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Zhao Y.,900 University Avenue | Liao J.,900 University Avenue | Liao J.,University of California at Riverside
Heterocycles | Year: 2011

GW1100 is an antagonist of GPR40 identified by high throughput screening recently. The feasible synthesis of GW1100 has been developed in mild conditions. The key step involves the cyclization of the 2-thiouracil heterocycle under acidic conditions at room temperature. © The Japan Institute of Heterocyclic Chemistry.

Evtyushkin D.,Binghamton University State University of New York | Ponomarev D.,Binghamton University State University of New York | Abu-Ghazaleh N.,University of California at Riverside | Abu-Ghazaleh N.,900 University Avenue
ACM Transactions on Architecture and Code Optimization | Year: 2016

Covert channels through shared processor resources provide secret communication between two malicious processes: the trojan and the spy. In this article, we classify, analyze, and compare covert channels through dynamic branch prediction units in modern processors. Through experiments on a real hardware platform, we compare contention-based channel and the channel that is based on exploiting the branch predictor's residual state. We analyze these channels in SMT and single-threaded environments under both clean and noisy conditions. Our results show that the residual state-based channel provides a cleaner signal and is effective even in noisy execution environments with another application sharing the same physical core with the trojan and the spy. We also estimate the capacity of the branch predictor covert channels and describe a software-only mitigation technique that is based on randomizing the state of the predictor tables on context switches. We show that this protection eliminates all covert channels through the branch prediction unit with minimal impact on performance. © 2016 ACM.

Pires M.N.,University of California at Riverside | Pires M.N.,900 University Avenue | Bassar R.D.,University of California at Riverside | Mcbride K.E.,University of California at Riverside | And 3 more authors.
Functional Ecology | Year: 2011

1. The Northern Clade of the fish genus Poeciliopsis includes six closely related species, three of which lack placentas and three that have placentas but vary in the extent of post-fertilization provisioning. 2. We used this diversity to evaluate a series of hypotheses proposed in earlier publications concerning why the placenta has evolved. All hypotheses share the attribute of arguing that the placenta evolved to enhance the evolution of some other life-history trait, such as to reduce the age at maturation or to increase offspring size. We refer to these hypotheses collectively as 'life-history facilitation hypotheses'. 3. A general way to evaluate the plausibility of such proposals is to ask whether the evolution of the placenta is predictably associated with the evolution of other components of the life history. 4. We evaluated such associations in two ways. First, we performed a multivariate analysis of life-history data for fish collected and preserved in nature. This analysis included 16 populations across all six species. Secondly, we performed a more complete quantification of the life histories of the laboratory descendents from five populations representing four species, then performed a similar multivariate analysis. The laboratory study added information about the timing of reproduction (age at maturity, frequency of reproduction). 5. Both analyses yielded similar results, which were that the evolution of increased placentation is correlated with the evolution of a smaller size at first reproduction, the production of fewer and smaller offspring per litter, but an increase in the number of litters that were developing simultaneously in the ovary (superfetation). Increased placentation is associated with progressively earlier ages at maturation and shorter intervals between the birth of successive litters of offspring. Overall, increased placentation was associated with an increase in the rate of production of offspring early in life. A peculiar attribute of placentation is that this increase in the rate of offspring production can be attained despite a simultaneous reduction in the proportional quantity of resources devoted to reproduction. 6. These trends support one of the life history facilitation hypotheses, which is that placentation facilitates earlier maturity and a higher rate of reproduction early in life. They also suggest a possible connection between the evolution of the placenta and the well-established theory of life-history evolution, since these same life history attributes are predicted to evolve in response to exposure to high extrinsic rates of adult mortality. © 2011 The Authors. Functional Ecology © 2011 British Ecological Society.

Malik-Chaudhry H.K.,900 University Avenue | Saavedra A.,900 University Avenue | Liao J.,900 University Avenue | Liao J.,University of California at Riverside
Biotechnology and Bioengineering | Year: 2014

Förster resonance energy transfer (FRET) technology has been widely used in biological and biomedical research and is a valuable tool for elucidating molecular interactions in vitro and in vivo. Quantitative FRET analysis is a powerful method for determining biochemical parameters and molecular distances at nanometer levels. Recently, we reported theoretical developments and experimental procedures for determining the dissociation constant, Kd and enzymatic kinetics parameters, Kcat and KM, of protein interactions with the engineered FRET pair, CyPet and YPet. The strong FRET signal from this pair made these developments possible. However, the direct link of fluorescent proteins with proteins of interests may interfere with the folding of some fusion proteins. Here, we report a new protein engineering strategy for improving FRET signals by adding a linker between the fluorescent protein and the targeted protein. This improvement allowed us to follow the covalent conjugation of NEDD8 to its E2 ligase in the presence of E1 and ATP, which was difficult to determine without linker. Three linkers, LAEAAAKEAA, TSGSPGLQEFGT, and LAAALAAA, which are alpha helix or random coil, all significantly improved the FRET signals. Our results show a general methodology for improving trans-FRET signals to effectively determine biochemical reaction intermediates. © 2014 Wiley Periodicals, Inc.

Kumar R.,Center for Environmental Research and Technology | Kumar R.,900 University Avenue | Kumar R.,Oak Ridge National Laboratory | Hu F.,Oak Ridge National Laboratory | And 10 more authors.
Biotechnology and Bioengineering | Year: 2013

Dilute acid as well as water only (hydrothermal) pretreatments often lead to a significant hemicellulose loss to soluble furans and insoluble degradation products, collectively termed as chars and/or pseudo-lignin. In order to understand the factors contributing to reducing sugar yields from pretreated biomass and the possible influence of hemicellulose derived pseudo-lignin on cellulose conversion at the moderate to low enzyme loadings necessary for favorable economics, dilute acid pretreatment of Avicel cellulose alone and mixed with beechwood xylan or xylose was performed at various severities. Following pretreatment, the solids were enzymatically hydrolyzed and characterized for chemical composition and physical properties by NMR, FT-IR, and SEM imaging. It was found that hemicelluloses (xylan) derived-pseudo-lignin was formed at even moderate severities and that these insoluble degradation products can significantly retard cellulose hydrolysis. Furthermore, although low severity (CSF∼1.94) dilute acid pretreatment of a xylan-Avicel mixture hydrolyzed most of the xylan (98%) and produced negligible amounts of pseudo-lignin, enzymatic conversion of cellulose dropped significantly (>25%) compared to cellulose pretreated alone at the same conditions. The drop in cellulose conversion was higher than realized for cellulase inhibition by xylooligomers reported previously. Plausible mechanisms are discussed to explain the observed reductions in cellulose conversions. © 2012 Wiley Periodicals, Inc.

Sharma K.R.,Auburn University | Sharma K.R.,900 University Avenue | Fadamiro H.Y.,Auburn University
Journal of Insect Physiology | Year: 2013

Pseudacteon tricuspis, Pseudacteon obtusus and Pseudacteon curvatus are three species of parasitic phorid flies (Diptera: Phoridae), which have been introduced as classical biological control agents of imported, Solenopsis fire ants (Hymenoptera: Formicidae) in the southern USA. Previous studies demonstrated the behavioral response of P. tricuspis to the venom alkaloids and alarm pheromone of the fire ant, S. invicta. In the present study, we compared the responses of P. tricuspis, P. obtusus and P. curvatus to Solenopsis invicta alarm pheromone, venom alkaloids, or a mixture of both chemicals in four-choice olfactometer bioassays. The main hypothesis tested was that the fire ant alarm pheromone and venom alkaloids act in concert to attract Pseudacteon phorid flies. Both sexes of all three Pseudacteon species were attracted to low doses of the fire ant alarm pheromone or venom alkaloids (i.e. 1 ant worker equivalent) alone. However, the flies were significantly more attracted to a mixture of both chemicals (i.e., 1:1 mixture of alarm pheromone. +. alkaloids) than to either chemical. The results suggest an additive rather than a synergistic effect of combining both chemicals. Comparing the fly species, P. tricuspis showed relatively greater attraction to cis alkaloids, whereas the alkaloid mixture (cis+. trans) was preferred by P. obtusus and P. curvatus. In general, no key sexual differences were recorded, although females of P. tricuspis and P. obtusus showed slightly higher response than conspecific males to lower doses of the alarm pheromone. The ecological significance of these findings is discussed, and a host location model is proposed for parasitic phorid flies involving the use of fire ant alarm pheromone and venom alkaloids as long range and short range attractants, respectively. © 2013 Elsevier Ltd.

Nguyen T.Y.,900 University Avenue | Guan R.G.,Northeastern University China | Cipriano A.F.,900 University Avenue | Zhao Z.Y.,Northeastern University China | Liu H.N.,900 University Avenue
Advanced Materials Research | Year: 2014

Magnesium (Mg) is an attractive biomaterial due to its desirable biodegradable and mechanical properties. In this study, we compared the degradation behavior of Mg and a new Mg alloy incubated in both whole blood and platelet rich plasma (PRP) for two hours under standard cell culture conditions. To avoid settling of red blood cells, tubes with whole blood were under constant rotation during the incubation. Post-incubation solutions were collected, centrifuged, and analyzed for pH and Mg ion concentration. Mg and Mg alloy samples were fixed with a 3% glutaraldehyde solution, dehydrated using an ethanol series, critical point dried, sputter coated, and imaged with a field emission scanning electron microscope. Analysis of the post-incubation solutions showed PRP had greater concentrations of Mg ions and higher pH values when compared with whole blood. This indicated that the Mg and Mg alloy degraded faster when incubated in PRP than in whole blood. When comparing the surface of the materials after incubation with whole blood and PRP, the surfaces of Mg and Mg alloy that was incubated in PRP had larger cracks and grain boundaries than the samples incubated in whole blood. Additionally, more particulate microstructures were observed on the samples incubated in PRP as opposed to whole blood. Further studies are still needed to elucidate the differences in degradation of Mg alloys in whole blood and PRP. © (2014) Trans Tech Publications, Switzerland.

Cruz J.,900 University Avenue | Mane-Padros D.,900 University Avenue | Zou Z.,900 University Avenue | Raikhel A.S.,900 University Avenue
Molecular and Cellular Endocrinology | Year: 2012

Mosquitoes are adapted to using vertebrate blood as a nutrient source to promote egg development and as a consequence serve as disease vectors. Blood-meal activated reproductive events in female mosquitoes are hormonally and nutritionally controlled with an insect steroid hormone 20-hydroxyecdysone (20E) playing a central role. The nuclear receptor E75 is an essential factor in the 20E genetic hierarchy, however functions of its three isoforms - E75A, E75B, and E75C - in mosquito reproduction are unclear. By means of specific RNA interference depletion of E75 isoforms, we identified their distinct roles in regulating the level and timing of expression of key genes involved in vitellogenesis in the fat body (an insect analog of vertebrate liver and adipose tissue) of the mosquito Aedes aegypti. Heme is required in a high level of expression of 20E-controlled genes in the fat body, and this heme action depends on E75. Thus, in mosquitoes, heme is an important signaling molecule, serving as a sensor of the availability of a protein meal for egg development. Disruption of this signaling pathway could be explored in the design of mosquito control approaches. © 2011 Elsevier Ireland Ltd.

Ounit R.,900 University Avenue | Close T.,900 University Avenue | Wanamaker S.,900 University Avenue | Lonardi S.,900 University Avenue
ACM BCB 2014 - 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics | Year: 2014

We present CLARK, a novel approach for classifying metagenomics and genomics sequences with high speed and accuracy. Copyright © 2014 ACM.

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