.8nm that is well below the smallest horizontal length scale envisioned in the international technology roadmap for semiconductors (ITRS). © 2012 American Physical Society.


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 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.


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.


Johnson I.,University of California at Riverside | Liu H.,University of California at Riverside
PLoS ONE | Year: 2013

Controlling degradation of magnesium or its alloys in physiological saline solutions is essential for their potential applications in clinically viable implants. Rapid degradation of magnesium-based materials reduces the mechanical properties of implants prematurely and severely increases alkalinity of the local environment. Therefore, the objective of this study is to investigate the effects of three interactive factors on magnesium degradation, specifically, the addition of yttrium to form a magnesium-yttrium alloy versus pure magnesium, the metallic versus oxide surfaces, and the presence versus absence of physiological salt ions in the immersion solution. In the immersion solution of phosphate buffered saline (PBS), the magnesium-yttrium alloy with metallic surface degraded the slowest, followed by pure magnesium with metallic or oxide surfaces, and the magnesium-yttrium alloy with oxide surface degraded the fastest. However, in deionized (DI) water, the degradation rate showed a different trend. Specifically, pure magnesium with metallic or oxide surfaces degraded the slowest, followed by the magnesium-yttrium alloy with oxide surface, and the magnesium-yttrium alloy with metallic surface degraded the fastest. Interestingly, only magnesium-yttrium alloy with metallic surface degraded slower in PBS than in DI water, while all the other samples degraded faster in PBS than in DI water. Clearly, the results showed that the alloy composition, presence or absence of surface oxide layer, and presence or absence of physiological salt ions in the immersion solution all influenced the degradation rate and mode. Moreover, these three factors showed statistically significant interactions. This study revealed the complex interrelationships among these factors and their respective contributions to degradation for the first time. The results of this study not only improved our understanding of magnesium degradation in physiological environment, but also presented the key factors to consider in order to satisfy the degradation requirements for next-generation biodegradable implants and devices. © 2013 Johnson and Liu.


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.


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.


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.


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.


Deslauriers S.D.,University of California at Riverside | Larsen P.B.,University of California at Riverside
Molecular Plant | Year: 2010

Ethylene signaling is a complex pathway that has been intensively analyzed partly due to its importance to the manifestation of horticultural phenomena, including fruit ripening and tissue senescence. In order to further our understanding of how this pathway is regulated, a screen for Arabidopsis mutants with increased ethylene response was conducted. From this, a mutant was identified as having a dark-grown hypocotyl that is indistinguishable from Col-0 wt in the presence of the ethylene perception inhibitor AgNO3, yet has extreme responsiveness to even low levels of ethylene. Map-based cloning of the mutation revealed a T-DNA insertion in the coding sequence of the receptor-like kinase FERONIA, which is required for normal pollen tube reception and cell elongation in a currently unknown capacity. In contrast to a previous report, analysis of our feronia knockout mutant shows it also has altered responsiveness to brassinosteroids, with etiolated fer-2 seedlings being partially brassinosteroid insensitive with regard to promotion of hypocotyl elongation. Our results indicate that FERONIA-dependent brassinosteroid response serves to antagonize the effect of ethylene on hypocotyl growth of etiolated seedlings, with loss of proper brassinosteroid signaling disrupting this balance and leading to a greater impact of ethylene on hypocotyl shortening. © The Author 2010. Published by the Molecular Plant Shanghai Editorial Office in association with Oxford University Press on behalf of CSPP and IPPE, SIBS, CAS.


Bower J.D.,University of California at Riverside | Andersen G.J.,University of California at Riverside
Vision Research | Year: 2012

In the present study we examined the use of perceptual learning to improve motion processing in older and younger individuals. Using the Perceptual Template Model (. Lu & Dosher, 1998, 1999), age-related differences in baseline perceptual inefficiencies and changes due to training were assessed for additive internal noise, tolerance to external noise, and internal multiplicative noise. In Experiments 1 and 2 we trained participants by manipulating contrast in noise embedded sine-wave gratings and Random Dot Cinematograms (RDCs). The results indicate that older observers have higher additive internal noise and lower tolerance to external noise compared to younger observers. The rate of perceptual learning in older observers was found to be similar to that of younger observers suggesting that plasticity of motion processing mechanisms is well preserved in advancing age. Transfer of learning between sine-wave gratings and RDCs for both older and younger observers was examined in an analysis of pre/post-test measurements. The results indicate that transfer of learning occurred for both age groups. This suggests that older individuals maintain a sufficient degree of plasticity to allow generalization between sine-wave gratings and RDCs. In addition, training with RDCs was found to produce greater perceptual learning than training with sine-wave gratings. These experiments provide important findings regarding changes in perceptual efficiency for motion perception in older adults and suggest that perceptual learning is an effective approach for recovering from age-related declines in visual processing. © 2011 Elsevier Ltd.


Reed C.A.,University of California at Riverside
Accounts of Chemical Research | Year: 2010

(Figure Presented) For decades, triflic acid, methyl triflate, and trialkylsilyl triflate reagents have served synthetic chemistry well as clean, strong electrophilic sources of H+, CH3 +, and R3Si+, respectively. However, a number of weakly basic substrates are unreactive toward these reagents. In addition, triflate anion can express undesired nucleophilicity toward electrophilically activated substrates. In this Account, we describe methods that replace triflatebased electrophilic reagents with carborane reagents. Using carborane anions of type CHB11R5X6 - (R = H, Me, X; X = Br, Cl), members of a class of notably inert, weakly nucleophilic anions, significantly increases the electrophilicity of these reagents and shuts down subsequent nucleophilic chemistry of the anion. Thus, H(carborane) acids cleanly protonate benzene, phosphabenzene, C60, etc., while triflic acid does not. Similarly, CH3 (carborane) reagents can methylate substrates that are inert to boiling neat methyl triflate, including benzene, phosphabenzenes, phosphazenes, and the pentamethylhydrazinium ion, which forms the dipositive ethane analogue, Me6N2 2+. Methyl carboranes are also surprisingly effective in abstracting hydride from simple alkanes to give isolable carbocation salts, e.g., t-butyl cation. Trialkylsilyl carborane reagents, R3Si(carborane), abstract halides from substrates to produce cations of unprecedented reactivity. For example, fluoride is extracted from freons to form carbocations; chloride is extracted from IrCl(CO) (PPh3)2 to form a coordinatively unsaturated iridium cation that undergoes oxidative addition with chlorobenzene at room temperature; and silylation of cyclo-N3P3Cl6 produces a catalyst for the polymerization of phosphazenes that functions at room temperature. Although currently too expensive for widespread use, carborane reagents are nevertheless of considerable interest as specialty reagents for making reactive cations and catalysts. © 2010 American Chemical Society.


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.


Jang W.,University of California at Riverside | Chen Z.,University of California at Riverside | Bao W.,University of California at Riverside | Lau C.N.,University of California at Riverside | Dames C.,University of California at Riverside
Nano Letters | Year: 2010

The thermal conductivity of graphene and ultrathin graphite (thickness from 1 to ∼20 layers) encased within silicon dioxide was measured using a heat spreader method. The thermal conductivity increases with the number of graphene layers, approaching the in-plane thermal conductivity of bulk graphite for the thickest samples, while showing suppression below 160 W/m-K at room temperature for single-layer graphene. These results show the strong effect of the encasing oxide in disrupting the thermal conductivity of adjacent graphene layers, an effect that penetrates a characteristic distance of approximately 2.5 nm (∼7 layers) into the core layers at room temperature. © 2010 American Chemical Society.


Teweldebrhan D.,University of California at Riverside | Goyal V.,University of California at Riverside | Balandin A.A.,University of California at Riverside
Nano Letters | Year: 2010

Bismuth telluride (Bi2Te3) and its alloys are the best bulk thermoelectric materials known today. In addition, stacked quasi-two-dimensional (2D) layers of Bi2Te3 were recently identified as promising topological insulators. In this Letter we describe a method for graphene-inspired" exfoliation of crystalline bismuth telluride films with a thickness of a few atoms. The atomically thin films were suspended across trenches in Si/SiO2 substrates, and subjected to detail material characterization, which included atomic force microscopy and micro-Raman spectroscopy. The presence of the van der Waals gaps allowed us to disassemble Bi2Te3 crystal into its quintuple building blocks - five monatomic sheets - consisting of Te(1)?Bi?Te (2)?Bi?Te(1). By altering the thickness and sequence of atomic planes, we were able to create "designer" nonstoichiometric quasi-2D crystalline films, change their composition and doping, the type of charge carriers as well as other properties. The exfoliated quintuples and ultrathin films have low thermal conductivity, high electrical conductivity, and enhanced thermoelectric properties. The obtained results pave the way for producing stacks of crystalline bismuth telluride quantum wells with the strong spatial confinement of charge carriers and acoustic phonons, beneficial for thermoelectric devices. The developed technology for producing free-standing quasi-2D layers of Te(1)?Bi?Te(2)?Bi?Te(1) creates an impetus for investigation of the topological insulators and their possible practical applications. © 2010 American Chemical Society.


Wang F.,University of California at Riverside | Itkis M.E.,University of California at Riverside | Haddon R.C.,University of California at Riverside
Nano Letters | Year: 2010

We report a comprehensive study of the gate-induced electromodulated transmittance of infrared light by single-walled carbon nanotube (SVVNT) thin films. The observed electromodulation is significantly enhanced by utilizing large diameter SWNTs, increasing the ratio of semiconducting to metal SWNTs, and by decreasing the SWNT film thickness. The amplitude of the effect reported herein (∼7%) is more than an order of magnitude larger than in previous SWNT thin film solid state devices. © 2010 American Chemical Society.


Sun H.,University of California at Riverside | Zaera F.,University of California at Riverside
Journal of Physical Chemistry C | Year: 2012

The growth of manganese-based films on silicon oxide substrates via the thermal decomposition of two Mn metalorganic complexes, bis(N,N'- diisopropylpentylamidinato)Mn(II) and methylcyclopentadienylmanganese(I) tricarbonyl, was characterized and contrasted by using an instrument equipped with a reactor coupled to a X-ray photoelectron spectroscopy (XPS) analytical chamber. The acetamidinate precursor proved highly reactive, affording the deposition of Mn at reasonable rates, higher at higher temperatures, but also leading to the incorporation of approximately 15% of nitrogen and additional carbon in the grown Mn(0) films. The methylcyclopentadienyl compound, by contrast, proved quite unreactive, even if an electron-impact gas-phase preactivation step recently developed in our laboratory was used. Slow deposition rates were seen with this precursor, appearing to be slower at higher temperature because of an unfavorable kinetic competition with Mn diffusion into the bulk. In both cases, a nonstoichiometric mixture of MnO x + SiO x and Mn silicate is formed first, possibly followed by the formation of a thin subsurface Mn silicide layer. The combined Mn silicate/Mn silicide structure acts as an effective diffusion barrier, after which Mn(0) metallic films can be grown on top. The implications of this behavior to the design of Mn chemical vapor deposition processes are briefly discussed. © 2012 American Chemical Society.


Wisotsky Z.,University of California at Riverside | Medina A.,University of California at Riverside | Freeman E.,University of California at Riverside | Dahanukar A.,University of California at Riverside
Nature Neuroscience | Year: 2011

Very little is known about how stimuli that are typically not rich in sugars, such as beer, trigger attractive gustatory responses in Drosophila. We identified a member of the gustatory receptor family, Gr64e, as a receptor that is required for feeding preference for beer and other sources that have fermenting yeast. We found that Gr64e is required for neuronal and behavioral responses to glycerol, an abundant component of growing yeast and fermentation products. Ectopic expression of Gr64e in an olfactory neuron conferred responsiveness to glycerol. We also found that Drosophila species that are predicted to carry pseudogenes of Gr64e had reduced glycerol sensitivity. Our results provide insight into the molecular mechanisms of feeding acceptance of yeast products and raise the possibility that Gr64e contributes to specific evolutionary variations in appetitive selectivity across Drosophila species. © 2011 Nature America, Inc. All rights reserved.


Bartnicki-Garcia S.,CICESE | Bartnicki-Garcia S.,University of California at Riverside
Nature Reviews Microbiology | Year: 2015

Midway through the twentieth century, the availability of new and improved optical and electronic microscopes facilitated rapid advances in the elucidation of the fine structure of fungal cells. In this Essay, I pay tribute to Manfred Girbardt (1919-1991) and Charles Bracker (1938-2012)-two individuals who, despite being separated by geography and the restrictions of the Cold War, both made equally fundamental discoveries in fungal cell ultrastructure and set high standards for specimen manipulation and image processing. © 2014 Macmillan Publishers Limited. All rights reserved.


Zhang F.,University of California at Riverside
Molecular & cellular proteomics : MCP | Year: 2012

5-Aza-2'-deoxycytidine (5-Aza-CdR), a nucleoside analog that can inhibit DNA cytosine methylation, possesses potent antitumorigenic activities for myeloid disorders. Although 5-Aza-CdR is known to be incorporated into DNA and inhibit DNA (cytosine-5)-methyltransferases, the precise mechanisms underlying the drug's antineoplastic activity remain unclear. Here we utilized a mass spectrometry-based quantitative proteomic method to analyze the 5-Aza-CdR-induced perturbation of protein expression in Jurkat-T cells at the global proteome scale. Among the ≈ 2780 quantified proteins, 188 exhibited significant alteration in expression levels upon a 24-hr treatment with 5 μm 5-Aza-CdR. In particular, we found that drug treatment led to substantially reduced expression of farnesyl diphosphate synthase (FDPS) and farnesyl diphosphate farnesyltransferase (FDFT1), two important enzymes involved in de novo cholesterol synthesis. Consistent with this finding, 5-Aza-CdR treatment of leukemia (Jurkat-T, K562 and HL60) and melanoma (WM-266-4) cells led to a marked decrease in cellular cholesterol content and pronounced growth inhibition, which could be rescued by externally added cholesterol. Exposure of these cells to 5-Aza-CdR also led to epigenetic reactivation of dipeptidyl peptidase 4 (DPP4) gene. Additionally, suppression of DPP4 expression with siRNA induced elevated protein levels of FDPS and FDFT1, and increased cholesterol biosynthesis in WM-266-4 cells. Together, the results from the present study revealed, for the first time, that 5-Aza-CdR exerts its cytotoxic effects in leukemia and melanoma cells through epigenetic reactivation of DPP4 gene and the resultant inhibition of cholesterol biosynthesis in these cells.


Wei H.,University of California at Riverside | Chao S.-P.,University of California at Riverside | Aji V.,University of California at Riverside
Physical Review Letters | Year: 2012

Systems with strong spin-orbit coupling, which competes with other interactions and energy scales, offer a fertile playground to explore new correlated phases of matter. Weyl semimetals are an example where the phenomenon leads to a low-energy effective theory in terms of massless linearly dispersing fermions in three dimensions. In the absence of interactions chirality is a conserved quantum number, protecting the semimetallic physics against perturbations that are translationally invariant. In this Letter we show that the interplay between interaction and topology yields a novel chiral excitonic insulator. The state is characterized by a complex vectorial order parameter leading to a gapping out of the Weyl nodes. A striking feature is that it is ferromagnetic, with the phase of the order parameter determining the direction of the induced magnetic moment. © 2012 American Physical Society.


Zeng X.,University of California at Riverside | Kinjo R.,University of California at Riverside | Donnadieu B.,University of California at Riverside | Bertrand G.,University of California at Riverside
Angewandte Chemie - International Edition | Year: 2010

(Chemical equation presented) The gold rush: A cationic gold (I) complex, supported by a CAAC ligand, promotes the intramolecular addition of N-H or N-Me bonds (from ammonium salts or tertiary amines, respectively) to carbon-carbon triple bonds; the same complex allows for the isolation of vinylgold intermediates. X= (C6F5)4B. CAAC = cyclic (alkyl) (amino)carbene. © 2010 Wiley-VCH Verlag GmbH & Co. KGaA.


Liu Y.,University of California at Riverside | Zhao S.,East China University of Science and Technology | Wu J.,University of California at Riverside
Journal of Chemical Theory and Computation | Year: 2013

We report a site density functional theory (SDFT) based on the conventional atomistic models of water and the universality ansatz of the bridge functional. The excess Helmholtz energy functional is formulated in terms of a quadratic expansion with respect to the local density deviation from that of a uniform system and a universal functional for all higher-order terms approximated by that of a reference hard-sphere system. With the atomistic pair direct correlation functions of the uniform system calculated from MD simulation and an analytical expression for the bridge functional from the modified fundamental measure theory, the SDFT can be used to predict the structure and thermodynamic properties of water under inhomogeneous conditions with a computational cost negligible in comparison to that of brute-force simulations. The numerical performance of the SDFT has been demonstrated with the predictions of the solvation free energies of 15 molecular analogs of amino acid side chains in water represented by SPC/E, SPC, and TIP3P models. For theTIP3P model, a comparison of the theoretical predictions with MD simulation and experimental data shows agreement within 0.64 and 1.09 kcal/mol on average, respectively. © 2013 American Chemical 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.


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
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.


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.


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.


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.


Tauxe G.M.,University of California at Riverside | Macwilliam D.,University of California at Riverside | Boyle S.M.,University of California at Riverside | Guda T.,University of California at Riverside | Ray A.,University of California at Riverside
Cell | Year: 2013

Female mosquitoes that transmit deadly diseases locate human hosts by detecting exhaled CO2 and skin odor. The identities of olfactory neurons and receptors required for attraction to skin odor remain a mystery. Here, we show that the CO2-sensitive olfactory neuron is also a sensitive detector of human skin odorants in both Aedes aegypti and Anopheles gambiae. We demonstrate that activity of this neuron is important for attraction to skin odor, establishing it as a key target for intervention. We screen ∼0.5 million compounds in silico and identify several CO2 receptor ligands, including an antagonist that reduces attraction to skin and an agonist that lures mosquitoes to traps as effectively as CO2. Analysis of the CO2 receptor ligand space provides a foundation for understanding mosquito host-seeking behavior and identifies odors that are potentially safe, pleasant, and affordable for use in a new generation of mosquito control strategies worldwide. PaperClip © 2013 Elsevier Inc.


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.


Mickelbart M.V.,Purdue University | Hasegawa P.M.,Purdue University | Bailey-Serres J.,University of California at Riverside | Bailey-Serres J.,University Utrecht
Nature Reviews Genetics | Year: 2015

Crop yield reduction as a consequence of increasingly severe climatic events threatens global food security. Genetic loci that ensure productivity in challenging environments exist within the germplasm of crops, their wild relatives and species that are adapted to extreme environments. Selective breeding for the combination of beneficial loci in germplasm has improved yields in diverse environments throughout the history of agriculture. An effective new paradigm is the targeted identification of specific genetic determinants of stress adaptation that have evolved in nature and their precise introgression into elite varieties. These loci are often associated with distinct regulation or function, duplication and/or neofunctionalization of genes that maintain plant homeostasis. © 2015 Macmillan Publishers Limited.


Beran G.J.O.,University of California at Riverside
Chemical Reviews | Year: 2016

Interest in molecular crystals has grown thanks to their relevance to pharmaceuticals, organic semiconductor materials, foods, and many other applications. Electronic structure methods have become an increasingly important tool for modeling molecular crystals and polymorphism. This article reviews electronic structure techniques used to model molecular crystals, including periodic density functional theory, periodic second-order Møller-Plesset perturbation theory, fragment-based electronic structure methods, and diffusion Monte Carlo. It also discusses the use of these models for predicting a variety of crystal properties that are relevant to the study of polymorphism, including lattice energies, structures, crystal structure prediction, polymorphism, phase diagrams, vibrational spectroscopies, and nuclear magnetic resonance spectroscopy. Finally, tools for analyzing crystal structures and intermolecular interactions are briefly discussed. © 2016 American Chemical Society.


Kim Y.J.,University of California at Riverside | Maizel A.,University of Heidelberg | Chen X.,University of California at Riverside | Chen X.,Howard Hughes Medical Institute
EMBO Journal | Year: 2014

microRNAs (miRNAs) and small interfering RNAs (siRNAs) are small RNAs that repress gene expression at the post-transcriptional level in plants and animals. Small RNAs guide Argonaute-containing RNA-induced silencing complexes to target RNAs in a sequence-specific manner, resulting in mRNA deadenylation followed by exonucleolytic decay, mRNA endonucleolytic cleavage, or translational inhibition. Although our knowledge of small RNA biogenesis, turnover, and mechanisms of action has dramatically expanded in the past decade, the subcellular location of small RNA-mediated RNA silencing still needs to be defined. In contrast to the prevalent presumption that RNA silencing occurs in the cytosol, emerging evidence reveals connections between the endomembrane system and small RNA activities in plants and animals. Here, we summarize the work that uncovered this link between small RNAs and endomembrane compartments and present an overview of the involvement of the endomembrane system in various aspects of RNA silencing. We propose that the endomembrane system is an integral component of RNA silencing that has been long overlooked and predict that a marriage between cell biology and RNA biology holds the key to a full understanding of post-transcriptional gene regulation by small RNAs. While extensive work has gone into clarifying the mechanistic basis for RNA silencing, our understanding of the cellular compartments involved is still in its infancy. This review discusses accumulating evidence that the endomembrane system plays a central role in orchestrating small RNA pathways. © 2014 The Authors. Published under the terms of the CC BY NC ND license.


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.


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.


Cassidy D.B.,University of California at Riverside | Meligne V.E.,University of California at Riverside | Mills A.P.,University of California at Riverside
Physical Review Letters | Year: 2010

Long-lived |m|=1 positronium (Ps) atoms are produced in vacuum when high density bursts of positrons with net polarization p0 are implanted into a porous silica film in a 2.3 T magnetic field. We observe a decrease in the |m|=1 population as the density of the incident positron beam is increased due to quenching interactions between oppositely polarized Ps atoms within the target. Saturation of this density dependent quenching indicates that the initial positron spin polarization p0=28±1%, and demonstrates the long term (102s) survival of positron polarization in a Surko-type buffer gas trap. We conclude that, at high Ps densities, the minority spin component is essentially eliminated and the remaining Ps is almost entirely (∼96%) polarized, as required for the formation of a Ps Bose-Einstein condensate. © 2010 The American Physical Society.


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.


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.


Miller T.A.,University of California at Riverside | DiMatteo M.R.,University of California at Riverside
Diabetes, Metabolic Syndrome and Obesity: Targets and Therapy | Year: 2013

Diabetes mellitus affects 24 million individuals in the US. In order to manage their diabetes successfully, patients must adhere to treatment regimens that include dietary restrictions, physical activity goals, and self-monitoring of glucose levels. Numerous factors affect patients' ability to adhere properly, eg, self-efficacy, treatment expectations, health beliefs, and lack of social support. Consequently, diabetes management can be quite complex, requiring lifelong commitment and drastic changes to the patient's lifestyle. Empirical studies have shown positive and significant relationships between social support and treatment adherence among patients with diabetes. Social support from family provides patients with practical help and can buffer the stresses of living with illness. However, the exact mechanism by which social support affects patient adherence is not yet completely understood. Further research is needed to address how the differences in types of support, such as functional or emotional support, are linked to outcomes for patients. The purpose of this review is to summarize what is known of the impact of social and family support on treatment adherence in patients with diabetes and to explore the current methods and interventions used to facilitate family support for diabetic patients. © 2013 Miller and DiMatteo.


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.


Murty S.,University of Exeter | Robert Russell R.,University of California at Riverside | Levkoff S.B.,University of California at Riverside
Journal of Environmental Economics and Management | Year: 2012

We argue analytically that many commonly used models of pollution-generating technologies, which treat pollution as a freely disposable input or as a weakly disposable and null-joint output, may generate unacceptable implications for the trade-offs among inputs, outputs, and pollution. We show that the correct trade-offs in production are best captured if a pollution-generating technology is modeled as an intersection of an intended-production technology of the firm and nature's residual-generation set. The former satisfies standard disposability properties, while the latter violates free (strong) disposability of pollution and pollution-causing inputs. As a result, the intersection-which we call a by-production technology-violates standard free disposability of pollution and pollution-causing inputs. Employing data envelopment analysis on an electric-power-plant database, we illustrate shortcomings, under by-production, of two popular efficiency indexes: the hyperbolic and directional-distance-function indexes. We propose and implement an alternative index with superior properties. Under by-production, most efficiency indexes decompose very naturally into intended-production and environmental efficiency indexes. This decomposition is difficult to find under alternative specifications of pollution-generating technologies. © 2012 Elsevier Inc..


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.


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.


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.


Banishev A.A.,University of California at Riverside | Klimchitskaya G.L.,Russian Academy of Sciences | Mostepanenko V.M.,Russian Academy of Sciences | Mohideen U.,University of California at Riverside
Physical Review Letters | Year: 2013

We demonstrate the Casimir interaction between two ferromagnetic boundary surfaces using the dynamic atomic force microscope. The experimental data are found to be in excellent agreement with the predictions of the Lifshitz theory for magnetic boundary surfaces combined with the plasma model approach. It is shown that for magnetic materials the role of hypothetical patch potentials is opposite to that required for reconciliation of the data with the Drude model. © 2013 American Physical Society.


Williams R.T.,University of California at Riverside | Wang Y.,University of California at Riverside
Biochemistry | Year: 2012

B3LYP/6-311+G(2d,p)//B3LYP/6-31+G(d) density functional theory calculations were employed to explore the kinetics and thermodynamics of gas-phase N-glycosidic bond cleavage induced by nucleophilic attack of C1′ with a hydroxide ion in 5-substituted 2′-deoxycytidines. The results showed that, among the 5-substituted 2′-deoxycytidine derivatives examined [XdC, where X = H (dC), CH 3 (medC), CH 2OH (hmdC), CHO (fmdC), COOH (cadC), F (FdC), or Br (BrdC)], fmdC and cadC exhibited the lowest energy barrier and largest exothermicity for N-glycosidic bond cleavage. These results paralleled previously reported nucleobase excision activities of human thymine DNA glycosylase (hTDG) toward duplex DNA substrates harboring a thymine and 5-substituted cytosine derivatives when paired with a guanine. Our study suggests that the inherent chemistry associated with the nucleophilic cleavage of N-glycosidic bond constitutes a major factor contributing to the selectivity of hTDG toward 5-substituted dC derivatives. These findings provided novel insights into the role of TDG in active cytosine demethylation. © 2012 American Chemical Society.


Lee I.,University of California at Riverside | Joo J.B.,University of California at Riverside | Yin Y.,University of California at Riverside | Zaera F.,University of California at Riverside
Angewandte Chemie - International Edition | Year: 2011

Trapped inside: A new catalyst was developed where gold nanoparticles are encased inside hollow titania nanospheres (see picture). The new nanoarchitecture prevents the nanoparticles from sintering and losing their activity while still providing the reactants free access to the metal surface. The result is a catalyst capable of promoting the oxidation of CO at room temperature while surviving calcination at temperatures above 775 K. © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Alfi M.,University of California at Riverside | Talbot P.,University of California at Riverside
Journal of Medical Internet Research | Year: 2013

Background: The health effects caused by electronic cigarette (e-cigarette) use are not well understood. Objective: 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. Methods: 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. Results: 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. Conclusions: 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.


Bardeen C.J.,University of California at Riverside
MRS Bulletin | Year: 2013

This article provides an overview of the basic aspects of the structure and dynamics of excitons in molecular crystals that give rise to their unique spectroscopic behavior. The two different types of optically accessible excitons, charge-transfer and Frenkel, are described and their different properties discussed. Particular attention is paid to the spin properties of Frenkel excitons (i.e., singlet and triplet) and also to their coupling to intramolecular vibrations. Experimental challenges in the study of molecular crystal optical properties are also reviewed, including their high optical density, complex refractive index behavior, and issues with sample crystallinity and chemical purity. Once created, excitons in molecular crystals can exhibit interesting dynamical behavior, including diffusion over large length scales and ionization into electron-hole pairs. Exciton-exciton interactions are also important, ranging from fusion or annihilation (two excitons combine into one exciton) to fission (one exciton splits into two excitons). The long-range diffusion and exciton fission effects have particular relevance for the design of organic photovoltaic materials. © 2013 Materials Research Society.


King E.G.,University of California at Riverside | Roff D.A.,University of California at Riverside
American Naturalist | Year: 2010

In nature, resource availability varies spatially and temporally both within and across generations, leading to variation in the amount of energy available to individuals. The optimal allocation strategy can change, depending on the amount of resources available to allocate to life-history functions. If so, selection should favor the evolution of allocation strategies that can respond to variation in environmental resource levels. We address this issue by using two quantitative genetic simulation models in a model system for studying trade-offs, wing-dimorphic insects. Wing dimorphic insects typically exhibit a trade-off in the allocation of resources between migratory ability and reproduction. In our models, we focus on allocation as a genetic trait and model the evolution of phenotypic plasticity in this trait in response to spatiotemporal variation in resource availability. We show that the evolved allocation strategy depends on the predictability of resource levels across time. Specifically, selection favors higher investment in flight under poor conditions in predictable environments and lower investment in unpredictable environments. © 2010 by The University of Chicago.


Low food availability during early growth and development can have long-term negative consequences for reproductive success. Phenotypic plasticity in adult life-history decisions may help to mitigate these potential costs, yet adult life-history responses to juvenile food conditions remain largely unexplored. I used a foodmanipulation experiment with female Trinidadian guppies (Poecilia reticulata) to examine age-related changes in adult life-history responses to early food conditions, whether these responses varied across different adult food conditions, and how these responses affected overall reproductive success. Guppy females reared on low food as juveniles matured at a later age, at a smaller size, and with less energy reserves than females reared on high food as juveniles. In response to this setback, they changed their investment in growth, reproduction, and fat storage throughout the adult stage such that they were able to catch up in body size, increase their reproductive output, and restore their energy reserves to levels comparable to those of females reared on high food as juveniles. The net effect was that adult female guppies did not merely mitigate but surprisingly were able to fully compensate for the potential long-term negative effects of poor juvenile food conditions on reproductive success. © 2010 by The University of Chicago.


Cao Y.,University of California at Riverside | Cao Y.,Air Force Research Lab | Ren W.,University of California at Riverside | Egerstedt M.,Georgia Institute of Technology
Automatica | Year: 2012

In this paper, we study the problem of distributed containment control of a group of mobile autonomous agents with multiple stationary or dynamic leaders under both fixed and switching directed network topologies. First, when the leaders are stationary and all followers share an inertial coordinate frame, we present necessary and sufficient conditions on the fixed or switching directed network topology such that all followers will ultimately converge to the stationary convex hull formed by the stationary leaders for arbitrary initial states in a space of any finite dimension. When the directed network topology is fixed, we partition the (nonsymmetric) Laplacian matrix and explore its properties to derive the convergence results. When the directed network topology is switching, the commonly adopted decoupling technique based on the Kronecker product in a high-dimensional space can no longer be applied and we hence present an important coordinate transformation technique to derive the convergence results. The proposed coordinate transformation technique also has potential applications in other high-dimensional distributed control scenarios and might be used to simplify the analysis of a high-dimensional system to that of a one-dimensional system when the decoupling technique based on the Kronecker product cannot be applied. Second, when the leaders are dynamic and all followers share an inertial coordinate frame, we propose a distributed tracking control algorithm without velocity measurements. When the directed network topology is fixed, we derive conditions on the network topology and the control gain to guarantee that all followers will ultimately converge to the dynamic convex hull formed by the dynamic leaders for arbitrary initial states in a space of any finite dimension. When the directed network topology is switching, we derive conditions on the network topology and the control gain such that all followers will ultimately converge to the minimal hyperrectangle that contains the dynamic leaders and each of its hyperplanes is normal to one axis of the inertial coordinate frame in any high-dimensional space. We also show via some counterexamples that it is, in general, impossible to find distribute containment control algorithms without velocity measurements to guarantee that all followers will ultimately converge to the convex hull formed by the dynamic leaders under a switching network topology in a high-dimensional space. Simulation results are presented as a proof of concept. © 2012 Elsevier Ltd. All rights reserved.


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.


Pham H.T.,University of California at Riverside | Julian R.R.,University of California at Riverside
Analytical Chemistry | Year: 2014

Phosphatidylethanolamines (PE) and phosphatidylcholines (PC) are important phospholipids frequently present in many types of cells. In some cases, PE has been equated with PC because they are chemically very similar and are often isomeric species. In this study, we demonstrate that noncovalent complexation between PE and 18-crown-6 ether (18C6) can be used to quantitatively mass shift and separate PE from PC phospholipids. Detection of PE is also more sensitive by approximately an order of magnitude with addition of 18C6. This noncovalent complexation approach is used to separate and quantitatively characterize PE in a soy bean asolectin extract. 18C6 (modified with an iodobenzoyl moiety) can also be used to efficiently generate radical PE lipids following photoactivation in the gas phase. Subsequent collisional activation of these lipid radical ions leads to radical directed dissociation (RDD), which generates unique fragment ions relative to dissociation of comparable even electron ions. Interestingly, RDD produces fragment ions that reveal carbon bonding features within the lipid acyl chain substituents, such as double bond location or the presence of branching. Furthermore, several novel and abundant fragments were observed in unsaturated lipids. Mechanisms that can account for the high abundance of some of these product ions are proposed. © 2014 American Chemical Society.


Berzenski S.R.,University of California at Riverside | Yates T.M.,University of California at Riverside
Child Maltreatment | Year: 2011

While the overwhelming majority of research on the consequences of childhood maltreatment reports differential outcomes of specific maltreatment subtypes (e.g., physical abuse vs. emotional abuse) as though they are independent, maltreatment experiences often occur in combination. The present study evaluated multiple maltreatment experiences in a sample of 2,637 undergraduate students who reported on childhood maltreatment and current adjustment. The authors used latent class analysis to examine predominant patterns of multiple maltreatment experiences and investigated indices of psychosocial adjustment associated with those patterns. Results suggested that specific constellations of multiple maltreatment have qualitatively different associations with adjustment. Emotional abuse, alone or in combination with other maltreatment types, was especially salient for psychopathology (e.g., anxiety, depression), while a combination of physical and emotional abuse was most strongly associated with conduct-related problems (e.g., substance use, risky sexual behavior). These findings have both practical and empirical significance for understanding and classifying experiences of maltreatment. © The Author(s) 2011.


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.


Richert R.A.,University of California at Riverside | Robb M.B.,University of California at Riverside | Smith E.I.,University of California at Riverside
Child Development | Year: 2011

Television has become a nearly ubiquitous feature in children's cultural landscape. A review of the research into young children's learning from television indicates that the likelihood that children will learn from screen media is influenced by their developing social relationships with on-screen characters, as much as by their developing perception of the screen and their symbolic understanding and comprehension of information presented on screen. Considering the circumstances in which children under 6 years learn from screen media can inform teachers, parents, and researchers about the important nature of social interaction in early learning and development. The findings reviewed in this article suggest the social nature of learning, even learning from screen media. © 2011 The Authors. Child Development © 2011 Society for Research in Child Development, Inc.


Roy S.,University of California at Riverside | Kagda M.,University of California at Riverside | Judelson H.S.,University of California at Riverside
PLoS Pathogens | Year: 2013

Most eukaryotic pathogens have complex life cycles in which gene expression networks orchestrate the formation of cells specialized for dissemination or host colonization. In the oomycete Phytophthora infestans, the potato late blight pathogen, major shifts in mRNA profiles during developmental transitions were identified using microarrays. We used those data with search algorithms to discover about 100 motifs that are over-represented in promoters of genes up-regulated in hyphae, sporangia, sporangia undergoing zoosporogenesis, swimming zoospores, or germinated cysts forming appressoria (infection structures). Most of the putative stage-specific transcription factor binding sites (TFBSs) thus identified had features typical of TFBSs such as position or orientation bias, palindromy, and conservation in related species. Each of six motifs tested in P. infestans transformants using the GUS reporter gene conferred the expected stage-specific expression pattern, and several were shown to bind nuclear proteins in gel-shift assays. Motifs linked to the appressoria-forming stage, including a functionally validated TFBS, were over-represented in promoters of genes encoding effectors and other pathogenesis-related proteins. To understand how promoter and genome architecture influence expression, we also mapped transcription patterns to the P. infestans genome assembly. Adjacent genes were not typically induced in the same stage, including genes transcribed in opposite directions from small intergenic regions, but co-regulated gene pairs occurred more than expected by random chance. These data help illuminate the processes regulating development and pathogenesis, and will enable future attempts to purify the cognate transcription factors. © 2013 Roy et al.


Yang Z.,University of California at Riverside | Lavagi I.,University of California at Riverside
Current Opinion in Plant Biology | Year: 2012

Breaking of the cell membrane symmetry to form polarized or localized domains/regions of the plasma membrane (PM) is a fundamental cellular process that occurs in essentially all cellular organisms, and is required for a wide variety of cellular functions/behaviors including cell morphogenesis, cell division and cell differentiation. In plants, the development of localized or polarized PM domains has been linked to a vast array of cellular and developmental processes such as polar cell expansion, asymmetric cell division, cell morphogenesis, the polarization of auxin transporters (and thus auxin polar transport), secondary cell wall patterning, cell type specification, and tissue pattern formation. Rho GTPases from plants (ROPs) are known to be involved in many of these processes. Here, we review the current knowledge on ROP involvement in breaking symmetry and propose that ROP-based self-organizing signaling may provide a common mechanism for the spatial control of PM domains required in various cellular and developmental processes in plants. © 2012.


Zaera F.,University of California at Riverside
Chemical Reviews | Year: 2012

A study was conducted to demonstrate probing techniques for liquid and solid interfaces at the molecular level. Investigations revealed that new approaches were needed to study liquid or solid interfaces at a molecular level. Some electron-based surface-science techniques were adapted to probe liquid and solid interfaces by minimizing the paths that the probing particles needed to travel through the liquid phase. The use of techniques based on light or other electromagnetic radiation for surface analysis had more potential to achieve these objectives. The potential use of techniques, such as X-ray photoelectron spectroscopy and nuclear magnetic and electron spin resonance spectroscopies for the characterization of liquid and solid interfaces was investigated. Investigations revealed that infrared (IR) absorption spectroscopy was the most commonly used technique for the molecular-level characterization of such liquid and solid interfaces.


Pierce C.J.,University of California at Riverside | Nguyen M.,University of California at Riverside | Larsen C.H.,University of California at Riverside
Angewandte Chemie - International Edition | Year: 2012

Three-component coupling, with a pair: The combination of CuII and TiIV catalyzes the first three-component coupling of unactivated ketones with a diverse range of amines and terminal alkynes. Tetrasubstituted propargylamines are formed under green, solvent-free conditions (see scheme). This dual metal system overcomes the barrier to ketimine formation and subsequent attack, opening a new path to multicomponent reactions of ketone electrophiles. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


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.


Chung H.,Howard Hughes Medical Institute | Loehlin D.W.,Howard Hughes Medical Institute | Dufour H.D.,Howard Hughes Medical Institute | Vaccarro K.,Howard Hughes Medical Institute | And 2 more authors.
Science | Year: 2014

Evolutionary changes in traits involved in both ecological divergence and mate choice may produce reproductive isolation and speciation. However, there are few examples of such dual traits, and the genetic and molecular bases of their evolution have not been identified. We show that methyl-branched cuticular hydrocarbons (mbCHCs) are a dual trait that affects both desiccation resistance and mate choice in Drosophila serrata. We identify a fatty acid synthase mFAS (CG3524) responsible for mbCHC production in Drosophila and find that expression of mFAS is undetectable in oenocytes (cells that produce CHCs) of a closely related, desiccation-sensitive species, D. birchii, due in part to multiple changes in cis-regulatory sequences of mFAS. We suggest that ecologically influenced changes in the production of mbCHCs have contributed to reproductive isolation between the two species.


Xie Y.,University of California at Riverside | Cwiertny D.M.,University of California at Riverside
Environmental Science and Technology | Year: 2010

Nanoscale zero-valent iron (NZVI) represents a promising approach for source zone control, but concerns over its reactive lifetime might limit application. Here, we demonstrate that dithionite (S 2O 4 2-), a reducing agent for in situ redox manipulation, can restore the reducing capacity of passivated NZVI. Slurries of NZVI were aged in the presence (3 days) and absence (60 days) of dissolved oxygen over a range of pH values (6-8). Upon loss of reactivity toward model pollutants {1,1,1,2-tetrachloroethane, hexavalent chromium [Cr(VI)], nitrobenzene}, aged suspensions were reacted with dithionite, and the composition and reactivity of the dithionite-treated materials were determined. NZVI aging products generally depended on pH and the presence of oxygen, whereas the amount of dithionite influenced the nature and reducing capacity of products generated from reaction with aged NZVI suspensions. Notably, air oxidation at pH ≥ 8 quickly exhausted NZVI reactivity despite preservation of significant Fe(0) in the particle core. Under these conditions, formation of a passive surface layer hindered the complete transformation of NZVI particles into iron(III) oxides, which occurred at lower pH. Reduction of this passive layer by low dithionite concentrations (<1 g/g of NZVI) restored suspension reactivity to levels equal to, and occasionally greater than, that of unaged NZVI. Multiple dithionite additions further improved pollutant removal, allowing at least a 15-fold increase in Cr(VI) removal [∼300 mg of Cr(VI)/g of NZVI] relative to that of as-received NZVI [∼20 mg of Cr(VI)/g of NZVI]. © 2010 American Chemical Society.


Freeman E.G.,University of California at Riverside | Wisotsky Z.,University of California at Riverside | Dahanukar A.,University of California at Riverside
Proceedings of the National Academy of Sciences of the United States of America | Year: 2014

Sweet taste cells play critical roles in food selection and feeding behaviors. Drosophila sweet neurons express eight gustatory receptors (Grs) belonging to a highly conserved clade in insects. Despite ongoing efforts, little is known about the fundamental principles that underlie how sweet tastants are detected by these receptors. Here, we provide a systematic functional analysis of Drosophila sweet receptors using the ab1C CO 2-sensing olfactory neuron as a unique in vivo decoder. We find that each of the eight receptors of this group confers sensitivity to one or more sweet tastants, indicating direct roles in ligand recognition for all sweet receptors. Receptor response profiles are validated by analysis of taste responses in corresponding Gr mutants. The response matrix shows extensive overlap in Gr-ligand interactions and loosely separates sweet receptors into two groups matching their relationships by sequence. We then show that expression of a bitter taste receptor confers sensitivity to selected aversive tastants that match the responses of the neuron that the Gr is derived from. Finally, we characterize an internal fructose-sensing receptor, Gr43a, and its ortholog in the malaria mosquito, AgGr25, in the ab1C expression system. We find that both receptors show robust responses to fructose along with a number of other sweet tastants. Our results provide a molecular basis for tastant detection by the entire repertoire of sweet taste receptors in the fly and lay the foundation for studying Grs in mosquitoes and other insects that transmit deadly diseases.


Li W.,University of California at Riverside | Jiang T.,University of California at Riverside | Jiang T.,Tsinghua University
Bioinformatics | Year: 2012

Motivation: RNA-Seq uses the high-throughput sequencing technology to identify and quantify transcriptome at an unprecedented high resolution and low cost. However, RNA-Seq reads are usually not uniformly distributed and biases in RNA-Seq data post great challenges in many applications including transcriptome assembly and the expression level estimation of genes or isoforms. Much effort has been made in the literature to calibrate the expression level estimation from biased RNA-Seq data, but the effect of biases on transcriptome assembly remains largely unexplored.Results: Here, we propose a statistical framework for both transcriptome assembly and isoform expression level estimation from biased RNA-Seq data. Using a quasi-multinomial distribution model, our method is able to capture various types of RNA-Seq biases, including positional, sequencing and mappability biases. Our experimental results on simulated and real RNA-Seq datasets exhibit interesting effects of RNA-Seq biases on both transcriptome assembly and isoform expression level estimation. The advantage of our method is clearly shown in the experimental analysis by its high sensitivity and precision in transcriptome assembly and the high concordance of its estimated expression levels with quantitative reverse transcription-polymerase chain reaction data. © 2012 The Author.


Weng Z.,University of California at Riverside | Zaera F.,University of California at Riverside
Journal of Physical Chemistry C | Year: 2014

Selectivity has become a critical consideration in the design of catalysts, but increases in selectivity are typically achieved at the expense of overall activity. Here we report on a unique case where the addition of alkyl thiol self-assembled monolayers to colloidal platinum nanoparticles leads to significant improvements in both activity and selectivity during the hydrogenation of α-keto esters with cinchonidine as a chiral modifier. These catalytic improvements may be explained by a kinetic effect in which the cinchonidine residence time on the surface is increased by the thiol self-assembled layers. More nuanced compromises between activity and selectivity are involved when using supported catalysts, but reasonable performances are still possible with Pt/Al2O3 catalysts treated with cinchonidine-derivatized thiols. Indeed, these all-heterogeneous catalysts can promote the α-keto ester hydrogenation reaction with almost the same enantioselectivity as the best naked supported Pt catalyst without the need to add cinchonidine to the reaction mixture. They are among the most enantioselective all-heterogeneous catalysts reported to date. © 2014 American Chemical Society.


Ma E.,University of California at Riverside | Wegman D.,University of California at Riverside
Physical Review Letters | Year: 2011

In the original 2004 paper which first derived tribimaximal mixing in the context of A4, i.e., the non-Abelian finite symmetry group of the tetrahedron, as its simplest application, it was also pointed out how θ13≠ 0 may be accommodated. On the strength of the new T2K result that 0.03(0.04)≤sin22θ13≤0.28(0.34) for δCP=0 and normal (inverted) neutrino mass hierarchy, we perform a more detailed analysis of how this original idea may be realized in the context of A4. © 2011 American Physical Society.


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.


Turcotte M.M.,University of Toronto | Reznick D.N.,University of California at Riverside | Hare J.D.,University of California at Riverside
Ecology Letters | Year: 2011

Rapid evolution challenges the assumption that evolution is too slow to impact short-term ecological dynamics. This insight motivates the study of 'Eco-Evolutionary Dynamics' or how evolution and ecological processes reciprocally interact on short time scales. We tested how rapid evolution impacts concurrent population dynamics using an aphid (Myzus persicae) and an undomesticated host (Hirschfeldia incana) in replicated wild populations. We manipulated evolvability by creating non-evolving (single clone) and potentially evolving (two-clone) aphid populations that contained genetic variation in intrinsic growth rate. We observed significant evolution in two-clone populations whether or not they were exposed to predators and competitors. Evolving populations grew up to 42% faster and attained up to 67% higher density, compared with non-evolving control populations but only in treatments exposed to competitors and predators. Increased density also correlates with relative fitness of competing clones suggesting a full eco-evolutionary dynamic cycle defined as reciprocal interactions between evolution and density. © 2011 Blackwell Publishing Ltd/CNRS.


Richert R.A.,University of California at Riverside | Smith E.I.,University of California at Riverside
Child Development | Year: 2011

Preschool-aged children are exposed to fantasy stories with the expectation that they will learn messages in those stories that are applied to real-world situations. We examined children's transfer from fantastical and real stories. Over the course of 2 studies, 31/2- to 51/2-year-old children were less likely to transfer problem solutions from stories about fantasy characters than stories about real people. A combined analysis of the participants in the 2 studies revealed that the factors predicting transfer differed for the fantasy and real stories. These findings are discussed within the context of their implications for preschoolers' developing boundaries between fantasy and real worlds. © 2011 The Authors. Child Development © 2011 Society for Research in Child Development, Inc.


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.


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.


Liu Y.,Northeastern University China | Guo L.,Northeastern University China | Wei X.,University of California at Riverside
Journal of Lightwave Technology | Year: 2012

Survivability is one of the key issues in hybrid wireless-optical broadband access networks (WOBAN) since the single segment failure can cause huge data loss. The single segment failure refers to a scenario where all optical-network-units (ONUs) are disconnected with the optical line terminal (OLT). Previous schemes focus on protecting WOBAN against single segment failure by deploying backup fibers. However, previous schemes suffer from two key problems. First, they ignore optimizing the selection of backup ONUs, which determines the cost of recovering the traffic interrupted by the failure. Second, they underutilize the residual capacity of segments, thus requiring higher backup fibers cost. In this paper, we propose a new and efficient scheme, called Optimizing Backup ONUs selection and backup Fibers deployment (OBOF), to enhance the survivability of WOBAN against the single segment failure. Our OBOF is composed of two consecutive steps, backup ONUs selection and backup fibers deployment. In the first step, aiming to minimize the cost of recovering the traffic interrupted by the failure, the simulated annealing (SA) algorithm is customized to optimize the selection of backup ONUs. In the second step, most importantly, an enhanced greedy cost-efficiency (EGCE) algorithm is proposed to optimize the deployment of backup fibers. Our EGCE consists of a novel remote backup segment (RBS) method, which can efficiently utilize the residual capacity of the segments, and a Bound on Length of Backup-optical-path (BLB) method, which limits the increase in recovery time induced by RBS. Extensive experimental results demonstrate that our OBOF scheme outperforms the previous schemes significantly, especially in the scenario of higher traffic demand. © 2012 IEEE.


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.


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.


Weirauch C.,University of California at Riverside | Schuh R.T.,American Museum of Natural History
Annual Review of Entomology | Year: 2011

Heteroptera, or true bugs, are part of the most successful radiation of nonholometabolous insects. Twenty-five years after the first review on the influence of cladistics on systematic research in Heteroptera, we summarize progress, problems, and future directions in the field. The few hypotheses on infraordinal relationships conflict on crucial points. Understanding relationships within Gerromorpha, Nepomorpha, Leptopodomorpha, Cimicomorpha, and Pentatomomorpha is improving, but progress within Enicocephalomorpha and Dipsocoromorpha is lagging behind. Nonetheless, the classifications of several erfamily-level taxa within the Pentatomomorpha, such as Aradoidea, Coreoidea, and Pyrrhocoroidea, are still unaffected by cladistic studies. Progress in comparative morphology is slow and drastically impedes our understanding of the evolution of major clades. Molecular systematics has dramatically contributed to accelerating the generation and testing of hypotheses. Given the fascinating natural history of true bugs and their status as model organisms for evolutionary studies, integration of cladistic analyses in a broader biogeographic and evolutionary context deserves increased attention. © 2011 by Annual Reviews. All rights reserved.


Hamdy O.M.,University of California at Riverside | Julian R.R.,University of California at Riverside
Journal of the American Society for Mass Spectrometry | Year: 2012

The connection between charge state distributions, protein structure, and mechanistic details of electrospray are discussed in relation to the emerging field of gas phase structural biology. Comparisons are drawn with the established area of enzymatic catalysis in organic solvents, which shares many similar challenges. Charge solvation emerges as a dominant force in both systems that must be dealt with to enable kinetic trapping of native structures in foreign environments. Potential methods for mediating unfavorable charge solvation effects are discussed and, ironically, do not include partial solvation by water. The importance of timescale in relation to the evolution of protein structure during the process of electrospray ionization is discussed. Finally several prospects for future endeavors are highlighted. © 2011 American Society for Mass Spectrometry.


Meyet C.E.,University of California at Riverside | Pierce C.J.,University of California at Riverside | Larsen C.H.,University of California at Riverside
Organic Letters | Year: 2012

A single Cu(II) catalyst without the addition of ligand or base couples a diverse range of nitrogen sources with alkynes and aldehydes bearing alkyl, halogenated, silyl, aryl, and heteroaryl groups. The first example of a copper-catalyzed alkynylation involving p-toluenesulfonamide provides high yields of N-Ts-protected propargylamines. The superior activity of copper(II) triflate also allows this three-component alkynylation to incorporate a ketone. © 2012 American Chemical Society.


Han W.,University of California at Riverside | Kawakami R.K.,University of California at Riverside
Physical Review Letters | Year: 2011

We investigate spin relaxation in graphene spin valves and observe strongly contrasting behavior for single-layer graphene (SLG) and bilayer graphene (BLG). In SLG, the spin lifetime (τs) varies linearly with the momentum scattering time (τp) as carrier concentration is varied, indicating the dominance of Elliot-Yafet (EY) spin relaxation at low temperatures. In BLG, τs and τp exhibit an inverse dependence, which indicates the dominance of Dyakonov-Perel spin relaxation at low temperatures. The different behavior is due to enhanced screening and/or reduced surface sensitivity of BLG, which greatly reduces the impurity-induced EY spin relaxation. © 2011 American Physical Society.


He Y.,University of California at Riverside | Varma C.M.,University of California at Riverside
Physical Review Letters | Year: 2011

We show that the two branches of collective modes discovered recently in underdoped cuprates with a large spectral weight are a necessary consequence of the loop-current state. Such a state has been shown in earlier experiments to be consistent with the symmetry of the order parameter competing with superconductivity in four families of cuprates. We also predict a third branch of excitations which cannot be discovered by neutron scattering but may be discovered by other techniques. Using parameters to fit the observed modes, we show that quantum fluctuations change the direction of the effective moments in the ground state to lie at an angle to the c axis as observed in experiments. © 2011 American Physical Society.


Goebl J.,University of California at Riverside | Zhang Q.,University of California at Riverside | He L.,University of California at Riverside | Yin Y.,University of California at Riverside
Angewandte Chemie - International Edition | Year: 2012

Out of the frame: A marker study using gold frames was designed to reveal that silver nanoplates undergo a shape transition during their seeded growth from triangular to circular to hexagonal plates before ultimately returning to triangular structures with an orientation 180° relative to that of the original triangular seeds (see picture, the original gold triangular frame is visible at the center of the silver nanoplate). Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Sarkar S.,University of California at Riverside | Bekyarova E.,University of California at Riverside | Haddon R.C.,University of California at Riverside
Angewandte Chemie - International Edition | Year: 2012

The Kolbe electrochemical oxidation strategy has been utilized to achieve an efficient quasireversible electrochemical grafting of the α-naphthylmethyl functional group to graphene. The method facilitates reversible bandgap engineering in graphene and preparation of electrochemically erasable organic dielectric films. The picture shows Raman D-band maps of both systems. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Liu Y.,University of California at Riverside | Han X.,University of California at Riverside | He L.,University of California at Riverside | Yin Y.,University of California at Riverside
Angewandte Chemie - International Edition | Year: 2012

Charged colloidal gold nanoparticles (AuNPs) can be assembled and disassembled in an aqueous solution in response to temperature change and display reversible thermoresponsive tuning of plasmon coupling. The reversible tuning was made possible by manipulating the electrostatic interaction through the temperature-dependent zeta potential of the charged AuNPs (see the extinction spectra of a typical AuNP dispersion). Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Martin D.,University of California at Riverside | Lassauque N.,University of California at Riverside | Donnadieu B.,University of California at Riverside | Bertrand G.,University of California at Riverside
Angewandte Chemie - International Edition | Year: 2012

An anti-Bredt NHC! Placing one of the adjacent nitrogen atoms of an NHC in the bridgehead position of a bicyclic scaffold prevents the donation of its lone pair. Thus, the π-electron-accepting properties of the carbene center are enhanced, while the strong -electron-donating properties of classical NHCs are retained. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Linic S.,University of Michigan | Christopher P.,University of Michigan | Christopher P.,University of California at Riverside | Xin H.,University of Michigan | Marimuthu A.,University of Michigan
Accounts of Chemical Research | Year: 2013

Heterogeneous catalysis by metals was among the first enabling technologies that extensively relied on nanoscience. The early intersections of catalysis and nanoscience focused on the synthesis of catalytic materials with high surface to volume ratio. These synthesis strategies mainly involved the impregnation of metal salts on high surface area supports. This would usually yield quasi-spherical nanoparticles capped by low-energy surface facets, typically with closely packed metal atoms. These high density areas often function as the catalytically active surface sites. Unfortunately, strategies to control the functioning surface facet (i.e., the geometry of active sites that performs catalytic turnover) are rare and represent a significant challenge in our ability to fine-tune and optimize the reactive surfaces.Through recent developments in colloidal chemistry, chemists have been able to synthesize metallic nanoparticles of both targeted size and desired shape. This has opened new possibilities for the design of heterogeneous catalytic materials, since metal nanoparticles of different shapes are terminated with different surface facets. By controlling the surface facet exposed to reactants, we can start affecting the chemical transformations taking place on the metal particles and changing the outcome of catalytic processes.Controlling the size and shape of metal nanoparticles also allows us to control the optical properties of these materials. For example, noble metals nanoparticles (Au, Ag, Cu) interact with UV-vis light through an excitation of localized surface plasmon resonance (LSPR), which is highly sensitive to the size and shape of the nanostructures. This excitation is accompanied by the creation of short-lived energetic electrons on the surface of the nanostructure. We showed recently that these energetic electrons could drive photocatalytic transformations on these nanostructures. The photocatalytic, electron-driven processes on metal nanoparticles represent a new family of chemical transformations exhibiting fundamentally different behavior compared with phonon-driven thermal processes, potentially allowing selective bond activation. In this Account, we discuss both the impact of the shape of metal nanoparticles on the outcome of heterogeneous catalytic reactions and the direct, electron-driven photocatalysis on plasmonic metal nanostructures of noble metals. These two phenomena are important examples of taking advantage of physical properties of metal materials that are controlled at nanoscales to affect chemical transformations. © 2013 American Chemical Society.


Carter W.P.L.,University of California at Riverside | Heo G.,University of California at Riverside
Atmospheric Environment | Year: 2013

The representation of the gas-phase atmospheric reactions of aromatic hydrocarbons in the SAPRC-07 chemical mechanism has been updated to give better simulations of recent environmental chamber experiments carried out under lower NOx conditions than used to develop SAPRC-07. SAPRC-07 consistently underpredicted NO oxidation and O3 formation rates observed in most of the newer experiments. The new aromatics mechanisms, designated as SAPRC-11, gave better simulations of O3 formation in almost all experiments, except for higher (> 100ppb) NOx benzene and (to a lesser extent) toluene experiments where O3 formation rates were consistently overpredicted. This overprediction athigher NOx can be corrected if the aromatics mechanism is parameterized to include a new NOx dependence on photoreactive product yields, but that parameterization was not incorporated in SAPRC-11 because it is inconsistent with available laboratory data. The mechanisms for phenolic compounds were also significantly revised to better simulate the new experiments. The base mechanism for SAPRC-11 incorporates a few minor updates, but otherwise is the same as SAPRC-07. The light source used in the chamber experiments had no significant effect on mechanism evaluation results, except possibly for cresols. The mechanisms still underpredict OH radical levels and further studies are needed to reduce uncertainties in aromatics mechanisms. © 2013 Elsevier Ltd.


Strollo C.M.,University of California at Riverside | Ziemann P.J.,University of California at Riverside
Atmospheric Environment | Year: 2013

The aerosol products of the OH radical-initiated reaction of 3-methylfuran in the presence of NOx was investigated in an environmental chamber using a combination of online and offline techniques. Aerosol mass spectra, thermal desorption profiles, O/C, H/C, and N/C ratios, functional group composition, UV absorption spectra, and time profiles of NO, O3, and organic aerosol mass were all consistent with a mechanism of secondary organic aerosol (SOA) formation under dry conditions in which three previously identified unsaturated C5 reaction products, a 1,4-dialdehyde, hydroxyfuranone, and 1,4-aldoacid, partitioned to the aerosol and then underwent acid-catalyzed heterogeneous/multiphase reactions to form two hemiacetals, a cyclic hemiacetal, an ester, and two acetals. SOA formed in the presence of aqueous seed particles appeared to be composed primarily of gem-diol oligomers formed through reactions of unsaturated 1,4-dialdehydes and 1,4-aldoacids with water. Second-generation products of gas-phase OH radical reactions, which should have been a significant fraction of the total products, made at most a minor contribution to SOA. Because unsaturated 1,4-dicarbonyls are major products of the oxidation of aromatic hydrocarbons, the results suggest that although those compounds may form SOA via oligomerization reactions, SOA formation from aromatic hydrocarbons is probably due primarily to other reaction products. © 2013 Elsevier Ltd.


Loope K.J.,Cornell University | Loope K.J.,University of California at Riverside
Current Biology | Year: 2015

Social insect colonies are pinnacles of evolved altruism but also exhibit dramatic conflict among relatives [1, 2]. In many species, a colony's workers compete with the queen and each other over the production of males. Interspecific comparisons demonstrate the importance of within-colony relatedness in determining the outcome of such conflicts [3, 4], but facultative responses to within-colony relatedness are rarely reported [5-7]. Here, I report facultative matricide (worker killing of a colony's queen) in the social wasp Dolichovespula arenaria. Matricide is strongly associated with high worker-worker relatedness, as predicted by theory, because closely related workers value nephews more than brothers [8]. This pattern is the result of variation in both paternity frequency and the paternity skew of colonies with multiple patrilines, implicating worker-worker relatedness rather than a direct effect of multiple mating on queen survival. Furthermore, occasional inbreeding can explain why some multiple-patriline colonies exhibit high paternity skew associated with matricide. In general, these results support the hypothesis that workers can facultatively respond to intracolony relatedness determined by queen mating behavior and demonstrate a novel benefit of polyandry in annual social insects. Facultative matricide shows dramatically how workers are evolutionary actors with interests that can diverge from the queen's, rather than being "extrasomatic projections of her personal genome" [9]. © 2015 Elsevier Ltd. All rights reserved.


Liu Y.,University of California at Riverside | Cheng Q.,University of California at Riverside
Analytical Chemistry | Year: 2012

We report here a surface plasmon resonance (SPR) method for detection of cell membrane binding proteins with high degree signal amplification carried out in an all-aqueous condition. Ultrahigh detection sensitivity was achieved for a membrane-based biosensing interface through the use of functional gold nanoparticles (AuNP) in combination with in situ atom transfer radical polymerization (ATRP) reaction. Fusion of phosphatidylcholine vesicles on a calcinated SPR gold chip established a supported bilayer membrane in which cell receptor monosialoganglioside GM1 was embedded for capture of bacterial cholera toxin (CT). The surface-bound CT was recognized with biotinylated anti-CT, which was linked to the biotin-AuNP through an avidin bridge. The biotin-AuNP surface was functionalized with ATRP initiator that triggers localized growth of poly(hydroxyl-ethyl methacrylate) (PHEMA) brush, contributing to marked SPR signal enhancement and quantitative measurement of CT at very low concentrations. The resulting polymer film has been characterized by optical and atomic force microscopy. A calibration curve for CT detection has been obtained displaying a response range from 6.3 × 10 -16 to 6.3 × 10 -8 M with a detection limit of 160 aM (equivalent to ∼9500 molecules in 100 μL sample solution). Sensitive detection of biomolecules in complex medium has been conducted with CT-spiked serum, and the detection limit can be effectively improved by 6 orders of magnitude compared to direct measurement in serum. The combined AuNP/ATRP method reported here opens new avenues for ultrasensitive detection of proteins on delicate sensor interfaces constructed by lipid membranes or cell membrane mimics. © 2012 American Chemical Society.


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.


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.


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.


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.


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.


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.


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.


Mueller U.G.,University of Texas at Austin | Sachs J.L.,University of California at Riverside
Trends in Microbiology | Year: 2015

Animal and plant microbiomes encompass diverse microbial communities that colonize every accessible host tissue. These microbiomes enhance host functions, contributing to host health and fitness. A novel approach to improve animal and plant fitness is to artificially select upon microbiomes, thus engineering evolved microbiomes with specific effects on host fitness. We call this engineering approach host-mediated microbiome selection, because this method selects upon microbial communities indirectly through the host and leverages host traits that evolved to influence microbiomes. In essence, host phenotypes are used as probes to gauge and manipulate those microbiome functions that impact host fitness. To facilitate research on host-mediated microbiome engineering, we explain and compare the principal methods to impose artificial selection on microbiomes; discuss advantages and potential challenges of each method; offer a skeptical appraisal of each method in light of these potential challenges; and outline experimental strategies to optimize microbiome engineering. Finally, we develop a predictive framework for microbiome engineering that organizes research around principles of artificial selection, quantitative genetics, and microbial community-ecology. © 2015 Elsevier Ltd.


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.


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.


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.


Kovalev A.A.,University of California at Riverside | Pryadko L.P.,University of California at Riverside
Physical Review A - Atomic, Molecular, and Optical Physics | Year: 2013

We introduce an ansatz for quantum codes which gives the hypergraph-product (generalized toric) codes by Tillich and Zémor and generalized bicycle codes by MacKay as limiting cases. The construction allows for both the lower and the upper bounds on the minimum distance; they scale as a square root of the block length. Many thus defined codes have a finite rate and limited-weight stabilizer generators, an analog of classical low-density parity-check (LDPC) codes. Compared to the hypergraph-product codes, hyperbicycle codes generally have a wider range of parameters; in particular, they can have a higher rate while preserving the estimated error threshold. © 2013 American Physical Society.


Kovalev A.A.,University of California at Riverside | Pryadko L.P.,University of California at Riverside
Physical Review A - Atomic, Molecular, and Optical Physics | Year: 2013

We study the fault tolerance of quantum low-density parity check (LDPC) codes, such as generalized toric codes with a finite rate suggested by Tillich and Zémor [in ISIT 2009: IEEE International Symposium on Information Theory (IEEE, New York, 2009)]. We show that any family of quantum LDPC codes where each syndrome measurement involves a limited number of qubits and each qubit is involved in a limited number of measurements (as well as any similarly limited family of classical LDPC codes), in which distance scales as a positive power α of the number of physical qubits (α<1 for "bad" codes), has a finite error probability threshold. We conclude that for sufficiently large quantum computers, quantum LDPC codes can offer an advantage over the toric codes. © 2013 American Physical Society.


Pierce C.J.,University of California at Riverside | Larsen C.H.,University of California at Riverside
Green Chemistry | Year: 2012

A high-yielding three-component reaction proceeds under mild, solvent-free conditions for access to a wide variety of fully-substituted propargylamines. Inexpensive copper(ii) chloride catalyzes the coupling of equimolar amounts of amines, alkynes, and cyclohexanone such that the only by-product is one equivalent of water. © 2012 The Royal Society of Chemistry.


Lucas K.J.,University of California at Riverside | Myles K.M.,Virginia Polytechnic Institute and State University | Raikhel A.S.,University of California at Riverside
Trends in Parasitology | Year: 2013

The discovery of small non-coding RNAs has revolutionized our understanding of regulatory networks governing multiple functions in animals and plants. However, our knowledge of mosquito small RNAs is limited. We discuss here the state of current knowledge regarding the roles of small RNAs and their targets in mosquitoes, and describe the ongoing efforts to understand the role of the RNA interference (RNAi) pathway in mosquito antiviral immunity and transposon silencing. Providing a clear picture into the role of small RNAs in mosquito vectors will pave the way to the utilization of these small molecules in developing novel control approaches that target mosquito immunity and/or reproductive events. Elucidation of the functions of small RNAs represents a new frontier in mosquito biology. © 2013 Elsevier Ltd.


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.


Araci I.E.,Howard Hughes Medical Institute | Brisk P.,University of California at Riverside
Current Opinion in Biotechnology | Year: 2014

In 2002, Thorsen et al. integrated thousands of micromechanical valves on a single microfluidic chip and demonstrated that the control of the fluidic networks can be simplified through multiplexors [. 1]. This enabled realization of highly parallel and automated fluidic processes with substantial sample economy advantage. Moreover, the fabrication of these devices by multilayer soft lithography was easy and reliable hence contributed to the power of the technology; microfluidic large scale integration (mLSI). Since then, mLSI has found use in wide variety of applications in biology and chemistry. In the meantime, efforts to improve the technology have been ongoing. These efforts mostly focus on; novel materials, components, micromechanical valve actuation methods, and chip architectures for mLSI. In this review, these technological advances are discussed and, recent examples of the mLSI applications are summarized. © 2013 Elsevier Ltd.


Qing Q.,University of California at Riverside | Wyman C.E.,University of California at Riverside
Bioresource Technology | Year: 2011

Commercial cellulase complexes produced by cellulolytic fungi contain enzyme activities that are capable of hydrolyzing non-cellulosic polysaccharides in biomass, primarily hemicellulose and pectins, in addition to cellulose. However, xylanase activities detected in most commercial enzyme preparations have been shown to be insufficient to completely hydrolyze xylan, resulting in high xylooligomer concentrations remaining in the hydrolysis broth. Our recent research showed that these xylooligomers are stronger inhibitors of cellulase activity than others have previously established for glucose and cellobiose, making their removal of great importance. In this study, a HPLC system that can measure xylooligomers with degrees of polymerization (DP) up to 30 was applied to assess how Spezyme CP cellulase, Novozyme 188 β-glucosidase, Multifect xylanase, and non-commercial β-xylosidase enzymes hydrolyze different chain length xylooligomers derived from birchwood xylan. Spezyme CP cellulase and Multifect xylanase partially hydrolyzed high DP xylooligomers to lower DP species and monomeric xylose, while β-xylosidase showed the strongest ability to degrade both high and low DP xylooligomers. However, about 10-30% of the higher DP xylooligomers were difficult to be breakdown by cellulase or xylanase and about 5% of low DP xylooligomers (mainly xylobiose) proved resistant to hydrolysis by cellulase or β-glucosidase, possibly due to low β-xylosidase activity in these enzymes and/or the precipitation of high DP xylooligomers. © 2010 Elsevier Ltd.


DeMartini J.D.,University of California at Riverside | Wyman C.E.,University of California at Riverside
Bioresource Technology | Year: 2011

Understanding structural characteristics that are responsible for biomass recalcitrance by identifying why it is more difficult for some plants, or portions of plants, to release their sugars would be extremely valuable in overcoming this barrier. With this in mind, this study investigated the recalcitrance of wood by considering the effects of aging in two Populus tremuloides cross sections. By applying our novel small scale systems, including a multi-well pretreatment and enzymatic hydrolysis system and a downscaled compositional analysis procedure, we were able to follow ring-by-ring compositions and sugar release patterns. Observed variations were then related to structural changes that occur across the radial direction of trees, providing an important step toward understanding the influence of these changes on recalcitrance. © 2010 Elsevier Ltd.


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.


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.


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.


Lee I.,University of California at Riverside | Zaera F.,University of California at Riverside
Journal of Catalysis | Year: 2010

The surface chemistry and catalytic conversion of cis- and trans-2-butenes on platinum (1 0 0) facets were characterized via surface-science and catalytic experiments. Temperature-programed desorption studies on Pt(1 0 0) single crystals pointed to the higher hydrogenation probability of the trans isomer at the expense of a lower extent of C{double bond, long}C double-bond isomerization. To test these trends under catalytic conditions, shape selective catalysts were prepared by dispersing cubic platinum colloidal nanoparticles (which expose only (1 0 0) facets) onto a high-surface-area silica xerogel support. Infrared absorption spectroscopy and transmission electron microscopy were used to determine the conditions needed to remove the organic surfactants without loosing the original narrow size distribution and cubic shape of the original metal nanoparticles. Catalytic kinetic measurements with these materials corroborated the surface-science predictions, and pointed to a switch in isomerization selectivity from preferential cis-to-trans conversion with Pt(1 0 0) surfaces to the reverse trans-to-cis reaction with Pt(1 1 1) facets. © 2009 Elsevier Inc. All rights reserved.


Kinjo R.,University of California at Riverside | Donnadieu B.,University of California at Riverside | Bertrand G.,University of California at Riverside
Angewandte Chemie - International Edition | Year: 2010

Carbenes can do better than metals: Phosphorus mononitride transition-metal complexes have never been isolated, but a PN fragment capped by two bulky, strongly electron-releasing singlet carbenes can be prepared at room temperature (see picture; P red, N blue, C gray). The one-electron oxidation produced the corresponding stable radical cation. (Figure Presented) © 2010 wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.


Russell J.E.,University of California at Riverside | Stouthamer R.,University of California at Riverside
Heredity | Year: 2011

Parthenogenesis-inducing (PI) Wolbachia belong to a class of intracellular symbionts that distort the offspring sex ratio of their hosts toward a female bias. In many PI Wolbachia-infected species sex ratio distortion has reached its ultimate expression-fixation of infection and all-female populations. This is only possible with thelytokous PI symbionts as they provide an alternative form of reproduction and remove the requirement for males and sexual reproduction. Many populations fixed for PI Wolbachia infection have lost the ability to reproduce sexually, even when cured of the infection. We examine one such population in the species Trichogramma pretiosum. Through a series of backcrossing experiments with an uninfected Trichogramma pretiosum population we were able to show that the genetic basis for the loss of female sexual function could be explained by a dominant nuclear effect. Male sexual function had not been completely lost, though some deterioration of male sexual function was also evident when males from the infected population (created through antibiotic curing of infected females) were mated to uninfected females. We discuss the dynamics of sex ratio selection in PI Wolbachia-infected populations and the evolution of non-fertilizing mutations. © 2011 Macmillan Publishers Limited All rights reserved.


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.


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.


Nava M.,University of California at Riverside | Reed C.A.,University of California at Riverside
Organometallics | Year: 2011

The commonly used triethylsilyl perfluoro-tetraphenylborate salt, [Et 3Si+][F20-BPh4-], has been misidentified. As prepared, the cation is a hydride-bridged silane adduct [R3Si-H-SiR3+]. Under favorable circumstances it can be an effective source of the triethylsilylium ion Et3Si +, but in the absence of a stabilizing base the potent electrophilicity of Et3Si+ decomposes the "inert" F20-BPh4- counterion. © 2011 American Chemical Society.


Lindsey J.S.,North Carolina State University | Bocian D.F.,University of California at Riverside
Accounts of Chemical Research | Year: 2011

The inexorable drive to miniaturize information storage and processing devices has fueled the dreams of scientists pursuing molecular electronics: researchers in the field envisage exquisitely tailored molecular materials fulfilling the functions now carried out by semiconductors. A bottom-up assembly of such all-molecular devices would complement, if not supplant, the present top-down lithographic procedures of modern semiconductor fabrication. Short of these grand aspirations, a more near-term objective is to construct hybrid architectures wherein molecules are incorporated in semiconductor-based devices. Such a combined approach exploits the advantages of molecules for selected device functions while retaining the well-developed lithographic approaches for fabrication of the overall chip.In this Account, we survey more than a decade of results from our research programs to employ porphyrin molecules as charge-storage elements in hybrid semiconductor-molecular dynamic random access memory. Porphyrins are attractive for a variety of reasons: they meet the stability criteria for use in real-world applications, they are readily prepared and tailored synthetically, they undergo read-write processes at low potential, and they store charge for extended periods (up to minutes) in the absence of applied potential. Porphyrins typically exhibit two cationic redox states. Molecular architectures with greater than two cationic redox states are achieved by combinations of porphyrins in a variety of structures (for example, dyads, wherein the porphyrins have distinct potentials, triple deckers, and dyads of triple deckers). The incorporation of porphyrins in hybrid architectures has also required diverse tethers (alkyl, alkenyl, alkynyl, aryl, and combinations thereof) and attachment groups (alcohol, thiol, selenol, phosphonate, and hydrocarbon) for linkage to a variety of surfaces (Au, Si, SiO2, TiN, Ge, and so forth).The porphyrins as monolayers exhibit high charge density and are robust to high-temperature excursions (400 °C for 30 min) under inert atmosphere conditions. Even higher charge densities, which are invaluable for device applications, were achieved by in situ formation of porphyrin polymers or by stepwise growth of porphyrin-imide oligomers. The various molecular architectures have been investigated by diverse surface characterization methods, including ellipsometry, atomic force microscopy, FTIR spectroscopy, and X-ray photoelectron spectroscopy, as well as a variety of electrochemical methods. These studies have further revealed that the porphyrin layers are robust under conditions of deposition of a top metal contact.The results to date indicate the superior features of selected molecular architectures for molecular electronics applications. The near-term utilization of such materials depends on further work for appropriate integration in semiconductor-based devices, whereas ultimate adoption may depend on advances that remain far afield, such as the development of fully bottom-up assembly processes. © 2011 American Chemical Society.


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.


Lin T.,University of California at Riverside | Tang C.,University of California at Riverside | Alyahayaei H.M.,University of California at Riverside | Shi J.,University of California at Riverside
Physical Review Letters | Year: 2014

In bilayers consisting of Pd and yttrium iron garnet (Y3Fe5O12 or YIG), we observe vanishingly small room-temperature conventional anisotropic magnetoresistance but large new magnetoresistance that is similar to the spin Hall magnetoresistance previously reported in Pt-YIG bilayers. We report a temperature dependence study of the two magnetoresistance effects in Pt-YIG bilayers. As the temperature is decreased, the new magnetoresistance shows a peak, whereas the anisotropic magnetoresistance effect starts to appear and increases monotonically. We find that the magnetoresistance peak shifts to lower temperatures in thicker Pd samples, a feature characteristic of the spin current effect. The distinct temperature dependence reveals fundamentally different mechanisms responsible for the two effects in such hybrid structures. © 2014 American Physical Society.


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.


Lin J.-L.,University of California at Riverside | Palomec L.,University of California at Riverside | Wheeldon I.,University of California at Riverside
ACS Catalysis | Year: 2014

New developments in nucleic acid nanotechnology and protein scaffold designs have enabled unparalleled control over the spatial organization of synthetic multienzyme cascade reactions. One of the goals of these new technologies is to create nanostructured enzyme cascade reactions that promote substrate channeling along the cascade and, in doing so, enhance cascade catalysis. The concept of substrate channeling has a long and rich history in biochemistry and has established methods of evaluation and quantification. In this Perspective, we review the most common of these methods and discuss them in the context of engineered multienzyme systems and natural bifunctional enzymes with known mechanisms of substrate channeling. In addition, we use experimental data and the results of simulations of coupled-enzyme reactions to develop a set of preliminary design rules for engineering multienzyme nanostructures. The design rules address the limitations on interenzyme distance and active site orientation in substrate channeling and suggest designs for promoting enhanced catalysis, specifically, that enzyme orientation should minimize interenzyme distance and that at distances greater than 1 nm between active sites, significant channeling occurs only if diffusion of the intermediate is bounded through interactions with the surface or scaffold between active sites. This field is rapidly developing and promises to create many more new and exciting technologies. © 2013 American Chemical 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.


De A.,University of California at Riverside | Pryadko L.P.,University of California at Riverside
Physical Review Letters | Year: 2013

We construct a universal set of high fidelity quantum gates to be used on a sparse bipartite lattice with always-on Ising couplings. The gates are based on dynamical decoupling sequences using shaped pulses, they protect against low-frequency phase noise, and can be run in parallel on non-neighboring qubits. This makes them suitable for implementing quantum error correction with low-density parity check codes like the surface codes and their finite-rate generalizations. We illustrate the construction by simulating the quantum Zeno effect with the [[4, 2, 2]] toric code on a spin chain. © 2013 American Physical Society.


Hamilton K.E.,University of California at Riverside | Pryadko L.P.,University of California at Riverside
Physical Review Letters | Year: 2014

We construct a tight lower bound for the site percolation threshold on an infinite graph, which becomes exact for an infinite tree. The bound is given by the inverse of the maximal eigenvalue of the Hashimoto matrix used to count nonbacktracking walks on the original graph. Our bound always exceeds the inverse spectral radius of the graph's adjacency matrix, and it is also generally tighter than the existing bound in terms of the maximum degree. We give a constructive proof for existence of such an eigenvalue in the case of a connected infinite quasitransitive graph, a graph-theoretic analog of a translationally invariant system. © 2014 American Physical Society.


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.


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.


Stoyanov E.S.,University of California at Riverside | Stoyanova I.V.,University of California at Riverside | Reed C.A.,University of California at Riverside
Chemical Science | Year: 2011

The H+(aq) ion in ionized strong aqueous acids is an unexpectedly unique H13O6 + entity, unlike those in gas phase H+(H2O)n clusters or typical crystalline acid hydrates. IR spectroscopy indicates that the core structure has neither C3v H3O+ Eigen-like nor typical H5O2 + Zundel-like character. Rather, extensive delocalization of the positive charge leads to a H13O6 + ion having an unexpectedly long central O O separation of ~2.57 A ° and four conjugated O O separations of ~2.7 Å. These dimensions are in conflict with the shorter O/O separations found in structures calculated by theory. Ultrafast dynamic properties of the five H atoms involved in these H-bonds lead to a substantial collapse of normal IR vibrations and the appearance of a continuous broad absorption (cba) across the entire IR spectrum. This cba is distinguishable from the broad IR bands associated with typical low-barrier H-bonds. The solvation shell outside of the H13O6 + ion defines the boundary of positive charge delocalization. At low acid concentrations, the H13O6+ ion is a constituent part of an ion pair that has contact with the first hydration shell of the conjugate base anion. At higher concentrations, or with weaker acids, one or two H2O molecules of H13O6 + cation are shared with the hydration shell of the anion. Even the strongest acids show evidence of ion pairing. © The Royal Society of Chemistry 2011.


Martin D.,University of California at Riverside | Soleilhavoup M.,University of California at Riverside | Bertrand G.,University of California at Riverside
Chemical Science | Year: 2011

This perspective summarizes recent results, which demonstrate that stable carbenes can activate small molecules (CO, H2, NH3 and P4) and stabilize highly reactive intermediates (main group elements in the zero oxidation state and paramagnetic species). These two tasks were previously exclusive for transitionmetal complexes. © The Royal Society of Chemistry 2011.


Guerra N.G.,University of California at Riverside | Williams K.R.,University of California at Riverside | Sadek S.,University of California at Riverside
Child Development | Year: 2011

In the present study, quantitative and qualitative data are presented to examine individual and contextual predictors of bullying and victimization and how they vary by age and gender. Two waves of survey data were collected from 2,678 elementary, middle, and high school youth attending 59 schools. In addition, 14 focus groups were conducted with 115 youth who did not participate in the survey. Changes in both bullying and victimization were predicted across gender and age by low self-esteem and negative school climate, with normative beliefs supporting bullying predicting increases in bullying only. Focus group comments provided insights into the dynamics of bullying, highlighting its connection to emergent sexuality and social identity during adolescence. Findings are discussed in terms of their implications for preventive antibullying interventions in schools. © 2011 The Authors. Child Development © 2011 Society for Research in Child Development, Inc..


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.


The relationship between vertebrate morphology and swimming performance has long interested biologists. Recent work on predator-induced morphological plasticity of anuran tadpoles has increased this interest. Here, I use data on five species of spadefoot toad tadpoles (Scaphiopodidae) to compare linear and geometric morphometrics. Linear measures explain only 7-26% of the variation in swimming speed, depending on species, whereas geometric morphometrics could explain 24-46% of the same variation. I also compare two methods for examining how similar the morphology-swimming speed relationship is among species. A canonical variate derived from a MANCOVA approach successfully detected species differences in these relationships, whether using linear or geometric methods, but a canonical correlation approach failed in both cases. Overall, tadpoles with smaller bodies, larger tails, and larger tail muscles are faster swimmers but the details of how these shape changes are achieved differed among species. For example, in some species a smaller body was achieved primarily by reducing abdomen size, whereas in others both the head and abdomen are smaller. Faster swimmers also had deeper tails, especially in the posterior half of the tail. This pattern would have been missed in standard linear morphometrics which usually only measures maximum tail depth. © 2010 Wiley-Liss, Inc.


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.


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.


Kale M.J.,University of California at Riverside | Avanesian T.,University of California at Riverside | Christopher P.,University of California at Riverside
ACS Catalysis | Year: 2014

Recent reports have shown that plasmonic nanostructures can be used to drive direct photocatalysis with visible photons, where nanostructures act as the light absorber and the catalytic active site. These reports have showcased direct plasmon driven photocatalysis as a route to concentrate and channel the energy of low intensity visible light into adsorbed molecules, enhancing the rates of chemical transformations, and offering pathways to control reaction selectivity. In this perspective, we will discuss the fundamental photophysics of localized surface plasmon resonance (LSPR) excitation in the context of driving chemical transformations. The various demonstrated chemical conversions executed using direct plasmonic photocatalysis will be reviewed. Experimental observations, such as the dependence of photocatalytic rate on illumination intensity and photon energy, will be related to microscopic mechanisms of photocatalysis. In addition, theoretical treatments of various mechanisms within the process of direct plasmonic photocatalysis will be discussed and related to experimental studies. Throughout the Perspective, the possibility of activating targeted adsorbate bonds to allow rational manipulation of reaction selectivity in direct plasmonic photocatalysis will be discussed. © 2013 American Chemical Society.


Hille R.,University of California at Riverside | Hall J.,University of California at Riverside | Basu P.,Duquesne University
Chemical Reviews | Year: 2014

A study is conducted to discuss the mononuclear molybdenum enzymes. Enzymes containing molybdenum in their active sites have been recognized with more than 50 molybdenum-containing enzymes being purified and biochemically characterized. It is well-established that all molybdenum-containing enzymes other than nitrogenase fall into three large and mutually exclusive families, as exemplified by the enzymes xanthine oxidase, sulfite oxidase, and DMSO reductase. The structures of the three canonical molybdenum centers in their oxidized Mo(VI) states are examined along with that for the pyranopterin cofactor. The active sites of members of the xanthine oxidase family ALSO have an LMoVIOS-(OH) structure with a square-pyramidal coordination geometry.


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.


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.


Roy S.G.,University of California at Riverside | Raikhel A.S.,University of California at Riverside
FASEB Journal | Year: 2012

Mosquitoes require blood for egg development, and, as a consequence, they transmit pathogens of devastating diseases. Target of rapamycin (TOR) signaling is a key pathway linking blood feeding and egg development in the mosquito Aedes aegypti. We show that the regulation of the TOR effector translational repressor 4E-BP is finely tuned to the nutritional requirements of the female mosquito, and it occurs at transcriptional and post-translational levels. Immediately after blood feeding, 4E-BP became hyperphosphorylated, suggesting rapid inhibition of its translational repression function. 4E-BP was highly phosphorylated after in vitro incubation of the fat body in the presence of amino acids; this phosphorylation was rapamycin insensitive, in contrast to another TOR target, S6K, phosphorylation of which was rapamycin sensitive. A high level of 4E-BP phosphorylation was also elicited by insulin. Rapamycin and the PI3K inhibitor LY294002 blocked insulin-mediated 4E-BP phosphorylation. RNA-interference depletion of the insulin receptor or Akt resulted in severe reduction of 4E-BP phosphorylation. Phosphorylation and stability of 4E-BP was dependent on its partner eIF4E translation initiation factor. Silencing of 4E-BP resulted in reduction of the life span of adult female mosquitoes. This study demonstrates a dual nutritional and hormonal control of 4E-BP and its role in mosquito egg development. © FASEB.


Maduro M.F.,University of California at Riverside
Molecular Reproduction and Development | Year: 2015

Developmental robustness is the ability of an embryo to develop normally despite many sources of variation, from differences in the environment to stochastic cell-to-cell differences in gene expression. The nematode Caenorhabditis elegans exhibits an additional level of robustness: Unlike most other animals, the embryonic pattern of cell divisions is nearly identical from animal to animal. The endoderm (gut) lineage is an ideal model for studying such robustness as the juvenile gut has a simple anatomy, consisting of 20 cells that are derived from a single cell, E, and the gene regulatory network that controls E specification shares features with developmental regulatory networks in many other systems, including genetic redundancy, parallel pathways, and feed-forward loops. Early studies were initially concerned with identifying the genes in the network, whereas recent work has focused on understanding how the endoderm produces a robust developmental output in the face of many sources of variation. Genetic control exists at three levels of endoderm development: Progenitor specification, cell divisions within the developing gut, and maintenance of gut differentiation. Recent findings show that specification genes regulate all three of these aspects of gut development, and that mutant embryos can experience a "partial" specification state in which some, but not all, E descendants adopt a gut fate. Ongoing studies using newer quantitative and genome-wide methods promise further insights into how developmental gene-regulatory networks buffer variation. © 2015 Wiley Periodicals, Inc.


Ge J.,University of California at Riverside | Ge J.,Tongji University | Yin Y.,University of California at Riverside
Angewandte Chemie - International Edition | Year: 2011

This Review summarizes recent developments in the field of responsive photonic crystal structures, including principles for design and fabrication and many strategies for applications, for example as optical switches or chemical and biological sensors. A number of fabrication methods are now available to realize responsive photonic structures, the majority of which rely on self-assembly processes to achieve ordering. Compared with microfabrication techniques, self-assembly approaches have lower processing costs and higher production efficiency, however, major efforts are still needed to further develop such approaches. In fact, some emerging techniques such as spin coating, magnetic assembly, and flow-induced self-assembly have already shown great promise in overcoming current challenges. When designing new systems with improved performance, it is always helpful to bear in mind the lessons learnt from natural photonic structures. © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Wang M.,University of California at Riverside | He L.,University of California at Riverside | Zorba S.,Whittier College | Yin Y.,University of California at Riverside
Nano Letters | Year: 2014

Ferrimagnetic inorganic nanorods have been used as building blocks to construct liquid crystals with optical properties that can be instantly and reversibly controlled by manipulating the nanorod orientation using considerably weak external magnetic fields (1 mT). Under an alternating magnetic field, they exhibit an optical switching frequency above 100 Hz, which is comparable to the performance of commercial liquid crystals based on electrical switching. By combining magnetic alignment and lithography processes, it is also possible to create patterns of different polarizations in a thin composite film and control over the transmittance of light in particular areas. Developing such magnetically responsive liquid crystals opens the door toward various applications, which may benefit from the instantaneous and contactless nature of magnetic manipulation. © 2014 American Chemical Society.


You C.,University of California at Riverside | Wang Y.,University of California at Riverside
Nature Protocols | Year: 2015

Aberrant transcription induced by DNA damage may confer risk for the development of cancer and other human diseases. Traditional methods for measuring lesion-induced transcriptional alterations often involve extensive colony screening and DNA sequencing procedures. Here we describe a protocol for the quantitative assessment of the effects of DNA lesions on the efficiency and fidelity of transcription in vitro and in mammalian cells. The method is also amenable to investigating the influence of specific DNA repair proteins on the biological response toward DNA damage during transcription by manipulating their gene expression. Specifically, we present detailed, step-by-step procedures, including DNA template preparation, in vitro and in vivo transcription, RNA purification, reverse-transcription PCR (RT-PCR) and restriction digestion of RT-PCR products. Analyses of restriction fragments of interest are performed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) and polyacrylamide gel electrophoresis (PAGE). The entire procedure described in this protocol can be completed in 15-20 d. © 2015 Nature America, Inc. All rights reserved.


Trtchounian A.,University of California at Riverside
Nicotine & tobacco research : official journal of the Society for Research on Nicotine and Tobacco | Year: 2010

Electronic cigarettes or e-cigarettes are marketed as tobacco-free nicotine delivery devices that have received little laboratory evaluation. In this study, the smoking properties of conventional and e-cigarettes were compared by examining the vacuum required to produce smoke (conventional cigarettes) or aerosol (e-cigarettes) and the density of the smoke/aerosol over time. Vacuum was measured using a manometer coupled to a smoking machine. The density of aerosol or smoke was measured spectrophotometrically. E-cigarettes were subjected to smoke-out experiments in which vacuum and aerosol density were measured until each cartridge was exhausted. The vacuum required to smoke conventional cigarettes varied among the eight brands tested. Lights and ultra-light brands required stronger vacuums to smoke than unfiltered and regular filtered brands. Except for one brand, higher vacuums were required to smoke e-cigarettes than conventional brands. Smoke/aerosol density was stable for conventional brands and for e-cigarettes over the first 10 puffs; however, aerosol density of e-cigarettes dropped during subsequent smoking, and higher vacuums were required to produce aerosol as the puff number increased. While conventional cigarettes were uniform in their smoking behavior within brands, vacuum and density varied within brands of e-cigarettes. Generally, e-cigarettes required stronger vacuums (suction) to smoke than conventional brands, and the effects of this on human health could be adverse. The amount of aerosol produced by e-cigarettes decreased during smoking, which necessitated increasing puff strength to produce aerosol. The decreased efficiency of aerosol production during e-cigarette smoking makes dosing nonuniform over time and calls into question their usefulness as nicotine delivery devices.


Shi J.-H.,University of California at Riverside | Yang Z.-B.,University of California at Riverside
Molecular Plant | Year: 2011

AUXIN BINDING PROTEIN 1 (ABP1) has long been proposed as an auxin receptor to regulate cell expansion. The embryo lethality of ABP1-null mutants demonstrates its fundamental role in plant development, but also hinders investigation of its involvement in post-embryonic processes and its mode of action. By taking advantage of weak alleles and inducible systems, several recent studies have revealed a role for ABP1 in organ development, cell polarization, and shape formation. In addition to its role in the regulation of auxin-induced gene expression, ABP1 has now been shown to modulate non-transcriptional auxin responses. ABP1 is required for activating two antagonizing ROP GTPase signaling pathways involved in cytoskeletal reorganization and cell shape formation, and participates in the regulation of clathrin-mediated endocytosis to subsequently affect PIN protein distribution. These exciting discoveries provide indisputable evidence for the auxin-induced signaling pathways that are downstream of ABP1 function, and suggest intriguing mechanisms for ABP1-mediated polar cell expansion and spatial coordination in response to auxin. © 2011 The Author.


Emotion regulation predicts positive academic outcomes like learning, but little is known about why. Effective emotion regulation likely promotes learning by broadening the scope of what may be attended to after an emotional event. One hundred twenty-six 6- to 13-year-olds' (54% boys) regulation of sadness was examined for changes in emotional experience, information processing, and memory for subsequent neutral information. Instructions to use specific strategies (distancing, positive reappraisal, rumination, or no strategy) predicted changes in sadness and happiness but did not predict information processing or memory. Effective regulation of sadness (regardless of instructions) predicted better memory through the indirect effect of broadened information processing but only for older children. Implications for emotion regulation processes in childhood are discussed. © 2016 The Author. Child Development © 2016 Society for Research in Child Development, Inc.


Allen R.J.,University of California at Riverside | Norris J.R.,University of California at San Diego | Kovilakam M.,University of California at Riverside
Nature Geoscience | Year: 2014

The tropical belt has widened by several degrees latitude since 1979, as evidenced by shifts in atmospheric circulation and climate zones. Global climate models also simulate tropical belt widening, but less so than observed. Reasons for this discrepancy and the mechanisms driving the expansion are uncertain. Here we analyse multidecadal variability in tropical belt width since 1950 using the Coupled Model Intercomparison Project Phase 5 climate model runs and find that simulated rates of tropical expansion over the past 30 years -particularly in the Northern Hemisphere -are in better agreement with observations than previous models. We find that models driven by observed sea surface temperatures over this interval yield the largest rate of tropical expansion. We link the tropical expansion in the Northern Hemisphere to the leading pattern of sea surface temperature variability in the North Pacific, the Pacific Decadal Oscillation. We also find, both from models and observations, that the tropical belt contracted in the Northern Hemisphere from 1950 to 1979, coincident with the reversal of the Pacific Decadal Oscillation trend. In both time periods, anthropogenic aerosols act to modify the Pacific Decadal Oscillation and therefore contribute to the width of the tropical belt. We conclude that tropical expansion and contraction are influenced by multidecadal sea surface temperature variability associated with both the Pacific Decadal Oscillation and anthropogenic aerosols. © 2014 Macmillan Publishers Limited. All rights reserved.


Hicks G.R.,University of California at Riverside | Raikhel N.V.,University of California at Riverside
Annual Review of Plant Biology | Year: 2012

Since the introduction of chemical genomics to plant biology as a tool for basic research, the field has advanced significantly. There are now examples of important basic discoveries that demonstrate the power and untapped potential of this approach. Given the combination of protein and small-molecule complexity, new phenotypes can be described through the perturbation of cellular functions that can be linked to growth and developmental phenotypes. There are now clear examples of overcoming functional redundancy in plants to dissect molecular mechanisms or critical pathways such as hormone signaling and dynamic intracellular processes. Owing to ongoing advances, including more sophisticated high-content screening and rapid approaches for target identification, the field is beginning to move forward. However, there are also challenges to improve automation, imaging, and analysis and provide chemical biology resources to the broader plant biology community. © 2012 by Annual Reviews. All rights reserved.


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.


Perales M.,University of California at Riverside | Reddy G.V.,University of California at Riverside
Current Opinion in Plant Biology | Year: 2012

Stem cell homeostasis in shoot apical meristems of higher plants is regulated through a dynamic balance between spatial regulation of gene expression, cell growth patterns and patterns of differentiation. Cell-cell communication mediated by both the local factors and long-range signals have been implicated in stem cell homeostasis. Here we have reviewed recent developments on spatio-temporal regulation of cell-cell communication processes with an emphasis on how ubiquitously utilized signals such as plant hormones function with local factors in mediating stem cell homeostasis. We also provide a brief overview of how the activity of ubiquitously utilized epigenetic regulators are modulated locally to orchestrate gene expression. © 2011 Elsevier Ltd.


Cassidy D.B.,University of California at Riverside | Mills A.P.,University of California at Riverside
Physical Review Letters | Year: 2011

Slow positrons implanted into a porous silica film may efficiently form positronium (Ps) atoms that diffuse through a network of interconnected pores. At high Ps densities, the long lifetime of ortho-positronium atoms is reduced due to Ps-Ps spin dependent interactions at a rate that implies an effective free-space scattering cross section, σe=(3.4±0.5) ×10-14cm-2, at least 25 times larger than the theoretical value. This enhanced interaction rate may be explained if the quantum confinement of Ps results in interpore tunneling rates that depend critically on the distribution of pore sizes, so that rather than uniformly sampling the porous matrix Ps diffusion is limited to a small subset of the pores. © 2011 American Physical Society.


Prokuda A.Y.,University of California at Riverside | Roff D.A.,University of California at Riverside
Journal of Evolutionary Biology | Year: 2014

The maintenance of variation in sexually selected traits is a puzzle that has received increasing attention in the past several decades. Traits that are related to fitness, such as life-history or sexually selected traits, are expected to have low additive genetic variance (and hence, heritability) due to the rapid fixation of advantageous alleles. However, previous analyses have suggested that the heritabilities of sexually selected traits are on average higher than nonsexually selected traits. We show that the heritabilities of sexually selected traits are not significantly different from those of nonsexually selected traits overall or when separated into the three trait categories: behavioural, morphological and physiological. In contrast with previous findings, the heritability of preference is quite low (h2 = 0.25 ± 0.06) and is in the same range as life-history traits. We distinguish preferred traits as a category of sexually selected traits and find that the heritability of the former is not significantly different than sexually selected traits overall (0.48 ± 0.04 vs. 0.46 ± 0.03). We test the hypothesis that the heritability of sexually selected traits is negatively correlated with the strength of sexual selection. As predicted, there is a significant negative correlation between the heritabilities of sexually selected traits and the strength of selection. This suggests that heritabilities do indeed decrease as sexual selection increases but sexual selection is not strong enough to cause heritabilities of sexually selected traits to deviate from the same type of nonsexually selected traits. © 2014 European Society For Evolutionary Biology.


Hille R.,University of California at Riverside | Nishino T.,University of California at Riverside | Nishino T.,Nippon Medical School | Bittner F.,TU Braunschweig
Coordination Chemistry Reviews | Year: 2011

Recent progress in our understanding of the structural and catalytic properties of molybdenum-containing enzymes in eukaryotes is reviewed, along with aspects of the biosynthesis of the cofactor and its insertion into apoprotein. © 2010 Elsevier B.V.


Chae K.,University of California at Riverside | Lord E.M.,University of California at Riverside
Annals of Botany | Year: 2011

Background Pollination is a crucial step in angiosperm (flowering plant) reproduction. Highly orchestrated pollenpistil interactions and signalling events enable plant species to avoid inbreeding and outcrossing as a species-specific barrier. In compatible pollination, pollen tubes carrying two sperm cells grow through the pistil transmitting tract and are precisely guided to the ovules, discharging the sperm cells to the embryo sac for fertilization. ScopeIn Lilium longiflorum pollination, growing pollen tubes utilize two critical mechanisms, adhesion and chemotropism, for directional growth to the ovules. Among several molecular factors discovered in the past decade, two small, secreted cysteine-rich proteins have been shown to play major roles in pollen tube adhesion and reorientation bioassays: stigma/style cysteine-rich adhesin (SCA, approx. 9·3 kDa) and chemocyanin (approx. 9·8 kDa). SCA, a lipid transfer protein (LTP) secreted from the stylar transmitting tract epidermis, functions in lily pollen tube tip growth as well as in forming the adhesive pectin matrix at the growing pollen tube wall back from the tip. Lily chemocyanin is a plantacyanin family member and acts as a directional cue for reorienting pollen tubes. Recent consecutive studies revealed that Arabidopsis thaliana homologues for SCA and chemocyanin play pivotal roles in tip polarity and directionality of pollen tube growth, respectively. This review outlines the biological roles of various secreted proteins in angiosperm pollination, focusing on plant LTPs and chemocyanin. © The Author 2011. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved.


Hilario E.,University of California at Riverside | Li Y.,University of California at Riverside | Nobumori Y.,University of California at Riverside | Liu X.,University of California at Riverside | Fan L.,University of California at Riverside
Acta Crystallographica Section D: Biological Crystallography | Year: 2013

XPB is a DNA-dependent helicase and a subunit of the TFIIH complex required for both transcription and DNA repair. XPB contains four domains: an N-terminal domain, two conserved helicase domains (HD1 and HD2) and a C-terminal extension. The C-terminal extension is important for DNA repair since the phosphorylation of Ser751 inhibits 5′-incision by ERCC1-XPF endonuclease. A disease-causing frameshift mutation (XP11BE) that changes the last 42 amino acids of XPB causes manifestations including impaired DNA repair and deficient transcription. Here, the crystal structure of the C-terminal half of XPB (residues 494-782) is reported at 1.8Å resolution. The structure contained the conserved XPB HD2 and a C-terminal extension which shares structural similarity with RIG-I, leading to a structural model of the XPF-XPB-DNA complex for 5′ incision during DNA repair. A mutation mimicking the XP11BE mutation produced the much less soluble mutant XPBm(494-781). Western blotting results confirmed that the intracellular levels of XPB and other TFIIH subunits in XP11BE patient cells were much lower than those from the healthy parents. Together, these results indicate that the XP11BE mutation not only divests the XPF-interaction motif, impairing DNA repair, but also reduces XPB solubility, leading to a lower intracellular level of TFIIH and deficient transcription.


Ding D.,Xi'an University of Science and Technology | Liu K.,Xi'an University of Science and Technology | He S.,Xi'an University of Science and Technology | Gao C.,Xi'an 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.


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.


Han X.,University of California at Riverside | Liu Y.,University of California at Riverside | Yin Y.,University of California at Riverside
Nano Letters | Year: 2014

We report the development of a stress-responsive colorimetric film that can memorize the stress it has experienced. The system is designed by taking advantage of the plasmonic shift associated with the disassembly of one-dimensional gold nanoparticle chains driven by the plastic deformation of the surrounding polymer matrix. By modifying the plasticity of the polymer, we demonstrate that the plasmonic shift and colorimetric change respond to a large range of stresses. This novel pressure indicating film can be used to capture and record the pressure distribution and magnitude between two contacting or impacting surfaces by outputting color information. © 2014 American Chemical Society.


Zhang H.,University of California at Riverside | Zhu J.-K.,University of California at Riverside
Current Opinion in Plant Biology | Year: 2011

DNA methylation is an important epigenetic mechanism for silencing transposons and other repetitive elements, and for stable repression of specific transgenes and endogenous genes. Plants can utilize small interfering RNAs (siRNAs) to guide de novo DNA methyltransferases for the establishment of sequence-specific DNA methylation. Genetic and biochemical approaches have identified many components involved in RNA-directed DNA methylation (RdDM). These components function in one or more of the following three aspects: biogenesis of siRNAs, production of scaffold RNAs, and the assembly of an effector complex that involves the complementary pairing between the guide siRNAs and nascent scaffold RNAs and that recruits the DNA methyltransferases. Recent studies not only unveiled new molecular players and novel interactions, but also suggested spatial and temporal segregation of the RdDM process within the nucleus. © 2011 Elsevier Ltd.


Zheng B.,University of California at Riverside | Chen X.,University of California at Riverside
Current Opinion in Plant Biology | Year: 2011

The development of multicellular organisms is governed partly by temporally and spatially controlled gene expression. DNA methylation, covalent modifications of histones, and the use of histone variants are the major epigenetic mechanisms governing gene expression in plant development. In this review, we zoom in onto histone H3 lysine 27 trimethylation (H3K27me3), a repressive mark that plays a crucial role in the dynamic regulation of gene expression in plant development, to discuss recent advances as well as outstanding questions in the deposition, recognition, and removal of the mark and the impacts of these molecular processes on plant development. © 2011 Elsevier Ltd.


Chen X.,University of California at Riverside | Chen X.,Howard Hughes Medical Institute
Current Opinion in Genetics and Development | Year: 2012

microRNAs (miRNAs) and small interfering RNAs (siRNAs), which constitute two major classes of endogenous small RNAs in plants, impact a multitude of developmental and physiological processes by imparting sequence specificity to gene and genome regulation. Although lacking the third major class of small RNAs found in animals, Piwi-interacting RNAs (piRNAs), plants have expanded their repertoire of endogenous siRNAs, some of which fulfill similar molecular and developmental functions as piRNAs in animals. Research on plant miRNAs and siRNAs has contributed invaluable insights into small RNA biology, thanks to the highly conserved molecular logic behind the biogenesis and actions of small RNAs. Here, I review progress in the plant small RNA field in the past two years, with an emphasis on recent findings related to plant development. I do not recount the numerous developmental processes regulated by small RNAs; instead, I focus on major principles that have been derived from recent studies and draw parallels, when applicable, between plants and animals. © 2012 Elsevier Ltd.


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
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.


Begum N.,University of California at Riverside | Keogh E.,University of California at Riverside
Proceedings of the VLDB Endowment | Year: 2014

The detection of time series motifs, which are approximately repeated subsequences in time series streams, has been shown to have great utility as a subroutine in many higher-level data mining algorithms. However, this detection becomes much harder in cases where the motifs of interest are vanishingly rare or when faced with a never-ending stream of data. In this work we investigate algorithms to find such rare motifs. We demonstrate that under reasonable assumptions we must abandon any hope of an exact solution to the motif problem as it is normally defined; however, we introduce algorithms that allow us to solve the underlying problem with high probability. © 2014 VLDB Endowment 2150-8097/14/10.


Henry H.L.,University of California at Riverside
Best Practice and Research: Clinical Endocrinology and Metabolism | Year: 2011

Fundamental to understanding the way in which perturbations in the vitamin D endocrine system can affect human health is an appreciation of the steps involved in the production of the well-recognized active hormonal form, 1,25-dihydroxyvitamin D 3. Thus this paper focuses first on the nature and regulation of the two enzymes responsible for the production of 1,25-dihydroxyvitamin D 3, the 25-hydroxylase in the liver and the 1α-hydroxylase in the kidney. The most important regulators of the 1α-hydroxylase in the kidney are 1,25-dihydroxyvitamin D 3 itself, parathyroid hormone and FGF23. The extent and importance of extra-renal, 1,25-dihydroxyvitamin D 3 synthesis is then considered. Finally the features of the 24R-hydroxylase, which produces 24R,25-dihydroxyvitamin D 3inthe kidney and is induced by and inactivated, 1,25- dihydroxyvitamin D 3in target cells are described. © 2010 Elsevier Masson SAS. All rights reserved.


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.


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.


Kain P.,University of California at Riverside | Boyle S.M.,University of California at Riverside | Tharadra S.K.,University of California at Riverside | Guda T.,University of California at Riverside | And 3 more authors.
Nature | Year: 2013

There are major impediments to finding improved DEET alternatives because the receptors causing olfactory repellency are unknown, and new chemicals require exorbitant costs to determine safety for human use. Here we identify DEET-sensitive neurons in a pit-like structure in the Drosophila melanogaster antenna called the sacculus. They express a highly conserved receptor, Ir40a, and flies in which these neurons are silenced or Ir40a is knocked down lose avoidance to DEET. We used a computational structure-activity screen of >400,000 compounds that identified >100 natural compounds as candidate repellents. We tested several and found that most activate Ir40a+ neurons and are repellents for Drosophila. These compounds are also strong repellents for mosquitoes. The candidates contain chemicals that do not dissolve plastic, are affordable and smell mildly like grapes, with three considered safe in human foods. Our findings pave the way to discover new generations of repellents that will help fight deadly insect-borne diseases worldwide. © 2013 Macmillan Publishers Limited. All rights reserved.


Messaoudi I.,University of California at Riverside | Basler C.F.,Mount Sinai School of Medicine
Current Opinion in Immunology | Year: 2015

Several enveloped RNA viruses of the arenavirus, bunyavirus, filovirus and flavivirus families are associated with a syndrome known as viral hemorrhagic fever (VHF). VHF is characterized by fever, vascular leakage, coagulation defects and multi organ system failure. VHF is currently viewed as a disease precipitated by viral suppression of innate immunity, which promotes systemic virus replication and excessive proinflammatory cytokine responses that trigger the manifestations of severe disease. However, the mechanisms by which immune dysregulation contributes to disease remain poorly understood. Infection of nonhuman primates closely recapitulates human VHF, notably Ebola and yellow fever, thereby providing excellent models to better define the immunological basis for this syndrome. Here we review the current state of our knowledge and suggest future directions that will better define the immunological mechanisms underlying VHF. © 2015 Elsevier Ltd.


Craddock C.,University of California at Riverside | Lavagi I.,University of California at Riverside | Yang Z.,University of California at Riverside
Trends in Cell Biology | Year: 2012

In animal and plant cells, a wide range of key cellular processes that require the establishment of cell polarity are governed by Rho-GTPases. In contrast to animals and yeast, however, plants possess a single Rho-GTPase subfamily called Rho-like GTPases from plants (ROPs). This raises the question of how plants achieve the high level of regulation required for polar cellular processes. It is becoming evident that plants have evolved specific regulators, including ROP-Guanine Exchange Factors (GEFs) and the Rop-interactive CRIB motif-containing protein (RIC) effectors. Recent research shows that the spatiotemporal dynamics of ROPs, the cytoskeleton, endocytosis, and exocytosis are intertwined. This review focuses on the proposed self-organizing nature of ROPs in plants and how ROP-mediated cellular mechanisms compare with those responsible for cell polarity in animals and yeast. © 2012 Elsevier Ltd.


Chen Z.-J.,University of California at Riverside | Ai H.-W.,University of California at Riverside
Biochemistry | Year: 2014

The discovery of hydrogen sulfide (H2S) as a novel gasotransmitter for cell signaling and other pathophysiological processes has spurred tremendous interest in developing analytical methods for its detection in biological systems. Herein, we report the development of a highly responsive and selective genetically encoded H2S probe, hsGFP, for the detection of H2S both in vitro and in living mammalian cells. hsGFP bestows a combination of favorable properties, including large fluorescence responses, high efficiency in folding and chromophore formation, and excellent sensitivity and selectivity toward H2S. As a genetically encoded probe, hsGFP can be readily and precisely localized to subcellular domains such as mitochondria, cell nuclei, and ion channels. hsGFP was further utilized to image H2S enzymatically produced from l-cysteine in human embryonic kidney (HEK) 293T cells. (Chemical Equation Presented). © 2014 American Chemical Society.


Canalizo G.,University of California at Riverside | Stockton A.,University of Hawaii at Manoa
Astrophysical Journal | Year: 2013

Although mergers and starbursts are often invoked in the discussion of quasi-stellar object (QSO) activity in the context of galaxy evolution, several studies have questioned their importance or even their presence in QSO host galaxies. Accordingly, we are conducting a study of z ∼ 0.2 QSO host galaxies previously classified as passively evolving elliptical galaxies. We present deep Keck/LRIS spectroscopy of a sample of 15 hosts and model their stellar absorption spectra using stellar synthesis models. The high signal-to-noise ratio of our spectra allows us to break various degeneracies that arise from different combinations of models, varying metallicities, and contamination from QSO light. We find that none of the host spectra can be modeled by purely old stellar populations and that the majority of the hosts (14/15) have a substantial contribution from intermediate-age populations with ages ranging from 0.7 to 2.4 Gyr. An average host spectrum is strikingly well fit by a combination of an old population and a 2.1 (+0.5, -0.7) Gyr population. The morphologies of the host galaxies suggest that these aging starbursts were induced during the early stages of the mergers that resulted in the elliptical-shaped galaxies that we observe. The current active galactic nucleus activity likely corresponds to the late episodes of accretion predicted by numerical simulations, which occur near the end of the mergers, whereas earlier episodes may be more difficult to observe due to obscuration. Our off-axis observations prevent us from detecting any current star formation or young stellar populations that may be present in the central few kiloparsecs. © 2013. The American Astronomical Society. All rights reserved.


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.


Fukao T.,University of California at Riverside | Yeung E.,University of California at Riverside | Bailey-Serres J.,University of California at Riverside
Plant Cell | Year: 2011

Submergence and drought are major constraints to rice (Oryza sativa) production in rain-fed farmlands, both of which can occur sequentially during a single crop cycle. SUB1A, an ERF transcription factor found in limited rice accessions, dampens ethylene production and gibberellic acid responsiveness during submergence, economizing carbohydrate reserves and significantly prolonging endurance. Here, we evaluated the functional role of SUB1A in acclimation to dehydration. Comparative analysis of genotypes with and without SUB1A revealed that SUB1A enhanced recovery from drought at the vegetative stage through reduction of leaf water loss and lipid peroxidation and increased expression of genes associated with acclimation to dehydration. Overexpression of SUB1A augmented ABA responsiveness, thereby activating stressinducible gene expression. Paradoxically, vegetative tissue undergoes dehydration upon desubmergence even though the soil contains sufficient water, indicating that leaf desiccation occurs in the natural progression of a flooding event. Desubmergence caused the upregulation of gene transcripts associated with acclimation to dehydration, with higher induction in SUB1A genotypes. SUB1A also restrained accumulation of reactive oxygen species (ROS) in aerial tissue during drought and desubmergence. Consistently, SUB1A increased the abundance of transcripts encoding ROS scavenging enzymes, resulting in enhanced tolerance to oxidative stress. Therefore, in addition to providing robust submergence tolerance, SUB1A improves survival of rapid dehydration following desubmergence and water deficit during drought. © 2011 American Society of Plant Biologists.


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.


Kamada A.,University of California at Riverside | Yu H.-B.,University of California at Riverside
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2015

The energy spectrum of high-energy neutrinos reported by the IceCube Collaboration shows a dip between 400 TeV and 1 PeV. One intriguing explanation is that high-energy neutrinos scatter with the cosmic neutrino background through an ∼MeV mediator. Taking the density matrix approach, we develop a formalism to study the propagation of PeV neutrinos in the presence of the new neutrino interaction. If the interaction is flavored such as the gauged Lμ-Lτ model we consider, the resonant collision may not suppress the PeV neutrino flux completely. The new force mediator may also contribute to the number of effectively massless degrees of freedom in the early Universe and change the diffusion time of neutrinos from the supernova core. Astrophysical observations such as big bang nucleosynthesis and supernova cooling provide an interesting test for the explanation. © 2015 American Physical Society.


Chen S.,University of California at Riverside | Chen Z.-J.,University of California at Riverside | Ren W.,University of California at Riverside | Ai H.-W.,University of California at Riverside
Journal of the American Chemical Society | Year: 2012

The detection of hydrogen sulfide (H 2S), a toxic gas and an important biological signaling molecule, has been a long-time challenge. Here we report genetically encoded fluorescent protein (FP)-based probes that can selectively detect H 2S. By expanding the genetic codes of E. coli and mammalian cells, FP chromophores were modified with the sulfide-reactive azide functional group. These structurally modified chromophores were selectively reduced by H 2S, resulting in sensitive fluorescence enhancement detectable by spectroscopic and microscopic techniques. Exploration of a circularly permuted FP led to an improved sensor with faster responses, and the feasibility of using such a genetically encoded probe to monitor H 2S in living mammalian cells has also been demonstrated. © 2012 American Chemical Society.


Rotschafer S.,University of California at Riverside | Razak K.,University of California at Riverside
Brain Research | Year: 2013

This study provides the first description of auditory cortical processing in a mouse model of Fragile X Syndrome (FXS). FXS is a genetic cause of intellectual impairment and is an autism spectrum disorder. Human studies with auditory evoked potentials indicate that FXS is associated with abnormal auditory processing. The Fmr1 knock-out (KO) mouse is a useful model for studying FXS. The KO mice show acoustic hypersensitivity and propensity for audiogenic seizures, suggesting altered auditory responses. However, the nature of changes at the neuronal level is not known. Here we conducted in vivo single unit extracellular electrophysiology in the auditory cortex of urethane/xylazine-anesthetized Fmr1 KO mice in response to tones and frequency modulated (FM) sweeps. Using tones as stimuli, we report expanded frequency tuning, enhanced response magnitude, and more variable first spike latencies in Fmr1 KO mice compared to wild-type controls. FM sweep stimuli revealed altered sensitivity to the rate of frequency change indicating abnormal spectrotemporal processing. There was no difference in FM sweep direction selectivity. Consistent with studies of the somatosensory cortex, these data point to hyper-responsiveness of auditory neurons as a key processing abnormality in FXS. Auditory neural responses can serve as outcome measures in preclinical trials of therapeutics for FXS as well as serve as physiological probes to study their mechanisms of action. © 2013 Elsevier B.V.


Gao Y.,University of California at Riverside | Tuncel E.,University of California at Riverside
IEEE Transactions on Information Theory | Year: 2011

A new hybrid digital/analog scheme is proposed for lossy transmission of a Gaussian source over a bandwidth-matched Gaussian broadcast channel with source side information available at each receiver. The proposed scheme combines two schemes that were previously shown to achieve optimal point-to-point distortion/power tradeoff simultaneously at all receivers under two distinct conditions stated in terms of channel and side information quality parameters. For the two-receiver case, the combined scheme is shown to achieve the same kind of optimality for the entire region in the parameter space sandwiched between those two conditions. Crucial to this result is a new degree of freedom discovered in designing point-to-point hybrid digital/analog schemes with side information. When superimposed with analog transmission, the proposed scheme outperforms all previously known schemes even outside the optimality region in the parameter space. © 2011 IEEE.


Gulotty R.,University of California at Riverside | Castellino M.,Polytechnic University of Turin | Jagdale P.,Polytechnic University of Turin | Tagliaferro A.,Polytechnic University of Turin | Balandin A.A.,University of California at Riverside
ACS Nano | Year: 2013

Carboxylic functionalization (-COOH groups) of carbon nanotubes is known to improve their dispersion properties and increase the electrical conductivity of carbon-nanotube-polymer nanocomposites. We have studied experimentally the effects of this type of functionalization on the thermal conductivity of the nanocomposites. It was found that while even small quantities of carbon nanotubes (∼1 wt %) can increase the electrical conductivity, a larger loading fraction (∼3 wt %) is required to enhance the thermal conductivity of nanocomposites. Functionalized multi-wall carbon nanotubes performed the best as filler material leading to a simultaneous improvement of the electrical and thermal properties of the composites. Functionalization of the single-wall carbon nanotubes reduced the thermal conductivity enhancement. The observed trends were explained by the fact that while surface functionalization increases the coupling between carbon nanotube and polymer matrix, it also leads to formation of defects, which impede the acoustic phonon transport in the single-wall carbon nanotubes. The obtained results are important for applications of carbon nanotubes and graphene flakes as fillers for improving thermal, electrical and mechanical properties of composites. © 2013 American Chemical Society.


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.


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.


Medina-Ortega K.J.,University of California at Riverside | Walker G.P.,University of California at Riverside
Journal of Experimental Botany | Year: 2013

To protect against loss of photo-assimilate-rich phloem sap, plants have evolved several mechanisms to plug phloem sieve tubes in response to damage. In many Fabaceae, each sieve element contains a discrete proteinaceous body called a forisome, which, in response to damage, rapidly transforms from a condensed configuration that does not impede the flow of sap to a dispersed configuration that plugs the sieve element. Aphids and other specialized phloem sap feeders can ingest phloem sap from a single sieve element for hours or days, and to do this, they must be able to suppress or reverse phloem plugging. A recent study provided in vitro evidence that aphid saliva can reverse forisome plugs. The present study tested this hypothesis in vivo by inducing forisome plugs which triggered aphids to switch behaviour from phloem sap ingestion to salivation into the sieve element. After salivating into the sieve element for various periods of time, the aphids were instantaneously cryofixed (freeze fixed) in situ on their leaf. The state of the forisome was then determined in the penetrated sieve element and in nearby non-penetrated sieve elements which served as controls for sieve elements not subjected to direct aphid salivation. Forisomes were almost always in close contact with the stylet tips and thus came into direct contact with the saliva. Nonetheless, forisome plugs in the penetrated sieve element did not revert back to a non-plugging state any faster than those in neighbouring sieve elements that were not subjected to direct aphid salivation. © The Author 2013. Published by Oxford University Press on behalf of the Society for Experimental Biology.


Straus D.S.,University of California at Riverside
Molecular Cancer | Year: 2013

Background: Inflammation is a well-known etiological factor for colorectal cancer, but mechanisms underlying the linkage between inflammation and cancer are incompletely understood. We hypothesized that two pro-inflammatory cytokines, TNFα and IL-17, might play a role in promoting colorectal carcinogenesis. Aerobic glycolysis is a metabolic adaptation that promotes the survival/proliferation of cancer cells. Paracrine signaling between tumor cells and cancer-associated fibroblasts also plays a role in carcinogenesis.Methods: The effect of TNFα and IL-17 on aerobic glycolysis and growth factor production in cultured human colorectal cancer cells was investigated. Glucose utilization and lactate production were quantified by measuring the disappearance of glucose and appearance of lactate in the culture medium. Glucose transporter and glycolytic enzyme expression levels were measured by immunoblotting.Results: TNFα and IL-17 cooperatively stimulated glycolysis in HT-29, T84, Caco-2 and HCT116 colorectal cancer cells. Treatment of HT-29 cells with TNFα plus IL-17 also increased the expression of HIF-1α and c-myc, two factors know to induce the transcription of genes encoding components of the glycolytic pathway. To further investigate mechanisms for cytokine-stimulated glycolysis, the effects of TNFα and IL-17 on expression of six members and one regulator of the glycolytic pathway were investigated. TNFα and IL-17 cooperatively increased the expression of the glucose transporter SLC2A1 and hexokinase-2 but did not regulate expression of glucose transporter SLC2A3, enolase-1, pyruvate kinase M2, lactate dehydrogenase A, or 6-phoshofructo-2-kinase/fructose-2,6-bisphosphatase-3 (PFKFB3). Experiments with inhibitors indicated that HIF-1α played a role in induction of SLC2A1 and that the transcription factor NF-κB played a role in induction of hexokinase-2 by TNFα and IL-17. TNFα and IL-17 also synergistically stimulated production by HT-29 cells of a growth factor that simulated proliferation/survival of NIL8 fibroblastic cells. The activity of this factor was not specifically inhibited by the EGFR inhibitor AG1478, indicating that it is not an EGFR ligand.Conclusions: Chronic inflammation is known to promote colorectal tumorigenesis. The pro-inflammatory cytokines TNFα and IL-17 may contribute to this effect by stimulating glycolysis and growth factor production in colorectal cancer cells. © 2013 Straus; licensee BioMed Central Ltd.


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.


Zhu Y.,University of California at Riverside | Nayak N.M.,University of California at Riverside | Roy-Chowdhury A.K.,University of California at Riverside
Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition | Year: 2013

In this paper, rather than modeling activities in videos individually, we propose a hierarchical framework that jointly models and recognizes related activities using motion and various context features. This is motivated from the observations that the activities related in space and time rarely occur independently and can serve as the context for each other. Given a video, action segments are automatically detected using motion segmentation based on a nonlinear dynamical model. We aim to merge these segments into activities of interest and generate optimum labels for the activities. Towards this goal, we utilize a structural model in a max-margin framework that jointly models the underlying activities which are related in space and time. The model explicitly learns the duration, motion and context patterns for each activity class, as well as the spatio-temporal relationships for groups of them. The learned model is then used to optimally label the activities in the testing videos using a greedy search method. We show promising results on the VIRAT Ground Dataset demonstrating the benefit of joint modeling and recognizing activities in a wide-area scene. © 2013 IEEE.


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

A special form of the 3×3 Majorana neutrino mass matrix derivable from μ-τ interchange symmetry accompanied by a generalized CP transformation was obtained many years ago. It predicts θ23=π/4 as well as δCP=±π/2, with θ13≠0. Whereas this is consistent with present data, we explore a deviation of this result which occurs naturally in a recent proposed model of radiative inverse seesaw neutrino mass. © 2015 Published by Elsevier B.V.


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 .


Gordon A.D.,University of California at Riverside | Zaera F.,University of California at Riverside
Angewandte Chemie - International Edition | Year: 2013

Chiral modification of catalysts: A comparative in situ reflection-absorption infrared spectroscopy study of the adsorption of 1-(1-naphthyl)ethylamine on Pt surfaces from solution indicated bonding mainly through the amine group and not the aromatic ring as commonly assumed (see picture). In light of these results, a rethinking of the existing model for chiral modification of catalysts may be needed. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Lavallo V.,University of California at Riverside | Wright II J.H.,University of California at Riverside | Tham F.S.,University of California at Riverside | Quinlivan S.,University of California at Riverside
Angewandte Chemie - International Edition | Year: 2013

Bigger and better! The single-component zwitterionic gold catalyst formed by the coordination of a phosphine ligand bearing an inert and noncoordinating carborane substituent, CB11Cl11 -, to an Au I ion exhibited the highest reported activity for the hydroamination of alkynes with amines (see scheme). The highest turnover number observed for hydroamination with this catalyst exceeded a stunning 95 000. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


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.


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.


Burdett J.J.,University of California at Riverside | Bardeen C.J.,University of California at Riverside
Journal of the American Chemical Society | Year: 2012

A detailed analysis of the oscillations seen in the delayed fluorescence of crystalline tetracene is presented in order to study the mechanism of singlet fission. Three quantum beat frequencies of 1.06 ± 0.05, 1.82 ± 0.05, and 2.92 ± 0.06 GHz are resolved, which are damped on a time scale of 20 ns. The effects of sample morphology, excitation wavelength, and temperature are examined. A density matrix model for singlet fission is developed that quantitatively describes the frequencies, amplitudes, and damping of the oscillations. The model assumes a direct coupling of the initially excited singlet exciton to the triplet pair manifold. There is no electronic coherence between the singlet and triplet pair states, but the rapid singlet decay time of ∼200 ps in solution-grown single crystals provides the impulsive population transfer necessary to create a coherent superposition of three zero-field triplet pair states |xx〉, |yy〉, and |zz〉 with overall singlet character. This superposition of the three states gives rise to the three quantum beat frequencies seen in the experiment. Damping of the quantum beats results from both population exchange between triplet and singlet manifolds and pure dephasing between the triplet pair states. By lowering the temperature and slowing the SF rate, the visibility of the oscillations decreases. There is no evidence of magnetic dipole-dipole coupling between the product triplets. Our model provides good overall agreement with the data, supporting the conclusion that singlet fission in tetracene proceeds through the "direct" mechanism without strong electronic coupling between the singlet and triplet pair states. © 2012 American Chemical Society.


Yates T.M.,University of California at Riverside | Grey I.K.,University of California at Riverside
Development and Psychopathology | Year: 2012

This investigation employed latent profile analysis to identify distinct patterns of multiform competence among 164 emancipated foster youth (Mage = 19.67 years, SD = 1.12; 64% female). Fit indices and conceptual interpretation converged on a four-profile solution. A subset of emancipated youth evidenced a maladaptive profile (16.5%; n = 27), which was characterized by low educational competence, low occupational competence, low civic engagement, problematic interpersonal relationships, low self-esteem, and high depressive symptoms. However, the largest group of emancipated youth exhibited a resilient profile in which they were faring reasonably well in all domains despite marked adversity (47%; n = 77). Two additional groups evidenced discordant adjustment patterns wherein they exhibited high levels of psychological competence despite behavioral difficulties (i.e., internally resilient; 30%; n = 49) or significant emotional difficulties despite manifest competence (i.e., externally resilient; 6.5%; n = 11). The obtained profiles were validated against independent measures of behavioral and socioemotional adjustment. Exploratory analyses examined etiological differences across profiles with respect to child welfare variables, such as age at entry into care, placement disruption, reason for placement, and severity of child maltreatment. The findings highlight the need for multidimensional models of risk and resilience and illustrate the importance of heretofore underappreciated heterogeneity in the adaptive outcomes of emancipated foster youth. © 2012 Cambridge University Press.


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.


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.


Jiang D.-E.,Oak Ridge National Laboratory | Jin Z.,University of California at Riverside | Henderson D.,Brigham Young University | Wu J.,University of California at Riverside
Journal of Physical Chemistry Letters | Year: 2012

Organic electrolytes such as tetraethylammonium tetrafluoroborate dissolved in acetonitrile (TEA-BF4/ACN) are widely used in commercial supercapacitors and academic research, but conflicting experimental results have been reported regarding the dependence of surface-area-normalized capacitance on the pore size. Here we show from a classical density functional theory the dependence of capacitance on the pore size from 0.5 to 3.0 nm for a model TEA-BF4/ACN electrolyte. We find that the capacitance-pore size curve becomes roughly flat after the first peak around the ion diameter, and the peak capacitance is not significantly higher than the large-pore average. We attribute the invariance of capacitance with the pore size to the formation of an electric double-layer structure that consists of counterions and highly organized solvent molecules. This work highlights the role of the solvent molecules in modulating the capacitance and reconciles apparently conflicting experimental reports. © 2012 American Chemical Society.


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.


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.


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.


Yang X.,Rice University | Liu G.,University of California at Riverside | Balandin A.A.,University of California at Riverside | Mohanram K.,Rice University
ACS Nano | Year: 2010

We propose and experimentally demonstrate a triple-mode single-transistor graphene amplifier utilizing a three-terminal back-gated single-layer graphene transistor. The ambipolar nature of electronic transport in graphene transistors leads to increased amplifier functionality as compared to amplifiers built with unipolar semiconductor devices. The ambipolar graphene transistors can be configured as n-type, p-type, or hybrid-type by changing the gate bias. As a result, the single-transistor graphene amplifier can operate in the common-source, common-drain, or frequency multiplication mode, respectively. This in-field controllability of the single-transistor graphene amplifier can be used to realize the modulation necessary for phase shift keying and frequency shift keying, which are widely used in wireless applications. It also offers new opportunities for designing analog circuits with simpler structure and higher integration densities for communications applications. © 2010 American Chemical Society.


Zaera F.,University of California at Riverside
Journal of Physical Chemistry Letters | Year: 2010

New self-assembly and nanotechnology synthetic methodology is finding its way into the preparation of heterogeneous catalysts. The new approaches afford better design of active sites to fine-tune the selectivity of specific catalytic processes. Examples are provided here for the preparation of supports for catalysts with well-defined structures, for the use of nanostructures with well-defined sizes and shapes as active phases, for the grafting of molecular functionality to solid surfaces, and for the assembly of complex nanostructures to illustrate the recent advances in this area of research. It is argued that by combining these new synthetic tools with mechanistic studies via surface science and theoretical studies, it should be finally possible to design highly selective catalysts from first principles, the holy grail of the field of catalysis. © 2010 American Chemical Society.


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.


Burnette J.M.,University of California at Riverside | Wessler S.R.,University of California at Riverside
Genetics | Year: 2013

Large lecture classes and standardized laboratory exercises are characteristic of introductory biology courses. Previous research has found that these courses do not adequately convey the process of scientific research and the excitement of discovery. Here we propose a model that provides beginning biology students with an inquiry-based, active learning laboratory experience. The Dynamic Genome course replicates a modern research laboratory focused on eukaryotic transposable elements where beginning undergraduates learn key genetics concepts, experimental design, and molecular biological skills. Here we report on two key features of the course, a didactic module and the capstone original research project. The module is a modified version of a published experiment where students experience how virtual transposable elements from rice (Oryza sativa) are assayed for function in transgenic Arabidopsis thaliana. As part of the module, students analyze the phenotypes and genotypes of transgenic plants to determine the requirements for transposition. After mastering the skills and concepts, students participate in an authentic research project where they use computational analysis and PCR to detect transposable element insertion site polymorphism in a panel of diverse maize strains. As a consequence of their engagement in this course, students report large gains in their ability to understand the nature of research and demonstrate that they can apply that knowledge to independent research projects. © 2013 by the Genetics Society of America.


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.


Kokoza V.A.,University of California at Riverside | Raikhel A.S.,University of California at Riverside
Insect Biochemistry and Molecular Biology | Year: 2011

In this study, we report the establishment of the binary Gal4/UAS system for the yellow fever mosquito Aedes aegypti. We utilized the 1.8-kb 5' upstream region of the vitellogenin gene (Vg) to genetically engineer mosquito lines with the Vg-Gal4 activator and established UAS-EGFP responder transgenic mosquito lines to evaluate the binary Gal4/UAS system. The results show that the Vg-Gal4 driver leads to a high level of tissue-, stage- and sex-specific expression of the EGFP reporter in the fat body of Vg-Gal4/UAS-EGFP hybrids after blood-meal activation. In addition, the applicability of this system to study hormonal regulation of gene expression was demonstrated in in vitro organ culture experiments in which the EGFP reporter was highly activated in isolated fat bodies of previtellogenic Vg-Gal4/UAS-EGFP females incubated in the presence of 20-hydroxyecdysone (20E). Hence, this study has opened the door for further refinement of genetic tools in mosquitoes. © 2011 Elsevier Ltd.


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.


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.


Layous K.,University of California at Riverside | Chancellor J.,University of California at Riverside | Lyubomirsky S.,University of California at Riverside
Journal of Abnormal Psychology | Year: 2014

Applying Nolen-Hoeksema and Watkins's (2011) transdiagnostic risk factor heuristic to our work on positive activities (i.e., practices that characterize naturally happy people, like expressing gratitude and practicing generosity), we propose that such activities may serve as protective factors that mitigate proximal risk factors both directly and by intervening with the mechanisms that give rise to them. First, we discuss theoretical and empirical support for the importance of well-being and the mechanisms that explain how positive activities promote well-being (by boosting positive emotions, positive thoughts, positive behaviors, and need satisfaction; Lyubomirsky & Layous, 2013). Second, we outline examples of how positive activities can mitigate two particular proximal risk factors (rumination and loneliness) and counteract environmental triggers (i.e., moderators) that might amplify them (e.g., through adaptive coping). Third, we argue that positive activities can be taught to youth to instill positive patterns of emotions, thoughts, and behaviors that may serve as protective factors over the course of their lifetimes. Lastly, we propose that certain positive activities might be particularly well-suited to certain individuals and to specific risk factors. © 2014 American Psychological Association.


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.


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.


Lew C.M.,University of California at Riverside | Cai R.,University of California at Riverside | Yan Y.,University of California at Riverside
Accounts of Chemical Research | Year: 2010

(Figure Presented) Zeolites are a class of crystalline oxides that have uniform and molecular-sized pores (3-12 À in diameter). Although natural zeolites were first discovered in 1756, significant commercial development did not begin until the 1950s when synthetic zeolites with high purity and controlled chemical composition became available. Since then, major commercial applications of zeolites have been limited to catalysis, adsorption, and ion exchange, all using zeolites in powder form. Although researchers have widely investigated zeolite thin films within the last 15 years, most of these studies were motivated by the potential application of these materials as separation membranes and membrane reactors. In the last decade, we have recognized and demonstrated that zeolite thin films can have new, diverse, and economically significant applications that others had not previously considered. In this Account, we high-light our work on the development of zeolite thin films as lowdielectric constant (low-k) insulators for future generation computer chips, environmentally benign corrosion-resistant coatings for aerospace alloys, and hydrophilic and microbiocidal coatings for gravity-independent water separation in space stations. Although these three applications might not seem directly related, they all rely on the ability to fine-tune important macroscopic properties of zeolites by changing their ratio of silicon to aluminum. For example, pure-silica zeolites (PSZs, Si/Al = ∞) are hydrophobic, acid stable, and have no ion exchange capacity, while low-silica zeolites (LSZs, Si/Al < 2) are hydrophilic, acid soluble, and have a high ion exchange capacity. These new thin films also take advantage of some unique properties of zeolites that have not been exploited before, such as a higher elastic modulus, hardness, and heat conductivity than those of amorphous porous silicas, and microbiocidal capabilities derived from their ion exchange capacities. Finally, we briefly discuss our more recent work on polycrystalline zeolite thin films as promising biocompatible coatings and environmentally benign wear-resistant and anifouling coatings. When zeolites are incorporated into polymer thin films in the form of nanocrystals, we also show that the resultant composite membranes can significantly improve the performance of reverse osmosis membranes for sea water desalination and proton exchange membrane fuel cells. These diverse applications of zeolites have the potential to initiate new industries while revolutionizing existing ones with a potential economic impact that could extend into the hundreds of billions of dollars. We have licensed several of these inventions to companies with millions of dollars invested in their commercial development We expect that other related technologies will be licensed in the near future. © 2010 American Chemical Society.


Wang M.,University of California at Riverside | He L.,University of California at Riverside | Yin Y.,University of California at Riverside
Materials Today | Year: 2013

We present here our recent studies on the magnetic-field-guided assembly of colloidal matter. Starting from a brief introduction of the magnetic interactions exerted on colloidal nanostructures, we discuss how magnetic fields drive their assembly into one-dimensional (1D), two-dimensional (2D), and three-dimensional (3D) ordered structures. This principle is further demonstrated in the assembly of colloidal matter on macroscopic and microscopic magnetized patterns with defined field strengths and spatial distributions. © 2013 Elsevier Ltd.


Lin P.,University of Electronic Science and Technology of China | Ren W.,University of California at Riverside
Proceedings of the IEEE Conference on Decision and Control | Year: 2012

In this paper, a constrained consensus problem is studied in unbalanced networks in the presence of communication delays. Here each agent needs to lie in a closed convex set while reaching a consensus. The communication graphs considered 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. It is showed 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 showed that the communication delays do not affect the consensus stability and consensus is achieved even though the communication delays are arbitrary bounded. © 2012 IEEE.


Barlas Y.,University of California at Riverside | Varma C.M.,University of California at Riverside
Physical Review B - Condensed Matter and Materials Physics | Year: 2013

In Lorentz-invariant systems spontaneously broken gauge symmetry results in three types of fundamental excitations: density excitations, Higgs bosons (amplitude modes), and Goldstone bosons (phase modes). The density and phase modes are coupled by electromagnetic interactions while the amplitude modes are not. In s-wave superconductors, the Higgs mode, which can be observed only under special conditions, has been detected. We show that unconventional d-wave superconductors, such as the high-temperature cuprate superconductors, should have a rich assortment of Higgs bosons, each in a different irreducible representation of the point-group symmetry of the lattice. We also show that these modes have a characteristic singular spectral structure and discuss conditions for their observability. © 2013 American Physical Society.


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.


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

A model proposed in 2004 using the non-Abelian discrete symmetry S3 for understanding the flavor structure of quarks and leptons is updated, with special focus on the quark and scalar sectors. We show how the approximate residual symmetries of this model explain both the pattern of the quark mixing matrix and why the recently observed particle of 126 GeV at the Large Hadron Collider is so much like the one Higgs boson of the Standard Model. We identify the strongest phenomenological bounds on the scalar masses of this model, and predict a possibly observable decay b→sτ-μ+ (Bs→τ+μ-), but not b→sτ+μ- (Bs→τ-μ+). © 2013 Elsevier B.V.


Hou Y.,University of California at Riverside | Zuo F.,University of California at Riverside | Dagg A.,University of California at Riverside | Feng P.,University of California at Riverside
Angewandte Chemie - International Edition | Year: 2013

Hitting water with nanotrees: A three-dimensional branched heterojunction array for water oxidation based on cobalt-doped α-Fe2O 3 nanorod cores and MgFe2O4 shells has been synthesized. Such an architecture not only has a large surface area and excellent light absorption properties, and shows fast charge transport, but also exhibits a very high photoelectrochemical activity for water oxidation and a high stability. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


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.


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.


Rumyantsev S.,Rensselaer Polytechnic Institute | Rumyantsev S.,RAS Ioffe Physical - Technical Institute | Liu G.,University of California at Riverside | Shur M.S.,Rensselaer Polytechnic Institute | And 2 more authors.
Nano Letters | Year: 2012

We show that vapors of different chemicals produce distinguishably different effects on the low-frequency noise spectra of graphene. It was found in a systematic study that some gases change the electrical resistance of graphene devices without changing their low-frequency noise spectra while other gases modify the noise spectra by inducing Lorentzian components with distinctive features. The characteristic frequency f c of the Lorentzian noise bulges in graphene devices is different for different chemicals and varies from f c = 10-20 Hz to f c = 1300-1600 Hz for tetrahydrofuran and chloroform vapors, respectively. The obtained results indicate that the low-frequency noise in combination with other sensing parameters can allow one to achieve the selective gas sensing with a single pristine graphene transistor. Our method of gas sensing with graphene does not require graphene surface functionalization or fabrication of an array of the devices with each tuned to a certain chemical. © 2012 American Chemical 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.


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.


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.


Sim C.K.,Stanford University | Perry S.,University of California at Riverside | Tharadra S.K.,University of California at Riverside | Lipsick J.S.,Stanford University | Ray A.,University of California at Riverside
Genes and Development | Year: 2012

In both mammals and insects, an olfactory neuron will usually select a single olfactory receptor and repress remaining members of large receptor families. Here we show that a conserved multiprotein complex, Myb-MuvB (MMB)/dREAM, plays an important role in mediating neuron-specific expression of the carbon dioxide (CO2) receptor genes (Gr63a/Gr21a) in Drosophila. Activity of Myb in the complex is required for expression of Gr63a/Gr21a and acts in opposition to the histone methyltransferase Su(var)3-9. Consistent with this, we observed repressive dimethylated H3K9 modifications at the receptor gene loci, suggesting a mechanism for silencing receptor gene expression. Conversely, other complex members, Mip120 (Myb-interacting protein 120) and E2F2, are required for repression of Gr63a in inappropriate neurons. Misexpression in mutants is accompanied by an increase in the H3K4me3 mark of active chromatin at the receptor gene locus. Nuclei of CO2 receptor-expressing neurons contain reduced levels of the repressive subunit Mip120 compared with surrounding neurons and increased levels of Myb, suggesting that activity of the complex can be regulated in a cell-specific manner. Our evidence suggests a model in which olfactory receptors are regulated epigenetically and the MMB/dREAM complex plays a critical role in specifying, maintaining, and modulating the receptor-to-neuron map. © 2012 by Cold Spring Harbor Laboratory Press.


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.


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.