Human Pol ζ purified with accessory subunits is active in translesion DNA synthesis and complements Pol η in cisplatin bypass

PubMed Central

Lee, Young-Sam; Gregory, Mark T.; Yang, Wei

2014-01-01

DNA polymerase ζ (Pol ζ) is a eukaryotic B-family DNA polymerase that specializes in translesion synthesis and is essential for normal embryogenesis. At a minimum, Pol ζ consists of a catalytic subunit Rev3 and an accessory subunit Rev7. Mammalian Rev3 contains >3,000 residues and is twice as large as the yeast homolog. To date, no vertebrate Pol ζ has been purified for biochemical characterization. Here we report purification of a series of human Rev3 deletion constructs expressed in HEK293 cells and identification of a minimally catalytically active human Pol ζ variant. With a tagged form of an active Pol ζ variant, we isolated two additional accessory subunits of human Pol ζ, PolD2 and PolD3. The purified four-subunit Pol ζ4 (Rev3–Rev7–PolD2–PolD3) is much more efficient and more processive at bypassing a 1,2-intrastrand d(GpG)-cisplatin cross-link than the two-subunit Pol ζ2 (Rev3–Rev7). We show that complete bypass of cisplatin lesions requires Pol η to insert dCTP opposite the 3′ guanine and Pol ζ4 to extend the primers. PMID:24449906

Human Pol ζ purified with accessory subunits is active in translesion DNA synthesis and complements Pol η in cisplatin bypass.

PubMed

Lee, Young-Sam; Gregory, Mark T; Yang, Wei

2014-02-25

DNA polymerase ζ (Pol ζ) is a eukaryotic B-family DNA polymerase that specializes in translesion synthesis and is essential for normal embryogenesis. At a minimum, Pol ζ consists of a catalytic subunit Rev3 and an accessory subunit Rev7. Mammalian Rev3 contains >3,000 residues and is twice as large as the yeast homolog. To date, no vertebrate Pol ζ has been purified for biochemical characterization. Here we report purification of a series of human Rev3 deletion constructs expressed in HEK293 cells and identification of a minimally catalytically active human Pol ζ variant. With a tagged form of an active Pol ζ variant, we isolated two additional accessory subunits of human Pol ζ, PolD2 and PolD3. The purified four-subunit Pol ζ4 (Rev3-Rev7-PolD2-PolD3) is much more efficient and more processive at bypassing a 1,2-intrastrand d(GpG)-cisplatin cross-link than the two-subunit Pol ζ2 (Rev3-Rev7). We show that complete bypass of cisplatin lesions requires Pol η to insert dCTP opposite the 3' guanine and Pol ζ4 to extend the primers.

Biallelic inactivation of REV7 is associated with Fanconi anemia.

PubMed

Bluteau, Dominique; Masliah-Planchon, Julien; Clairmont, Connor; Rousseau, Alix; Ceccaldi, Raphael; Dubois d'Enghien, Catherine; Bluteau, Olivier; Cuccuini, Wendy; Gachet, Stéphanie; Peffault de Latour, Régis; Leblanc, Thierry; Socié, Gérard; Baruchel, André; Stoppa-Lyonnet, Dominique; D'Andrea, Alan D; Soulier, Jean

2016-09-01

Fanconi anemia (FA) is a recessive genetic disease characterized by congenital abnormalities, chromosome instability, progressive bone marrow failure (BMF), and a strong predisposition to cancer. Twenty FA genes have been identified, and the FANC proteins they encode cooperate in a common pathway that regulates DNA crosslink repair and replication fork stability. We identified a child with severe BMF who harbored biallelic inactivating mutations of the translesion DNA synthesis (TLS) gene REV7 (also known as MAD2L2), which encodes the mutant REV7 protein REV7-V85E. Patient-derived cells demonstrated an extended FA phenotype, which included increased chromosome breaks and G2/M accumulation upon exposure to DNA crosslinking agents, γH2AX and 53BP1 foci accumulation, and enhanced p53/p21 activation relative to cells derived from healthy patients. Expression of WT REV7 restored normal cellular and functional phenotypes in the patient's cells, and CRISPR/Cas9 inactivation of REV7 in a non-FA human cell line produced an FA phenotype. Finally, silencing Rev7 in primary hematopoietic cells impaired progenitor function, suggesting that the DNA repair defect underlies the development of BMF in FA. Taken together, our genetic and functional analyses identified REV7 as a previously undescribed FA gene, which we term FANCV.

Biallelic inactivation of REV7 is associated with Fanconi anemia

PubMed Central

Masliah-Planchon, Julien; Clairmont, Connor; Rousseau, Alix; Ceccaldi, Raphael; Dubois d’Enghien, Catherine; Bluteau, Olivier; Cuccuini, Wendy; Gachet, Stéphanie; Peffault de Latour, Régis; Leblanc, Thierry; Socié, Gérard; Baruchel, André; Stoppa-Lyonnet, Dominique; D’Andrea, Alan D.

2016-01-01

Fanconi anemia (FA) is a recessive genetic disease characterized by congenital abnormalities, chromosome instability, progressive bone marrow failure (BMF), and a strong predisposition to cancer. Twenty FA genes have been identified, and the FANC proteins they encode cooperate in a common pathway that regulates DNA crosslink repair and replication fork stability. We identified a child with severe BMF who harbored biallelic inactivating mutations of the translesion DNA synthesis (TLS) gene REV7 (also known as MAD2L2), which encodes the mutant REV7 protein REV7-V85E. Patient-derived cells demonstrated an extended FA phenotype, which included increased chromosome breaks and G2/M accumulation upon exposure to DNA crosslinking agents, γH2AX and 53BP1 foci accumulation, and enhanced p53/p21 activation relative to cells derived from healthy patients. Expression of WT REV7 restored normal cellular and functional phenotypes in the patient’s cells, and CRISPR/Cas9 inactivation of REV7 in a non-FA human cell line produced an FA phenotype. Finally, silencing Rev7 in primary hematopoietic cells impaired progenitor function, suggesting that the DNA repair defect underlies the development of BMF in FA. Taken together, our genetic and functional analyses identified REV7 as a previously undescribed FA gene, which we term FANCV. PMID:27500492

Computing Critical Properties with Yang-Yang Anomalies

NASA Astrophysics Data System (ADS)

Orkoulas, Gerassimos; Cerdeirina, Claudio; Fisher, Michael

2017-01-01

Computation of the thermodynamics of fluids in the critical region is a challenging task owing to divergence of the correlation length and lack of particle-hole symmetries found in Ising or lattice-gas models. In addition, analysis of experiments and simulations reveals a Yang-Yang (YY) anomaly which entails sharing of the specific heat singularity between the pressure and the chemical potential. The size of the YY anomaly is measured by the YY ratio Rμ =C μ /CV of the amplitudes of C μ = - T d2 μ /dT2 and of the total specific heat CV. A ``complete scaling'' theory, in which the pressure mixes into the scaling fields, accounts for the YY anomaly. In Phys. Rev. Lett. 116, 040601 (2016), compressible cell gas (CCG) models which exhibit YY and singular diameter anomalies, have been advanced for near-critical fluids. In such models, the individual cell volumes are allowed to fluctuate. The thermodynamics of CCGs can be computed through mapping onto the Ising model via the seldom-used great grand canonical ensemble. The computations indicate that local free volume fluctuations are the origins of the YY effects. Furthermore, local energy-volume coupling (to model water) is another crucial factor underlying the phenomena.

Expansion of effective wet bulb globe temperature for vapor impermeable protective clothing.

PubMed

Sakoi, Tomonori; Mochida, Tohru; Kurazumi, Yoshihito; Sawada, Shin-Ichi; Horiba, Yosuke; Kuwabara, Kohei

2018-01-01

The wet bulb globe temperature (WBGT) is an effective measure for risk screening to prevent heat dISOrders. However, a heat risk evaluation by WBGT requires adjustments depending on the clothing. In this study, we proposed a new effective WBGT (WBGT eff * ) for general vapor permeable clothing ensembles and vapor impermeable protective clothing that is applicable to occupants engaged in moderate intensity work with a metabolic heat production value of around 174W/m 2 . WBGT eff * enables the conversion of heat stress into the scale experienced by the occupant dressed in the basic clothing ensemble (work clothes) based on the heat balances for a human body. We confirmed that WBGT eff * was effective for expressing the critical thermal environments for the prescriptive zones for occupants wearing vapor impermeable protective clothing. Based on WBGT eff * , we succeeded in clarifying how the weights for natural wet bulb, globe, and air temperatures and the intercept changed depending on clothing properties and the surrounding environmental factors when heat stress is expressed by the weighted sum of natural wet bulb, globe, and air temperatures and the intercept. The weight of environmental temperatures (globe and air temperatures) for WBGT eff * for vapor impermeable protective clothing increased compared with that for general vapor permeable clothing, whereas that of the natural wet bulb temperature decreased. For WBGT eff * in outdoor conditions with a solar load, the weighting ratio of globe temperature increased and that of air temperature decreased with air velocity. Approximation equations of WBGT eff * were proposed for both general vapor permeable clothing ensembles and for vapor impermeable protective clothing. Copyright © 2017 Elsevier Ltd. All rights reserved.

Historeceptomic Fingerprints for Drug-Like Compounds.

PubMed

Shmelkov, Evgeny; Grigoryan, Arsen; Swetnam, James; Xin, Junyang; Tivon, Doreen; Shmelkov, Sergey V; Cardozo, Timothy

2015-01-01

Most drugs exert their beneficial and adverse effects through their combined action on several different molecular targets (polypharmacology). The true molecular fingerprint of the direct action of a drug has two components: the ensemble of all the receptors upon which a drug acts and their level of expression in organs/tissues. Conversely, the fingerprint of the adverse effects of a drug may derive from its action in bystander tissues. The ensemble of targets is almost always only partially known. Here we describe an approach improving upon and integrating both components: in silico identification of a more comprehensive ensemble of targets for any drug weighted by the expression of those receptors in relevant tissues. Our system combines more than 300,000 experimentally determined bioactivity values from the ChEMBL database and 4.2 billion molecular docking scores. We integrated these scores with gene expression data for human receptors across a panel of human tissues to produce drug-specific tissue-receptor (historeceptomics) scores. A statistical model was designed to identify significant scores, which define an improved fingerprint representing the unique activity of any drug. These multi-dimensional historeceptomic fingerprints describe, in a novel, intuitive, and easy to interpret style, the holistic, in vivo picture of the mechanism of any drug's action. Valuable applications in drug discovery and personalized medicine, including the identification of molecular signatures for drugs with polypharmacologic modes of action, detection of tissue-specific adverse effects of drugs, matching molecular signatures of a disease to drugs, target identification for bioactive compounds with unknown receptors, and hypothesis generation for drug/compound phenotypes may be enabled by this approach. The system has been deployed at drugable.org for access through a user-friendly web site.

Quantum-Critical Dynamics of the Skyrmion Lattice.

NASA Astrophysics Data System (ADS)

Green, Andrew G.

2002-03-01

Slightly away from exact filling of the lowest Landau level, the quantum Hall ferromagnet contains a finite density of magnetic vortices or Skyrmions[1,2]. These Skyrmions are expected to form a square lattice[3], the low energy excitations of which (translation/phonon modes and rotation/breathing modes) lead to dramatically enhanced nuclear relaxation[4,5]. Upon changing the filling fraction, the rotational modes undergo a quantum phase transition where zero-point fluctuations destroy the orientational order of the Skyrmions[4,6]. I will discuss the effect of this quantum critical point upon nuclear spin relaxation[7]. [1]S. L. Sondhi et al., Phys. Rev. B47, 16419 (1993). [2]S. E. Barrett et al., Phys. Rev. Lett. 74, 5112 (1995), A. Schmeller et al., Phys. Rev. Lett. 75, 4290 (1995). [3]L. Brey et al, Phys. Rev. Lett. 75, 2562 (1995). [4]R. Côté et al., Phys. Rev. Lett. 78, 4825 (1997). [5]R. Tycko et al., Science 268, 1460 (1995). [6]Yu V. Nazarov and A. V. Khaetskii, Phys. Rev. Lett. 80, 576 (1998). [7]A. G. Green, Phys. Rev. B61, R16 299 (2000).

A comparison of breeding and ensemble transform vectors for global ensemble generation

NASA Astrophysics Data System (ADS)

Deng, Guo; Tian, Hua; Li, Xiaoli; Chen, Jing; Gong, Jiandong; Jiao, Meiyan

2012-02-01

To compare the initial perturbation techniques using breeding vectors and ensemble transform vectors, three ensemble prediction systems using both initial perturbation methods but with different ensemble member sizes based on the spectral model T213/L31 are constructed at the National Meteorological Center, China Meteorological Administration (NMC/CMA). A series of ensemble verification scores such as forecast skill of the ensemble mean, ensemble resolution, and ensemble reliability are introduced to identify the most important attributes of ensemble forecast systems. The results indicate that the ensemble transform technique is superior to the breeding vector method in light of the evaluation of anomaly correlation coefficient (ACC), which is a deterministic character of the ensemble mean, the root-mean-square error (RMSE) and spread, which are of probabilistic attributes, and the continuous ranked probability score (CRPS) and its decomposition. The advantage of the ensemble transform approach is attributed to its orthogonality among ensemble perturbations as well as its consistence with the data assimilation system. Therefore, this study may serve as a reference for configuration of the best ensemble prediction system to be used in operation.

Reply to "Comment on `Particle path through a nested Mach-Zehnder interferometer' "

NASA Astrophysics Data System (ADS)

Griffiths, Robert B.

2018-02-01

While much of the technical analysis in the preceding Comment is correct, in the end it confirms the conclusion reached in my previous work [Phys. Rev. A 94, 032115 (2016), 10.1103/PhysRevA.94.032115]: A consistent histories analysis provides no support for the claim of counterfactual quantum communication put forward by Salih et al. [Phys. Rev. Lett. 110, 170502 (2013), 10.1103/PhysRevLett.110.170502].

α-decay systematics for superheavy elements

NASA Astrophysics Data System (ADS)

Duarte, S. B.; Teruya, N.

2012-01-01

In this Brief Report we extend the α-decay half-life calculation to the superheavy emitter region to verify whether these nuclei satisfy the recently observed systematics [D. N. Poenaru , Phys. Rev. CPRVCAN0556-281310.1103/PhysRevC.83.014601 83, 014601 (2011);C. Qi , Phys. Rev. CPRVCAN0556-281310.1103/PhysRevC.80.044326 80, 044326 (2009)]. To establish the systematics, we have used the α-cluster potential description, which was originally developed to study α decay in connection with nuclear energy level structure [B. Buck , Phys. Rev. CPRVCAN0556-281310.1103/PhysRevC.51.559 51, 559 (1995)]. The quantum-mechanical tunneling calculation has been employed to obtain the half-lives, showing that with this treatment the systematics are well reproduced in the region of heavy nuclei. Finally, the half-life calculation has been extended to the superheavy emitters to verify whether the systematics can still be observed.

The Proliferating Cell Nuclear Antigen (PCNA)-interacting Protein (PIP) Motif of DNA Polymerase η Mediates Its Interaction with the C-terminal Domain of Rev1*

PubMed Central

Boehm, Elizabeth M.; Powers, Kyle T.; Kondratick, Christine M.; Spies, Maria; Houtman, Jon C. D.; Washington, M. Todd

2016-01-01

Y-family DNA polymerases, such as polymerase η, polymerase ι, and polymerase κ, catalyze the bypass of DNA damage during translesion synthesis. These enzymes are recruited to sites of DNA damage by interacting with the essential replication accessory protein proliferating cell nuclear antigen (PCNA) and the scaffold protein Rev1. In most Y-family polymerases, these interactions are mediated by one or more conserved PCNA-interacting protein (PIP) motifs that bind in a hydrophobic pocket on the front side of PCNA as well as by conserved Rev1-interacting region (RIR) motifs that bind in a hydrophobic pocket on the C-terminal domain of Rev1. Yeast polymerase η, a prototypical translesion synthesis polymerase, binds both PCNA and Rev1. It possesses a single PIP motif but not an RIR motif. Here we show that the PIP motif of yeast polymerase η mediates its interactions both with PCNA and with Rev1. Moreover, the PIP motif of polymerase η binds in the hydrophobic pocket on the Rev1 C-terminal domain. We also show that the RIR motif of human polymerase κ and the PIP motif of yeast Msh6 bind both PCNA and Rev1. Overall, these findings demonstrate that PIP motifs and RIR motifs have overlapping specificities and can interact with both PCNA and Rev1 in structurally similar ways. These findings also suggest that PIP motifs are a more versatile protein interaction motif than previously believed. PMID:26903512

Selective suppression of autocatalytic caspase-3 driven by two-step transcriptional amplified human telomerase reverse transcriptase promoter on ovarian carcinoma growth in vitro and in mice.

PubMed

Song, Yue; Xin, Xing; Xia, Zhijun; Zhai, Xingyue; Shen, Keng

2014-07-01

The objective of our study was to construct recombinant adenovirus (rAd) AdHTVP2G5-rev-casp3, which expresses autocatalytic caspase-3 driven by human telomerase reverse transcriptase promoter (hTERTp) with a two-step transcription amplification (TSTA) system and investigate its antitumor effects on ovarian cancer in vitro and in vivo. Fluorescent detection was used to detect EGFP expression in various cells. Cell viabilities were determined using the Cell Counting Kit-8 and flow cytometry. RT-PCR and immunoblotting assays were used to detect cellular apoptotic activities. Tumor growth and survival of tumor-bearing mice were studied. The hTERTp-TSTA system showed the strongest activity in hTERT-positive cancer cells when compared with hTERTp and cytomeglovirus promoter (CMVp). In contrast, it showed no activity in hTERT‑negative HUVECs. AdHTVP2G5‑rev-casp3 markedly suppressed the survival of AO cells in a dose-dependent modality with a viability rate of 17.8 ± 3.5% at an MOI of 70, which was significantly lower than that by AdHT-rev-casp3 and Ad-rev-casp3 (rAds which express rev-caspase-3 driven by hTERTp and CMVp, respectively). In contrast, AdHTVP2G5‑rev-casp3 induced little HUVEC death with a viability rate of 92.7 ± 5.2% at the same MOI. Additionally, AdHTVP2G5-rev-casp3 (MOI=70) caused significant apoptosis in AO cells with an apoptotic rate of 42%. The tumor growth suppression rate of AdHTVP2G5-rev-casp3 was 81.52%, significantly higher than that of AdHT-rev-casp3 (54.94%) or Ad-rev-casp3 (21.35%). AdHTVP2G5-rev-casp3 significantly improved the survival of tumor-bearing mice with little liver damage, with a mean survival of 258 ± 28 days. These results showed that AdHTVP2G5-rev-casp3 caused effective apoptosis with significant tumor selectivity, strongly suppressed tumor growth and improved mouse survival with little liver toxicity. It can be a potent therapeutic agent for tumor targeted treatment of ovarian cancer.

The Ensembl REST API: Ensembl Data for Any Language.

PubMed

Yates, Andrew; Beal, Kathryn; Keenan, Stephen; McLaren, William; Pignatelli, Miguel; Ritchie, Graham R S; Ruffier, Magali; Taylor, Kieron; Vullo, Alessandro; Flicek, Paul

2015-01-01

We present a Web service to access Ensembl data using Representational State Transfer (REST). The Ensembl REST server enables the easy retrieval of a wide range of Ensembl data by most programming languages, using standard formats such as JSON and FASTA while minimizing client work. We also introduce bindings to the popular Ensembl Variant Effect Predictor tool permitting large-scale programmatic variant analysis independent of any specific programming language. The Ensembl REST API can be accessed at http://rest.ensembl.org and source code is freely available under an Apache 2.0 license from http://github.com/Ensembl/ensembl-rest. © The Author 2014. Published by Oxford University Press.

Ensembl BioMarts: a hub for data retrieval across taxonomic space.

PubMed

Kinsella, Rhoda J; Kähäri, Andreas; Haider, Syed; Zamora, Jorge; Proctor, Glenn; Spudich, Giulietta; Almeida-King, Jeff; Staines, Daniel; Derwent, Paul; Kerhornou, Arnaud; Kersey, Paul; Flicek, Paul

2011-01-01

For a number of years the BioMart data warehousing system has proven to be a valuable resource for scientists seeking a fast and versatile means of accessing the growing volume of genomic data provided by the Ensembl project. The launch of the Ensembl Genomes project in 2009 complemented the Ensembl project by utilizing the same visualization, interactive and programming tools to provide users with a means for accessing genome data from a further five domains: protists, bacteria, metazoa, plants and fungi. The Ensembl and Ensembl Genomes BioMarts provide a point of access to the high-quality gene annotation, variation data, functional and regulatory annotation and evolutionary relationships from genomes spanning the taxonomic space. This article aims to give a comprehensive overview of the Ensembl and Ensembl Genomes BioMarts as well as some useful examples and a description of current data content and future objectives. Database URLs: http://www.ensembl.org/biomart/martview/; http://metazoa.ensembl.org/biomart/martview/; http://plants.ensembl.org/biomart/martview/; http://protists.ensembl.org/biomart/martview/; http://fungi.ensembl.org/biomart/martview/; http://bacteria.ensembl.org/biomart/martview/.

Reply to "Comment on `Protecting bipartite entanglement by quantum interferences' "

NASA Astrophysics Data System (ADS)

Das, Sumanta; Agarwal, G. S.

2018-03-01

In a recent Comment Nair and Arun, Phys. Rev. A 97, 036301 (2018), 10.1103/PhysRevA.97.036301, it was concluded that the two-qubit entanglement protection reported in our work [Das and Agarwal, Phys. Rev. A 81, 052341 (2010), 10.1103/PhysRevA.81.052341] is erroneous. While we acknowledge the error in analytical results on concurrence when dipole matrix elements were unequal, the essential conclusions on entanglement protection are not affected.

Bibliography of Leishmania and Leishmanial Diseases. Volume 1

DTIC Science & Technology

1980-06-01

Sea 7 Rev. Med.- Yucatan Paulo, REVISTA MEDICA DE YUCATAN . Merida. Rev, Paliclin, Caracas Rev. Menn. Med. , Brazil REVISTA DE LA POLICLINICA, CARACAc...Parasit., 41(2):126-136. 799 pp. CHAKG, P. Y.; TENG, L. T.; SUNG, Y. (1957A) Interactions T. & LIU, Y. C. (1958A) Kala-azar between nutrition and...of nutrition in experimental Infectivan. Bact. Rev. , 13:99-134. CLINTON, B. A.; STAUBER, L. A.& CLRT .(1959A) Comparative PALCZUK, N. C. (1969A

Ensemble Density Functional Approach to the Quantum Hall Effect

NASA Astrophysics Data System (ADS)

Heinonen, O.

1997-03-01

The fractional quantum Hall effect (FQHE) occurs in a two-dimensional electron gas of density n when a strong magnetic field perpendicular to the plane of the electron gas takes on certain strengths B(n). At these magnetic field strengths the system is incompressible, i.e., there is a finite cost in energy for creating charge density fluctuations in the bulk. Even so the boundary of the electron gas supports gapless modes of density waves. The bulk energy gap arises because of the strong electron-electron interactions. There are very good models for infinite homogeneous systems and for the gapless excitations of the boundary of the electron gas. But in order to explain experiments on quantum Hall systems, including Hall bars and quantum dots, new approaches are needed which can accurately describe inhomogeneous systems, including Landau level mixing and the spin degree of freedom. One possibility is an ensemble density functional theory approach that we have developed.(O. Heinonen, M.I. Lubin, and M.D. Johnson, Phys. Rev. Lett. 75), 4110 (1995)(O. Heinonen, M.I. Lubin, and M.D. Johnson, Int. J. Quant. Chem, December 1996) We have applied this to study edge reconstructions of spin-polarized quantum dots. The results for a six-electron test case are in excellent agreement with numerical diagonalizations. For larger systems, compressible and incompressible strips appear as the magnetic field is increased from the region in which a dot forms a compact so-called maximum density droplet. We have recently included spin degree of freedom to study the stability of a maximum density droplet, and charge-spin textures in inhomogeneous systems. As an example, when the Zeeman coupling is decreased, we find that the maximum density droplet develops a spin-structured edge instability. This implies that the spin degree of freedom may play a significant role in the study of edge modes at low or moderate magnetic fields.

Avoidance of APOBEC3B-induced mutation by error-free lesion bypass

PubMed Central

Hoopes, James I.; Hughes, Amber L.; Hobson, Lauren A.; Cortez, Luis M.; Brown, Alexander J.

2017-01-01

Abstract APOBEC cytidine deaminases mutate cancer genomes by converting cytidines into uridines within ssDNA during replication. Although uracil DNA glycosylases limit APOBEC-induced mutation, it is unknown if subsequent base excision repair (BER) steps function on replication-associated ssDNA. Hence, we measured APOBEC3B-induced CAN1 mutation frequencies in yeast deficient in BER endonucleases or DNA damage tolerance proteins. Strains lacking Apn1, Apn2, Ntg1, Ntg2 or Rev3 displayed wild-type frequencies of APOBEC3B-induced canavanine resistance (CanR). However, strains without error-free lesion bypass proteins Ubc13, Mms2 and Mph1 displayed respective 4.9-, 2.8- and 7.8-fold higher frequency of APOBEC3B-induced CanR. These results indicate that mutations resulting from APOBEC activity are avoided by deoxyuridine conversion to abasic sites ahead of nascent lagging strand DNA synthesis and subsequent bypass by error-free template switching. We found this mechanism also functions during telomere re-synthesis, but with a diminished requirement for Ubc13. Interestingly, reduction of G to C substitutions in Ubc13-deficient strains uncovered a previously unknown role of Ubc13 in controlling the activity of the translesion synthesis polymerase, Rev1. Our results highlight a novel mechanism for error-free bypass of deoxyuridines generated within ssDNA and suggest that the APOBEC mutation signature observed in cancer genomes may under-represent the genomic damage these enzymes induce. PMID:28334887

Altered Sleep Homeostasis in Rev-erbα Knockout Mice

PubMed Central

Mang, Géraldine M.; La Spada, Francesco; Emmenegger, Yann; Chappuis, Sylvie; Ripperger, Jürgen A.; Albrecht, Urs; Franken, Paul

2016-01-01

Study Objectives: The nuclear receptor REV-ERBα is a potent, constitutive transcriptional repressor critical for the regulation of key circadian and metabolic genes. Recently, REV-ERBα's involvement in learning, neurogenesis, mood, and dopamine turnover was demonstrated suggesting a specific role in central nervous system functioning. We have previously shown that the brain expression of several core clock genes, including Rev-erbα, is modulated by sleep loss. We here test the consequences of a loss of REV-ERBα on the homeostatic regulation of sleep. Methods: EEG/EMG signals were recorded in Rev-erbα knockout (KO) mice and their wild type (WT) littermates during baseline, sleep deprivation, and recovery. Cortical gene expression measurements after sleep deprivation were contrasted to baseline. Results: Although baseline sleep/wake duration was remarkably similar, KO mice showed an advance of the sleep/wake distribution relative to the light-dark cycle. After sleep onset in baseline and after sleep deprivation, both EEG delta power (1–4 Hz) and sleep consolidation were reduced in KO mice indicating a slower increase of homeostatic sleep need during wakefulness. This slower increase might relate to the smaller increase in theta and gamma power observed in the waking EEG prior to sleep onset under both conditions. Indeed, the increased theta activity during wakefulness predicted delta power in subsequent NREM sleep. Lack of Rev-erbα increased Bmal1, Npas2, Clock, and Fabp7 expression, confirming the direct regulation of these genes by REV-ERBα also in the brain. Conclusions: Our results add further proof to the notion that clock genes are involved in sleep homeostasis. Because accumulating evidence directly links REV-ERBα to dopamine signaling the altered homeostatic regulation of sleep reported here are discussed in that context. Citation: Mang GM, La Spada F, Emmenegger Y, Chappuis S, Ripperger JA, Albrecht U, Franken P. Altered sleep homeostasis in Rev-erbα knockout mice. SLEEP 2016;39(3):589–601. PMID:26564124

HIV-1 Rev protein specifies the viral RNA export pathway by suppressing TAP/NXF1 recruitment

PubMed Central

Taniguchi, Ichiro; Mabuchi, Naoto; Ohno, Mutsuhito

2014-01-01

Nuclear RNA export pathways in eukaryotes are often linked to the fate of a given RNA. Therefore, the choice of export pathway should be well-controlled to avoid an unfavorable effect on gene expression. Although some RNAs could be exported by more than one pathway, little is known about how the choice is regulated. This issue is highlighted when the human immunodeficiency virus type 1 (HIV-1) Rev protein induces the export of singly spliced and unspliced HIV-1 transcripts. How these RNAs are exported is not well understood because such transcripts should have the possibility of utilizing CRM1-dependent export via Rev or cellular TAP/NXF1-dependent export via the transcription/export (TREX) complex, or both. Here we found that Rev suppressed TAP/NXF1-dependent export of model RNA substrates that recapitulated viral transcripts. In this effect, Rev interacted with the cap-binding complex and inhibited the recruitment of the TREX complex. Thus, Rev controls the identity of the factor occupying the cap-proximal region that determines the RNA export pathway. This ribonucleoprotein remodeling activity of Rev may favor viral gene expression. PMID:24753416

Magnetic and structural X-ray dichroïsms of metallic multilayers

NASA Astrophysics Data System (ADS)

Pizzini, Stefania; Fontaine, A.; Baudelet, F.; Minr, S.; Giorgetti, C.; Dartyge, E.; Bobo, J. F.; Piecuch, M.

1995-05-01

Fe/Cu and Co/Cu multilayers are intensively studied because of their exceptional magnetic properties, i.e., their giant magnetoresistance and the oscillations of the magnetic coupling between magnetic layers as a function of the thickness of the copper spacer [S.S. Parkin et al., Phys. Rev. Lett. 66 (1991) 2152; F. Petroff et al., Phys. Rev. B 44 (1991) 5355]. Spectroscopic approaches to the understanding of the coupling of ferromagnetic layers through a noble metal layer have been recently introduced, in particular spin-resolved photoemission [N.B. Brookes et al., Phys. Rev. Lett. 67 (1991) 354; C. Carbone et al., PRL 71 (1993) 2805] inverse photoemission [J.E. Ortega et al., Phys. Rev. Lett. 69 (1992) 844; Phys. Rev. B 47 (1993) 1540] and magnetic circular dichroism [S. Pizzini et al., MRS Symp. Proc., vol. 313 (1993); M.G. Samant et al. Phys. Rev. Lett. 72 (1994) 2152; S. Pizzini et al., Phys. Rev. Lett. 74 (1995) 1470]. X-ray absorption spectroscopy appears to be effective both for determination of the local structure, specific to the bidimensionality of the system but also for the electron symmetry-dependent evaluation of the spin polarisation of the noble metal as well as the magnetic element.

RNA helicase MOV10 functions as a co-factor of HIV-1 Rev to facilitate Rev/RRE-dependent nuclear export of viral mRNAs.

PubMed

Huang, Feng; Zhang, Junsong; Zhang, Yijun; Geng, Guannan; Liang, Juanran; Li, Yingniang; Chen, Jingliang; Liu, Chao; Zhang, Hui

2015-12-01

Human immunodeficiency virus type 1 (HIV-1) exploits multiple host factors during its replication. The REV/RRE-dependent nuclear export of unspliced/partially spliced viral transcripts needs the assistance of host proteins. Recent studies have shown that MOV10 overexpression inhibited HIV-1 replication at various steps. However, the endogenous MOV10 was required in certain step(s) of HIV-1 replication. In this report, we found that MOV10 potently enhances the nuclear export of viral mRNAs and subsequently increases the expression of Gag protein and other late products through affecting the Rev/RRE axis. The co-immunoprecipitation analysis indicated that MOV10 interacts with Rev in an RNA-independent manner. The DEAG-box of MOV10 was required for the enhancement of Rev/RRE-dependent nuclear export and the DEAG-box mutant showed a dominant-negative activity. Our data propose that HIV-1 utilizes the anti-viral factor MOV10 to function as a co-factor of Rev and demonstrate the complicated effects of MOV10 on HIV-1 life cycle. Copyright © 2015 Elsevier Inc. All rights reserved.

Biological responses of beef steers to steroidal implants and zilpaterol hydrochloride.

PubMed

Parr, S L; Brown, T R; Ribeiro, F R B; Chung, K Y; Hutcheson, J P; Blackwell, B R; Smith, P N; Johnson, B J

2014-08-01

British × Continental steers (n = 168; 7 pens/treatment; initial BW = 362 kg) were used to evaluate the effect of dose/payout pattern of trenbolone acetate (TBA) and estradiol-17β (E2) and feeding of zilpaterol hydrochloride (ZH) on serum urea-N (SUN), NEFA, IGF-I, and E2 concentrations and LM mRNA expression of the estrogen (ER), androgen (ANR), IGF-I (IGF-IR), β1-adrenergic (β1-AR), and β2-adrenergic (β2-AR) receptors and IGF-I. A randomized complete block design was used with a 3 × 2 factorial arrangement of treatments. Main effects were implant (no implant [NI], Revalor-S [REV-S; 120 mg TBA + 24 mg E2], and Revalor-XS [REV-X; 200 mg TBA + 40 mg E2]) and ZH (0 or 8.3 mg/kg of DM for 20 d with a 3-d withdrawal). Steers were fed for 153 or 174 d. Blood was collected (2 steers/pen) at d -1, 2, 6, 13, 27, 55, 83, 111, and 131 relative to implanting; LM biopsies (1 steer/pen) were collected at d -1, 27, 55, and 111. Blood and LM samples were collected at d -1, 11, and 19 relative to ZH feeding. A greater dose of TBA + E2 in combination with ZH increased ADG and HCW in an additive manner, suggesting a different mechanism of action for ZH and steroidal implants. Implanting decreased (P < 0.05) SUN from d 2 through 131. Feeding ZH decreased (P < 0.05) SUN. Serum NEFA concentrations were not affected by implants (P = 0.44). There was a day × ZH interaction (P = 0.06) for NEFA; ZH steers had increased (P < 0.01) NEFA concentrations at d 11 of ZH feeding. Serum E2 was greater (P < 0.05) for implanted steers by d 27. Serum trenbolone-17β was greater (P < 0.05) for implanted steers by d 2 followed by a typical biphasic release rate, with a secondary peak at d 111 for REV-X (P < 0.05) implanted steers. Implanting did not affect mRNA expression of the ANR or ER, but the IGF-IR and the β1-AR and β2-AR were less (P < 0.05) for REV-S than NI at d 55 and β2-AR mRNA was less (P < 0.05) for REV-S than for REV-X. Expression of the IGF-IR and the β1-AR at d 111 was greater (P< 0.05) for REV-X than for REV-S and NI at d 111, and the β2-AR was less (P< 0.05) for REV-S than for REV-X. Feeding ZH did not affect mRNA expression of the β1-AR and β2-AR. Both implanting and feeding ZH decreased SUN, but a greater dose of TBA + E2 did not result in further decreases. In addition, feeding ZH increased serum NEFA concentrations. Metabolic changes resulting from implanting and feeding ZH may aid in explaining steer performance and carcass responses to these growth promotants.

User Instructions for the Systems Assessment Capability, Rev. 1, Computer Codes Volume 3: Utility Codes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eslinger, Paul W.; Aaberg, Rosanne L.; Lopresti, Charles A.

2004-09-14

This document contains detailed user instructions for a suite of utility codes developed for Rev. 1 of the Systems Assessment Capability. The suite of computer codes for Rev. 1 of Systems Assessment Capability performs many functions.

Low Temperature Power Coating (LTPC) Phase 2 Laboratory Test Plan and Procedures for PACAF (Rev D)

DTIC Science & Technology

2018-03-20

Δa*, LTPC Phase II Laboratory Test Plan and Procedures Rev D (CDRL A004) BATTELLE | 20 March 2018 | 6 Δb* and ΔE will be calculated post ...BATTELLE | CONTRACT NUMBER: FA8532-17-C-0008 (CDRL A004) LTPC Phase II Laboratory Test Plan and Procedures (Rev D) Prepared by... Test Plan and Procedures Rev D (CDRL A004) BATTELLE | 20 March 2018 | i List of Acronyms AGE Aircraft Ground Equipment ASTM American

Multiplicity-dependent and nonbinomial efficiency corrections for particle number cumulants

NASA Astrophysics Data System (ADS)

Bzdak, Adam; Holzmann, Romain; Koch, Volker

2016-12-01

In this article we extend previous work on efficiency corrections for cumulant measurements [Bzdak and Koch, Phys. Rev. C 86, 044904 (2012), 10.1103/PhysRevC.86.044904; Phys. Rev. C 91, 027901 (2015), 10.1103/PhysRevC.91.027901]. We will discuss the limitations of the methods presented in these papers. Specifically we will consider multiplicity dependent efficiencies as well as nonbinomial efficiency distributions. We will discuss the most simple and straightforward methods to implement those corrections.

Aging and Rejuvenation with Fractional Derivatives

DTIC Science & Technology

2004-09-10

Chechkin , J. Klafter, V . Yu . Gonchar , R. Metzler, and L. V . Tanatarov, Phys. Rev. E 67, 010102(R) (2003). [12] I. M. Sokolov and R. Metzler, Phys. Rev. E 67...051106 (2001). [7] A . V . Chechkin , R. Gorenflo, and I. M. Sokolov, Phys. Rev. E 66, 046129 (2002). [8] J. Bisquert, Phys. Rev. Lett. 91, 010602 (2003...9] R. Metzler and J. Klafter, J. Phys. Chem. B 104 3851 (2000). [10] E. Barkai and R. J. Silbey, J. Phys. Chem. B 104 3866 (2000).

Reply to "Comment on `Troublesome aspects of the Renyi-MaxEnt treatment' "

NASA Astrophysics Data System (ADS)

Plastino, A.; Rocca, M. C.; Pennini, F.

2017-11-01

This Reply is intended as a refutation of the preceding Comment [Oikonomou and Bagci, Phys. Rev. E 96, 056101 (2017), 10.1103/PhysRevE.96.056101] on our paper [Plastino et al., Phys. Rev. E 94, 012145 (2016)., 10.1103/PhysRevE.94.012145]. We show that the Tsallis probability distribution of our paper does not coincide with the Tsallis distribution studied by Oikonomou and Bagci. Consequently, their findings do not apply to our paper.

Reply to "Comment on 'Troublesome aspects of the Renyi-MaxEnt treatment' ".

PubMed

Plastino, A; Rocca, M C; Pennini, F

2017-11-01

This Reply is intended as a refutation of the preceding Comment [Oikonomou and Bagci, Phys. Rev. E 96, 056101 (2017)10.1103/PhysRevE.96.056101] on our paper [Plastino et al., Phys. Rev. E 94, 012145 (2016).1539-375510.1103/PhysRevE.94.012145]. We show that the Tsallis probability distribution of our paper does not coincide with the Tsallis distribution studied by Oikonomou and Bagci. Consequently, their findings do not apply to our paper.

Optimized Chemical Probes for REV-ERBα

PubMed Central

Trump, Ryan P.; Bresciani, Stefano; Cooper, Anthony W. J.; Tellam, James P.; Wojno, Justyna; Blaikley, John; Orband-Miller, Lisa A.; Kashatus, Jennifer A.; Dawson, Helen C.; Loudon, Andrew; Ray, David; Grant, Daniel; Farrow, Stuart N.; Willson, Timothy M.; Tomkinson, Nicholas C. O.

2015-01-01

REV-ERBα has emerged as an important target for regulation of circadian rhythm and its associated physiology. Herein, we report on the optimization of a series of REV-ERBα agonists based on GSK4112 (1) for potency, selectivity, and bioavailability. Potent REV-ERBα agonists 4, 10, 16, and 23 are detailed for their ability to suppress BMAL and IL-6 expression from human cells while also demonstrating excellent selectivity over LXRα. Amine 4 demonstrated in vivo bioavailability after either IV or oral dosing. PMID:23656296

Multiplicity-dependent and nonbinomial efficiency corrections for particle number cumulants

DOE PAGES

Bzdak, Adam; Holzmann, Romain; Koch, Volker

2016-12-19

Here, we extend previous work on efficiency corrections for cumulant measurements [Bzdak and Koch, Phys. Rev. C 86, 044904 (2012)PRVCAN0556-281310.1103/PhysRevC.86.044904; Phys. Rev. C 91, 027901 (2015)PRVCAN0556-281310.1103/PhysRevC.91.027901]. We will then discuss the limitations of the methods presented in these papers. Specifically we will consider multiplicity dependent efficiencies as well as nonbinomial efficiency distributions. We will discuss the most simple and straightforward methods to implement those corrections.

Stabilizing IkappaBalpha by "consensus" design.

PubMed

Ferreiro, Diego U; Cervantes, Carla F; Truhlar, Stephanie M E; Cho, Samuel S; Wolynes, Peter G; Komives, Elizabeth A

2007-01-26

IkappaBalpha is the major regulator of transcription factor NF-kappaB function. The ankyrin repeat region of IkappaBalpha mediates specific interactions with NF-kappaB dimers, but ankyrin repeats 1, 5 and 6 display a highly dynamic character when not in complex with NF-kappaB. Using chemical denaturation, we show here that IkappaBalpha displays two folding transitions: a non-cooperative conversion under weak perturbation, and a major cooperative folding phase upon stronger insult. Taking advantage of a native Trp residue in ankyrin repeat (AR) 6 and engineered Trp residues in AR2, AR4 and AR5, we show that the cooperative transition involves AR2 and AR3, while the non-cooperative transition involves AR5 and AR6. The major structural transition can be affected by single amino acid substitutions converging to the "consensus" ankyrin repeat sequence, increasing the native state stability significantly. We further characterized the structural and dynamic properties of the native state ensemble of IkappaBalpha and the stabilized mutants by H/(2)H exchange mass spectrometry and NMR. The solution experiments were complemented with molecular dynamics simulations to elucidate the microscopic origins of the stabilizing effect of the consensus substitutions, which can be traced to the fast conformational dynamics of the folded ensemble.

Should future wind speed changes be taken into account in wind farm development?

NASA Astrophysics Data System (ADS)

Devis, Annemarie; Van Lipzig, Nicole P. M.; Demuzere, Matthias

2018-06-01

Accurate wind resource assessments are crucial in the development of wind farm projects. However, it is common practice to estimate the wind yield over the next 20 years from short-term measurements and reanalysis data of the past 20 years, even though wind climatology is expected to change under the future climate. The present work examines future changes in wind power output over Europe using an ensemble of ESMs. The power output is calculated using the entire wind speed PDF and a non-constant power conversion coefficient. Based on this method, the ESM ensemble projects changes in near-future power outputs with a spatially varying magnitude between ‑12% and 8%. The most extreme changes occur over the Mediterranean region. For the first time, the sensitivity of these future change in power output to the type of wind turbine is also investigated. The analysis reveals that the projected wind power changes may vary in up to half of their magnitude, depending on the type of turbine and region of interest. As such, we recommend that wind industries fully account for projected near-future changes in wind power output by taking them into account as a well-defined loss/gain and uncertainty when estimating the yield of a future wind farm.

Seasonal hydroclimatic impacts of Brazilian sugar cane expansion

NASA Astrophysics Data System (ADS)

Georgescu, M.; Lobell, D. B.; Field, C. B.; Mahalov, A.

2012-12-01

Brazil is the leading producer of sugar cane in the world with roughly half used for ethanol production. Because of suitable climatic growing conditions, the majority of biofuel production is derived from sugar plantations in southeastern states. Anticipated increases in global demand for biofuels are expected to lead to future sugar cane expansion extending into Brazilian pasturelands and native cerrado. Prior to undergoing large-scale expansion an evaluation of impacts on the region's hydroclimate is warranted. Using a suite of multi-year ensemble-based simulations with the WRF modeling system, we quantify hydroclimatic consequences of sugar cane expansion across portions of south-central Brazil. Conversion from current land use to sugar cane causes opposing seasonal impacts on near-surface temperature. Proggresively greater cooling is simulated during the course of the growing season, followed by an abrupt warming shift post-harvest. Although seasonal impacts on near-surface temperature are significant, with cooling of 1C occurring during the peak of the growing season followed by warming of similar magnitude, impacts are small when annually averaged. Ensemble mean differences between the imposed sugar cane expansion and non-expansion scenario are suggestive of a drying precipitation trend, yet large uncertainty among individual members precludes definitive statements about impacts on the region's rainfall.

Unveiling Inherent Degeneracies in Determining Population-weighted Ensembles of Inter-domain Orientational Distributions Using NMR Residual Dipolar Couplings: Application to RNA Helix Junction Helix Motifs

PubMed Central

Yang, Shan; Al-Hashimi, Hashim M.

2016-01-01

A growing number of studies employ time-averaged experimental data to determine dynamic ensembles of biomolecules. While it is well known that different ensembles can satisfy experimental data to within error, the extent and nature of these degeneracies, and their impact on the accuracy of the ensemble determination remains poorly understood. Here, we use simulations and a recently introduced metric for assessing ensemble similarity to explore degeneracies in determining ensembles using NMR residual dipolar couplings (RDCs) with specific application to A-form helices in RNA. Various target ensembles were constructed representing different domain-domain orientational distributions that are confined to a topologically restricted (<10%) conformational space. Five independent sets of ensemble averaged RDCs were then computed for each target ensemble and a ‘sample and select’ scheme used to identify degenerate ensembles that satisfy RDCs to within experimental uncertainty. We find that ensembles with different ensemble sizes and that can differ significantly from the target ensemble (by as much as ΣΩ ~ 0.4 where ΣΩ varies between 0 and 1 for maximum and minimum ensemble similarity, respectively) can satisfy the ensemble averaged RDCs. These deviations increase with the number of unique conformers and breadth of the target distribution, and result in significant uncertainty in determining conformational entropy (as large as 5 kcal/mol at T = 298 K). Nevertheless, the RDC-degenerate ensembles are biased towards populated regions of the target ensemble, and capture other essential features of the distribution, including the shape. Our results identify ensemble size as a major source of uncertainty in determining ensembles and suggest that NMR interactions such as RDCs and spin relaxation, on their own, do not carry the necessary information needed to determine conformational entropy at a useful level of precision. The framework introduced here provides a general approach for exploring degeneracies in ensemble determination for different types of experimental data. PMID:26131693

Involvement of the Clock Gene Rev-erb alpha in the Regulation of Glucagon Secretion in Pancreatic Alpha-Cells

PubMed Central

Vieira, Elaine; Marroquí, Laura; Figueroa, Ana Lucia C.; Merino, Beatriz; Fernandez-Ruiz, Rebeca; Nadal, Angel; Burris, Thomas P.; Gomis, Ramon; Quesada, Ivan

2013-01-01

Disruption of pancreatic clock genes impairs pancreatic beta-cell function, leading to the onset of diabetes. Despite the importance of pancreatic alpha-cells in the regulation of glucose homeostasis and in diabetes pathophysiology, nothing is known about the role of clock genes in these cells. Here, we identify the clock gene Rev-erb alpha as a new intracellular regulator of glucagon secretion. Rev-erb alpha down-regulation by siRNA (60–70% inhibition) in alphaTC1-9 cells inhibited low-glucose induced glucagon secretion (p<0.05) and led to a decrease in key genes of the exocytotic machinery. The Rev-erb alpha agonist GSK4112 increased glucagon secretion (1.6 fold) and intracellular calcium signals in alphaTC1-9 cells and mouse primary alpha-cells, whereas the Rev-erb alpha antagonist SR8278 produced the opposite effect. At 0.5 mM glucose, alphaTC1-9 cells exhibited intrinsic circadian Rev-erb alpha expression oscillations that were inhibited by 11 mM glucose. In mouse primary alpha-cells, glucose induced similar effects (p<0.001). High glucose inhibited key genes controlled by AMPK such as Nampt, Sirt1 and PGC-1 alpha in alphaTC1-9 cells (p<0.05). AMPK activation by metformin completely reversed the inhibitory effect of glucose on Nampt-Sirt1-PGC-1 alpha and Rev-erb alpha. Nampt inhibition decreased Sirt1, PGC-1 alpha and Rev-erb alpha mRNA expression (p<0.01) and glucagon release (p<0.05). These findings identify Rev-erb alpha as a new intracellular regulator of glucagon secretion via AMPK/Nampt/Sirt1 pathway. PMID:23936124

Altered Sleep Homeostasis in Rev-erbα Knockout Mice.

PubMed

Mang, Géraldine M; La Spada, Francesco; Emmenegger, Yann; Chappuis, Sylvie; Ripperger, Jürgen A; Albrecht, Urs; Franken, Paul

2016-03-01

The nuclear receptor REV-ERBα is a potent, constitutive transcriptional repressor critical for the regulation of key circadian and metabolic genes. Recently, REV-ERBα's involvement in learning, neurogenesis, mood, and dopamine turnover was demonstrated suggesting a specific role in central nervous system functioning. We have previously shown that the brain expression of several core clock genes, including Rev-erbα, is modulated by sleep loss. We here test the consequences of a loss of REV-ERBα on the homeostatic regulation of sleep. EEG/EMG signals were recorded in Rev-erbα knockout (KO) mice and their wild type (WT) littermates during baseline, sleep deprivation, and recovery. Cortical gene expression measurements after sleep deprivation were contrasted to baseline. Although baseline sleep/wake duration was remarkably similar, KO mice showed an advance of the sleep/wake distribution relative to the light-dark cycle. After sleep onset in baseline and after sleep deprivation, both EEG delta power (1-4 Hz) and sleep consolidation were reduced in KO mice indicating a slower increase of homeostatic sleep need during wakefulness. This slower increase might relate to the smaller increase in theta and gamma power observed in the waking EEG prior to sleep onset under both conditions. Indeed, the increased theta activity during wakefulness predicted delta power in subsequent NREM sleep. Lack of Rev-erbα increased Bmal1, Npas2, Clock, and Fabp7 expression, confirming the direct regulation of these genes by REV-ERBα also in the brain. Our results add further proof to the notion that clock genes are involved in sleep homeostasis. Because accumulating evidence directly links REV-ERBα to dopamine signaling the altered homeostatic regulation of sleep reported here are discussed in that context. © 2016 Associated Professional Sleep Societies, LLC.

Background field removal technique using regularization enabled sophisticated harmonic artifact reduction for phase data with varying kernel sizes.

PubMed

Kan, Hirohito; Kasai, Harumasa; Arai, Nobuyuki; Kunitomo, Hiroshi; Hirose, Yasujiro; Shibamoto, Yuta

2016-09-01

An effective background field removal technique is desired for more accurate quantitative susceptibility mapping (QSM) prior to dipole inversion. The aim of this study was to evaluate the accuracy of regularization enabled sophisticated harmonic artifact reduction for phase data with varying spherical kernel sizes (REV-SHARP) method using a three-dimensional head phantom and human brain data. The proposed REV-SHARP method used the spherical mean value operation and Tikhonov regularization in the deconvolution process, with varying 2-14mm kernel sizes. The kernel sizes were gradually reduced, similar to the SHARP with varying spherical kernel (VSHARP) method. We determined the relative errors and relationships between the true local field and estimated local field in REV-SHARP, VSHARP, projection onto dipole fields (PDF), and regularization enabled SHARP (RESHARP). Human experiment was also conducted using REV-SHARP, VSHARP, PDF, and RESHARP. The relative errors in the numerical phantom study were 0.386, 0.448, 0.838, and 0.452 for REV-SHARP, VSHARP, PDF, and RESHARP. REV-SHARP result exhibited the highest correlation between the true local field and estimated local field. The linear regression slopes were 1.005, 1.124, 0.988, and 0.536 for REV-SHARP, VSHARP, PDF, and RESHARP in regions of interest on the three-dimensional head phantom. In human experiments, no obvious errors due to artifacts were present in REV-SHARP. The proposed REV-SHARP is a new method combined with variable spherical kernel size and Tikhonov regularization. This technique might make it possible to be more accurate backgroud field removal and help to achive better accuracy of QSM. Copyright © 2016 Elsevier Inc. All rights reserved.

Pharmacological Targeting the REV-ERBs in Sleep/Wake Regulation

PubMed Central

Amador, Ariadna; Huitron-Resendiz, Salvador; Roberts, Amanda J.; Kamenecka, Theodore M.; Solt, Laura A.; Burris, Thomas P.

2016-01-01

The circadian clock maintains appropriate timing for a wide range of behaviors and physiological processes. Circadian behaviors such as sleep and wakefulness are intrinsically dependent on the precise oscillation of the endogenous molecular machinery that regulates the circadian clock. The identical core clock machinery regulates myriad endocrine and metabolic functions providing a link between sleep and metabolic health. The REV-ERBs (REV-ERBα and REV-ERBβ) are nuclear receptors that are key regulators of the molecular clock and have been successfully targeted using small molecule ligands. Recent studies in mice suggest that REV-ERB-specific synthetic agonists modulate metabolic activity as well as alter sleep architecture, inducing wakefulness during the light period. Therefore, these small molecules represent unique tools to extensively study REV-ERB regulation of sleep and wakefulness. In these studies, our aim was to further investigate the therapeutic potential of targeting the REV-ERBs for regulation of sleep by characterizing efficacy, and optimal dosing time of the REV-ERB agonist SR9009 using electroencephalographic (EEG) recordings. Applying different experimental paradigms in mice, our studies establish that SR9009 does not lose efficacy when administered more than once a day, nor does tolerance develop when administered once a day over a three-day dosing regimen. Moreover, through use of a time response paradigm, we determined that although there is an optimal time for administration of SR9009 in terms of maximal efficacy, there is a 12-hour window in which SR9009 elicited a response. Our studies indicate that the REV-ERBs are potential therapeutic targets for treating sleep problems as those encountered as a consequence of shift work or jet lag. PMID:27603791

Potent Inhibition of Human Immunodeficiency Virus Type 1 Replication by an Intracellular Anti-Rev Single-Chain Antibody

NASA Astrophysics Data System (ADS)

Duan, Lingxun; Bagasra, Omar; Laughlin, Mark A.; Oakes, Joseph W.; Pomerantz, Roger J.

1994-05-01

Human immunodeficiency virus type 1 (HIV-1) has a complex life cycle, which has made it a difficult target for conventional therapeutic modalities. A single-chain antibody moiety, directed against the HIV-1 regulatory protein Rev, which rescues unspliced viral RNA from the nucleus of infected cells, has now been developed. This anti-Rev single-chain construct (SFv) consists of both light and heavy chain variable regions of an anti-Rev monoclonal antibody, which, when expressed intracellularly within human cells, potently inhibits HIV-1 replication. This intracellular SFv molecule is demonstrated to specifically antagonize Rev function. Thus, intracellular SFv expression, against a retroviral regulatory protein, may be useful as a gene therapeutic approach to combat HIV-1 infections.

REV-ERB and ROR nuclear receptors as drug targets

PubMed Central

Kojetin, Douglas J.; Burris, Thomas P.

2016-01-01

The nuclear receptors REV-ERB (consisting of REV-ERBα and REV-ERBβ) and retinoic acid receptor-related orphan receptors (RORs; consisting of RORα, RORβ and RORγ) are involved in many physiological processes, including regulation of metabolism, development and immunity as well as the circadian rhythm. The recent characterization of endogenous ligands for these former orphan nuclear receptors has stimulated the development of synthetic ligands and opened up the possibility of targeting these receptors to treat several diseases, including diabetes, atherosclerosis, autoimmunity and cancer. This Review focuses on the latest developments in ROR and REV-ERB pharmacology indicating that these nuclear receptors are druggable targets and that ligands targeting these receptors may be useful in the treatment of several disorders. PMID:24577401

Residue-level global and local ensemble-ensemble comparisons of protein domains.

PubMed

Clark, Sarah A; Tronrud, Dale E; Karplus, P Andrew

2015-09-01

Many methods of protein structure generation such as NMR-based solution structure determination and template-based modeling do not produce a single model, but an ensemble of models consistent with the available information. Current strategies for comparing ensembles lose information because they use only a single representative structure. Here, we describe the ENSEMBLATOR and its novel strategy to directly compare two ensembles containing the same atoms to identify significant global and local backbone differences between them on per-atom and per-residue levels, respectively. The ENSEMBLATOR has four components: eePREP (ee for ensemble-ensemble), which selects atoms common to all models; eeCORE, which identifies atoms belonging to a cutoff-distance dependent common core; eeGLOBAL, which globally superimposes all models using the defined core atoms and calculates for each atom the two intraensemble variations, the interensemble variation, and the closest approach of members of the two ensembles; and eeLOCAL, which performs a local overlay of each dipeptide and, using a novel measure of local backbone similarity, reports the same four variations as eeGLOBAL. The combination of eeGLOBAL and eeLOCAL analyses identifies the most significant differences between ensembles. We illustrate the ENSEMBLATOR's capabilities by showing how using it to analyze NMR ensembles and to compare NMR ensembles with crystal structures provides novel insights compared to published studies. One of these studies leads us to suggest that a "consistency check" of NMR-derived ensembles may be a useful analysis step for NMR-based structure determinations in general. The ENSEMBLATOR 1.0 is available as a first generation tool to carry out ensemble-ensemble comparisons. © 2015 The Protein Society.

Residue-level global and local ensemble-ensemble comparisons of protein domains

PubMed Central

Clark, Sarah A; Tronrud, Dale E; Andrew Karplus, P

2015-01-01

Many methods of protein structure generation such as NMR-based solution structure determination and template-based modeling do not produce a single model, but an ensemble of models consistent with the available information. Current strategies for comparing ensembles lose information because they use only a single representative structure. Here, we describe the ENSEMBLATOR and its novel strategy to directly compare two ensembles containing the same atoms to identify significant global and local backbone differences between them on per-atom and per-residue levels, respectively. The ENSEMBLATOR has four components: eePREP (ee for ensemble-ensemble), which selects atoms common to all models; eeCORE, which identifies atoms belonging to a cutoff-distance dependent common core; eeGLOBAL, which globally superimposes all models using the defined core atoms and calculates for each atom the two intraensemble variations, the interensemble variation, and the closest approach of members of the two ensembles; and eeLOCAL, which performs a local overlay of each dipeptide and, using a novel measure of local backbone similarity, reports the same four variations as eeGLOBAL. The combination of eeGLOBAL and eeLOCAL analyses identifies the most significant differences between ensembles. We illustrate the ENSEMBLATOR's capabilities by showing how using it to analyze NMR ensembles and to compare NMR ensembles with crystal structures provides novel insights compared to published studies. One of these studies leads us to suggest that a “consistency check” of NMR-derived ensembles may be a useful analysis step for NMR-based structure determinations in general. The ENSEMBLATOR 1.0 is available as a first generation tool to carry out ensemble-ensemble comparisons. PMID:26032515

The Ensembl REST API: Ensembl Data for Any Language

PubMed Central

Yates, Andrew; Beal, Kathryn; Keenan, Stephen; McLaren, William; Pignatelli, Miguel; Ritchie, Graham R. S.; Ruffier, Magali; Taylor, Kieron; Vullo, Alessandro; Flicek, Paul

2015-01-01

Motivation: We present a Web service to access Ensembl data using Representational State Transfer (REST). The Ensembl REST server enables the easy retrieval of a wide range of Ensembl data by most programming languages, using standard formats such as JSON and FASTA while minimizing client work. We also introduce bindings to the popular Ensembl Variant Effect Predictor tool permitting large-scale programmatic variant analysis independent of any specific programming language. Availability and implementation: The Ensembl REST API can be accessed at http://rest.ensembl.org and source code is freely available under an Apache 2.0 license from http://github.com/Ensembl/ensembl-rest. Contact: ayates@ebi.ac.uk or flicek@ebi.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25236461

Complete set of essential parameters of an effective theory

NASA Astrophysics Data System (ADS)

Ioffe, M. V.; Vereshagin, V. V.

2018-04-01

The present paper continues the series [V. V. Vereshagin, True self-energy function and reducibility in effective scalar theories, Phys. Rev. D 89, 125022 (2014); , 10.1103/PhysRevD.89.125022A. Vereshagin and V. Vereshagin, Resultant parameters of effective theory, Phys. Rev. D 69, 025002 (2004); , 10.1103/PhysRevD.69.025002K. Semenov-Tian-Shansky, A. Vereshagin, and V. Vereshagin, S-matrix renormalization in effective theories, Phys. Rev. D 73, 025020 (2006), 10.1103/PhysRevD.73.025020] devoted to the systematic study of effective scattering theories. We consider matrix elements of the effective Lagrangian monomials (in the interaction picture) of arbitrary high dimension D and show that the full set of corresponding coupling constants contains parameters of both kinds: essential and redundant. Since it would be pointless to formulate renormalization prescriptions for redundant parameters, it is necessary to select the full set of the essential ones. This is done in the present paper for the case of the single scalar field.

Reversible polymorphism-aware phylogenetic models and their application to tree inference.

PubMed

Schrempf, Dominik; Minh, Bui Quang; De Maio, Nicola; von Haeseler, Arndt; Kosiol, Carolin

2016-10-21

We present a reversible Polymorphism-Aware Phylogenetic Model (revPoMo) for species tree estimation from genome-wide data. revPoMo enables the reconstruction of large scale species trees for many within-species samples. It expands the alphabet of DNA substitution models to include polymorphic states, thereby, naturally accounting for incomplete lineage sorting. We implemented revPoMo in the maximum likelihood software IQ-TREE. A simulation study and an application to great apes data show that the runtimes of our approach and standard substitution models are comparable but that revPoMo has much better accuracy in estimating trees, divergence times and mutation rates. The advantage of revPoMo is that an increase of sample size per species improves estimations but does not increase runtime. Therefore, revPoMo is a valuable tool with several applications, from speciation dating to species tree reconstruction. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Binding and thermodynamics of REV peptide-ctDNA interaction.

PubMed

Upadhyay, Santosh Kumar

2017-03-01

The thermodynamics of DNA-ligand binding is important as it provides useful information to understand the details of binding processes. HIV-1 REV response element (RRE) located in the env coding region of the viral genome is reported to be well conserved across different HIV-1 isolates. In this study, the binding characteristics of Calf thymus DNA (ctDNA) and REV peptide from HIV-1 were investigated using spectroscopic (UV-visible, fluorescence, and circular dichroism (CD)) and isothermal titration calorimetric (ITC) techniques. Thermal stability and ligand binding properties of the ctDNA revealed that native ctDNA had a T m of 75.5 °C, whereas the ctDNA-REV peptide complex exhibited an incremental shift in the T m by 8 °C, indicating thermal stability of the complex. CD data indicated increased ellipticity due to large conformational changes in ctDNA molecule upon binding with REV peptide and two binding stoichiometric modes are apparent. The ctDNA experienced condensation due to large conformational changes in the presence of REV peptide and positive B→Ψ transition was observed at higher molar charge ratios. Fluorescence studies performed at several ligand concentrations revealed a gradual decrease in the fluorescence intensity of EtBr-bound ctDNA in response to increasing ligand concentrations. The fluorescence data further confirmed two stoichiometric modes of binding for ctDNA-REV peptide complex as previously observed with CD studies. The binding enthalpies were determined using ITC in the temperature range of 293 K-308 K. The ITC binding isotherm was exothermic at all temperatures examined, with low ΔH values indicating that the ctDNA-REV peptide interaction is driven largely by entropy. The heat capacity change (ΔC p ) was insignificant, an unusual finding in the area of DNA-peptide interaction studies. The variation in the values obtained for ΔH, ΔS, and ΔG with temperature further suggests that ctDNA-REV peptide interaction is entropically driven. ITC based analysis of salt dependence of binding constant gave a charge value (Z) = +4.01, as determined for the δlnK/δln[Na + ] parameter, suggesting the participation of only 3-4 Arg out of 11 Arg charge from REV peptide. The stoichiometry observed for the complex was three molar charge of REV peptide binding per molar charge of ctDNA. ITC based analysis further confirmed that the binding between ctDNA and REV peptide is governed by electrostatic interaction. Molecular interactions including H-bonding, van der Waals forces, and solvent molecules rearrangement, underlie the binding of REV peptide to ctDNA. © 2016 Wiley Periodicals, Inc.

HLPI-Ensemble: Prediction of human lncRNA-protein interactions based on ensemble strategy.

PubMed

Hu, Huan; Zhang, Li; Ai, Haixin; Zhang, Hui; Fan, Yetian; Zhao, Qi; Liu, Hongsheng

2018-03-27

LncRNA plays an important role in many biological and disease progression by binding to related proteins. However, the experimental methods for studying lncRNA-protein interactions are time-consuming and expensive. Although there are a few models designed to predict the interactions of ncRNA-protein, they all have some common drawbacks that limit their predictive performance. In this study, we present a model called HLPI-Ensemble designed specifically for human lncRNA-protein interactions. HLPI-Ensemble adopts the ensemble strategy based on three mainstream machine learning algorithms of Support Vector Machines (SVM), Random Forests (RF) and Extreme Gradient Boosting (XGB) to generate HLPI-SVM Ensemble, HLPI-RF Ensemble and HLPI-XGB Ensemble, respectively. The results of 10-fold cross-validation show that HLPI-SVM Ensemble, HLPI-RF Ensemble and HLPI-XGB Ensemble achieved AUCs of 0.95, 0.96 and 0.96, respectively, in the test dataset. Furthermore, we compared the performance of the HLPI-Ensemble models with the previous models through external validation dataset. The results show that the false positives (FPs) of HLPI-Ensemble models are much lower than that of the previous models, and other evaluation indicators of HLPI-Ensemble models are also higher than those of the previous models. It is further showed that HLPI-Ensemble models are superior in predicting human lncRNA-protein interaction compared with previous models. The HLPI-Ensemble is publicly available at: http://ccsipb.lnu.edu.cn/hlpiensemble/ .

Tamavidin 2-REV: an engineered tamavidin with reversible biotin-binding capability.

PubMed

Takakura, Yoshimitsu; Sofuku, Kozue; Tsunashima, Masako

2013-03-10

A biotin-binding protein with reversible biotin-binding capability is of great technical value in the affinity purification of biotinylated biomolecules. Although several proteins, chemically or genetically modified from avidin or streptavidin, with reversible biotin-binding have been reported, they have been problematic in one way or another. Tamavidin 2 is a fungal protein similar to avidin and streptavidin in biotin-binding. Here, a mutein, tamavidin 2-REV, was engineered from tamavidin 2 by replacing the serine at position 36 (S36) with alanine. S36 is thought to form a hydrogen bond with biotin in tamavidin 2/biotin complexes and two hydrogen bonds with V38 within the protein. Tamavidin 2-REV bound to biotin-agarose and was eluted with excess free biotin at a neutral pH. In addition, the model substrate biotinylated bovine serum albumin was efficiently purified from a crude extract from Escherichia coli by means of single-step affinity chromatography with tamavidin 2-REV-immobilized resin. Tamavidin 2-REV thus demonstrated reversible biotin-binding capability. The Kd value of tamavidin 2-REV to biotin was 2.8-4.4×10(-7)M.Tamavidin 2-REV retained other convenient characteristics of tamavidin 2, such as high-level expression in E. coli, resistance to proteases, and a neutral isoelectric point, demonstrating that tamavidin 2-REV is a powerful tool for the purification of biotinylated biomolecules. Copyright © 2013 Elsevier B.V. All rights reserved.

Comment on "Many-body localization in Ising models with random long-range interactions"

NASA Astrophysics Data System (ADS)

Maksymov, Andrii O.; Rahman, Noah; Kapit, Eliot; Burin, Alexander L.

2017-11-01

This Comment is dedicated to the investigation of many-body localization in a quantum Ising model with long-range power-law interactions r-α, relevant for a variety of systems ranging from electrons in Anderson insulators to spin excitations in chains of cold atoms. It has earlier been argued [arXiv:cond-mat/0611387 (2005); Phys. Rev. B 91, 094202 (2015), 10.1103/PhysRevB.91.094202] that this model obeys the dimensional constraint suggesting the delocalization of all finite-temperature states in the thermodynamic limit for α ≤2 d in a d -dimensional system. This expectation conflicts with the recent numerical studies of the specific interacting spin model of Li et al. [Phys. Rev. A 94, 063625 (2016), 10.1103/PhysRevA.94.063625]. To resolve this controversy we reexamine the model of Li et al. [Phys. Rev. A 94, 063625 (2016), 10.1103/PhysRevA.94.063625] and demonstrate that the infinite-temperature states there obey the dimensional constraint. The earlier developed scaling theory for the critical system size required for delocalization is extended to small exponents 0 ≤α ≤d . The disagreements between the two works are explained by the nonstandard selection of investigated states in the ordered phase in the work of Li et al. [Phys. Rev. A 94, 063625 (2016)10.1103/PhysRevA.94.063625].

HIV-1 Rev expressed in recombinant Escherichia coli: purification, polymerization, and conformational properties.

PubMed

Wingfield, P T; Stahl, S J; Payton, M A; Venkatesan, S; Misra, M; Steven, A C

1991-07-30

The high-level expression of HIV-1 Rev in Escherichia coli is described. Protein in crude bacterial extracts was dissociated from bound nucleic acid with urea. A simple purification and renaturation protocol, monitored by circular dichroism, is described which results in high yields of pure protein. The purified protein binds with high affinity to the Rev-responsive element mRNA and has nativelike spectroscopic properties. The protein exhibits concentration-dependent self-association as judged by analytical ultracentrifugation and gel filtration measurements. Purified Rev showed reversible heat-induced aggregation over the temperature range 0-30 degrees C. This hydrophobic-driven and nonspecific protein association was inhibited by low concentrations of sulfate ions. Rev solutions at greater than 80 micrograms/mL, incubated at 0-4 degrees C, slowly polymerized to form long hollow fibers of 20-nm diameter. Filament formation occurs at a lower protein concentration and more rapidly in the presence of Rev-responsive mRNA. The nucleic acid containing filaments are about 8 nm in diameter and up to 0.4 micron in length. On the basis of physical properties of the purified protein, we have suggested that in the nucleus of infected cells, Rev binding to the Rev-responsive region of env mRNA may be followed by helical polymerization of the protein which results in coating of the nucleic acid. Coated nucleic acid could be protected from splicing in the nucleus and exported to the cytoplasm.

Autocatalytic caspase-3 driven by human telomerase reverse transcriptase promoter suppresses human ovarian carcinoma growth in vitro and in mice.

PubMed

Song, Yue; Xia, Zhijun; Shen, Keng; Zhai, Xingyue

2013-05-01

To construct recombinant adenoviruses AdHT-rev-casp3 and Ad-rev-casp3, which express autocatalysis caspase-3 driven by human telomerase reverse transcriptase promoter and cytomegalovirus promoter, respectively; and to investigate their antitumor effects on ovarian cancer in vitro and in vivo. Cell viabilities were determined using the cell counting kit 8 and flow cytometry. Reverse transcriptase polymerase chain reaction and immunoblotting assays were used to detect cellular apoptotic activities after treatments. Tumor growth and survival of mice bearing AO cells were studied. AdHT-rev-casp3 significantly suppressed the survival of AO cells in a dose-dependent modality with a viability rate of 60.45% ± 7.8% at an multiplicity of infection (MOI) of 70 and 42.18 ± 5.3% at an MOI of 100, which was somewhat lower than that of the AO cells treated with Ad-rev-casp3 (32.28% ± 5.3% and 21.84% ± 3.4%, respectively). In contrast, AdHT-rev-casp3 induced little human umbilical vein epithelial cell (HUVEC) death with a viability rate of 98.52% ± 6.9% at an MOI of 70, whereas Ad-rev-casp3 induced significant cell death in HUVEC with a viability rate of 27.14% ± 5.4%. Additionally, AdHT-rev-casp3 (MOI = 70) caused significant apoptosis in AO cells with an apoptotic rate of 25.97%, whereas it caused undetectable apoptosis in HUVECs with the rate of only 1.75%. Ad-rev-casp3 (MOI = 70) caused strong apoptosis in both AO and HUVECs, with the rate of 35.82% and 38.12%, respectively. AdHT-rev-casp3 caused markedly higher levels of active caspase-3, causing no detectable active caspase-3 expression in HUVECs. The tumor growth suppression rate of AdHT-rev-casp3 was 54.94%, significantly higher than that of phosphate-buffered saline at the end point of the study. AdHT-rev-casp3 significantly improved the survival of mice receiving intraperitoneal inoculation of AO cells with little liver damage, with the mean survival of 177 ± 12 days. AdHT-rev-casp3 causes effective apoptosis with significant tumor selectivity, suppresses tumor growth, and improves the mouse survival with little liver toxicity. It can be a potent therapeutic agent for the tumor-targeting treatment of ovarian cancer.

Relativistically induced transparency acceleration of light ions by an ultrashort laser pulse interacting with a heavy-ion-plasma density gradient

NASA Astrophysics Data System (ADS)

Sahai, Aakash A.; Tsung, Frank S.; Tableman, Adam R.; Mori, Warren B.; Katsouleas, Thomas C.

2013-10-01

The relativistically induced transparency acceleration (RITA) scheme of proton and ion acceleration using laser-plasma interactions is introduced, modeled, and compared to the existing schemes. Protons are accelerated with femtosecond relativistic pulses to produce quasimonoenergetic bunches with controllable peak energy. The RITA scheme works by a relativistic laser inducing transparency [Akhiezer and Polovin, Zh. Eksp. Teor. Fiz 30, 915 (1956); Kaw and Dawson, Phys. FluidsPFLDAS0031-917110.1063/1.1692942 13, 472 (1970); Max and Perkins, Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.27.1342 27, 1342 (1971)] to densities higher than the cold-electron critical density, while the background heavy ions are stationary. The rising laser pulse creates a traveling acceleration structure at the relativistic critical density by ponderomotively [Lindl and Kaw, Phys. FluidsPFLDAS0031-917110.1063/1.1693437 14, 371 (1971); Silva , Phys. Rev. E1063-651X10.1103/PhysRevE.59.2273 59, 2273 (1999)] driving a local electron density inflation, creating an electron snowplow and a co-propagating electrostatic potential. The snowplow advances with a velocity determined by the rate of the rise of the laser's intensity envelope and the heavy-ion-plasma density gradient scale length. The rising laser is incrementally rendered transparent to higher densities such that the relativistic-electron plasma frequency is resonant with the laser frequency. In the snowplow frame, trace density protons reflect off the electrostatic potential and get snowplowed, while the heavier background ions are relatively unperturbed. Quasimonoenergetic bunches of velocity equal to twice the snowplow velocity can be obtained and tuned by controlling the snowplow velocity using laser-plasma parameters. An analytical model for the proton energy as a function of laser intensity, rise time, and plasma density gradient is developed and compared to 1D and 2D PIC OSIRIS [Fonseca , Lect. Note Comput. Sci.9783-540410.1007/3-540-47789-6_36 2331, 342 (2002)] simulations. We model the acceleration of protons to GeV energies with tens-of-femtoseconds laser pulses of a few petawatts. The scaling of proton energy with laser power compares favorably to other mechanisms for ultrashort pulses [Schreiber , Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.97.045005 97, 045005 (2006); Esirkepov , Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.92.175003 92, 175003 (2004); Silva , Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.92.015002 92, 015002 (2004); Fiuza , Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.109.215001 109, 215001 (2012)].

Quicklook overview of model changes in Melcor 2.2: Rev 6342 to Rev 9496

DOE Office of Scientific and Technical Information (OSTI.GOV)

Humphries, Larry L.

2017-05-01

MELCOR 2.2 is a significant official release of the MELCOR code with many new models and model improvements. This report provides the code user with a quick review and characterization of new models added, changes to existing models, the effect of code changes during this code development cycle (rev 6342 to rev 9496), a preview of validation results with this code version. More detailed information is found in the code Subversion logs as well as the User Guide and Reference Manuals.

Upper bound on three-tangles of reduced states of four-qubit pure states

NASA Astrophysics Data System (ADS)

Sharma, S. Shelly; Sharma, N. K.

2017-06-01

Closed formulas for upper bounds on three-tangles of three-qubit reduced states in terms of three-qubit-invariant polynomials of pure four-qubit states are obtained. Our results offer tighter constraints on total three-way entanglement of a given qubit with the rest of the system than those used by Regula et al. [Phys. Rev. Lett. 113, 110501 (2014), 10.1103/PhysRevLett.113.110501 and Phys. Rev. Lett. 116, 049902(E) (2016)], 10.1103/PhysRevLett.116.049902 to verify monogamy of four-qubit quantum entanglement.

Adaptive clustering procedure for continuous gravitational wave searches

NASA Astrophysics Data System (ADS)

Singh, Avneet; Papa, Maria Alessandra; Eggenstein, Heinz-Bernd; Walsh, Sinéad

2017-10-01

In hierarchical searches for continuous gravitational waves, clustering of candidates is an important post-processing step because it reduces the number of noise candidates that are followed up at successive stages [J. Aasi et al., Phys. Rev. Lett. 88, 102002 (2013), 10.1103/PhysRevD.88.102002; B. Behnke, M. A. Papa, and R. Prix, Phys. Rev. D 91, 064007 (2015), 10.1103/PhysRevD.91.064007; M. A. Papa et al., Phys. Rev. D 94, 122006 (2016), 10.1103/PhysRevD.94.122006]. Previous clustering procedures bundled together nearby candidates ascribing them to the same root cause (be it a signal or a disturbance), based on a predefined cluster volume. In this paper, we present a procedure that adapts the cluster volume to the data itself and checks for consistency of such volume with what is expected from a signal. This significantly improves the noise rejection capabilities at fixed detection threshold, and at fixed computing resources for the follow-up stages, this results in an overall more sensitive search. This new procedure was employed in the first Einstein@Home search on data from the first science run of the advanced LIGO detectors (O1) [LIGO Scientific Collaboration and Virgo Collaboration, arXiv:1707.02669 [Phys. Rev. D (to be published)

Ultra-powerful compact amplifiers for short laser pulses

NASA Astrophysics Data System (ADS)

Malkin, Vladimir

1999-11-01

Laser compressors-amplifiers more powerful and compact than ones based on the currently most advanced chirped pulse amplification technique must handle ultrahigh laser intensities. The medium capable of bearing those is plasma. An interesting kinetic regime of short laser pulse amplification by Compton backscattering of counterpropagating laser pump in plasma, akin to superradiant amplification in free-electron lasers, has been proposed recently (Shvets G., Fisch N. J., Pukhov A., and Meyer-ter-Vehn J., Phys. Rev. Lett., v.81, 4879 (1998)). However, the conversion efficiency of pump energy into a short pulse appears to be higher in a transient Raman backscattering regime (Malkin V. M., Shvets G. and Fisch N. J., Phys. Rev. Lett., v.82, 4448 (1999)), where the integrity of the three-wave interaction is maintained. In this regime the pump is completely depleted through the full nonlinear stage of the interaction, so that unwanted Raman and modulational instabilities limit just the amplification time, while the efficiency is kept about 100%. For instance, a 2*10^14 W/cm^2, 1 μm-wavelength laser pump can be compressed within 5 mm length, which is less than the length for filamentation instabilities to develop, to a 30--40 fsec pulse with fluence 6 kJ/cm^2. Such an output pulse is a thousand times shorter and a million time more intensive than outputs of conventional Raman amplifiers operating in a stationary regime. Yet larger amplification distances and output energies can be achieved by suppressing filamentation instabilities. It appears (Malkin V. M., Shvets G. and Fisch N. J., Submitted to Phys. Rev. Lett.) that appropriate detuning of the resonance (by plasma density gradient or/and chirping the pump laser) suppresses the Raman near-forward scattering instability of the pumped pulse, as well as the pump Raman backscattering instability to noise, while the high efficiency of the amplification still persists. The respective new class of transient amplification regimes, generalizing the classical pi-pulse regime of exactly resonant amplification, is described quantitatively. These regimes are of broad interest, being applicable also to other processes such as Brillouin scattering.

Exploring the calibration of a wind forecast ensemble for energy applications

NASA Astrophysics Data System (ADS)

Heppelmann, Tobias; Ben Bouallegue, Zied; Theis, Susanne

2015-04-01

In the German research project EWeLiNE, Deutscher Wetterdienst (DWD) and Fraunhofer Institute for Wind Energy and Energy System Technology (IWES) are collaborating with three German Transmission System Operators (TSO) in order to provide the TSOs with improved probabilistic power forecasts. Probabilistic power forecasts are derived from probabilistic weather forecasts, themselves derived from ensemble prediction systems (EPS). Since the considered raw ensemble wind forecasts suffer from underdispersiveness and bias, calibration methods are developed for the correction of the model bias and the ensemble spread bias. The overall aim is to improve the ensemble forecasts such that the uncertainty of the possible weather deployment is depicted by the ensemble spread from the first forecast hours. Additionally, the ensemble members after calibration should remain physically consistent scenarios. We focus on probabilistic hourly wind forecasts with horizon of 21 h delivered by the convection permitting high-resolution ensemble system COSMO-DE-EPS which has become operational in 2012 at DWD. The ensemble consists of 20 ensemble members driven by four different global models. The model area includes whole Germany and parts of Central Europe with a horizontal resolution of 2.8 km and a vertical resolution of 50 model levels. For verification we use wind mast measurements around 100 m height that corresponds to the hub height of wind energy plants that belong to wind farms within the model area. Calibration of the ensemble forecasts can be performed by different statistical methods applied to the raw ensemble output. Here, we explore local bivariate Ensemble Model Output Statistics at individual sites and quantile regression with different predictors. Applying different methods, we already show an improvement of ensemble wind forecasts from COSMO-DE-EPS for energy applications. In addition, an ensemble copula coupling approach transfers the time-dependencies of the raw ensemble to the calibrated ensemble. The calibrated wind forecasts are evaluated first with univariate probabilistic scores and additionally with diagnostics of wind ramps in order to assess the time-consistency of the calibrated ensemble members.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Das, Anirban; Dighe, Amol; Sen, Manibrata, E-mail: anirbandas@theory.tifr.res.in, E-mail: amol@theory.tifr.res.in, E-mail: manibrata@theory.tifr.res.in

Neutrino self-interactions are known to lead to non-linear collective flavor oscillations in a core-collapse supernova. We point out new possible effects of non-standard self-interactions (NSSI) of neutrinos on flavor conversions in a two-flavor framework. We show that, for a single-energy neutrino-antineutrino ensemble, a flavor instability is generated even in normal hierarchy for large enough NSSI. Using a toy model for the neutrino spectra, we show that flavor-preserving NSSI lead to pinching of spectral swaps, while flavor-violating NSSI cause swaps to develop away from a spectral crossing or even in the absence of a spectral crossing. Consequently, NSSI could give risemore » to collective oscillations and spectral splits even during neutronization burst, for both hierarchies.« less

Human protein Staufen-2 promotes HIV-1 proliferation by positively regulating RNA export activity of viral protein Rev.

PubMed

Banerjee, Atoshi; Benjamin, Ronald; Balakrishnan, Kannan; Ghosh, Payel; Banerjee, Sharmistha

2014-02-13

The export of intron containing viral RNAs from the nucleus to the cytoplasm is an essential step in the life cycle of Human Immunodeficiency Virus-1 (HIV-1). As the eukaryotic system does not permit the transport of intron containing RNA out of the nucleus, HIV-1 makes a regulatory protein, Rev, that mediates the transportation of unspliced and partially spliced viral mRNA from the nucleus to the cytoplasm, thereby playing a decisive role in the generation of new infectious virus particles. Therefore, the host factors modulating the RNA export activity of Rev can be major determinants of virus production in an infected cell. In this study, human Staufen-2 (hStau-2) was identified as a host factor interacting with HIV-1 Rev through affinity chromatography followed by MALDI analyses. Our experiments involving transient expressions, siRNA mediated knockdowns and infection assays conclusively established that hStau-2 is a positive regulator of HIV-1 pathogenesis. We demonstrated that Rev-hStau-2 interactions positively regulated the RNA export activity of Rev and promoted progeny virus synthesis. The Rev-hStau-2 interaction was independent of RNA despite both being RNA binding proteins. hStau-2 mutant, with mutations at Q314R-A318F-K319E, deficient of binding Rev, failed to promote hStau-2 dependent Rev activity and viral production, validating the essentiality of this protein-protein interaction. The expression of this positive regulator was elevated upon HIV-1 infection in both human T-lymphocyte and astrocyte cell lines. With this study, we establish that human Staufen-2, a host factor which is up-regulated upon HIV-1 infection, interacts with HIV-1 Rev, thereby promoting its RNA export activity and progeny virus formation. Altogether, our study provides new insights into the emerging role of the Staufen family of mRNA transporters in host-pathogen interaction and supports the notion that obliterating interactions between viral and host proteins that positively regulate HIV-1 proliferation can significantly contribute to anti-retroviral treatments.

Proflavine acts as a Rev inhibitor by targeting the high-affinity Rev binding site of the Rev responsive element of HIV-1.

PubMed

DeJong, Eric S; Chang, Chia-en; Gilson, Michael K; Marino, John P

2003-07-08

Rev is an essential regulatory HIV-1 protein that binds the Rev responsive element (RRE) within the env gene of the HIV-1 RNA genome, activating the switch between viral latency and active viral replication. Previously, we have shown that selective incorporation of the fluorescent probe 2-aminopurine (2-AP) into a truncated form of the RRE sequence (RRE-IIB) allowed the binding of an arginine-rich peptide derived from Rev and aminoglycosides to be characterized directly by fluorescence methods. Using these fluorescence and nuclear magnetic resonance (NMR) methods, proflavine has been identified, through a limited screen of selected small heterocyclic compounds, as a specific and high-affinity RRE-IIB binder which inhibits the interaction of the Rev peptide with RRE-IIB. Direct and competitive 2-AP fluorescence binding assays reveal that there are at least two classes of proflavine binding sites on RRE-IIB: a high-affinity site that competes with the Rev peptide for binding to RRE-IIB (K(D) approximately 0.1 +/- 0.05 microM) and a weaker binding site(s) (K(D) approximately 1.1 +/- 0.05 microM). Titrations of RRE-IIB with proflavine, monitored using (1)H NMR, demonstrate that the high-affinity proflavine binding interaction occurs with a 2:1 (proflavine:RRE-IIB) stoichiometry, and NOEs observed in the NOESY spectrum of the 2:1 proflavine.RRE-IIB complex indicate that the two proflavine molecules bind specifically and close to each other within a single binding site. NOESY data further indicate that formation of the 2:1 proflavine.RRE-IIB complex stabilizes base pairing and stacking within the internal purine-rich bulge of RRE-IIB in a manner analogous to what has been observed in the Rev peptide.RRE-IIB complex. The observation that proflavine competes with Rev for binding to RRE-IIB by binding as a dimer to a single high-affinity site opens the possibility for rational drug design based on linking and modifying it and related compounds.

Contributions of individual domains to function of the HIV-1 Rev response element.

PubMed

O'Carroll, Ina P; Thappeta, Yashna; Fan, Lixin; Ramirez-Valdez, Edric A; Smith, Sean; Wang, Yun-Xing; Rein, Alan

2017-08-16

The HIV-1 Rev response element (RRE) is a 351-base element in unspliced and partially spliced viral RNA; binding of the RRE by the viral Rev protein induces nuclear export of RRE-containing RNAs, as required for virus replication. It contains one long, imperfect double helix (domain I), one branched domain (domain II) containing a high-affinity Rev-binding site, and two or three additional domains. We previously reported that the RRE assumes an "A" shape in solution and suggested that the location of the Rev binding sites in domains I and II, opposite each other on the two legs of the A, is optimal for Rev binding and explains Rev's specificity for RRE-containing RNAs. Using SAXS and a quantitative functional assay, we have now analyzed a panel of RRE mutants. All the results support the essential role of the A shape for RRE function. Moreover, they suggest that the distal portion of domain I and the three crowning domains all contribute to the maintenance of the A shape. Domains I and II are necessary and sufficient for substantial RRE function, provided they are joined by a flexible linker that allows the two domains to face each other. IMPORTANCE Retroviral replication requires that some of the viral RNAs transcribed in the cell nucleus be exported to the cytoplasm without being spliced. To achieve this, HIV-1 encodes a protein, Rev, which binds to a complex, highly structured element within viral RNA, the Rev Response Element (RRE), and escorts RRE-containing RNAs from the nucleus. We previously reported that the RRE is "A"-shaped and suggested that this architecture, with the 2 legs opposite one another, can explain the specificity of Rev for the RRE. We have analyzed the functional contributions of individual RRE domains, and now report that several domains contribute, with some redundancy, to maintenance of the overall RRE shape. The data strongly support the hypothesis that the opposed placement of the 2 legs is essential for RRE function. Copyright © 2017 American Society for Microbiology.

Contributions of Individual Domains to Function of the HIV-1 Rev Response Element

PubMed Central

O'Carroll, Ina P.; Thappeta, Yashna; Fan, Lixin; Ramirez-Valdez, Edric A.; Smith, Sean; Wang, Yun-Xing

2017-01-01

ABSTRACT The HIV-1 Rev response element (RRE) is a 351-base element in unspliced and partially spliced viral RNA; binding of the RRE by the viral Rev protein induces nuclear export of RRE-containing RNAs, as required for virus replication. It contains one long, imperfect double helix (domain I), one branched domain (domain II) containing a high-affinity Rev-binding site, and two or three additional domains. We previously reported that the RRE assumes an “A” shape in solution and suggested that the location of the Rev binding sites in domains I and II, opposite each other on the two legs of the A, is optimal for Rev binding and explains Rev's specificity for RRE-containing RNAs. Using small-angle X-ray scattering (SAXS) and a quantitative functional assay, we have now analyzed a panel of RRE mutants. All the results support the essential role of the A shape for RRE function. Moreover, they suggest that the distal portion of domain I and the three crowning domains all contribute to the maintenance of the A shape. Domains I and II are necessary and sufficient for substantial RRE function, provided they are joined by a flexible linker that allows the two domains to face each other. IMPORTANCE Retroviral replication requires that some of the viral RNAs transcribed in the cell nucleus be exported to the cytoplasm without being spliced. To achieve this, HIV-1 encodes a protein, Rev, which binds to a complex, highly structured element within viral RNA, the Rev response element (RRE), and escorts RRE-containing RNAs from the nucleus. We previously reported that the RRE is “A” shaped and suggested that this architecture, with the 2 legs opposite one another, can explain the specificity of Rev for the RRE. We have analyzed the functional contributions of individual RRE domains and now report that several domains contribute, with some redundancy, to maintenance of the overall RRE shape. The data strongly support the hypothesis that the opposed placement of the 2 legs is essential for RRE function. PMID:28814520

Spin-symmetry conversion and internal rotation in high J molecular systems

NASA Astrophysics Data System (ADS)

Mitchell, Justin; Harter, William

2006-05-01

Dynamics and spectra of molecules with internal rotation or rovibrational coupling is approximately modeled by rigid or semi-rigid rotors with attached gyroscopes. Using Rotational Energy (RE)^1 surfaces, high resolution molecular spectra for high angular momentum show two distinct but related phenomena; spin-symmetry conversion and internal rotation. For both cases the high total angular momentum allows for transitions that would otherwise be forbidden. Molecular body-frame J-localization effects associated with tight energy level-clusters dominate the rovibronic spectra of high symmetry molecules, particularly spherical tops at J>10. ^2 The effects include large and widespread spin-symmetry mixing contrary to conventional wisdom^3 about weak nuclear moments. Such effects are discussed showing how RE surface plots may predict them even at low J. Classical dynamics of axially constrained rotors are approximated by intersecting rotational-energy-surfaces (RES) that have (J-S).B.(J-S) forms in the limit of constraints that do no work. Semi-classical eigensolutions are compared to those found by direct diagonalization. ^1 W.G Hater, in Handbook of Atomic, Molecular and Optical Physics, edited by G.W.F Drake (Springer, Germany 2006) ^2 W. G. Harter, Phys. Rev. A24,192-262(1981). ^3 G. Herzberg, Infrared and Raman Spectra (VanNostrand 1945) pp. 458,463.

Computational investigation of the HIV-1 Rev multimerization using molecular dynamics simulations and binding free energy calculations.

PubMed

Venken, Tom; Daelemans, Dirk; De Maeyer, Marc; Voet, Arnout

2012-06-01

The HIV Rev protein mediates the nuclear export of viral mRNA, and is thereby essential for the production of late viral proteins in the replication cycle. Rev forms a large organized multimeric protein-protein complex for proper functioning. Recently, the three-dimensional structures of a Rev dimer and tetramer have been resolved and provide the basis for a thorough structural analysis of the binding interaction. Here, molecular dynamics (MD) and binding free energy calculations were performed to elucidate the forces thriving dimerization and higher order multimerization of the Rev protein. It is found that despite the structural differences between each crystal structure, both display a similar behavior according to our calculations. Our analysis based on a molecular mechanics-generalized Born surface area (MM/GBSA) and a configurational entropy approach demonstrates that the higher order multimerization site is much weaker than the dimerization site. In addition, a quantitative hot spot analysis combined with a mutational analysis reveals the most contributing amino acid residues for protein interactions in agreement with experimental results. Additional residues were found in each interface, which are important for the protein interaction. The investigation of the thermodynamics of the Rev multimerization interactions performed here could be a further step in the development of novel antiretrovirals using structure based drug design. Moreover, the variability of the angle between each Rev monomer as measured during the MD simulations suggests a role of the Rev protein in allowing flexibility of the arginine rich domain (ARM) to accommodate RNA binding. Copyright © 2012 Wiley Periodicals, Inc.

REV-ERB-ALPHA circadian gene variant associates with obesity in two independent populations: Mediterranean and North American.

PubMed

Garaulet, Marta; Smith, Caren E; Gomez-Abellán, Purificación; Ordovás-Montañés, María; Lee, Yu-Chi; Parnell, Laurence D; Arnett, Donna K; Ordovás, José M

2014-04-01

Despite the solid connection between REV-ERB and obesity, the information about whether genetic variations at this locus may be associated with obesity traits is scarce. Therefore our objective was to study the association between REV-ERB-ALPHA1 rs2314339 and obesity in two independent populations. Participants were 2214 subjects from Spanish Mediterranean (n = 1404) and North American (n = 810) populations. Anthropometric, biochemical, dietary, and genotype analyses were performed. We found novel associations between the REV-ERB-ALPHA1 rs2314339 genotype and obesity in two independent populations: in Spanish Mediterranean and North American groups, the frequency of the minor-allele-carriers (AA+ AG) was significantly lower in the "abdominally obese" group than in those of the "nonabdominally obese" group (p < 0.05). Minor allele carriers had lower probability of abdominal obesity than noncarriers, and the effect was of similar magnitude for both populations (OR ≈ 1.50). There were consistent associations between REV-ERB-ALPHA1 genotype and obesity-related traits (p < 0.05). Energy intake was not significantly associated with REV-ERB-ALPHA1 rs2314339. However, physical activity significantly differed by genotype. A significant interaction between the REV-ERB-ALPHA1 variant and monounsaturated-fatty-acids (MUFA) intake for obesity was also detected in the Mediterranean population. This new discovery highlights the importance of REV-ERB-ALPHA1 in obesity and provides evidence for the connection between our biological clock and obesity-related traits. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Generic revision of the ant subfamily Dorylinae (Hymenoptera, Formicidae)

PubMed Central

Borowiec, Marek L.

2016-01-01

Abstract The generic classification of the ant subfamily Dorylinae is revised, with the aim of facilitating identification of easily-diagnosable monophyletic genera. The new classification is based on recent molecular phylogenetic evidence and a critical reappraisal of doryline morphology. New keys and diagnoses based on workers and males are provided, along with reviews of natural history and phylogenetic relationships, distribution maps, and a list of valid species for each lineage. Twenty-eight genera (27 extant and 1 extinct) are recognized within the subfamily, an increase from 20 in the previous classification scheme. Species classified in the polyphyletic Cerapachys and Sphinctomyrmex prior to this publication are here distributed among 9 and 3 different genera, respectively. Amyrmex and Asphinctanilloides are synonymized under Leptanilloides and the currently recognized subgenera are synonymized for Dorylus. No tribal classification is proposed for the subfamily, but several apparently monophyletic genus-groups are discussed. Valid generic names recognized here include: Acanthostichus (= Ctenopyga), Aenictogiton, Aenictus (= Paraenictus, Typhlatta), Cerapachys (= Ceratopachys), Cheliomyrmex, Chrysapace gen. rev., Cylindromyrmex (= Holcoponera, Hypocylindromyrmex, Metacylindromyrmex), Dorylus (= Alaopone syn. n., Anomma syn. n., Cosmaecetes, Dichthadia syn. n., Rhogmus syn. n., Shuckardia, Sphecomyrmex, Sphegomyrmex, Typhlopone syn. n.), Eburopone gen. n., Eciton (= Camptognatha, Holopone, Mayromyrmex), Eusphinctus gen. rev., Labidus (= Nycteresia, Pseudodichthadia), Leptanilloides (= Amyrmex syn. n., Asphinctanilloides syn. n.), Lioponera gen. rev. (= Neophyracaces syn. n., Phyracaces syn. n.), Lividopone, Neivamyrmex (= Acamatus, Woitkowskia), Neocerapachys gen. n., Nomamyrmex, Ooceraea gen. rev. (= Cysias syn. n.), Parasyscia gen. rev., †Procerapachys, Simopone, Sphinctomyrmex, Syscia gen. rev., Tanipone, Vicinopone, Yunodorylus gen. rev., Zasphinctus gen. rev. (= Aethiopopone syn. n., Nothosphinctus syn. n.). PMID:27559303

Estimation of representative elementary volume for DNAPL saturation and DNAPL-water interfacial areas in 2D heterogeneous porous media

NASA Astrophysics Data System (ADS)

Wu, Ming; Cheng, Zhou; Wu, Jianfeng; Wu, Jichun

2017-06-01

Representative elementary volume (REV) is important to determine properties of porous media and those involved in migration of contaminants especially dense nonaqueous phase liquids (DNAPLs) in subsurface environment. In this study, an experiment of long-term migration of the commonly used DNAPL, perchloroethylene (PCE), is performed in a two dimensional (2D) sandbox where several system variables including porosity, PCE saturation (Soil) and PCE-water interfacial area (AOW) are accurately quantified by light transmission techniques over the entire PCE migration process. Moreover, the REVs for these system variables are estimated by a criterion of relative gradient error (εgi) and results indicate that the frequency of minimum porosity-REV size closely follows a Gaussian distribution in the range of 2.0 mm and 8.0 mm. As experiment proceeds in PCE infiltration process, the frequency and cumulative frequency of both minimum Soil-REV and minimum AOW-REV sizes change their shapes from the irregular and random to the regular and smooth. When experiment comes into redistribution process, the cumulative frequency of minimum Soil-REV size reveals a linear positive correlation, while frequency of minimum AOW-REV size tends to a Gaussian distribution in the range of 2.0 mm-7.0 mm and appears a peak value in 13.0 mm-14.0 mm. Undoubtedly, this study will facilitate the quantification of REVs for materials and fluid properties in a rapid, handy and economical manner, which helps enhance our understanding of porous media and DNAPL properties at micro scale, as well as the accuracy of DNAPL contamination modeling at field-scale.

Asymptotics of the monomer-dimer model on two-dimensional semi-infinite lattices

NASA Astrophysics Data System (ADS)

Kong, Yong

2007-05-01

By using the asymptotic theory of Pemantle and Wilson [R. Pemantle and M. C. Wilson, J. Comb. Theory, Ser. AJCBTA70097-316510.1006/jcta.2001.3201 97, 129 (2002)], asymptotic expansions of the free energy of the monomer-dimer model on two-dimensional semi-infinite ∞×n lattices in terms of dimer density are obtained for small values of n , at both high- and low-dimer-density limits. In the high-dimer-density limit, the theoretical results confirm the dependence of the free energy on the parity of n , a result obtained previously by computational methods by Y. Kong [Y. Kong, Phys. Rev. EPLEEE81063-651X10.1103/PhysRevE.74.061102 74, 061102 (2006); Phys. Rev. EPLEEE81063-651X10.1103/PhysRevE.73.016106 73, 016106 (2006);Phys. Rev. EPLEEE81063-651X10.1103/PhysRevE.74.011102 74, 011102 (2006)]. In the low-dimer-density limit, the free energy on a cylinder ∞×n lattice strip has exactly the same first n terms in the series expansion as that of an infinite ∞×∞ lattice.

B23/nucleophosmin interacts with bovine immunodeficiency virus Rev protein and facilitates viral replication.

PubMed

Passos-Castilho, Ana Maria; Marchand, Claude; Archambault, Denis

2018-02-01

The bovine immunodeficiency virus (BIV) Rev shuttling protein contains nuclear/nucleolar localization signals and nuclear import/export mechanisms that are novel among lentivirus Rev proteins. Several viral proteins localize to the nucleolus, which may play a role in processes that are essential to the outcome of viral replication. Although BIV Rev localizes to the nucleoli of transfected/infected cells and colocalizes with one of its major proteins, nucleophosmin (NPM1, also known as B23), the role of the nucleolus and B23 in BIV replication remains to be determined. Here, we demonstrate for the first time that BIV Rev interacts with nucleolar phosphoprotein B23 in cells. Using small interfering RNA (siRNA) technology, we show that depletion of B23 expression inhibits virus production by BIV-infected cells, indicating that B23 plays an important role in BIV replication. The interaction between Rev and B23 may represent a potential new target for the development of antiviral drugs against lentiviruses. Copyright © 2017 Elsevier Inc. All rights reserved.

Reynolds number effects on the single-mode Richtmyer-Meshkov instability

NASA Astrophysics Data System (ADS)

Walchli, B.; Thornber, B.

2017-01-01

The Reynolds number effects on the nonlinear growth rates of the Richtmyer-Meshkov instability are investigated using two-dimensional numerical simulations. A decrease in Reynolds number gives an increased time to reach nonlinear saturation, with Reynolds number effects only significant in the range Re<256 . Within this range there is a sharp change in instability properties. The bubble and spike amplitudes move towards equal size at lower Reynolds numbers and the bubble velocities decay faster than predicted by Sohn's model [S.-I. Sohn, Phys. Rev. E 80, 055302 (2009), 10.1103/PhysRevE.80.055302]. Predicted amplitudes show reasonable agreement with the existing theory of Carles and Popinet [P. Carles and S. Popinet, Phys. Fluids Lett. 13, 1833 (2001), 10.1063/1.1377863; Eur. J. Mech. B 21, 511 (2002), 10.1016/S0997-7546(02)01199-8] and Mikaelian [K. O. Mikaelian, Phys. Rev. E 47, 375 (1993), 10.1103/PhysRevE.47.375; K. O. Mikaelian, Phys. Rev. E 87, 031003 (2013), 10.1103/PhysRevE.87.031003], with the former being the closest match to the current computations.

Ionic Dependence of Reversal Voltage of the Light Response in Limulus Ventral Photoreceptors

PubMed Central

Brown, J. E.; Mote, M. I.

1974-01-01

The light-induced current as measured using a voltage clamp (holding voltage at resting potential) is attenuated when sodium ions in the bathing solution, Nao, are replaced by Tris, choline, or Li or when NaCl is replaced by sucrose. After replacement of NaCl by sucrose, the reversal voltage, V rev, for the light response becomes more negative. In this case, the slope of the V rev vs. log Nao near Nao = 425 mM is approximately 55 mV/decade increase of Nao (mean for 13 cells). The slope decreases at lower values of Nao. Choline is not impermeant and partially substitutes for Na; the slope of V rev vs. log Nao is 20 mV/decade (mean for three cells). V rev does not change when Na is replaced by Li. Decreases in the bath concentrations of Ca, Mg, Cl, or K do not affect V rev. When Nao = 212 mM, V rev becomes more positive when Ko is increased. Thus, light induces a change in membrane permeability to Na and probably also to K. PMID:4817353

Reply to "Comment on `Conductance scaling in Kondo-correlated quantum dots: Role of level asymmetry and charging energy'"

NASA Astrophysics Data System (ADS)

Merker, L.; Kirchner, S.; Muñoz, E.; Costi, T. A.

2014-08-01

The Comment of A. A. Aligia claims that the superperturbation theory (SPT) approach [E. Muñoz, C. J. Bolech, and S. Kirchner, Phys. Rev. Lett. 110, 016601 (2013), 10.1103/PhysRevLett.110.016601] formulated using dual fermions [A. N. Rubtsov, M. I. Katsnelson, and A. I. Lichtenstein, Phys. Rev. B 77, 033101 (2008), 10.1103/PhysRevB.77.033101] and used by us to compare with numerical renormalization group (NRG) results for the conductance [L. Merker, S. Kirchner, E. Muñoz, and T. A. Costi, Phys. Rev. B 87, 165132 (2013), 10.1103/PhysRevB.87.165132], fails to correctly extend the results of the symmetric Anderson impurity model (SIAM) for general values of the local level Ed in the Kondo regime. We answer this criticism. We also compare new NRG results for cB, with cB calculated directly from the low-field conductance, with new higher-order SPT calculations for this quantity, finding excellent agreement for all Ed and for U /πΔ extending into the strong coupling regime.

Lessons learned from the recovered heatshield of the USERS REV capsule

NASA Astrophysics Data System (ADS)

Yamada, Tetsuya; Matsuda, Seiji; Okuyama, Keiichi; Ishii, Nobuaki

2008-01-01

The USERS Reentry Vehicle (REV) capsule carried out reentry flight from the low earth orbit and was successfully recovered on the sea in May, 2003. This paper presents the post-flight analysis of the recovered heatshield of REV capsule and summarizes the lessons learned. REV capsule, totally about 670 kg, has the combined shape of the nose hemisphere and the rear cone part, and its size is about 1.5 m in diameter and 1.9 m in length. REV is thermally protected against the aerodynamic heating by the carbon phenolic ablator heatshield. The recovered REV heatshield was scrutinized based on the outside aspect and the cross-sections. In general, the temperature profiles of the heatshield have been compared between the flight data and the prediction. The origin of the surface shallow cracks and slight delamination observed in the heatshield have been investigated based on the flight data and taking account of the ablator internal pyrolysis gas pressure, the thermal stress, and the allowable stress. The heatshield has proven to satisfy thermal protection requirements, and the validity of the designing has been confirmed.

Analysis of mutagenic DNA repair in a thermoconditional mutant of Saccharomyces cerevisiae. IV. Influence of DNA replication and excision repair on REV2 dependent UV-mutagenesis and repair.

PubMed

Siede, W; Eckardt, F

1986-01-01

A double mutant being thermoconditionally defective in mutation induction as well as in repair of pre-lethal UV-induced DNA damage (rev2ts) and deficient in excision repair (rad3-2) was studied in temperature-shift experiments. The influence of inhibitors of DNA replication (hydroxyurea, aphidicolin) was determined. Additionally, an analysis of the dose-response pattern of mutation induction ("mutation kinetics") at several ochre alleles was carried out. It was concluded that the UV-inducible REV2 dependent mutagenic repair process is not induced in excision-deficient cells. In excision-deficient cells, REV2 dependent mutation fixation is slow and mostly post-replicative though not dependent on DNA replication. The REV2 mediated mutagenic process could be separated from the repair function.

MSEBAG: a dynamic classifier ensemble generation based on `minimum-sufficient ensemble' and bagging

NASA Astrophysics Data System (ADS)

Chen, Lei; Kamel, Mohamed S.

2016-01-01

In this paper, we propose a dynamic classifier system, MSEBAG, which is characterised by searching for the 'minimum-sufficient ensemble' and bagging at the ensemble level. It adopts an 'over-generation and selection' strategy and aims to achieve a good bias-variance trade-off. In the training phase, MSEBAG first searches for the 'minimum-sufficient ensemble', which maximises the in-sample fitness with the minimal number of base classifiers. Then, starting from the 'minimum-sufficient ensemble', a backward stepwise algorithm is employed to generate a collection of ensembles. The objective is to create a collection of ensembles with a descending fitness on the data, as well as a descending complexity in the structure. MSEBAG dynamically selects the ensembles from the collection for the decision aggregation. The extended adaptive aggregation (EAA) approach, a bagging-style algorithm performed at the ensemble level, is employed for this task. EAA searches for the competent ensembles using a score function, which takes into consideration both the in-sample fitness and the confidence of the statistical inference, and averages the decisions of the selected ensembles to label the test pattern. The experimental results show that the proposed MSEBAG outperforms the benchmarks on average.

Simulation studies of the fidelity of biomolecular structure ensemble recreation

NASA Astrophysics Data System (ADS)

Lätzer, Joachim; Eastwood, Michael P.; Wolynes, Peter G.

2006-12-01

We examine the ability of Bayesian methods to recreate structural ensembles for partially folded molecules from averaged data. Specifically we test the ability of various algorithms to recreate different transition state ensembles for folding proteins using a multiple replica simulation algorithm using input from "gold standard" reference ensembles that were first generated with a Gō-like Hamiltonian having nonpairwise additive terms. A set of low resolution data, which function as the "experimental" ϕ values, were first constructed from this reference ensemble. The resulting ϕ values were then treated as one would treat laboratory experimental data and were used as input in the replica reconstruction algorithm. The resulting ensembles of structures obtained by the replica algorithm were compared to the gold standard reference ensemble, from which those "data" were, in fact, obtained. It is found that for a unimodal transition state ensemble with a low barrier, the multiple replica algorithm does recreate the reference ensemble fairly successfully when no experimental error is assumed. The Kolmogorov-Smirnov test as well as principal component analysis show that the overlap of the recovered and reference ensembles is significantly enhanced when multiple replicas are used. Reduction of the multiple replica ensembles by clustering successfully yields subensembles with close similarity to the reference ensembles. On the other hand, for a high barrier transition state with two distinct transition state ensembles, the single replica algorithm only samples a few structures of one of the reference ensemble basins. This is due to the fact that the ϕ values are intrinsically ensemble averaged quantities. The replica algorithm with multiple copies does sample both reference ensemble basins. In contrast to the single replica case, the multiple replicas are constrained to reproduce the average ϕ values, but allow fluctuations in ϕ for each individual copy. These fluctuations facilitate a more faithful sampling of the reference ensemble basins. Finally, we test how robustly the reconstruction algorithm can function by introducing errors in ϕ comparable in magnitude to those suggested by some authors. In this circumstance we observe that the chances of ensemble recovery with the replica algorithm are poor using a single replica, but are improved when multiple copies are used. A multimodal transition state ensemble, however, turns out to be more sensitive to large errors in ϕ (if appropriately gauged) and attempts at successful recreation of the reference ensemble with simple replica algorithms can fall short.

Revised PROPELLER for T2-weighted imaging of the prostate at 3 Tesla: impact on lesion detection and PI-RADS classification.

PubMed

Meier-Schroers, Michael; Marx, Christian; Schmeel, Frederic Carsten; Wolter, Karsten; Gieseke, Jürgen; Block, Wolfgang; Sprinkart, Alois Martin; Traeber, Frank; Willinek, Winfried; Schild, Hans Heinz; Kukuk, Guido Matthias

2018-01-01

To evaluate revised PROPELLER (RevPROP) for T2-weighted imaging (T2WI) of the prostate as a substitute for turbo spin echo (TSE). Three-Tesla MR images of 50 patients with 55 cancer-suspicious lesions were prospectively evaluated. Findings were correlated with histopathology after MRI-guided biopsy. T2 RevPROP, T2 TSE, diffusion-weighted imaging, dynamic contrast enhancement, and MR-spectroscopy were acquired. RevPROP was compared to TSE concerning PI-RADS scores, lesion size, lesion signal-intensity, lesion contrast, artefacts, and image quality. There were 41 carcinomas in 55 cancer-suspicious lesions. RevPROP detected 41 of 41 carcinomas (100%) and 54 of 55 lesions (98.2%). TSE detected 39 of 41 carcinomas (95.1%) and 51 of 55 lesions (92.7%). RevPROP showed fewer artefacts and higher image quality (each p < 0.001). No differences were observed between single and overall PI-RADS scores based on RevPROP or TSE (p = 0.106 and p = 0.107). Lesion size was not different (p = 0.105). T2-signal intensity of lesions was higher and T2-contrast of lesions was lower on RevPROP (each p < 0.001). For prostate cancer detection RevPROP is superior to TSE with respect to motion robustness, image quality and detection rates of lesions. Therefore, RevPROP might be used as a substitute for T2WI. • Revised PROPELLER can be used as a substitute for T2-weighted prostate imaging. • Revised PROPELLER detected more carcinomas and more suspicious lesions than TSE. • Revised PROPELLER showed fewer artefacts and better image quality compared to TSE. • There were no significant differences in PI-RADS scores between revised PROPELLER and TSE. • The lower T2-contrast of revised PROPELLER did not impair its diagnostic quality.

Impact of production strategies and animal performance on economic values of dairy sheep traits.

PubMed

Krupová, Z; Wolfová, M; Krupa, E; Oravcová, M; Daňo, J; Huba, J; Polák, P

2012-03-01

The objective of this study was to carry out a sensitivity analysis on the impact of various production strategies and performance levels on the relative economic values (REVs) of traits in dairy sheep. A bio-economic model implemented in the program package ECOWEIGHT was used to simulate the profit function for a semi-extensive production system with the Slovak multi-purpose breed Improved Valachian and to calculate the REV of 14 production and functional traits. The following production strategies were analysed: differing proportions of milk processed to cheese, customary weaning and early weaning of lambs with immediate sale or sale after artificial rearing, seasonal lambing in winter and aseasonal lambing in autumn. Results of the sensitivity analysis are presented in detail for the four economically most important traits: 150 days milk yield, conception rate of ewes, litter size and ewe productive lifetime. Impacts of the differences in the mean value of each of these four traits on REVs of all other traits were also examined. Simulated changes in the production circumstances had a higher impact on the REV for milk yield than on REVs of the other traits investigated. The proportion of milk processed to cheese, weaning management strategy for lambs and level of milk yield were the main factors influencing the REV of milk yield. The REVs for conception rate of ewes were highly sensitive to the current mean level of the trait. The REV of ewe productive lifetime was most sensitive to variation in ewe conception rate, and the REV of litter size was most affected by weaning strategy for lambs. On the basis of the results of sensitivity analyses, it is recommended that economic values of traits for the overall breeding objective for dairy sheep be calculated as the weighted average of the economic values obtained for the most common production strategies of Slovak dairy sheep farms and that economic values be adjusted after substantial changes in performance levels of the traits.

Monthly ENSO Forecast Skill and Lagged Ensemble Size

PubMed Central

DelSole, T.; Tippett, M.K.; Pegion, K.

2018-01-01

Abstract The mean square error (MSE) of a lagged ensemble of monthly forecasts of the Niño 3.4 index from the Climate Forecast System (CFSv2) is examined with respect to ensemble size and configuration. Although the real‐time forecast is initialized 4 times per day, it is possible to infer the MSE for arbitrary initialization frequency and for burst ensembles by fitting error covariances to a parametric model and then extrapolating to arbitrary ensemble size and initialization frequency. Applying this method to real‐time forecasts, we find that the MSE consistently reaches a minimum for a lagged ensemble size between one and eight days, when four initializations per day are included. This ensemble size is consistent with the 8–10 day lagged ensemble configuration used operationally. Interestingly, the skill of both ensemble configurations is close to the estimated skill of the infinite ensemble. The skill of the weighted, lagged, and burst ensembles are found to be comparable. Certain unphysical features of the estimated error growth were tracked down to problems with the climatology and data discontinuities. PMID:29937973

Monthly ENSO Forecast Skill and Lagged Ensemble Size

NASA Astrophysics Data System (ADS)

Trenary, L.; DelSole, T.; Tippett, M. K.; Pegion, K.

2018-04-01

The mean square error (MSE) of a lagged ensemble of monthly forecasts of the Niño 3.4 index from the Climate Forecast System (CFSv2) is examined with respect to ensemble size and configuration. Although the real-time forecast is initialized 4 times per day, it is possible to infer the MSE for arbitrary initialization frequency and for burst ensembles by fitting error covariances to a parametric model and then extrapolating to arbitrary ensemble size and initialization frequency. Applying this method to real-time forecasts, we find that the MSE consistently reaches a minimum for a lagged ensemble size between one and eight days, when four initializations per day are included. This ensemble size is consistent with the 8-10 day lagged ensemble configuration used operationally. Interestingly, the skill of both ensemble configurations is close to the estimated skill of the infinite ensemble. The skill of the weighted, lagged, and burst ensembles are found to be comparable. Certain unphysical features of the estimated error growth were tracked down to problems with the climatology and data discontinuities.

Generalized canonical ensembles and ensemble equivalence

DOE Office of Scientific and Technical Information (OSTI.GOV)

Costeniuc, M.; Ellis, R.S.; Turkington, B.

2006-02-15

This paper is a companion piece to our previous work [J. Stat. Phys. 119, 1283 (2005)], which introduced a generalized canonical ensemble obtained by multiplying the usual Boltzmann weight factor e{sup -{beta}}{sup H} of the canonical ensemble with an exponential factor involving a continuous function g of the Hamiltonian H. We provide here a simplified introduction to our previous work, focusing now on a number of physical rather than mathematical aspects of the generalized canonical ensemble. The main result discussed is that, for suitable choices of g, the generalized canonical ensemble reproduces, in the thermodynamic limit, all the microcanonical equilibriummore » properties of the many-body system represented by H even if this system has a nonconcave microcanonical entropy function. This is something that in general the standard (g=0) canonical ensemble cannot achieve. Thus a virtue of the generalized canonical ensemble is that it can often be made equivalent to the microcanonical ensemble in cases in which the canonical ensemble cannot. The case of quadratic g functions is discussed in detail; it leads to the so-called Gaussian ensemble.« less

Elastic fields, dipole tensors, and interaction between self-interstitial atom defects in bcc transition metals

NASA Astrophysics Data System (ADS)

Dudarev, S. L.; Ma, Pui-Wai

2018-03-01

Density functional theory (DFT) calculations show that self-interstitial atom (SIA) defects in nonmagnetic body-centered-cubic (bcc) metals adopt strongly anisotropic configurations, elongated in the <111 > direction [S. Han et al., Phys. Rev. B 66, 220101 (2002), 10.1103/PhysRevB.66.220101; D. Nguyen-Manh et al., Phys. Rev. B 73, 020101 (2006), 10.1103/PhysRevB.73.020101; P. M. Derlet et al., Phys. Rev. B 76, 054107 (2007), 10.1103/PhysRevB.76.054107; S. L. Dudarev, Annu. Rev. Mater. Res. 43, 35 (2013), 10.1146/annurev-matsci-071312-121626]. Elastic distortions, associated with such anisotropic atomic structures, appear similar to distortions around small prismatic dislocation loops, although the extent of this similarity has never been quantified. We derive analytical formulas for the dipole tensors of SIA defects, which show that, in addition to the prismatic dislocation looplike character, the elastic field of a SIA defect also has a significant isotropic dilatation component. Using empirical potentials and DFT calculations, we parametrize dipole tensors of <111 > defects for all the nonmagnetic bcc transition metals. This enables a quantitative evaluation of the energy of elastic interaction between the defects, which also shows that in a periodic three-dimensional simple cubic arrangement of crowdions, long-range elastic interactions between a defect and all its images favor a <111 > orientation of the defect.

RevEcoR: an R package for the reverse ecology analysis of microbiomes.

PubMed

Cao, Yang; Wang, Yuanyuan; Zheng, Xiaofei; Li, Fei; Bo, Xiaochen

2016-07-29

All species live in complex ecosystems. The structure and complexity of a microbial community reflects not only diversity and function, but also the environment in which it occurs. However, traditional ecological methods can only be applied on a small scale and for relatively well-understood biological systems. Recently, a graph-theory-based algorithm called the reverse ecology approach has been developed that can analyze the metabolic networks of all the species in a microbial community, and predict the metabolic interface between species and their environment. Here, we present RevEcoR, an R package and a Shiny Web application that implements the reverse ecology algorithm for determining microbe-microbe interactions in microbial communities. This software allows users to obtain large-scale ecological insights into species' ecology directly from high-throughput metagenomic data. The software has great potential for facilitating the study of microbiomes. RevEcoR is open source software for the study of microbial community ecology. The RevEcoR R package is freely available under the GNU General Public License v. 2.0 at http://cran.r-project.org/web/packages/RevEcoR/ with the vignette and typical usage examples, and the interactive Shiny web application is available at http://yiluheihei.shinyapps.io/shiny-RevEcoR , or can be installed locally with the source code accessed from https://github.com/yiluheihei/shiny-RevEcoR .

Detection of reticuloendotheliosis virus as a contaminant of fowl pox vaccines.

PubMed

Awad, A M; Abd El-Hamid, H S; Abou Rawash, A A; Ibrahim, H H

2010-11-01

This study was designed to detect reticuloendotheliosis virus (REV) as a contaminant in fowl pox vaccines. A total of 30 fowl pox vaccine samples were examined for the presence of REV using both in vitro and in vivo methods. In in vitro testing, the fowl pox vaccine samples were inoculated into chicken embryo fibroblast cultures prepared from specific-pathogen-free embryonated chicken eggs, and the cultures were examined using PCR to detect REV. In in vivo testing, each fowl pox vaccine sample was inoculated into 5-d-old specific-pathogen-free chicks, which were kept under observation for up to 12 wk postinoculation; serum samples were collected at 15, 30, and 45 d postinoculation for the detection of REV-specific antibodies using ELISA. Tissue samples were collected at 8 and 12 wk postinoculation for histopathological examination. Of the tested vaccines, only one imported vaccine sample tested positive for REV using PCR. Serum samples collected from chicks infected with the PCR-positive vaccine batch also tested positive for REV-specific antibodies using ELISA. Histopathological examination of the liver, spleen, and bursa of Fabricius demonstrated the presence of tumor cells in these organs, confirming the results obtained using PCR and ELISA, and indicating that the sample was contaminated with REV. These data clearly indicate that the screening of all commercial poultry vaccines for viruses is an important factor in assuring the biosafety of animal vaccines.

Post-processing ECMWF precipitation and temperature ensemble reforecasts for operational hydrologic forecasting at various spatial scales

NASA Astrophysics Data System (ADS)

Verkade, J. S.; Brown, J. D.; Reggiani, P.; Weerts, A. H.

2013-09-01

The ECMWF temperature and precipitation ensemble reforecasts are evaluated for biases in the mean, spread and forecast probabilities, and how these biases propagate to streamflow ensemble forecasts. The forcing ensembles are subsequently post-processed to reduce bias and increase skill, and to investigate whether this leads to improved streamflow ensemble forecasts. Multiple post-processing techniques are used: quantile-to-quantile transform, linear regression with an assumption of bivariate normality and logistic regression. Both the raw and post-processed ensembles are run through a hydrologic model of the river Rhine to create streamflow ensembles. The results are compared using multiple verification metrics and skill scores: relative mean error, Brier skill score and its decompositions, mean continuous ranked probability skill score and its decomposition, and the ROC score. Verification of the streamflow ensembles is performed at multiple spatial scales: relatively small headwater basins, large tributaries and the Rhine outlet at Lobith. The streamflow ensembles are verified against simulated streamflow, in order to isolate the effects of biases in the forcing ensembles and any improvements therein. The results indicate that the forcing ensembles contain significant biases, and that these cascade to the streamflow ensembles. Some of the bias in the forcing ensembles is unconditional in nature; this was resolved by a simple quantile-to-quantile transform. Improvements in conditional bias and skill of the forcing ensembles vary with forecast lead time, amount, and spatial scale, but are generally moderate. The translation to streamflow forecast skill is further muted, and several explanations are considered, including limitations in the modelling of the space-time covariability of the forcing ensembles and the presence of storages.

REV-ERB-ALPHA circadian gene variant associates with obesity in two independent populations: Mediterranean and North American

USDA-ARS?s Scientific Manuscript database

Despite the solid connection between REV-ERB and obesity, the information about whether genetic variations at this locus may be associated with obesity traits is scarce. Therefore our objective was to study the association between REV-ERB-ALPHA1 rs2314339 and obesity in two independent populations. ...

NREL Fuels and Engines R&D Revs Up Vehicle Efficiency, Performance (Text

Science.gov Websites

Version) | News | NREL Fuels and Engines R&D Revs Up Vehicle Efficiency, Performance (Text Version) NREL Fuels and Engines R&D Revs Up Vehicle Efficiency, Performance (Text Version) NREL's combustion to the evolution of how fuels interact with engine and vehicle design. This is a text version of

Equilibrium Structure and Vibrational Spectra of Sila-Adamantane

DTIC Science & Technology

2006-10-27

42, 3276 (1990); M. R. Pederson, K. A. Jackson, Phys. Rev. B. 43, 7312 ( 1991 ); M. R. Pederson, D. V. Porezag, J. Kortus, and D. C. Patton, Phys... Pankratov , Phys. Rev. B 68, 085310 (2003); P. H. Han, W. G. Schmidt, and F. Becstedt, Phys. Rev. B 72, 245425 (2005). [13] T. Yamada, T. Inoue, K. Yamada, N

Biological Characterization of CVRM2-BAC, A Recombinant CV1988 Virus Containing an REV LTR Insertion

USDA-ARS?s Scientific Manuscript database

It has been previously reported that avian retroviruses, i.e. avian leukosis virus (ALV) and reticoloendotheliosis virus (REV), integrate in the Marek’s disease virus genome affecting MDV pathogenicity. RM-2 is an attenuated serotype 1 MDV virus generated by insertion of the REV LTR in the genome of...

46 CFR 160.047-1 - Incorporation by reference.

Code of Federal Regulations, 2010 CFR

2010-10-01

..., Models AK-1, and AF-1. Sheet 2, Rev. 2—Cutting Pattern and General Arrangement, Models CKM-1 and CFM-1. Sheet 3, Rev. 2—Cutting Pattern and General Arrangement, Models CKS-1 and CFS-1. Sheet 4, Rev. 1—Pad... Business Service Center, General Services Administration, Washington, DC 20407; (3) The military...

A Theoretical Analysis of Why Hybrid Ensembles Work.

PubMed

Hsu, Kuo-Wei

2017-01-01

Inspired by the group decision making process, ensembles or combinations of classifiers have been found favorable in a wide variety of application domains. Some researchers propose to use the mixture of two different types of classification algorithms to create a hybrid ensemble. Why does such an ensemble work? The question remains. Following the concept of diversity, which is one of the fundamental elements of the success of ensembles, we conduct a theoretical analysis of why hybrid ensembles work, connecting using different algorithms to accuracy gain. We also conduct experiments on classification performance of hybrid ensembles of classifiers created by decision tree and naïve Bayes classification algorithms, each of which is a top data mining algorithm and often used to create non-hybrid ensembles. Therefore, through this paper, we provide a complement to the theoretical foundation of creating and using hybrid ensembles.

Individual differences in ensemble perception reveal multiple, independent levels of ensemble representation.

PubMed

Haberman, Jason; Brady, Timothy F; Alvarez, George A

2015-04-01

Ensemble perception, including the ability to "see the average" from a group of items, operates in numerous feature domains (size, orientation, speed, facial expression, etc.). Although the ubiquity of ensemble representations is well established, the large-scale cognitive architecture of this process remains poorly defined. We address this using an individual differences approach. In a series of experiments, observers saw groups of objects and reported either a single item from the group or the average of the entire group. High-level ensemble representations (e.g., average facial expression) showed complete independence from low-level ensemble representations (e.g., average orientation). In contrast, low-level ensemble representations (e.g., orientation and color) were correlated with each other, but not with high-level ensemble representations (e.g., facial expression and person identity). These results suggest that there is not a single domain-general ensemble mechanism, and that the relationship among various ensemble representations depends on how proximal they are in representational space. (c) 2015 APA, all rights reserved).

National Centers for Environmental Prediction

Science.gov Websites

Ensemble Users Meetings 7th NCEP/NWS Ensemble User Workshop 13-15 June 2016 6th NCEP/NWS Ensemble User Workshop 25 - 27 March 2014 5th NCEP/NWS Ensemble User Workshop 10 - 12 May, 2011 4th NCEP/NWS Ensemble User Workshop 13 - 15 May, 2008 3rd NCEP/NWS Ensemble User Workshop 31 Oct - 2 Nov, 2006 2nd NCEP/NWS

On the generation of climate model ensembles

NASA Astrophysics Data System (ADS)

Haughton, Ned; Abramowitz, Gab; Pitman, Andy; Phipps, Steven J.

2014-10-01

Climate model ensembles are used to estimate uncertainty in future projections, typically by interpreting the ensemble distribution for a particular variable probabilistically. There are, however, different ways to produce climate model ensembles that yield different results, and therefore different probabilities for a future change in a variable. Perhaps equally importantly, there are different approaches to interpreting the ensemble distribution that lead to different conclusions. Here we use a reduced-resolution climate system model to compare three common ways to generate ensembles: initial conditions perturbation, physical parameter perturbation, and structural changes. Despite these three approaches conceptually representing very different categories of uncertainty within a modelling system, when comparing simulations to observations of surface air temperature they can be very difficult to separate. Using the twentieth century CMIP5 ensemble for comparison, we show that initial conditions ensembles, in theory representing internal variability, significantly underestimate observed variance. Structural ensembles, perhaps less surprisingly, exhibit over-dispersion in simulated variance. We argue that future climate model ensembles may need to include parameter or structural perturbation members in addition to perturbed initial conditions members to ensure that they sample uncertainty due to internal variability more completely. We note that where ensembles are over- or under-dispersive, such as for the CMIP5 ensemble, estimates of uncertainty need to be treated with care.

Identification of nonclassical properties of light with multiplexing layouts

PubMed Central

Sperling, J.; Eckstein, A.; Clements, W. R.; Moore, M.; Renema, J. J.; Kolthammer, W. S.; Nam, S. W.; Lita, A.; Gerrits, T.; Walmsley, I. A.; Agarwal, G. S.; Vogel, W.

2018-01-01

In Sperling et al. [Phys. Rev. Lett. 118, 163602 (2017)], we introduced and applied a detector-independent method to uncover nonclassicality. Here, we extend those techniques and give more details on the performed analysis. We derive a general theory of the positive-operator-valued measure that describes multiplexing layouts with arbitrary detectors. From the resulting quantum version of a multinomial statistics, we infer nonclassicality probes based on a matrix of normally ordered moments. We discuss these criteria and apply the theory to our data which are measured with superconducting transition-edge sensors. Our experiment produces heralded multiphoton states from a parametric down-conversion light source. We show that the known notions of sub-Poisson and sub-binomial light can be deduced from our general approach, and we establish the concept of sub-multinomial light, which is shown to outperform the former two concepts of nonclassicality for our data. PMID:29670949

Analysis of mutagenic DNA repair in a thermoconditional mutant of Saccharomyces cerevisiae. III. Dose-response pattern of mutation induction in UV-irradiated rev2ts cells.

PubMed

Siede, W; Eckardt, F

1986-01-01

Recent studies regarding the influence of cycloheximide on the temperature-dependent increase in survival and mutation frequencies of a thermoconditional rev2 mutant lead to the suggestion that the REV2-coded mutagenic repair function is UV-inducible. In the present study we show that stationary-phase rev2ts cells are characterized by a biphasic linear-quadratic dose-dependence of mutation induction ("mutation kinetics") of ochre alleles at 23 degrees C (permissive temperature) but linear kinetics at the restrictive temperature of 36 degrees C. Mathematical analysis using a model based on Poisson statistics and a further mathematical procedure, the calculation of "apparent survival", support the assumption that the quadratic component of the reverse mutation kinetics investigated can be attributed to a UV-inducible component of mutagenic DNA repair controlled by the REV2 gene.

OHD/HL - XEFS

Science.gov Websites

Assimilator Ensemble Post-processor (EnsPost) Hydrologic Model Output Statistics (HMOS) Ensemble Verification capabilities (see diagram below): the Ensemble Pre-processor, the Ensemble Post-processor, the Hydrologic Model (OpenDA, http://www.openda.org/joomla/index.php) to be used within the CHPS environment. Ensemble Post

Heat-bath algorithmic cooling with correlated qubit-environment interactions

NASA Astrophysics Data System (ADS)

Rodríguez-Briones, Nayeli A.; Li, Jun; Peng, Xinhua; Mor, Tal; Weinstein, Yossi; Laflamme, Raymond

2017-11-01

Cooling techniques are essential to understand fundamental thermodynamic questions of the low-energy states of physical systems, furthermore they are at the core of practical applications of quantum information science. In quantum computing, this controlled preparation of highly pure quantum states is required from the state initialization of most quantum algorithms to a reliable supply of ancilla qubits that satisfy the fault-tolerance threshold for quantum error correction. Heat-bath algorithmic cooling has been shown to purify qubits by controlled redistribution of entropy and multiple contact with a bath, not only for ensemble implementations but also for technologies with strong but imperfect measurements. In this paper, we show that correlated relaxation processes between the system and environment during rethermalization when we reset hot ancilla qubits, can be exploited to enhance purification. We show that a long standing upper bound on the limits of algorithmic cooling Schulman et al (2005 Phys. Rev. Lett. 94, 120501) can be broken by exploiting these correlations. We introduce a new tool for cooling algorithms, which we call ‘state-reset’, obtained when the coupling to the environment is generalized from individual-qubits relaxation to correlated-qubit relaxation. Furthermore, we present explicit improved cooling algorithms which lead to an increase of purity beyond all the previous work, and relate our results to the Nuclear Overhauser Effect.

Discriminating strength: a bona fide measure of non-classical correlations

NASA Astrophysics Data System (ADS)

Farace, A.; De Pasquale, A.; Rigovacca, L.; Giovannetti, V.

2014-07-01

A new measure of non-classical correlations is introduced and characterized. It tests the ability of using a state ρ of a composite system AB as a probe for a quantum illumination task (e.g. see Lloyd 2008 Science 321 1463), in which one is asked to remotely discriminate between the two following scenarios: (i) either nothing happens to the probe, or (ii) the subsystem A is transformed via a local unitary {{R}_{A}} whose properties are partially unspecified when producing ρ. This new measure can be seen as the discrete version of the recently introduced interferometric power measure (Girolami et al 2013 e-print arXiv:1309.1472) and, at least for the case in which A is a qubit, it is shown to coincide (up to an irrelevant scaling factor) with the local quantum uncertainty measure of Girolami, Tufarelli and Adesso (2013 Phys. Rev. Lett. 110 240402). Analytical expressions are derived which allow us to formally prove that, within the set of separable configurations, the maximum value of our non-classicality measure is achieved over the set of quantum-classical states (i.e. states ρ which admit a statistical unravelling where each element of the associated ensemble is distinguishable via local measures on B).

On the Dominant Factor Controlling Seasonal Hydrological Forecast Skill in China

DOE PAGES

Zhang, Xuejun; Tang, Qiuhong; Leng, Guoyong; ...

2017-11-20

Initial conditions (ICs) and climate forecasts (CFs) are the two primary sources of seasonal hydrological forecast skill. However, their relative contribution to predictive skill remains unclear in China. In this study, we investigate the relative roles of ICs and CFs in cumulative runoff (CR) and soil moisture (SM) forecasts using 31-year (1980–2010) ensemble streamflow prediction (ESP) and reverse-ESP (revESP) simulations with the Variable Capacity Infiltration (VIC) hydrologic model. The results show that the relative importance of ICs and CFs largely depends on climate regimes. The influence of ICs is stronger in a dry or wet-to-dry climate regime that covers themore » northern and western interior regions during the late fall to early summer. In particular, ICs may dominate the forecast skill for up to three months or even six months during late fall and winter months, probably due to the low precipitation value and variability in the dry period. In contrast, CFs become more important for most of southern China or during summer months. The impact of ICs on SM forecasts tends to cover larger domains than on CR forecasts. These findings will greatly benefit future work that will target efforts towards improving current forecast levels for the particular regions and forecast periods.« less

On the Dominant Factor Controlling Seasonal Hydrological Forecast Skill in China

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Xuejun; Tang, Qiuhong; Leng, Guoyong

Initial conditions (ICs) and climate forecasts (CFs) are the two primary sources of seasonal hydrological forecast skill. However, their relative contribution to predictive skill remains unclear in China. In this study, we investigate the relative roles of ICs and CFs in cumulative runoff (CR) and soil moisture (SM) forecasts using 31-year (1980–2010) ensemble streamflow prediction (ESP) and reverse-ESP (revESP) simulations with the Variable Capacity Infiltration (VIC) hydrologic model. The results show that the relative importance of ICs and CFs largely depends on climate regimes. The influence of ICs is stronger in a dry or wet-to-dry climate regime that covers themore » northern and western interior regions during the late fall to early summer. In particular, ICs may dominate the forecast skill for up to three months or even six months during late fall and winter months, probably due to the low precipitation value and variability in the dry period. In contrast, CFs become more important for most of southern China or during summer months. The impact of ICs on SM forecasts tends to cover larger domains than on CR forecasts. These findings will greatly benefit future work that will target efforts towards improving current forecast levels for the particular regions and forecast periods.« less

A simple analytical model for dynamics of time-varying target leverage ratios

NASA Astrophysics Data System (ADS)

Lo, C. F.; Hui, C. H.

2012-03-01

In this paper we have formulated a simple theoretical model for the dynamics of the time-varying target leverage ratio of a firm under some assumptions based upon empirical observations. In our theoretical model the time evolution of the target leverage ratio of a firm can be derived self-consistently from a set of coupled Ito's stochastic differential equations governing the leverage ratios of an ensemble of firms by the nonlinear Fokker-Planck equation approach. The theoretically derived time paths of the target leverage ratio bear great resemblance to those used in the time-dependent stationary-leverage (TDSL) model [Hui et al., Int. Rev. Financ. Analy. 15, 220 (2006)]. Thus, our simple model is able to provide a theoretical foundation for the selected time paths of the target leverage ratio in the TDSL model. We also examine how the pace of the adjustment of a firm's target ratio, the volatility of the leverage ratio and the current leverage ratio affect the dynamics of the time-varying target leverage ratio. Hence, with the proposed dynamics of the time-dependent target leverage ratio, the TDSL model can be readily applied to generate the default probabilities of individual firms and to assess the default risk of the firms.

Project fires. Volume 2: Protective ensemble performance standards, phase 1B

NASA Astrophysics Data System (ADS)

Abeles, F. J.

1980-05-01

The design of the prototype protective ensemble was finalized. Prototype ensembles were fabricated and then subjected to a series of qualification tests which were based upon the protective ensemble performance standards PEPS requirements. Engineering drawings and purchase specifications were prepared for the new protective ensemble.

Ensemble training to improve recognition using 2D ear

NASA Astrophysics Data System (ADS)

Middendorff, Christopher; Bowyer, Kevin W.

2009-05-01

The ear has gained popularity as a biometric feature due to the robustness of the shape over time and across emotional expression. Popular methods of ear biometrics analyze the ear as a whole, leaving these methods vulnerable to error due to occlusion. Many researchers explore ear recognition using an ensemble, but none present a method for designing the individual parts that comprise the ensemble. In this work, we introduce a method of modifying the ensemble shapes to improve performance. We determine how different properties of an ensemble training system can affect overall performance. We show that ensembles built from small parts will outperform ensembles built with larger parts, and that incorporating a large number of parts improves the performance of the ensemble.

A Theoretical Analysis of Why Hybrid Ensembles Work

PubMed Central

2017-01-01

Inspired by the group decision making process, ensembles or combinations of classifiers have been found favorable in a wide variety of application domains. Some researchers propose to use the mixture of two different types of classification algorithms to create a hybrid ensemble. Why does such an ensemble work? The question remains. Following the concept of diversity, which is one of the fundamental elements of the success of ensembles, we conduct a theoretical analysis of why hybrid ensembles work, connecting using different algorithms to accuracy gain. We also conduct experiments on classification performance of hybrid ensembles of classifiers created by decision tree and naïve Bayes classification algorithms, each of which is a top data mining algorithm and often used to create non-hybrid ensembles. Therefore, through this paper, we provide a complement to the theoretical foundation of creating and using hybrid ensembles. PMID:28255296

On the predictability of outliers in ensemble forecasts

NASA Astrophysics Data System (ADS)

Siegert, S.; Bröcker, J.; Kantz, H.

2012-03-01

In numerical weather prediction, ensembles are used to retrieve probabilistic forecasts of future weather conditions. We consider events where the verification is smaller than the smallest, or larger than the largest ensemble member of a scalar ensemble forecast. These events are called outliers. In a statistically consistent K-member ensemble, outliers should occur with a base rate of 2/(K+1). In operational ensembles this base rate tends to be higher. We study the predictability of outlier events in terms of the Brier Skill Score and find that forecast probabilities can be calculated which are more skillful than the unconditional base rate. This is shown analytically for statistically consistent ensembles. Using logistic regression, forecast probabilities for outlier events in an operational ensemble are calculated. These probabilities exhibit positive skill which is quantitatively similar to the analytical results. Possible causes of these results as well as their consequences for ensemble interpretation are discussed.

The Contribution of Object Shape and Surface Properties to Object Ensemble Representation in Anterior-medial Ventral Visual Cortex.

PubMed

Cant, Jonathan S; Xu, Yaoda

2017-02-01

Our visual system can extract summary statistics from large collections of objects without forming detailed representations of the individual objects in the ensemble. In a region in ventral visual cortex encompassing the collateral sulcus and the parahippocampal gyrus and overlapping extensively with the scene-selective parahippocampal place area (PPA), we have previously reported fMRI adaptation to object ensembles when ensemble statistics repeated, even when local image features differed across images (e.g., two different images of the same strawberry pile). We additionally showed that this ensemble representation is similar to (but still distinct from) how visual texture patterns are processed in this region and is not explained by appealing to differences in the color of the elements that make up the ensemble. To further explore the nature of ensemble representation in this brain region, here we used PPA as our ROI and investigated in detail how the shape and surface properties (i.e., both texture and color) of the individual objects constituting an ensemble affect the ensemble representation in anterior-medial ventral visual cortex. We photographed object ensembles of stone beads that varied in shape and surface properties. A given ensemble always contained beads of the same shape and surface properties (e.g., an ensemble of star-shaped rose quartz beads). A change to the shape and/or surface properties of all the beads in an ensemble resulted in a significant release from adaptation in PPA compared with conditions in which no ensemble feature changed. In contrast, in the object-sensitive lateral occipital area (LO), we only observed a significant release from adaptation when the shape of the ensemble elements varied, and found no significant results in additional scene-sensitive regions, namely, the retrosplenial complex and occipital place area. Together, these results demonstrate that the shape and surface properties of the individual objects comprising an ensemble both contribute significantly to object ensemble representation in anterior-medial ventral visual cortex and further demonstrate a functional dissociation between object- (LO) and scene-selective (PPA) visual cortical regions and within the broader scene-processing network itself.

Far Infrared, Magnetic and Electronic Studies of High Tc Superconducting Materials

DTIC Science & Technology

1992-09-30

Phys. Rev. Left. 63, 2421(1989). 8. K. H. Fischer and T. Nattermann, Phys. Rev. .43, 10372(1991). 9. R. E. Walstedt, R. F. Bell, and D. B. Mitzi , Phys...Duran, J. Yazyi, F. dela Cruz, D. J. Bishop, D. B. Mitzi , and A. Kapitulnik, Phys. Rev. B 44, 17737(1991). 14. Y. Yeshurun and A. P. Malozemoff, Phys

Experimental Test of Nonlocal Realism Using a Fiber-Based Source of Polarization-Entangled Photon Paris

DTIC Science & Technology

2008-03-25

J. F. Clauser and M. A. Horne, Phys. Rev. D 10, 526 1974. 6 A. Zeilinger , Rev. Mod. Phys. 71, S288 1999; A. Aspect, Nature London 398, 189...Jennewein, M. Zukowski, M. Aspelmeyer, and A. Zeilinger , Phys. Rev. Lett. 99, 210406 2007; C. Branciard, A. Ling, N. Gisin, C. Kurt- siefer, A. Lamas

75 FR 69741 - Proposed Collection; Comment Request for Rev. Proc. 2007-99 (RP-127367-07), 9100 Relief Under...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-11-15

.... Proc. 2007-99 (RP- 127367-07), 9100 Relief Under Sections 897 and 1445 AGENCY: Internal Revenue Service...)). Currently, the IRS is soliciting comments concerning Rev. Proc. 2007-99 (RP-127367-07), 9100 Relief Under...: Rev. Proc. 2007-99 (RP-127367-07), 9100 Relief Under Sections 897 and 1445. OMB Number: 1545-2098...

Weak measurement combined with quantum delayed-choice experiment and implementation in optomechanical system

NASA Astrophysics Data System (ADS)

Li, Gang; Wang, Tao; Ye, Ming-Yong; Song, He-Shan

2015-12-01

Weak measurement [Y. Aharonov, D.Z. Albert, L. Vaidman, Phys. Rev. Lett. 60, 1351 (1988); C. Simon, E.S. Polzik, Phys. Rev. A 83, 040101(R) (2011)] combined with quantum delayed-choice experiment that use Controlled Hadamard gate instead of Hadamard gate in quantum networks give rise to a surprising amplification effect, i.e., counterintuitive negative amplification effect. We show that this effect is caused by the wave and particle behaviours of the system, and it can't be explained by a semiclassical wave theory [D. Suter, Phys. Rev. A 51, 45 (1995); J.C. Howell, D.J. Starling, P.B. Dixon, P.K. Vudyasetu, A.N. Jordan, Phys. Rev. A 81, 033813 (2010); N. Brunner, A. Acín, D. Collins, N. Gisin, V. Scarani, Phys. Rev. Lett. 91, 180402 (2003)] and by the statistical feature of preselection and postselection with disturbance [C. Ferrie, J. Combes, Phys. Rev. Lett. 113, 120404 (2014)], due to the entanglement of the system and the ancilla in Controlled Hadamard gate. The generation mechanism with wave-particle duality in quantum mechanics lead us to a scheme for implementation of weak measurement in optomechanical system.

Isolation and characterization of a virus-specific ribonucleoprotein complex from reticuloendotheliosis virus-transformed chicken bone marrow cells.

PubMed Central

Wong, T C; Kang, C Y

1978-01-01

Chicken bone marrow cells transformed by reticuloendotheliosis virus (REV) produce in the cytoplasm a ribonucleoprotein (RNP) complex which has a sedimentation value of approximately 80 to 100S and a density of 1.23 g/cm3. This RNP complex is not derived from the mature virion. An endogenous RNA-directed DNA polymerase activity is associated with the RNP complex. The enzyme activity was completely neutralized by anti-REV DNA polymerase antibody but not by anti-avian myeloblastosis virus DNA polymerase antibody. The DNA product from the endogenous RNA-directed DNA polymerase reaction of the RNP complex hybridized to REV RNA but not to avian leukosis virus RNA. The RNA extracted from the RNP hybridized only to REV-specific complementary DNA synthesized from an endogenous DNA polymerase reaction of purified REV. The size of the RNA in the RNP is 30 to 35S, which represents the subunit size of the genomic RNA. No 60S mature genomic RNA was found within the RNP complex. The significance of finding the endogenous DNA polymerase activity in the viral RNP in infected cells and the maturation process of 60S virion RNA of REV are discussed. PMID:81319

Reynolds number effects on the single-mode Richtmyer-Meshkov instability.

PubMed

Walchli, B; Thornber, B

2017-01-01

The Reynolds number effects on the nonlinear growth rates of the Richtmyer-Meshkov instability are investigated using two-dimensional numerical simulations. A decrease in Reynolds number gives an increased time to reach nonlinear saturation, with Reynolds number effects only significant in the range Re<256. Within this range there is a sharp change in instability properties. The bubble and spike amplitudes move towards equal size at lower Reynolds numbers and the bubble velocities decay faster than predicted by Sohn's model [S.-I. Sohn, Phys. Rev. E 80, 055302 (2009)PLEEE81539-375510.1103/PhysRevE.80.055302]. Predicted amplitudes show reasonable agreement with the existing theory of Carles and Popinet [P. Carles and S. Popinet, Phys. Fluids Lett. 13, 1833 (2001)10.1063/1.1377863; Eur. J. Mech. B 21, 511 (2002)EJBFEV0997-754610.1016/S0997-7546(02)01199-8] and Mikaelian [K. O. Mikaelian, Phys. Rev. E 47, 375 (1993)1063-651X10.1103/PhysRevE.47.375; K. O. Mikaelian, Phys. Rev. E 87, 031003 (2013)PLEEE81539-375510.1103/PhysRevE.87.031003], with the former being the closest match to the current computations.

Kinetic Basis of Nucleotide Selection Employed by a Protein Template-Dependent DNA Polymerase†

PubMed Central

Brown, Jessica A.; Fowler, Jason D.; Suo, Zucai

2010-01-01

Rev1, a Y-family DNA polymerase, contributes to spontaneous and DNA damage-induced mutagenic events. In this paper, we have employed pre-steady state kinetic methodology to establish a kinetic basis for nucleotide selection by human Rev1, a unique nucleotidyl transferase that uses a protein template-directed mechanism to preferentially instruct dCTP incorporation. This work demonstrated that the high incorporation efficiency of dCTP is dependent on both substrates: an incoming dCTP and a templating base dG. The extremely low base substitution fidelity of human Rev1 (100 to 10-5) was due to the preferred misincorporation of dCTP with templating bases dA, dT, and dC over correct dNTPs. Using non-natural nucleotide analogs, we showed that hydrogen bonding interactions between residue R357 of human Rev1 and an incoming dNTP are not essential for DNA synthesis. Lastly, human Rev1 discriminates between ribonucleotides and deoxyribonucleotides mainly by reducing the rate of incorporation, and the sugar selectivity of human Rev1 is sensitive to both the size and orientation of the 2′-substituent of a ribonucleotide. PMID:20518555

The HIV-1 Rev/RRE system is required for HIV-1 5' UTR cis elements to augment encapsidation of heterologous RNA into HIV-1 viral particles

PubMed Central

2011-01-01

Background The process of HIV-1 genomic RNA (gRNA) encapsidation is governed by a number of viral encoded components, most notably the Gag protein and gRNA cis elements in the canonical packaging signal (ψ). Also implicated in encapsidation are cis determinants in the R, U5, and PBS (primer binding site) from the 5' untranslated region (UTR). Although conventionally associated with nuclear export of HIV-1 RNA, there is a burgeoning role for the Rev/RRE in the encapsidation process. Pleiotropic effects exhibited by these cis and trans viral components may confound the ability to examine their independent, and combined, impact on encapsidation of RNA into HIV-1 viral particles in their innate viral context. We systematically reconstructed the HIV-1 packaging system in the context of a heterologous murine leukemia virus (MLV) vector RNA to elucidate a mechanism in which the Rev/RRE system is central to achieving efficient and specific encapsidation into HIV-1 viral particles. Results We show for the first time that the Rev/RRE system can augment RNA encapsidation independent of all cis elements from the 5' UTR (R, U5, PBS, and ψ). Incorporation of all the 5' UTR cis elements did not enhance RNA encapsidation in the absence of the Rev/RRE system. In fact, we demonstrate that the Rev/RRE system is required for specific and efficient encapsidation commonly associated with the canonical packaging signal. The mechanism of Rev/RRE-mediated encapsidation is not a general phenomenon, since the combination of the Rev/RRE system and 5' UTR cis elements did not enhance encapsidation into MLV-derived viral particles. Lastly, we show that heterologous MLV RNAs conform to transduction properties commonly associated with HIV-1 viral particles, including in vivo transduction of non-dividing cells (i.e. mouse neurons); however, the cDNA forms are episomes predominantly in the 1-LTR circle form. Conclusions Premised on encapsidation of a heterologous RNA into HIV-1 viral particles, our findings define a functional HIV-1 packaging system as comprising the 5' UTR cis elements, Gag, and the Rev/RRE system, in which the Rev/RRE system is required to make the RNA amenable to the ensuing interaction between Gag and the canonical packaging signal for subsequent encapsidation. PMID:21702950

Dirac Magnons in Honeycomb Ferromagnets

NASA Astrophysics Data System (ADS)

Pershoguba, Sergey S.; Banerjee, Saikat; Lashley, J. C.; Park, Jihwey; Ågren, Hans; Aeppli, Gabriel; Balatsky, Alexander V.

2018-01-01

The discovery of the Dirac electron dispersion in graphene [A. H. Castro Neto, et al., The Electronic Properties of Graphene, Rev. Mod. Phys. 81, 109 (2009), 10.1103/RevModPhys.81.109] led to the question of the Dirac cone stability with respect to interactions. Coulomb interactions between electrons were shown to induce a logarithmic renormalization of the Dirac dispersion. With a rapid expansion of the list of compounds and quasiparticle bands with linear band touching [T. O. Wehling, et al., Dirac Materials, Adv. Phys. 63, 1 (2014), 10.1080/00018732.2014.927109], the concept of bosonic Dirac materials has emerged. We consider a specific case of ferromagnets consisting of van der Waals-bonded stacks of honeycomb layers, e.g., chromium trihalides CrX3 (X =F , Cl, Br and I), that display two spin wave modes with energy dispersion similar to that for the electrons in graphene. At the single-particle level, these materials resemble their fermionic counterparts. However, how different particle statistics and interactions affect the stability of Dirac cones has yet to be determined. To address the role of interacting Dirac magnons, we expand the theory of ferromagnets beyond the standard Dyson theory [F. J. Dyson, General Theory of Spin-Wave Interactions, Phys. Rev. 102, 1217 (1956), 10.1103/PhysRev.102.1217, F. J. Dyson, Thermodynamic Behavior of an Ideal Ferromagnet, Phys. Rev. 102, 1230 (1956), 10.1103/PhysRev.102.1230] to the case of non-Bravais honeycomb layers. We demonstrate that magnon-magnon interactions lead to a significant momentum-dependent renormalization of the bare band structure in addition to strongly momentum-dependent magnon lifetimes. We show that our theory qualitatively accounts for hitherto unexplained anomalies in nearly half-century-old magnetic neutron-scattering data for CrBr3 [W. B. Yelon and R. Silberglitt, Renormalization of Large-Wave-Vector Magnons in Ferromagnetic CrBr3 Studied by Inelastic Neutron Scattering: Spin-Wave Correlation Effects, Phys. Rev. B 4, 2280 (1971), 10.1103/PhysRevB.4.2280, E. J. Samuelsen, et al., Spin Waves in Ferromagnetic CrBr3 Studied by Inelastic Neutron Scattering, Phys. Rev. B 3, 157 (1971), 10.1103/PhysRevB.3.157]. We also show that honeycomb ferromagnets display dispersive surface and edge states, unlike their electronic analogs.

Simulated hydroclimatic impacts of projected Brazilian sugarcane expansion

NASA Astrophysics Data System (ADS)

Georgescu, M.; Lobell, D. B.; Field, C. B.; Mahalov, A.

2013-03-01

Sugarcane area is currently expanding in Brazil, largely in response to domestic and international demand for sugar-based ethanol. To investigate the potential hydroclimatic impacts of future expansion, a regional climate model is used to simulate 5 years of a scenario in which cerrado and cropland areas (~1.1E6 km2) within south-central Brazil are converted to sugarcane. Results indicate a cooling of up to ~1.0°C during the peak of the growing season, mainly as a result of increased albedo of sugarcane relative to the previous landscape. After harvest, warming of similar magnitude occurs from a significant decline in evapotranspiration and a repartitioning toward greater sensible heating. Overall, annual temperature changes from large-scale conversion are expected to be small because of offsetting reductions in net radiation absorption and evapotranspiration. The decline in net water flux from land to the atmosphere implies a reduction in regional precipitation, which is consistent with progressively decreasing simulated average rainfall for the study period, upon conversion to sugarcane. However, rainfall changes were not robust across three ensemble members. The results suggest that sugarcane expansion will not drastically alter the regional energy or water balance, but could result in important local and seasonal effects.

Time of arrival in quantum and Bohmian mechanics

NASA Astrophysics Data System (ADS)

Leavens, C. R.

1998-08-01

In a recent paper Grot, Rovelli, and Tate (GRT) [Phys. Rev. A 54, 4676 (1996)] derived an expression for the probability distribution π(TX) of intrinsic arrival times T(X) at position x=X for a quantum particle with initial wave function ψ(x,t=0) freely evolving in one dimension. This was done by quantizing the classical expression for the time of arrival of a free particle at X, assuming a particular choice of operator ordering, and then regulating the resulting time of arrival operator. For the special case of a minimum-uncertainty-product wave packet at t=0 with average wave number and variance Δk they showed that their analytical expression for π(TX) agreed with the probability current density J(x=X,t=T) only to terms of order Δk/. They dismissed the probability current density as a viable candidate for the exact arrival time distribution on the grounds that it can sometimes be negative. This fact is not a problem within Bohmian mechanics where the arrival time distribution for a particle, either free or in the presence of a potential, is rigorously given by \\|J(X,T)\\| (suitably normalized) [W. R. McKinnon and C. R. Leavens, Phys. Rev. A 51, 2748 (1995); C. R. Leavens, Phys. Lett. A 178, 27 (1993); M. Daumer et al., in On Three Levels: The Mathematical Physics of Micro-, Meso-, and Macro-Approaches to Physics, edited by M. Fannes et al. (Plenum, New York, 1994); M. Daumer, in Bohmian Mechanics and Quantum Theory: An Appraisal, edited by J. T. Cushing et al. (Kluwer Academic, Dordrecht, 1996)]. The two theories are compared in this paper and a case presented for which the results could not differ more: According to GRT's theory, every particle in the ensemble reaches a point x=X, where ψ(x,t) and J(x,t) are both zero for all t, while no particle ever reaches X according to the theory based on Bohmian mechanics. Some possible implications are discussed.

Multi-scale dynamical behavior of spatially distributed systems: a deterministic point of view

NASA Astrophysics Data System (ADS)

Mangiarotti, S.; Le Jean, F.; Drapeau, L.; Huc, M.

2015-12-01

Physical and biophysical systems are spatially distributed systems. Their behavior can be observed or modelled spatially at various resolutions. In this work, a deterministic point of view is adopted to analyze multi-scale behavior taking a set of ordinary differential equation (ODE) as elementary part of the system.To perform analyses, scenes of study are thus generated based on ensembles of identical elementary ODE systems. Without any loss of generality, their dynamics is chosen chaotic in order to ensure sensitivity to initial conditions, that is, one fundamental property of atmosphere under instable conditions [1]. The Rössler system [2] is used for this purpose for both its topological and algebraic simplicity [3,4].Two cases are thus considered: the chaotic oscillators composing the scene of study are taken either independent, or in phase synchronization. Scale behaviors are analyzed considering the scene of study as aggregations (basically obtained by spatially averaging the signal) or as associations (obtained by concatenating the time series). The global modeling technique is used to perform the numerical analyses [5].One important result of this work is that, under phase synchronization, a scene of aggregated dynamics can be approximated by the elementary system composing the scene, but modifying its parameterization [6]. This is shown based on numerical analyses. It is then demonstrated analytically and generalized to a larger class of ODE systems. Preliminary applications to cereal crops observed from satellite are also presented.[1] Lorenz, Deterministic nonperiodic flow. J. Atmos. Sci., 20, 130-141 (1963).[2] Rössler, An equation for continuous chaos, Phys. Lett. A, 57, 397-398 (1976).[3] Gouesbet & Letellier, Global vector-field reconstruction by using a multivariate polynomial L2 approximation on nets, Phys. Rev. E 49, 4955-4972 (1994).[4] Letellier, Roulin & Rössler, Inequivalent topologies of chaos in simple equations, Chaos, Solitons & Fractals, 28, 337-360 (2006).[5] Mangiarotti, Coudret, Drapeau, & Jarlan, Polynomial search and global modeling, Phys. Rev. E 86(4), 046205 (2012).[6] Mangiarotti, Modélisation globale et Caractérisation Topologique de dynamiques environnementales. Habilitation à Diriger des Recherches, Univ. Toulouse 3 (2014).

Rethinking the Default Construction of Multimodel Climate Ensembles

DOE PAGES

Rauser, Florian; Gleckler, Peter; Marotzke, Jochem

2015-07-21

Here, we discuss the current code of practice in the climate sciences to routinely create climate model ensembles as ensembles of opportunity from the newest phase of the Coupled Model Intercomparison Project (CMIP). We give a two-step argument to rethink this process. First, the differences between generations of ensembles corresponding to different CMIP phases in key climate quantities are not large enough to warrant an automatic separation into generational ensembles for CMIP3 and CMIP5. Second, we suggest that climate model ensembles cannot continue to be mere ensembles of opportunity but should always be based on a transparent scientific decision process.more » If ensembles can be constrained by observation, then they should be constructed as target ensembles that are specifically tailored to a physical question. If model ensembles cannot be constrained by observation, then they should be constructed as cross-generational ensembles, including all available model data to enhance structural model diversity and to better sample the underlying uncertainties. To facilitate this, CMIP should guide the necessarily ongoing process of updating experimental protocols for the evaluation and documentation of coupled models. Finally, with an emphasis on easy access to model data and facilitating the filtering of climate model data across all CMIP generations and experiments, our community could return to the underlying idea of using model data ensembles to improve uncertainty quantification, evaluation, and cross-institutional exchange.« less

Simulation of DNAPL migration in heterogeneous translucent porous media based on estimation of representative elementary volume

NASA Astrophysics Data System (ADS)

Wu, Ming; Wu, Jianfeng; Wu, Jichun

2017-10-01

When the dense nonaqueous phase liquid (DNAPL) comes into the subsurface environment, its migration behavior is crucially affected by the permeability and entry pressure of subsurface porous media. A prerequisite for accurately simulating DNAPL migration in aquifers is then the determination of the permeability, entry pressure and corresponding representative elementary volumes (REV) of porous media. However, the permeability, entry pressure and corresponding representative elementary volumes (REV) are hard to determine clearly. This study utilizes the light transmission micro-tomography (LTM) method to determine the permeability and entry pressure of two dimensional (2D) translucent porous media and integrates the LTM with a criterion of relative gradient error to quantify the corresponding REV of porous media. As a result, the DNAPL migration in porous media might be accurately simulated by discretizing the model at the REV dimension. To validate the quantification methods, an experiment of perchloroethylene (PCE) migration is conducted in a two-dimensional heterogeneous bench-scale aquifer cell. Based on the quantifications of permeability, entry pressure and REV scales of 2D porous media determined by the LTM and relative gradient error, different models with different sizes of discretization grid are used to simulate the PCE migration. It is shown that the model based on REV size agrees well with the experimental results over the entire migration period including calibration, verification and validation processes. This helps to better understand the microstructures of porous media and achieve accurately simulating DNAPL migration in aquifers based on the REV estimation.

Trans-Lesion DNA Polymerases May Be Involved in Yeast Meiosis

PubMed Central

Arbel-Eden, Ayelet; Joseph-Strauss, Daphna; Masika, Hagit; Printzental, Oxana; Rachi, Eléanor; Simchen, Giora

2013-01-01

Trans-lesion DNA polymerases (TLSPs) enable bypass of DNA lesions during replication and are also induced under stress conditions. Being only weakly dependent on their template during replication, TLSPs introduce mutations into DNA. The low processivity of these enzymes ensures that they fall off their template after a few bases are synthesized and are then replaced by the more accurate replicative polymerase. We find that the three TLSPs of budding yeast Saccharomyces cerevisiae Rev1, PolZeta (Rev3 and Rev7), and Rad30 are induced during meiosis at a time when DNA double-strand breaks (DSBs) are formed and homologous chromosomes recombine. Strains deleted for one or any combination of the three TLSPs undergo normal meiosis. However, in the triple-deletion mutant, there is a reduction in both allelic and ectopic recombination. We suggest that trans-lesion polymerases are involved in the processing of meiotic double-strand breaks that lead to mutations. In support of this notion, we report significant yeast two-hybrid (Y2H) associations in meiosis-arrested cells between the TLSPs and DSB proteins Rev1-Spo11, Rev1-Mei4, and Rev7-Rec114, as well as between Rev1 and Rad30. We suggest that the involvement of TLSPs in processing of meiotic DSBs could be responsible for the considerably higher frequency of mutations reported during meiosis compared with that found in mitotically dividing cells, and therefore may contribute to faster evolutionary divergence than previously assumed. PMID:23550131

Estimation of the REV Size and Equivalent Permeability Coefficient of Fractured Rock Masses with an Emphasis on Comparing the Radial and Unidirectional Flow Configurations

NASA Astrophysics Data System (ADS)

Wang, Zhechao; Li, Wei; Bi, Liping; Qiao, Liping; Liu, Richeng; Liu, Jie

2018-05-01

A method to estimate the representative elementary volume (REV) size for the permeability and equivalent permeability coefficient of rock mass with a radial flow configuration was developed. The estimations of the REV size and equivalent permeability for the rock mass around an underground oil storage facility using a radial flow configuration were compared with those using a unidirectional flow configuration. The REV sizes estimated using the unidirectional flow configuration are much higher than those estimated using the radial flow configuration. The equivalent permeability coefficient estimated using the radial flow configuration is unique, while those estimated using the unidirectional flow configuration depend on the boundary conditions and flow directions. The influences of the fracture trace length, spacing and gap on the REV size and equivalent permeability coefficient were investigated. The REV size for the permeability of fractured rock mass increases with increasing the mean trace length and fracture spacing. The influence of the fracture gap length on the REV size is insignificant. The equivalent permeability coefficient decreases with the fracture spacing, while the influences of the fracture trace length and gap length are not determinate. The applicability of the proposed method to the prediction of groundwater inflow into rock caverns was verified using the measured groundwater inflow into the facility. The permeability coefficient estimated using the radial flow configuration is more similar to the representative equivalent permeability coefficient than those estimated with different boundary conditions using the unidirectional flow configuration.

The sensitivity of predicted financial and genetic gains in Holsteins to changes in the economic value of traits.

PubMed

Cottle, D J; Coffey, M P

2013-02-01

The objective of this study was to assess the impact of using different relative economic values (REVs) in selection indices on predicted financial and trait gains from selection of sires of cows and on the choice of leading Holstein bulls available in the UK dairy industry. Breeding objective traits were milk yield, fat yield, protein yield, lifespan, mastitis, non-return rate, calving interval and lameness. Relative importance of a trait, as estimated by a.h(2), was only moderately related to the rate of financial loss or total economic merit (ΔTEM) per percentage under- or overestimation of REV (r = 0.38 and 0.29, respectively) as a result of the variance-covariance structure of traits. The effects on TEM of under- or overestimating trait REVs were non-symmetrical. TEM was most sensitive to incorrect REVs for protein, fat, milk and lifespan and least sensitive to incorrect calving interval, lameness, non-return and mastitis REVs. A guide to deciding which dairy traits require the most rigorous analysis in the calculation of their REVs is given. Varying the REVs within a fairly wide range resulted in different bulls being selected by index and their differing predicted transmitting abilities would result in the herds moving in different directions in the long term (20 years). It is suggested that customized indices, where the farmer creates rankings of bulls tailored to their specific farm circumstances, can be worthwhile. © 2012 Blackwell Verlag GmbH.

Ligand-dependent exciton dynamics and photovoltaic properties of PbS quantum dot heterojunction solar cells.

PubMed

Chang, Jin; Ogomi, Yuhei; Ding, Chao; Zhang, Yao Hong; Toyoda, Taro; Hayase, Shuzi; Katayama, Kenji; Shen, Qing

2017-03-01

The surface chemistry of colloidal quantum dots (QDs) plays an important role in determining the photoelectric properties of QD films and the corresponding quantum dot heterojunction solar cells (QDHSCs). To investigate the effects of the ligand structure on the photovoltaic performance and exciton dynamics of QDHSCs, PbS QDHSCs were fabricated by the solid state ligand exchange method with mercaptoalkanoic acid as the cross-linking ligand. Temperature-dependent photoluminescence and ultrafast transient absorption spectra show that the electronic coupling and charge transfer rate within QD ensembles were monotonically enhanced as the ligand length decreased. However, in practical QDHSCs, the second shortest ligand 3-mercaptopropionic acid (MPA) showed higher power conversion efficiency than the shortest ligand thioglycolic acid (TGA). This could be attributed to the difference in their surface trap states, supported by thermally stimulated current measurements. Moreover, compared with the non-conjugated ligand MPA, the conjugated ligand 4-mercaptobenzoic acid (MBA) introduces less trap states and has a similar charge transfer rate in QD ensembles, but has poor photovoltaic properties. This unexpected result could be contributed by the QD-ligand orbital mixing, leading to the charge transfer from QDs to ligands instead of charge transfer between adjacent QDs. This work highlights the significant effects of ligand structures on the photovoltaic properties and exciton dynamics of QDHSCs, which would shed light on the further development of QD-based photoelectric devices.

Project FIRES [Firefighters' Integrated Response Equipment System]. Volume 2: Protective Ensemble Performance Standards, Phase 1B

NASA Technical Reports Server (NTRS)

Abeles, F. J.

1980-01-01

The design of the prototype protective ensemble was finalized. Prototype ensembles were fabricated and then subjected to a series of qualification tests which were based upon the protective ensemble performance standards PEPS requirements. Engineering drawings and purchase specifications were prepared for the new protective ensemble.

Verifying and Postprocesing the Ensemble Spread-Error Relationship

NASA Astrophysics Data System (ADS)

Hopson, Tom; Knievel, Jason; Liu, Yubao; Roux, Gregory; Wu, Wanli

2013-04-01

With the increased utilization of ensemble forecasts in weather and hydrologic applications, there is a need to verify their benefit over less expensive deterministic forecasts. One such potential benefit of ensemble systems is their capacity to forecast their own forecast error through the ensemble spread-error relationship. The paper begins by revisiting the limitations of the Pearson correlation alone in assessing this relationship. Next, we introduce two new metrics to consider in assessing the utility an ensemble's varying dispersion. We argue there are two aspects of an ensemble's dispersion that should be assessed. First, and perhaps more fundamentally: is there enough variability in the ensembles dispersion to justify the maintenance of an expensive ensemble prediction system (EPS), irrespective of whether the EPS is well-calibrated or not? To diagnose this, the factor that controls the theoretical upper limit of the spread-error correlation can be useful. Secondly, does the variable dispersion of an ensemble relate to variable expectation of forecast error? Representing the spread-error correlation in relation to its theoretical limit can provide a simple diagnostic of this attribute. A context for these concepts is provided by assessing two operational ensembles: 30-member Western US temperature forecasts for the U.S. Army Test and Evaluation Command and 51-member Brahmaputra River flow forecasts of the Climate Forecast and Applications Project for Bangladesh. Both of these systems utilize a postprocessing technique based on quantile regression (QR) under a step-wise forward selection framework leading to ensemble forecasts with both good reliability and sharpness. In addition, the methodology utilizes the ensemble's ability to self-diagnose forecast instability to produce calibrated forecasts with informative skill-spread relationships. We will describe both ensemble systems briefly, review the steps used to calibrate the ensemble forecast, and present verification statistics using error-spread metrics, along with figures from operational ensemble forecasts before and after calibration.

Imprinting and recalling cortical ensembles.

PubMed

Carrillo-Reid, Luis; Yang, Weijian; Bando, Yuki; Peterka, Darcy S; Yuste, Rafael

2016-08-12

Neuronal ensembles are coactive groups of neurons that may represent building blocks of cortical circuits. These ensembles could be formed by Hebbian plasticity, whereby synapses between coactive neurons are strengthened. Here we report that repetitive activation with two-photon optogenetics of neuronal populations from ensembles in the visual cortex of awake mice builds neuronal ensembles that recur spontaneously after being imprinted and do not disrupt preexisting ones. Moreover, imprinted ensembles can be recalled by single- cell stimulation and remain coactive on consecutive days. Our results demonstrate the persistent reconfiguration of cortical circuits by two-photon optogenetics into neuronal ensembles that can perform pattern completion. Copyright © 2016, American Association for the Advancement of Science.

Anomaly transform methods based on total energy and ocean heat content norms for generating ocean dynamic disturbances for ensemble climate forecasts

NASA Astrophysics Data System (ADS)

Romanova, Vanya; Hense, Andreas

2017-08-01

In our study we use the anomaly transform, a special case of ensemble transform method, in which a selected set of initial oceanic anomalies in space, time and variables are defined and orthogonalized. The resulting orthogonal perturbation patterns are designed such that they pick up typical balanced anomaly structures in space and time and between variables. The metric used to set up the eigen problem is taken either as the weighted total energy with its zonal, meridional kinetic and available potential energy terms having equal contributions, or the weighted ocean heat content in which a disturbance is applied only to the initial temperature fields. The choices of a reference state for defining the initial anomalies are such that either perturbations on seasonal timescales and or on interannual timescales are constructed. These project a-priori only the slow modes of the ocean physical processes, such that the disturbances grow mainly in the Western Boundary Currents, in the Antarctic Circumpolar Current and the El Nino Southern Oscillation regions. An additional set of initial conditions is designed to fit in a least square sense data from global ocean reanalysis. Applying the AT produced sets of disturbances to oceanic initial conditions initialized by observations of the MPIOM-ESM coupled model on T63L47/GR15 resolution, four ensemble and one hind-cast experiments were performed. The weighted total energy norm is used to monitor the amplitudes and rates of the fastest growing error modes. The results showed minor dependence of the instabilities or error growth on the selected metric but considerable change due to the magnitude of the scaling amplitudes of the perturbation patterns. In contrast to similar atmospheric applications, we find an energy conversion from kinetic to available potential energy, which suggests a different source of uncertainty generation in the ocean than in the atmosphere mainly associated with changes in the density field.

Naval Sea Systems Command > Home > Warfare Centers > NSWC Corona

Science.gov Websites

Modernization Inactive Ships International Fleet Support Surface Ship Readiness and Sustainment SURFMEPP Surface ; Schemas MIL-DTL-24784C IM/IP DTD Suite IWS6 Common Schema NAVSEA Class 2 ETM DTD Changes from the ETM Class 2 Revision E History Early Revisions Early Revisions Rev E Changes Rev D Changes Rev C 1.2 Changes

Annual Gaseous Electronics Conference (44TH) Held in Albuquerque, New Mexico on 22-25 October 1991

DTIC Science & Technology

1992-05-01

Phys. Rev. A 38, 2471 (1988); J. E. Lawler et al., Phys. Rev. A 43, 4427 1991). T. J. Sommerer et al., Phys. Rev. A39, 6356 (1989). EA-2 Diagnostics and...Charged Ions with a Metal Surface.* F.W. MEYER, S.H. OVERBURY, CC. HAVENER, PA. ZEULMANS VAN EMMICHOVEN, and D.M. ZEHNER, ORNL -- Projectile K-Auger

Treatment with the Fusion Inhibitor Enfuvirtide Influences the Appearance of Mutations in the Human Immunodeficiency Virus Type 1 Regulatory Protein Rev▿

PubMed Central

Svicher, Valentina; Alteri, Claudia; D'Arrigo, Roberta; Laganà, Alessandro; Trignetti, Maria; Lo Caputo, Sergio; Callegaro, Anna Paola; Maggiolo, Franco; Mazzotta, Francesco; Ferro, Alfredo; Dimonte, Salvatore; Aquaro, Stefano; di Perri, Giovanni; Bonora, Stefano; Tommasi, Chiara; Trotta, Maria Paola; Narciso, Pasquale; Antinori, Andrea; Perno, Carlo Federico; Ceccherini-Silberstein, Francesca

2009-01-01

The gp41-encoding sequence of the env gene contains in two separate regions the Rev-responsive elements (RRE) and the alternative open reading frame of the second exon of the regulatory protein Rev. The binding of Rev to the RRE allows the transport of unspliced/singly spliced viral mRNAs out of the nucleus, an essential step in the life cycle of human immunodeficiency virus type 1 (HIV-1). In this study, we have investigated whether the fusion-inhibitor enfuvirtide (ENF) can induce mutations in Rev and if these mutations correlate with the classical ENF resistance gp41 mutations and with viremia and CD4 cell count. Specific Rev mutations were positively associated with ENF treatment and significantly correlated with classical ENF resistance gp41 mutations. In particular, a cluster was observed for the Rev mutations E57A (E57Arev) and N86Srev with the ENF resistance gp41 mutations Q40H (Q40Hgp41) and L45Mgp41. In addition, the presence at week 48 of the E57Arev correlates with a significant viremia increase from baseline to week 48 and with a CD4 cell count loss from baseline to week 48. By modeling the RRE structure, we found that the Q40gp41 and L45gp41 codons form complementary base pairs in a region of the RRE involved in Rev binding. The conformation of this Rev-binding site is disrupted when Q40Hgp41 and L45Mgp41 occur alone while it is restored when both mutations are present. In conclusion, our study shows that ENF pressure may also affect both Rev and RRE structures and can provide an excellent example of compensatory evolution. This highlights the multiple roles of ENF (and perhaps other entry inhibitors) in modulating the correct interplay between the different HIV-1 genes and proteins during the HIV-1 life cycle. PMID:19124665

Conservation of Mass and Preservation of Positivity with Ensemble-Type Kalman Filter Algorithms

NASA Technical Reports Server (NTRS)

Janjic, Tijana; Mclaughlin, Dennis; Cohn, Stephen E.; Verlaan, Martin

2014-01-01

This paper considers the incorporation of constraints to enforce physically based conservation laws in the ensemble Kalman filter. In particular, constraints are used to ensure that the ensemble members and the ensemble mean conserve mass and remain nonnegative through measurement updates. In certain situations filtering algorithms such as the ensemble Kalman filter (EnKF) and ensemble transform Kalman filter (ETKF) yield updated ensembles that conserve mass but are negative, even though the actual states must be nonnegative. In such situations if negative values are set to zero, or a log transform is introduced, the total mass will not be conserved. In this study, mass and positivity are both preserved by formulating the filter update as a set of quadratic programming problems that incorporate non-negativity constraints. Simple numerical experiments indicate that this approach can have a significant positive impact on the posterior ensemble distribution, giving results that are more physically plausible both for individual ensemble members and for the ensemble mean. In two examples, an update that includes a non-negativity constraint is able to properly describe the transport of a sharp feature (e.g., a triangle or cone). A number of implementation questions still need to be addressed, particularly the need to develop a computationally efficient quadratic programming update for large ensemble.

EEMD-based wind turbine bearing failure detection using the generator stator current homopolar component

NASA Astrophysics Data System (ADS)

Amirat, Yassine; Choqueuse, Vincent; Benbouzid, Mohamed

2013-12-01

Failure detection has always been a demanding task in the electrical machines community; it has become more challenging in wind energy conversion systems because sustainability and viability of wind farms are highly dependent on the reduction of the operational and maintenance costs. Indeed the most efficient way of reducing these costs would be to continuously monitor the condition of these systems. This allows for early detection of the generator health degeneration, facilitating a proactive response, minimizing downtime, and maximizing productivity. This paper provides then an assessment of a failure detection techniques based on the homopolar component of the generator stator current and attempts to highlight the use of the ensemble empirical mode decomposition as a tool for failure detection in wind turbine generators for stationary and non-stationary cases.

Circular-polarization-sensitive metamaterial based on triple-quantum-dot molecules.

PubMed

Kotetes, Panagiotis; Jin, Pei-Qing; Marthaler, Michael; Schön, Gerd

2014-12-05

We propose a new type of chiral metamaterial based on an ensemble of artificial molecules formed by three identical quantum dots in a triangular arrangement. A static magnetic field oriented perpendicular to the plane breaks mirror symmetry, rendering the molecules sensitive to the circular polarization of light. By varying the orientation and magnitude of the magnetic field one can control the polarization and frequency of the emission spectrum. We identify a threshold frequency Ω, above which we find strong birefringence. In addition, Kerr rotation and circular-polarized lasing action can be implemented. We investigate the single-molecule lasing properties for different energy-level arrangements and demonstrate the possibility of circular-polarization conversion. Finally, we analyze the effect of weak stray electric fields or deviations from the equilateral triangular geometry.

Ocean Predictability and Uncertainty Forecasts Using Local Ensemble Transfer Kalman Filter (LETKF)

NASA Astrophysics Data System (ADS)

Wei, M.; Hogan, P. J.; Rowley, C. D.; Smedstad, O. M.; Wallcraft, A. J.; Penny, S. G.

2017-12-01

Ocean predictability and uncertainty are studied with an ensemble system that has been developed based on the US Navy's operational HYCOM using the Local Ensemble Transfer Kalman Filter (LETKF) technology. One of the advantages of this method is that the best possible initial analysis states for the HYCOM forecasts are provided by the LETKF which assimilates operational observations using ensemble method. The background covariance during this assimilation process is implicitly supplied with the ensemble avoiding the difficult task of developing tangent linear and adjoint models out of HYCOM with the complicated hybrid isopycnal vertical coordinate for 4D-VAR. The flow-dependent background covariance from the ensemble will be an indispensable part in the next generation hybrid 4D-Var/ensemble data assimilation system. The predictability and uncertainty for the ocean forecasts are studied initially for the Gulf of Mexico. The results are compared with another ensemble system using Ensemble Transfer (ET) method which has been used in the Navy's operational center. The advantages and disadvantages are discussed.

Comment on "Generalization of the Kohn-Sham system that can represent arbitrary one-electron density matrices"

NASA Astrophysics Data System (ADS)

Piris, Mario; Pernal, Katarzyna

2017-10-01

van Dam [Phys. Rev. A 93, 052512 (2016), 10.1103/PhysRevA.93.052512] claims that the one-particle reduced density matrix (1RDM) of an interacting system can be represented by means of a single-determinant wave function of fictitious noninteracting particles. van Dam [Phys. Rev. A 93, 052512 (2016), 10.1103/PhysRevA.93.052512] introduced orbitals within a mean-field framework that produce energy levels similar to Hartree-Fock orbital energies, therefore he also claims that conventional analyses based on Koopmans' theorem are possible in 1RDM functional theory. In this Comment, we demonstrate that both claims are unfounded.

Devil's staircases and continued fractions in Josephson junctions

NASA Astrophysics Data System (ADS)

Shukrinov, Yu. M.; Medvedeva, S. Yu.; Botha, A. E.; Kolahchi, M. R.; Irie, A.

2013-12-01

Detailed numerical simulations of the IV characteristics of a Josephson junction under external electromagnetic radiation show the devil's staircase within different bias current intervals. We have found that the observed steps form very precisely continued fractions. Increase of the amplitude of the radiation shifts the devil's staircase to higher Shapiro steps. An algorithm for the appearance and detection of subharmonics with increasing radiation amplitude is proposed. We demonstrate that the subharmonic steps registered in the well-known experiments by Dayem and Wiegand [Phys. Rev. 155, 419 (1967), 10.1103/PhysRev.155.419] and Clarke [Phys. Rev. B 4, 2963 (1971), 10.1103/PhysRevB.4.2963] also form continued fractions.

Classical capacity of Gaussian thermal memory channels

NASA Astrophysics Data System (ADS)

De Palma, G.; Mari, A.; Giovannetti, V.

2014-10-01

The classical capacity of phase-invariant Gaussian channels has been recently determined under the assumption that such channels are memoryless. In this work we generalize this result by deriving the classical capacity of a model of quantum memory channel, in which the output states depend on the previous input states. In particular we extend the analysis of Lupo et al. [Phys. Rev. Lett. 104, 030501 (2010), 10.1103/PhysRevLett.104.030501 and Phys. Rev. A 82, 032312 (2010), 10.1103/PhysRevA.82.032312] from quantum limited channels to thermal attenuators and thermal amplifiers. Our result applies in many situations in which the physical communication channel is affected by nonzero memory and by thermal noise.

Comment on "Modified quantum-speed-limit bounds for open quantum dynamics in quantum channels"

NASA Astrophysics Data System (ADS)

Mirkin, Nicolás; Toscano, Fabricio; Wisniacki, Diego A.

2018-04-01

In a recent paper [Phys. Rev. A 95, 052118 (2017), 10.1103/PhysRevA.95.052118], the authors claim that our criticism, in Phys. Rev. A 94, 052125 (2016), 10.1103/PhysRevA.94.052125, to some quantum speed limit bounds for open quantum dynamics that appeared recently in literature are invalid. According to the authors, the problem with our analysis would be generated by an artifact of the finite-precision numerical calculations. We analytically show here that it is not possible to have any inconsistency associated with the numerical precision of calculations. Therefore, our criticism of the quantum speed limit bounds continues to be valid.

Joys of Community Ensemble Playing: The Case of the Happy Roll Elastic Ensemble in Taiwan

ERIC Educational Resources Information Center

Hsieh, Yuan-Mei; Kao, Kai-Chi

2012-01-01

The Happy Roll Elastic Ensemble (HREE) is a community music ensemble supported by Tainan Culture Centre in Taiwan. With enjoyment and friendship as its primary goals, it aims to facilitate the joys of ensemble playing and the spirit of social networking. This article highlights the key aspects of HREE's development in its first two years…

Ensemble coding of face identity is not independent of the coding of individual identity.

PubMed

Neumann, Markus F; Ng, Ryan; Rhodes, Gillian; Palermo, Romina

2018-06-01

Information about a group of similar objects can be summarized into a compressed code, known as ensemble coding. Ensemble coding of simple stimuli (e.g., groups of circles) can occur in the absence of detailed exemplar coding, suggesting dissociable processes. Here, we investigate whether a dissociation would still be apparent when coding facial identity, where individual exemplar information is much more important. We examined whether ensemble coding can occur when exemplar coding is difficult, as a result of large sets or short viewing times, or whether the two types of coding are positively associated. We found a positive association, whereby both ensemble and exemplar coding were reduced for larger groups and shorter viewing times. There was no evidence for ensemble coding in the absence of exemplar coding. At longer presentation times, there was an unexpected dissociation, where exemplar coding increased yet ensemble coding decreased, suggesting that robust information about face identity might suppress ensemble coding. Thus, for face identity, we did not find the classic dissociation-of access to ensemble information in the absence of detailed exemplar information-that has been used to support claims of distinct mechanisms for ensemble and exemplar coding.

Ocean state and uncertainty forecasts using HYCOM with Local Ensemble Transfer Kalman Filter (LETKF)

NASA Astrophysics Data System (ADS)

Wei, Mozheng; Hogan, Pat; Rowley, Clark; Smedstad, Ole-Martin; Wallcraft, Alan; Penny, Steve

2017-04-01

An ensemble forecast system based on the US Navy's operational HYCOM using Local Ensemble Transfer Kalman Filter (LETKF) technology has been developed for ocean state and uncertainty forecasts. One of the advantages is that the best possible initial analysis states for the HYCOM forecasts are provided by the LETKF which assimilates the operational observations using ensemble method. The background covariance during this assimilation process is supplied with the ensemble, thus it avoids the difficulty of developing tangent linear and adjoint models for 4D-VAR from the complicated hybrid isopycnal vertical coordinate in HYCOM. Another advantage is that the ensemble system provides the valuable uncertainty estimate corresponding to every state forecast from HYCOM. Uncertainty forecasts have been proven to be critical for the downstream users and managers to make more scientifically sound decisions in numerical prediction community. In addition, ensemble mean is generally more accurate and skilful than the single traditional deterministic forecast with the same resolution. We will introduce the ensemble system design and setup, present some results from 30-member ensemble experiment, and discuss scientific, technical and computational issues and challenges, such as covariance localization, inflation, model related uncertainties and sensitivity to the ensemble size.

The export receptor Crm1 forms a dimer to promote nuclear export of HIV RNA.

PubMed

Booth, David S; Cheng, Yifan; Frankel, Alan D

2014-12-08

The HIV Rev protein routes viral RNAs containing the Rev Response Element (RRE) through the Crm1 nuclear export pathway to the cytoplasm where viral proteins are expressed and genomic RNA is delivered to assembling virions. The RRE assembles a Rev oligomer that displays nuclear export sequences (NESs) for recognition by the Crm1-Ran(GTP) nuclear receptor complex. Here we provide the first view of an assembled HIV-host nuclear export complex using single-particle electron microscopy. Unexpectedly, Crm1 forms a dimer with an extensive interface that enhances association with Rev-RRE and poises NES binding sites to interact with a Rev oligomer. The interface between Crm1 monomers explains differences between Crm1 orthologs that alter nuclear export and determine cellular tropism for viral replication. The arrangement of the export complex identifies a novel binding surface to possibly target an HIV inhibitor and may point to a broader role for Crm1 dimerization in regulating host gene expression.

Circadian Amplitude Regulation via FBXW7-Targeted REV-ERBα Degradation.

PubMed

Zhao, Xuan; Hirota, Tsuyoshi; Han, Xuemei; Cho, Han; Chong, Ling-Wa; Lamia, Katja; Liu, Sihao; Atkins, Annette R; Banayo, Ester; Liddle, Christopher; Yu, Ruth T; Yates, John R; Kay, Steve A; Downes, Michael; Evans, Ronald M

2016-06-16

Defects in circadian rhythm influence physiology and behavior with implications for the treatment of sleep disorders, metabolic disease, and cancer. Although core regulatory components of clock rhythmicity have been defined, insight into the mechanisms underpinning amplitude is limited. Here, we show that REV-ERBα, a core inhibitory component of clock transcription, is targeted for ubiquitination and subsequent degradation by the F-box protein FBXW7. By relieving REV-ERBα-dependent repression, FBXW7 provides an unrecognized mechanism for enhancing the amplitude of clock gene transcription. Cyclin-dependent kinase 1 (CDK1)-mediated phosphorylation of REV-ERBα is necessary for FBXW7 recognition. Moreover, targeted hepatic disruption of FBXW7 alters circadian expression of core clock genes and perturbs whole-body lipid and glucose levels. This CDK1-FBXW7 pathway controlling REV-ERBα repression defines an unexpected molecular mechanism for re-engaging the positive transcriptional arm of the clock, as well as a potential route to manipulate clock amplitude via small molecule CDK1 inhibition. Copyright © 2016 Elsevier Inc. All rights reserved.

Tissue damage drives co-localization of NF-κB, Smad3, and Nrf2 to direct Rev-erb sensitive wound repair in mouse macrophages

PubMed Central

Eichenfield, Dawn Z; Troutman, Ty Dale; Link, Verena M; Lam, Michael T; Cho, Han; Gosselin, David; Spann, Nathanael J; Lesch, Hanna P; Tao, Jenhan; Muto, Jun; Gallo, Richard L; Evans, Ronald M; Glass, Christopher K

2016-01-01

Although macrophages can be polarized to distinct phenotypes in vitro with individual ligands, in vivo they encounter multiple signals that control their varied functions in homeostasis, immunity, and disease. Here, we identify roles of Rev-erb nuclear receptors in regulating responses of mouse macrophages to complex tissue damage signals and wound repair. Rather than reinforcing a specific program of macrophage polarization, Rev-erbs repress subsets of genes that are activated by TLR ligands, IL4, TGFβ, and damage-associated molecular patterns (DAMPS). Unexpectedly, a complex damage signal promotes co-localization of NF-κB, Smad3, and Nrf2 at Rev-erb-sensitive enhancers and drives expression of genes characteristic of multiple polarization states in the same cells. Rev-erb-sensitive enhancers thereby integrate multiple damage-activated signaling pathways to promote a wound repair phenotype. DOI: http://dx.doi.org/10.7554/eLife.13024.001 PMID:27462873

Exploring diversity in ensemble classification: Applications in large area land cover mapping

NASA Astrophysics Data System (ADS)

Mellor, Andrew; Boukir, Samia

2017-07-01

Ensemble classifiers, such as random forests, are now commonly applied in the field of remote sensing, and have been shown to perform better than single classifier systems, resulting in reduced generalisation error. Diversity across the members of ensemble classifiers is known to have a strong influence on classification performance - whereby classifier errors are uncorrelated and more uniformly distributed across ensemble members. The relationship between ensemble diversity and classification performance has not yet been fully explored in the fields of information science and machine learning and has never been examined in the field of remote sensing. This study is a novel exploration of ensemble diversity and its link to classification performance, applied to a multi-class canopy cover classification problem using random forests and multisource remote sensing and ancillary GIS data, across seven million hectares of diverse dry-sclerophyll dominated public forests in Victoria Australia. A particular emphasis is placed on analysing the relationship between ensemble diversity and ensemble margin - two key concepts in ensemble learning. The main novelty of our work is on boosting diversity by emphasizing the contribution of lower margin instances used in the learning process. Exploring the influence of tree pruning on diversity is also a new empirical analysis that contributes to a better understanding of ensemble performance. Results reveal insights into the trade-off between ensemble classification accuracy and diversity, and through the ensemble margin, demonstrate how inducing diversity by targeting lower margin training samples is a means of achieving better classifier performance for more difficult or rarer classes and reducing information redundancy in classification problems. Our findings inform strategies for collecting training data and designing and parameterising ensemble classifiers, such as random forests. This is particularly important in large area remote sensing applications, for which training data is costly and resource intensive to collect.

Pauci ex tanto numero: reducing redundancy in multi-model ensembles

NASA Astrophysics Data System (ADS)

Solazzo, E.; Riccio, A.; Kioutsioukis, I.; Galmarini, S.

2013-02-01

We explicitly address the fundamental issue of member diversity in multi-model ensembles. To date no attempts in this direction are documented within the air quality (AQ) community, although the extensive use of ensembles in this field. Common biases and redundancy are the two issues directly deriving from lack of independence, undermining the significance of a multi-model ensemble, and are the subject of this study. Shared biases among models will determine a biased ensemble, making therefore essential the errors of the ensemble members to be independent so that bias can cancel out. Redundancy derives from having too large a portion of common variance among the members of the ensemble, producing overconfidence in the predictions and underestimation of the uncertainty. The two issues of common biases and redundancy are analysed in detail using the AQMEII ensemble of AQ model results for four air pollutants in two European regions. We show that models share large portions of bias and variance, extending well beyond those induced by common inputs. We make use of several techniques to further show that subsets of models can explain the same amount of variance as the full ensemble with the advantage of being poorly correlated. Selecting the members for generating skilful, non-redundant ensembles from such subsets proved, however, non-trivial. We propose and discuss various methods of member selection and rate the ensemble performance they produce. In most cases, the full ensemble is outscored by the reduced ones. We conclude that, although independence of outputs may not always guarantee enhancement of scores (but this depends upon the skill being investigated) we discourage selecting the members of the ensemble simply on the basis of scores, that is, independence and skills need to be considered disjointly.

Public Data Set: Erratum: "Multi-point, high-speed passive ion velocity distribution diagnostic on the Pegasus Toroidal Experiment" [Rev. Sci. Instrum. 83, 10D516 (2012)

DOE Data Explorer

Burke, Marcus G. [University of Wisconsin-Madison] (ORCID:0000000176193724); Fonck, Raymond J. [University of Wisconsin-Madison] (ORCID:0000000294386762); Bongard, Michael W. [University of Wisconsin-Madison] (ORCID:0000000231609746); Schlossberg, David J. [University of Wisconsin-Madison] (ORCID:0000000287139448); Winz, Gregory R. [University of Wisconsin-Madison] (ORCID:0000000177627184)

2016-07-18

This data set contains openly-documented, machine readable digital research data corresponding to figures published in M.G. Burke et al., 'Erratum: "Multi-point, high-speed passive ion velocity distribution diagnostic on the Pegasus Toroidal Experiment" [Rev. Sci. Instrum. 83, 10D516 (2012)],' Rev. Sci. Instrum. 87, 079902 (2016).

The Role of Stat3 Activation in Androgen Receptor Signaling and Prostate Cancer

DTIC Science & Technology

2006-07-01

S. C. & Xiao, G. (2003) Cancer Metastasis Rev. 22, 405–422. 10. Karin, M. & Greten , F. R. (2005) Nat. Rev. Immunol. 5, 749–759. 11. Karin, M., Cao, Y... Greten , F. R. & Li, Z. W. (2002) Nat. Rev. Cancer 2, 301–310. 12. Fan, C. M. & Maniatis, T. (1991) Nature 354, 395–398. 13. Betts, J. C. & Nabel, G

B80 and B101-103 clusters: Remarkable stability of the core-shell structures established by validated density functionalsa)

NASA Astrophysics Data System (ADS)

Li, Fengyu; Jin, Peng; Jiang, De-en; Wang, Lu; Zhang, Shengbai B.; Zhao, Jijun; Chen, Zhongfang

2012-02-01

Prompted by the very recent claim that the volleyball-shaped B80 fullerene [X. Wang, Phys. Rev. B 82, 153409 (2010), 10.1103/PhysRevB.82.153409] is lower in energy than the B80 buckyball [N. G. Szwacki, A. Sadrzadeh, and B. I. Yakobson, Phys. Rev. Lett. 98, 166804 (2007), 10.1103/PhysRevLett.98.166804] and core-shell structure [J. Zhao, L. Wang, F. Li, and Z. Chen, J. Phys. Chem. A 114, 9969 (2010), 10.1021/jp1018873], and inspired by the most recent finding of another core-shell isomer as the lowest energy B80 isomer [S. De, A. Willand, M. Amsler, P. Pochet, L. Genovese, and S. Goedecher, Phys. Rev. Lett. 106, 225502 (2011), 10.1103/PhysRevLett.106.225502], we carefully evaluated the performance of the density functional methods in the energetics of boron clusters and confirmed that the core-shell construction (stuffed fullerene) is thermodynamically the most favorable structural pattern for B80. Our global minimum search showed that both B101 and B103 also prefer a core-shell structure and that B103 can reach the complete core-shell configuration. We called for great attention to the theoretical community when using density functionals to investigate boron-related nanomaterials.

Analytical results for a conditional phase shift between single-photon pulses in a nonlocal nonlinear medium

NASA Astrophysics Data System (ADS)

Viswanathan, Balakrishnan; Gea-Banacloche, Julio

2018-03-01

It has been suggested that second-order nonlinearities could be used for quantum logic at the single-photon level. Specifically, successive two-photon processes in principle could accomplish the phase shift (conditioned on the presence of two photons in the low-frequency modes) |011 〉→i |100 〉→-|011 〉 . We have analyzed a recent scheme proposed by Xia et al. [Phys. Rev. Lett. 116, 023601 (2016)], 10.1103/PhysRevLett.116.023601 to induce such a conditional phase shift between two single-photon pulses propagating at different speeds through a nonlinear medium with a nonlocal response. We present here an analytical solution for the most general case, i.e., for an arbitrary response function, initial state, and pulse velocity, which supports their numerical observation that a π phase shift with unit fidelity is possible, in principle, in an appropriate limit. We also discuss why this is possible in this system, despite the theoretical objections to the possibility of conditional phase shifts on single photons that were raised some time ago by Shapiro [Phys. Rev. A 73, 062305 (2006)], 10.1103/PhysRevA.73.062305 and by Gea-Banacloche [Phys. Rev. A 81, 043823 (2010)], 10.1103/PhysRevA.81.043823 one of us.

The physiological and biomechanical effects of forwards and reverse sports wheelchair propulsion.

PubMed

Mason, Barry S; Lenton, John P; Goosey-Tolfrey, Victoria L

2015-07-01

To explore the physiological and biomechanical differences between forwards (FOR) and reverse (REV) sports wheelchair propulsion. Fourteen able-bodied males with previous wheelchair propulsion experience pushed a sports wheelchair on a single-roller ergometer in a FOR and REV direction at three sub-maximal speeds (4, 6, and 8 km/hour). Each trial lasted 3 minutes, and during the final minute physiological and biomechanical measures was collected. The physiological results revealed that oxygen uptake (1.51 ± 0.29 vs. 1.38 ± 0.26 L/minute, P = 0.005) and heart rate (121 ± 19 vs. 109 ± 14 beats/minute, P < 0.0005) were significantly greater during REV than FOR only during the 8 km/hour trials. From a biomechanical perspective, push frequencies were similar between FOR and REV across all speeds (P > 0.05). However, greater mean resultant forces were applied during FOR (P < 0.0005) at 4 km/hour (66.7 ± 19.5 vs. 49.2 ± 10.3 N), 6 km/hour (90.7 ± 21.9 vs. 65.3 ± 18.6 N), and 8 km/hour (102.5 ± 17.6 vs. 68.7 ± 13.5 N) compared to REV. Alternatively, push times and push angles were significantly lower (P ≤ 0.001) during FOR at each speed. The current study demonstrated that at higher speeds physiological demand becomes elevated during REV. This was likely to be associated with an inability to apply sufficient force to the wheels, thus requiring kinematic adaptations in order to maintain constant speeds in REV.

Impacts of calibration strategies and ensemble methods on ensemble flood forecasting over Lanjiang basin, Southeast China

NASA Astrophysics Data System (ADS)

Liu, Li; Xu, Yue-Ping

2017-04-01

Ensemble flood forecasting driven by numerical weather prediction products is becoming more commonly used in operational flood forecasting applications.In this study, a hydrological ensemble flood forecasting system based on Variable Infiltration Capacity (VIC) model and quantitative precipitation forecasts from TIGGE dataset is constructed for Lanjiang Basin, Southeast China. The impacts of calibration strategies and ensemble methods on the performance of the system are then evaluated.The hydrological model is optimized by parallel programmed ɛ-NSGAII multi-objective algorithm and two respectively parameterized models are determined to simulate daily flows and peak flows coupled with a modular approach.The results indicatethat the ɛ-NSGAII algorithm permits more efficient optimization and rational determination on parameter setting.It is demonstrated that the multimodel ensemble streamflow mean have better skills than the best singlemodel ensemble mean (ECMWF) and the multimodel ensembles weighted on members and skill scores outperform other multimodel ensembles. For typical flood event, it is proved that the flood can be predicted 3-4 days in advance, but the flows in rising limb can be captured with only 1-2 days ahead due to the flash feature. With respect to peak flows selected by Peaks Over Threshold approach, the ensemble means from either singlemodel or multimodels are generally underestimated as the extreme values are smoothed out by ensemble process.

Lessons from Climate Modeling on the Design and Use of Ensembles for Crop Modeling

NASA Technical Reports Server (NTRS)

Wallach, Daniel; Mearns, Linda O.; Ruane, Alexander C.; Roetter, Reimund P.; Asseng, Senthold

2016-01-01

Working with ensembles of crop models is a recent but important development in crop modeling which promises to lead to better uncertainty estimates for model projections and predictions, better predictions using the ensemble mean or median, and closer collaboration within the modeling community. There are numerous open questions about the best way to create and analyze such ensembles. Much can be learned from the field of climate modeling, given its much longer experience with ensembles. We draw on that experience to identify questions and make propositions that should help make ensemble modeling with crop models more rigorous and informative. The propositions include defining criteria for acceptance of models in a crop MME, exploring criteria for evaluating the degree of relatedness of models in a MME, studying the effect of number of models in the ensemble, development of a statistical model of model sampling, creation of a repository for MME results, studies of possible differential weighting of models in an ensemble, creation of single model ensembles based on sampling from the uncertainty distribution of parameter values or inputs specifically oriented toward uncertainty estimation, the creation of super ensembles that sample more than one source of uncertainty, the analysis of super ensemble results to obtain information on total uncertainty and the separate contributions of different sources of uncertainty and finally further investigation of the use of the multi-model mean or median as a predictor.

Decadal climate prediction in the large ensemble limit

NASA Astrophysics Data System (ADS)

Yeager, S. G.; Rosenbloom, N. A.; Strand, G.; Lindsay, K. T.; Danabasoglu, G.; Karspeck, A. R.; Bates, S. C.; Meehl, G. A.

2017-12-01

In order to quantify the benefits of initialization for climate prediction on decadal timescales, two parallel sets of historical simulations are required: one "initialized" ensemble that incorporates observations of past climate states and one "uninitialized" ensemble whose internal climate variations evolve freely and without synchronicity. In the large ensemble limit, ensemble averaging isolates potentially predictable forced and internal variance components in the "initialized" set, but only the forced variance remains after averaging the "uninitialized" set. The ensemble size needed to achieve this variance decomposition, and to robustly distinguish initialized from uninitialized decadal predictions, remains poorly constrained. We examine a large ensemble (LE) of initialized decadal prediction (DP) experiments carried out using the Community Earth System Model (CESM). This 40-member CESM-DP-LE set of experiments represents the "initialized" complement to the CESM large ensemble of 20th century runs (CESM-LE) documented in Kay et al. (2015). Both simulation sets share the same model configuration, historical radiative forcings, and large ensemble sizes. The twin experiments afford an unprecedented opportunity to explore the sensitivity of DP skill assessment, and in particular the skill enhancement associated with initialization, to ensemble size. This talk will highlight the benefits of a large ensemble size for initialized predictions of seasonal climate over land in the Atlantic sector as well as predictions of shifts in the likelihood of climate extremes that have large societal impact.

Summary statistics in the attentional blink.

PubMed

McNair, Nicolas A; Goodbourn, Patrick T; Shone, Lauren T; Harris, Irina M

2017-01-01

We used the attentional blink (AB) paradigm to investigate the processing stage at which extraction of summary statistics from visual stimuli ("ensemble coding") occurs. Experiment 1 examined whether ensemble coding requires attentional engagement with the items in the ensemble. Participants performed two sequential tasks on each trial: gender discrimination of a single face (T1) and estimating the average emotional expression of an ensemble of four faces (or of a single face, as a control condition) as T2. Ensemble coding was affected by the AB when the tasks were separated by a short temporal lag. In Experiment 2, the order of the tasks was reversed to test whether ensemble coding requires more working-memory resources, and therefore induces a larger AB, than estimating the expression of a single face. Each condition produced a similar magnitude AB in the subsequent gender-discrimination T2 task. Experiment 3 additionally investigated whether the previous results were due to participants adopting a subsampling strategy during the ensemble-coding task. Contrary to this explanation, we found different patterns of performance in the ensemble-coding condition and a condition in which participants were instructed to focus on only a single face within an ensemble. Taken together, these findings suggest that ensemble coding emerges automatically as a result of the deployment of attentional resources across the ensemble of stimuli, prior to information being consolidated in working memory.

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Science.gov Websites

2008073000 2008072900 2008072800 Background information bias reduction = ( | domain-averaged ensemble mean bias | - | domain-averaged bias-corrected ensemble mean bias | / | domain-averaged bias-corrected ensemble mean bias | NAEFS Products | NAEFS | EMC Ensemble Products EMC | NCEP | National Weather Service

How accurate are the parametrized correlation energies of the uniform electron gas?

NASA Astrophysics Data System (ADS)

Bhattarai, Puskar; Patra, Abhirup; Shahi, Chandra; Perdew, John P.

2018-05-01

Density functional approximations to the exchange-correlation energy are designed to be exact for an electron gas of uniform density parameter rs and relative spin polarization ζ , requiring a parametrization of the correlation energy per electron ɛc(rs,ζ ) . We consider three widely used parametrizations [J. P. Perdew and A. Zunger, Phys. Rev. B 23, 5048 (1981), 10.1103/PhysRevB.23.5048 or PZ81, S. H. Vosko, L. Wilk, and M. Nusair, Can. J. Phys. 58, 1200 (1980), 10.1139/p80-159 or VWN80, and J. P. Perdew and Y. Wang, Phys. Rev. B 45, 13244 (1992), 10.1103/PhysRevB.45.13244 or PW92] that interpolate the quantum Monte Carlo (QMC) correlation energies of Ceperley-Alder [Phys. Rev. Lett. 45, 566 (1980), 10.1103/PhysRevLett.45.566], while extrapolating them to known high-(rs→0 ) and low- (rs→∞ ) density limits. For the physically important range 0.5 ≤rs≤20 , they agree closely with one another, with differences of 0.01 eV (0.5%) or less between the latter two. The density parameter interpolation (DPI), designed to predict these energies by interpolation between the known high- and low-density limits, with almost no other input (and none for ζ =0 ), is also reasonably close, both in its original version and with corrections for ζ ≠0 . Moreover, the DPI and PW92 at rs=0.5 are very close to the high-density expansion. The larger discrepancies with the QMC of Spink et al. [Phys. Rev. B 88, 085121 (2013), 10.1103/PhysRevB.88.085121], of order 0.1 eV (5%) at rs=0.5 , are thus surprising, suggesting that the constraint-based PW92 and VWN80 parametrizations are more accurate than the QMC for rs<2 . For rs>2 , however, the QMC of Spink et al. confirms the dependence upon relative spin polarization predicted by the parametrizations.

DNA Polymerase ζ is essential for hexavalent chromium-induced mutagenesis

PubMed Central

O'Brien, Travis J.; Witcher, Preston; Brooks, Bradford; Patierno, Steven R.

2009-01-01

Translesion synthesis (TLS) is a unique DNA damage tolerance mechanism involved in the replicative bypass of genetic lesions in favor of uninterrupted DNA replication. TLS is critical for the generation of mutations by many different chemical and physical agents, however, there is no information available regarding the role of TLS in carcinogenic metal-induced mutagenesis. Hexavalent chromium (Cr(VI))-containing compounds are highly complex genotoxins possessing both mutagenic and clastogenic activities. The focus of this work was to determine the impact that TLS has on Cr(VI)-induced mutagenesis in S. cerevisiae. Wild-type yeast and strains deficient in TLS polymerases (i.e. Polζ (rev3), Polη (rad30)) were exposed to Cr(VI) and monitored for cell survival and forward mutagenesis at the CAN1 locus. In general, TLS deficiency had little impact on Cr(VI)-induced clonogenic lethality or cell growth. rad30 yeast exhibited higher levels of basal and induced mutagenesis compared to Wt and rev3 yeast. In contrast, rev3 yeast displayed attenuated Cr(VI)-induced mutagenesis. Moreover, deletion of REV3 in rad30 yeast (rad30 rev3) resulted in a significant decrease in basal and Cr(VI) mutagenesis relative to Wt and rad30 single mutants indicating that mutagenesis primarily depended upon Polζ. Interestingly, rev3 yeast were similar to Wt yeast in susceptibility to Cr(VI)-induced frameshift mutations. Mutational analysis of the CAN1 gene revealed that Cr(VI)-induced base substitution mutations accounted for 83.9% and 100.0% of the total mutations in Wt and rev3 yeast, respectively. Insertions and deletions comprised 16.1% of the total mutations in Cr(VI) treated Wt yeast but were not observed rev3 yeast. This work provides novel information regarding the molecular mechanisms of Cr(VI)-induced mutagenesis and is the first report demonstrating a role for TLS in the fixation of mutations induced by a carcinogenic metal. PMID:19428373

Specificity of RSG-1.2 Peptide Binding to RRE-IIB RNA Element of HIV-1 over Rev Peptide Is Mainly Enthalpic in Origin

PubMed Central

Kumar, Santosh; Bose, Debojit; Suryawanshi, Hemant; Sabharwal, Harshana; Mapa, Koyeli; Maiti, Souvik

2011-01-01

Rev is an essential HIV-1 regulatory protein which binds to the Rev responsive element (RRE) present within the env gene of HIV-1 RNA genome. This binding facilitates the transport of the RNA to the cytoplasm, which in turn triggers the switch between viral latency and active viral replication. Essential components of this complex have been localized to a minimal arginine rich Rev peptide and stem IIB region of RRE. A synthetic peptide known as RSG-1.2 binds with high binding affinity and specificity to the RRE-IIB than the Rev peptide, however the thermodynamic basis of this specificity has not yet been addressed. The present study aims to probe the thermodynamic origin of this specificity of RSG-1.2 over Rev Peptide for RRE-IIB. The temperature dependent melting studies show that RSG-1.2 binding stabilizes the RRE structure significantly (ΔT m = 4.3°C), in contrast to Rev binding. Interestingly the thermodynamic signatures of the binding have also been found to be different for both the peptides. At pH 7.5, RSG-1.2 binds RRE-IIB with a Ka = 16.2±0.6×107 M−1 where enthalpic change ΔH = −13.9±0.1 kcal/mol is the main driving force with limited unfavorable contribution from entropic change TΔS = −2.8±0.1 kcal/mol. A large part of ΔH may be due to specific stacking between U72 and Arg15. In contrast binding of Rev (Ka = 3.1±0.4×107 M−1) is driven mainly by entropy (ΔH = 0 kcal/mol and TΔS = 10.2±0.2 kcal/mol) which arises from major conformational changes in the RNA upon binding. PMID:21853108

Specificity of RSG-1.2 peptide binding to RRE-IIB RNA element of HIV-1 over Rev peptide is mainly enthalpic in origin.

PubMed

Kumar, Santosh; Bose, Debojit; Suryawanshi, Hemant; Sabharwal, Harshana; Mapa, Koyeli; Maiti, Souvik

2011-01-01

Rev is an essential HIV-1 regulatory protein which binds to the Rev responsive element (RRE) present within the env gene of HIV-1 RNA genome. This binding facilitates the transport of the RNA to the cytoplasm, which in turn triggers the switch between viral latency and active viral replication. Essential components of this complex have been localized to a minimal arginine rich Rev peptide and stem IIB region of RRE. A synthetic peptide known as RSG-1.2 binds with high binding affinity and specificity to the RRE-IIB than the Rev peptide, however the thermodynamic basis of this specificity has not yet been addressed. The present study aims to probe the thermodynamic origin of this specificity of RSG-1.2 over Rev Peptide for RRE-IIB. The temperature dependent melting studies show that RSG-1.2 binding stabilizes the RRE structure significantly (ΔT(m) = 4.3°C), in contrast to Rev binding. Interestingly the thermodynamic signatures of the binding have also been found to be different for both the peptides. At pH 7.5, RSG-1.2 binds RRE-IIB with a K(a) = 16.2±0.6×10(7) M(-1) where enthalpic change ΔH = -13.9±0.1 kcal/mol is the main driving force with limited unfavorable contribution from entropic change TΔS = -2.8±0.1 kcal/mol. A large part of ΔH may be due to specific stacking between U72 and Arg15. In contrast binding of Rev (K(a) = 3.1±0.4×10(7) M(-1)) is driven mainly by entropy (ΔH = 0 kcal/mol and TΔS = 10.2±0.2 kcal/mol) which arises from major conformational changes in the RNA upon binding.

Families of quantum fingerprinting protocols

NASA Astrophysics Data System (ADS)

Lovitz, Benjamin; Lütkenhaus, Norbert

2018-03-01

We introduce several families of quantum fingerprinting protocols to evaluate the equality function on two n -bit strings in the simultaneous message passing model. The original quantum fingerprinting protocol uses a tensor product of a small number of O (logn ) -qubit high-dimensional signals [H. Buhrman et al., Phys. Rev. Lett. 87, 167902 (2001), 10.1103/PhysRevLett.87.167902], whereas a recently proposed optical protocol uses a tensor product of O (n ) single-qubit signals, while maintaining the O (logn ) information leakage of the original protocol [J. M. Arazola and N. Lütkenhaus, Phys. Rev. A 89, 062305 (2014), 10.1103/PhysRevA.89.062305]. We find a family of protocols which interpolate between the original and optical protocols while maintaining the O (logn ) information leakage, thus demonstrating a tradeoff between the number of signals sent and the dimension of each signal. There has been interest in experimental realization of the recently proposed optical protocol using coherent states [F. Xu et al., Nat. Commun. 6, 8735 (2015), 10.1038/ncomms9735; J.-Y. Guan et al., Phys. Rev. Lett. 116, 240502 (2016), 10.1103/PhysRevLett.116.240502], but as the required number of laser pulses grows linearly with the input size n , eventual challenges for the long-time stability of experimental setups arise. We find a coherent state protocol which reduces the number of signals by a factor 1/2 while also reducing the information leakage. Our reduction makes use of a simple modulation scheme in optical phase space, and we find that more complex modulation schemes are not advantageous. Using a similar technique, we improve a recently proposed coherent state protocol for evaluating the Euclidean distance between two real unit vectors [N. Kumar et al., Phys. Rev. A 95, 032337 (2017), 10.1103/PhysRevA.95.032337] by reducing the number of signals by a factor 1/2 and also reducing the information leakage.

Statistical Ensemble of Large Eddy Simulations

NASA Technical Reports Server (NTRS)

Carati, Daniele; Rogers, Michael M.; Wray, Alan A.; Mansour, Nagi N. (Technical Monitor)

2001-01-01

A statistical ensemble of large eddy simulations (LES) is run simultaneously for the same flow. The information provided by the different large scale velocity fields is used to propose an ensemble averaged version of the dynamic model. This produces local model parameters that only depend on the statistical properties of the flow. An important property of the ensemble averaged dynamic procedure is that it does not require any spatial averaging and can thus be used in fully inhomogeneous flows. Also, the ensemble of LES's provides statistics of the large scale velocity that can be used for building new models for the subgrid-scale stress tensor. The ensemble averaged dynamic procedure has been implemented with various models for three flows: decaying isotropic turbulence, forced isotropic turbulence, and the time developing plane wake. It is found that the results are almost independent of the number of LES's in the statistical ensemble provided that the ensemble contains at least 16 realizations.

Invariant measures in brain dynamics

NASA Astrophysics Data System (ADS)

Boyarsky, Abraham; Góra, Paweł

2006-10-01

This note concerns brain activity at the level of neural ensembles and uses ideas from ergodic dynamical systems to model and characterize chaotic patterns among these ensembles during conscious mental activity. Central to our model is the definition of a space of neural ensembles and the assumption of discrete time ensemble dynamics. We argue that continuous invariant measures draw the attention of deeper brain processes, engendering emergent properties such as consciousness. Invariant measures supported on a finite set of ensembles reflect periodic behavior, whereas the existence of continuous invariant measures reflect the dynamics of nonrepeating ensemble patterns that elicit the interest of deeper mental processes. We shall consider two different ways to achieve continuous invariant measures on the space of neural ensembles: (1) via quantum jitters, and (2) via sensory input accompanied by inner thought processes which engender a “folding” property on the space of ensembles.

High energy neutrinos from astrophysical accelerators of cosmic ray nuclei

NASA Astrophysics Data System (ADS)

Anchordoqui, Luis A.; Hooper, Dan; Sarkar, Subir; Taylor, Andrew M.

2008-02-01

Ongoing experimental efforts to detect cosmic sources of high energy neutrinos are guided by the expectation that astrophysical accelerators of cosmic ray protons would also generate neutrinos through interactions with ambient matter and/or photons. However, there will be a reduction in the predicted neutrino flux if cosmic ray sources accelerate not only protons but also significant numbers of heavier nuclei, as is indicated by recent air shower data. We consider plausible extragalactic sources such as active galactic nuclei, gamma ray bursts and starburst galaxies and demand consistency with the observed cosmic ray composition and energy spectrum at Earth after allowing for propagation through intergalactic radiation fields. This allows us to calculate the expected neutrino fluxes from the sources, normalized to the observed cosmic ray spectrum. We find that the likely signals are still within reach of next generation neutrino telescopes such as IceCube.PACS95.85.Ry98.70.Rz98.54.Cm98.54.EpReferencesFor a review, see:F.HalzenD.HooperRep. Prog. Phys.6520021025A.AchterbergIceCube CollaborationPhys. Rev. Lett.972006221101A.AchterbergIceCube CollaborationAstropart. Phys.262006282arXiv:astro-ph/0611063arXiv:astro-ph/0702265V.NiessANTARES CollaborationAIP Conf. Proc.8672006217I.KravchenkoPhys. Rev. D732006082002S.W.BarwickANITA CollaborationPhys. Rev. Lett.962006171101V.Van ElewyckPierre Auger CollaborationAIP Conf. Proc.8092006187For a survey of possible sources and event rates in km3 detectors see e.g.,W.BednarekG.F.BurgioT.MontaruliNew Astron. Rev.4920051M.D.KistlerJ.F.BeacomPhys. Rev. D742006063007A. Kappes, J. Hinton, C. Stegmann, F.A. Aharonian, arXiv:astro-ph/0607286.A.LevinsonE.WaxmanPhys. Rev. Lett.872001171101C.DistefanoD.GuettaE.WaxmanA.LevinsonAstrophys. J.5752002378F.A.AharonianL.A.AnchordoquiD.KhangulyanT.MontaruliJ. Phys. Conf. Ser.392006408J.Alvarez-MunizF.HalzenAstrophys. J.5762002L33F.VissaniAstropart. Phys.262006310F.W.SteckerC.DoneM.H.SalamonP.SommersPhys. Rev. Lett.6619912697(Erratum-ibid. 69 (1992) 2738)F.W.SteckerPhys. Rev. D722005107301A.AtoyanC.D.DermerPhys. Rev. Lett.872001221102L.A.AnchordoquiH.GoldbergF.HalzenT.J.WeilerPhys. Lett. B6002004202E.WaxmanJ.N.BahcallPhys. Rev. Lett.7819972292C.D.DermerA.AtoyanPhys. Rev. Lett.912003071102D.GuettaD.HooperJ.Alvarez-MunizF.HalzenE.ReuveniAstropart. Phys.202004429J.Alvarez-MunizF.HalzenD.W.HooperPhys. Rev. D622000093015A.LoebE.WaxmanJCAP06052006003S. Inoue, G. Sigl, F. Miniati, E. Armengaud, arXiv:astro-ph/0701167.E.WaxmanJ.N.BahcallPhys. Rev. D591999023002Phys. Rev. D642001023002K.MannheimR.J.ProtheroeJ.P.RachenPhys. Rev. D632001023003arXiv:astro-ph/9908031M.AhlersL.A.AnchordoquiH.GoldbergF.HalzenA.RingwaldT.J.WeilerPhys. Rev. D722005023001E.WaxmanAstrophys. J.4521995L1Note that the neutrino spectral shape can deviate from that for protons if the Feynman plateau is not flat in pseudo-rapidity space;L.AnchordoquiH.GoldbergC.NunezPhys. Rev. D712005065014This is in fact suggested by Tevatron data;F.AbeCDF CollaborationPhys. Rev. D4119902330J.G.LearnedS.PakvasaAstropart. Phys.31995267F.HalzenD.SaltzbergPhys. Rev. Lett.8119984305J.F.BeacomN.F.BellD.HooperS.PakvasaT.J.WeilerPhys. Rev. D682003093005(Erratum-ibid. D 72 (2005) 019901)L.A.AnchordoquiH.GoldbergF.HalzenT.J.WeilerPhys. Lett. B593200442L.A.AnchordoquiH.GoldbergF.HalzenT.J.WeilerPhys. Lett. B621200518A.M.HillasAnn. Rev. Astron. Astrophys.221984425For a general discussion on the acceleration time-scale in these sources see, e.g.,D.F.TorresL.A.AnchordoquiRep. Prog. Phys.6720041663M.C.BegelmanB.RudakM.SikoraAstrophys. J.362199038M.J.ChodorowskiA.A.ZdziarskiM.SikoraAstrophys. J.4001992181S.MichalowskiD.AndrewsJ.EickmeyerT.GentileN.MistryR.TalmanK.UenoPhys. Rev. Lett.391977737J.L.PugetF.W.SteckerJ.H.BredekampAstrophys. J.2051976638D.HooperS.SarkarA.M.TaylorAstropart. Phys.272007199The non-thermal energy release in GRBs is much smaller than that output by AGN.P.L.BiermannP.A.StrittmatterAstrophys. J.3221987643R.J.ProtheroeA.P.SzaboPhys. Rev. Lett.6919922885J.P.RachenP.L.BiermannAstron. Astrophys.2721993161J.P.RachenT.StanevP.L.BiermannAstron. Astrophys.2731993377R.C.HartmanEGRET CollaborationAstrophys. J. Suppl.123199979See e.g.,M.PunchNature3581992477D.PetryHEGRA CollaborationAstron. Astrophys.3111996L13P.M.ChadwickAstrophys. J.5131999161C.D.DermerR.SchlickeiserA.MastichiadisAstron. Astrophys.2561992L27S.D.BloomA.P.MarscherAstrophys. J.4611996657K.MannheimAstron. Astrophys.269199367K.MannheimScience2791998684A.DarA.LaorAstrophys. J.4781997L5F.A.AharonianNew Astron.52000377M.BoettcherAstrophys. J.5151999L21C.D.DermerR.SchlickeiserAstrophys. J.4161993458F.W.SteckerPhys. Rev. Lett.2119681016G.J.FishmanC.A.MeeganAnn. Rev. Astron. Astrophys.331995415For a list of papers related to SWIFT, see: http://swift.gsfc.nasa.gov/docs/swift/results/publist/.B.LinkR.I.EpsteinAstrophys. J.4661996764C.A.MeeganNature3551992143M.R.MetzgerNature3871997878See e.g.,T.PiranPhys. Rep.3141999575T.PiranPhys. Rep.3332000529For a recent review of GRB phenomenology, see:P.MeszarosRep. Prog. Phys.6920062259E.WaxmanLect. Notes Phys.5762001122M.MilgromV.UsovAstrophys. J.4491995L37E.WaxmanPhys. Rev. Lett.751995386M.VietriPhys. Rev. Lett.7819974328D.BandAstrophys. J.4131993281F. Halzen, in: K. Oliver (Ed.), Proceedings of the TASI’98, Boulder, 1998, p. 524.J.W.ElbertP.SommersAstrophys. J.4411995151L.A.AnchordoquiG.E.RomeroJ.A.CombiPhys. Rev. D601999103001L.A. Anchordoqui, J.F. Beacom, H. Goldberg, S. Palomares-Ruiz, T.J. Weiler, arXiv:astro-ph/0611580; arXiv:astro-ph/0611581.The factor 9/(4R) results from calculating ∫dr∫dr|r-r|(4πR/3), where r is the position of a star and r is the position of an observer (the position of the reaction), in a region of radius R uniformly filled with sources.D.A.ForbesM.J.WardV.RotaciucM.BlietzR.GenzelS.DrapatzP.P.van der WerfA.KrabbeAstrophys. J.4061993L11P. Chanial, H. Flores, B. Guiderdoni, D. Elbaz, F. Hammer, L. Vigroux, arXiv:astro-ph/0610900.P.O.LagageC.J.CesarskyAstron. Astrophys.1181983223S.P.LaiJ.M.GirartR.CrutcherAstrophys. J.5982003392W.BednarekMon. Not. R. Astron. Soc.3452003847W.BednarekR.J.ProtheroeAstropart. Phys.162002397P.BlasiA.V.OlintoPhys. Rev. D591999023001F.W.SteckerAstropart. Phys.262007398F.W. Stecker, arXiv:astro-ph/0610208.A γ-ray signal from the nearby starburst galaxy NGC253 was reported by the CANGAROO-II Collaboration but their subsequent re-analysis of the data is consistent with the expectation from backgrounds:C.ItohCANGAROO-II CollaborationAstron. Astrophys.3962002L1(Erratum-ibid. 462 (2007) 67)T.A. Thompson, E. Quataert, E. Waxman, A. Loeb, arXiv:astro-ph/0608699.D.J.BirdFly’s Eye CollaborationPhys. Rev. Lett.7119933401D.R.BergmanHiRes CollaborationNucl. Phys. Proc. Suppl.136200440T.Abu-ZayyadHiRes-MIA CollaborationAstrophys. J.5572001686M.NaganoJ. Phys. G181992423V.BerezinskyA.Z.GazizovS.I.GrigorievaPhys. Rev. D742006043005R.U.AbbasiHiRes CollaborationPhys. Rev. Lett.922004151101V.BerezinskyA.Z.GazizovS.I.GrigorievaPhys. Lett. B6122005147V.S.BerezinskyS.I.GrigorievaB.I.HnatykAstropart. Phys.212004617See Fig. 21 in:L.AnchordoquiM.T.DovaA.MariazziT.McCauleyT.PaulS.ReucroftJ.SwainAnn. Phys.3142004145D.AllardE.ParizotE.KhanS.GorielyA.V.OlintoAstron. Astrophys.4432005L29D.AllardE.ParizotA.V.OlintoAstropart. Phys.27200761T.Abu-ZayyadHigh Resolution Fly’s Eye CollaborationAstropart. Phys.232005157P. Sommers, et al., Pierre Auger Collaboration, arXiv:astro-ph/0507150.R.U.AbbasiHiRes CollaborationAstrophys. J.6222005910B.N. Afanasiev, et al., Yakutsk Collaboration, in: M. Nagano (Ed.), Proceedings of the Tokyo Workshop on Techniques for the Study of the Extremely High Energy Cosmic Rays, 1993.J. Knapp, private communication.J.RanftPhys. Rev. D51199564R.S.FletcherT.K.GaisserP.LipariT.StanevPhys. Rev. D5019945710J.EngelT.K.GaisserT.StanevP.LipariPhys. Rev. D4619925013N.N.KalmykovS.S.OstapchenkoA.I.PavlovNucl. Phys. Proc. Suppl.52B19977It is important to stress that the Auger data are still at a preliminary stage and the reconstruction procedures are still to be finalised. However, even allowing for the systematic uncertainties still present, it does appear that at the highest energies fewer events are seen than expected from the AGASA analysis.V.S.BerezinskyG.T.ZatsepinPhys. Lett. B281969423F.W.SteckerAstrophys. J.2281979919R.EngelD.SeckelT.StanevPhys. Rev. D642001093010Z.FodorS.D.KatzA.RingwaldH.TuJCAP03112003015D.De MarcoT.StanevF.W.SteckerPhys. Rev. D732006043003D.HooperA.TaylorS.SarkarAstropart. Phys.23200511M.AveN.BuscaA.V.OlintoA.A.WatsonT.YamamotoAstropart. Phys.23200519A point worth noting at this juncture: If iron nuclei are accelerated to very high energies (much higher than the energy spectrum has been measured), then disintegration can lead to large numbers of protons above the spectrum cutoff. In this case, the resulting cosmogenic neutrino flux is not dramatically suppressed. On the other hand, if iron nuclei are only largely accelerated to around 10eV or less, then the liberated protons will only rarely interact with the CMB to produce pions, hence the cosmogenic neutrino flux will be significantly reduced.

Distinct cognitive mechanisms involved in the processing of single objects and object ensembles

PubMed Central

Cant, Jonathan S.; Sun, Sol Z.; Xu, Yaoda

2015-01-01

Behavioral research has demonstrated that the shape and texture of single objects can be processed independently. Similarly, neuroimaging results have shown that an object's shape and texture are processed in distinct brain regions with shape in the lateral occipital area and texture in parahippocampal cortex. Meanwhile, objects are not always seen in isolation and are often grouped together as an ensemble. We recently showed that the processing of ensembles also involves parahippocampal cortex and that the shape and texture of ensemble elements are processed together within this region. These neural data suggest that the independence seen between shape and texture in single-object perception would not be observed in object-ensemble perception. Here we tested this prediction by examining whether observers could attend to the shape of ensemble elements while ignoring changes in an unattended texture feature and vice versa. Across six behavioral experiments, we replicated previous findings of independence between shape and texture in single-object perception. In contrast, we observed that changes in an unattended ensemble feature negatively impacted the processing of an attended ensemble feature only when ensemble features were attended globally. When they were attended locally, thereby making ensemble processing similar to single-object processing, interference was abolished. Overall, these findings confirm previous neuroimaging results and suggest that distinct cognitive mechanisms may be involved in single-object and object-ensemble perception. Additionally, they show that the scope of visual attention plays a critical role in determining which type of object processing (ensemble or single object) is engaged by the visual system. PMID:26360156

Effects of ensemble and summary displays on interpretations of geospatial uncertainty data.

PubMed

Padilla, Lace M; Ruginski, Ian T; Creem-Regehr, Sarah H

2017-01-01

Ensemble and summary displays are two widely used methods to represent visual-spatial uncertainty; however, there is disagreement about which is the most effective technique to communicate uncertainty to the general public. Visualization scientists create ensemble displays by plotting multiple data points on the same Cartesian coordinate plane. Despite their use in scientific practice, it is more common in public presentations to use visualizations of summary displays, which scientists create by plotting statistical parameters of the ensemble members. While prior work has demonstrated that viewers make different decisions when viewing summary and ensemble displays, it is unclear what components of the displays lead to diverging judgments. This study aims to compare the salience of visual features - or visual elements that attract bottom-up attention - as one possible source of diverging judgments made with ensemble and summary displays in the context of hurricane track forecasts. We report that salient visual features of both ensemble and summary displays influence participant judgment. Specifically, we find that salient features of summary displays of geospatial uncertainty can be misunderstood as displaying size information. Further, salient features of ensemble displays evoke judgments that are indicative of accurate interpretations of the underlying probability distribution of the ensemble data. However, when participants use ensemble displays to make point-based judgments, they may overweight individual ensemble members in their decision-making process. We propose that ensemble displays are a promising alternative to summary displays in a geospatial context but that decisions about visualization methods should be informed by the viewer's task.

Measuring social interaction in music ensembles

PubMed Central

D'Ausilio, Alessandro; Badino, Leonardo; Camurri, Antonio; Fadiga, Luciano

2016-01-01

Music ensembles are an ideal test-bed for quantitative analysis of social interaction. Music is an inherently social activity, and music ensembles offer a broad variety of scenarios which are particularly suitable for investigation. Small ensembles, such as string quartets, are deemed a significant example of self-managed teams, where all musicians contribute equally to a task. In bigger ensembles, such as orchestras, the relationship between a leader (the conductor) and a group of followers (the musicians) clearly emerges. This paper presents an overview of recent research on social interaction in music ensembles with a particular focus on (i) studies from cognitive neuroscience; and (ii) studies adopting a computational approach for carrying out automatic quantitative analysis of ensemble music performances. PMID:27069054

Measuring social interaction in music ensembles.

PubMed

Volpe, Gualtiero; D'Ausilio, Alessandro; Badino, Leonardo; Camurri, Antonio; Fadiga, Luciano

2016-05-05

Music ensembles are an ideal test-bed for quantitative analysis of social interaction. Music is an inherently social activity, and music ensembles offer a broad variety of scenarios which are particularly suitable for investigation. Small ensembles, such as string quartets, are deemed a significant example of self-managed teams, where all musicians contribute equally to a task. In bigger ensembles, such as orchestras, the relationship between a leader (the conductor) and a group of followers (the musicians) clearly emerges. This paper presents an overview of recent research on social interaction in music ensembles with a particular focus on (i) studies from cognitive neuroscience; and (ii) studies adopting a computational approach for carrying out automatic quantitative analysis of ensemble music performances. © 2016 The Author(s).

Method and apparatus for quantum information processing using entangled neutral-atom qubits

DOEpatents

Jau, Yuan Yu; Biedermann, Grant; Deutsch, Ivan

2018-04-03

A method for preparing an entangled quantum state of an atomic ensemble is provided. The method includes loading each atom of the atomic ensemble into a respective optical trap; placing each atom of the atomic ensemble into a same first atomic quantum state by impingement of pump radiation; approaching the atoms of the atomic ensemble to within a dipole-dipole interaction length of each other; Rydberg-dressing the atomic ensemble; during the Rydberg-dressing operation, exciting the atomic ensemble with a Raman pulse tuned to stimulate a ground-state hyperfine transition from the first atomic quantum state to a second atomic quantum state; and separating the atoms of the atomic ensemble by more than a dipole-dipole interaction length.

Evaluation of protective ensemble thermal characteristics through sweating hot plate, sweating thermal manikin, and human tests.

PubMed

Kim, Jung-Hyun; Powell, Jeffery B; Roberge, Raymond J; Shepherd, Angie; Coca, Aitor

2014-01-01

The purpose of this study was to evaluate the predictive capability of fabric Total Heat Loss (THL) values on thermal stress that Personal Protective Equipment (PPE) ensemble wearers may encounter while performing work. A series of three tests, consisting of the Sweating Hot Plate (SHP) test on two sample fabrics and the Sweating Thermal Manikin (STM) and human performance tests on two single-layer encapsulating ensembles (fabric/ensemble A = low THL and B = high THL), was conducted to compare THL values between SHP and STM methods along with human thermophysiological responses to wearing the ensembles. In human testing, ten male subjects performed a treadmill exercise at 4.8 km and 3% incline for 60 min in two environmental conditions (mild = 22°C, 50% relative humidity (RH) and hot/humid = 35°C, 65% RH). The thermal and evaporative resistances were significantly higher on a fabric level as measured in the SHP test than on the ensemble level as measured in the STM test. Consequently the THL values were also significantly different for both fabric types (SHP vs. STM: 191.3 vs. 81.5 W/m(2) in fabric/ensemble A, and 909.3 vs. 149.9 W/m(2) in fabric/ensemble B (p < 0.001). Body temperature and heart rate response between ensembles A and B were consistently different in both environmental conditions (p < 0.001), which is attributed to significantly higher sweat evaporation in ensemble B than in A (p < 0.05), despite a greater sweat production in ensemble A (p < 0.001) in both environmental conditions. Further, elevation of microclimate temperature (p < 0.001) and humidity (p < 0.01) was significantly greater in ensemble A than in B. It was concluded that: (1) SHP test determined THL values are significantly different from the actual THL potential of the PPE ensemble tested on STM, (2) physiological benefits from wearing a more breathable PPE ensemble may not be feasible with incremental THL values (SHP test) less than approximately 150-200 W·m(2), and (3) the effects of thermal environments on a level of heat stress in PPE ensemble wearers are greater than ensemble thermal characteristics.

Minimalist ensemble algorithms for genome-wide protein localization prediction.

PubMed

Lin, Jhih-Rong; Mondal, Ananda Mohan; Liu, Rong; Hu, Jianjun

2012-07-03

Computational prediction of protein subcellular localization can greatly help to elucidate its functions. Despite the existence of dozens of protein localization prediction algorithms, the prediction accuracy and coverage are still low. Several ensemble algorithms have been proposed to improve the prediction performance, which usually include as many as 10 or more individual localization algorithms. However, their performance is still limited by the running complexity and redundancy among individual prediction algorithms. This paper proposed a novel method for rational design of minimalist ensemble algorithms for practical genome-wide protein subcellular localization prediction. The algorithm is based on combining a feature selection based filter and a logistic regression classifier. Using a novel concept of contribution scores, we analyzed issues of algorithm redundancy, consensus mistakes, and algorithm complementarity in designing ensemble algorithms. We applied the proposed minimalist logistic regression (LR) ensemble algorithm to two genome-wide datasets of Yeast and Human and compared its performance with current ensemble algorithms. Experimental results showed that the minimalist ensemble algorithm can achieve high prediction accuracy with only 1/3 to 1/2 of individual predictors of current ensemble algorithms, which greatly reduces computational complexity and running time. It was found that the high performance ensemble algorithms are usually composed of the predictors that together cover most of available features. Compared to the best individual predictor, our ensemble algorithm improved the prediction accuracy from AUC score of 0.558 to 0.707 for the Yeast dataset and from 0.628 to 0.646 for the Human dataset. Compared with popular weighted voting based ensemble algorithms, our classifier-based ensemble algorithms achieved much better performance without suffering from inclusion of too many individual predictors. We proposed a method for rational design of minimalist ensemble algorithms using feature selection and classifiers. The proposed minimalist ensemble algorithm based on logistic regression can achieve equal or better prediction performance while using only half or one-third of individual predictors compared to other ensemble algorithms. The results also suggested that meta-predictors that take advantage of a variety of features by combining individual predictors tend to achieve the best performance. The LR ensemble server and related benchmark datasets are available at http://mleg.cse.sc.edu/LRensemble/cgi-bin/predict.cgi.

Minimalist ensemble algorithms for genome-wide protein localization prediction

PubMed Central

2012-01-01

Background Computational prediction of protein subcellular localization can greatly help to elucidate its functions. Despite the existence of dozens of protein localization prediction algorithms, the prediction accuracy and coverage are still low. Several ensemble algorithms have been proposed to improve the prediction performance, which usually include as many as 10 or more individual localization algorithms. However, their performance is still limited by the running complexity and redundancy among individual prediction algorithms. Results This paper proposed a novel method for rational design of minimalist ensemble algorithms for practical genome-wide protein subcellular localization prediction. The algorithm is based on combining a feature selection based filter and a logistic regression classifier. Using a novel concept of contribution scores, we analyzed issues of algorithm redundancy, consensus mistakes, and algorithm complementarity in designing ensemble algorithms. We applied the proposed minimalist logistic regression (LR) ensemble algorithm to two genome-wide datasets of Yeast and Human and compared its performance with current ensemble algorithms. Experimental results showed that the minimalist ensemble algorithm can achieve high prediction accuracy with only 1/3 to 1/2 of individual predictors of current ensemble algorithms, which greatly reduces computational complexity and running time. It was found that the high performance ensemble algorithms are usually composed of the predictors that together cover most of available features. Compared to the best individual predictor, our ensemble algorithm improved the prediction accuracy from AUC score of 0.558 to 0.707 for the Yeast dataset and from 0.628 to 0.646 for the Human dataset. Compared with popular weighted voting based ensemble algorithms, our classifier-based ensemble algorithms achieved much better performance without suffering from inclusion of too many individual predictors. Conclusions We proposed a method for rational design of minimalist ensemble algorithms using feature selection and classifiers. The proposed minimalist ensemble algorithm based on logistic regression can achieve equal or better prediction performance while using only half or one-third of individual predictors compared to other ensemble algorithms. The results also suggested that meta-predictors that take advantage of a variety of features by combining individual predictors tend to achieve the best performance. The LR ensemble server and related benchmark datasets are available at http://mleg.cse.sc.edu/LRensemble/cgi-bin/predict.cgi. PMID:22759391

Optimization of oligomeric enzyme activity in ionic liquids using Rhodotorula glutinis yeast phenylalanine ammonia lyase.

PubMed

Barron, Christiaan C; Sponagle, Brandon J D; Arivalagan, Pugazhendhi; D'Cunha, Godwin B

2017-01-01

Phenylalanine ammonia lyase (E.C.4.3.1.24, PAL) activity of Rhodotorula glutinis yeast has been demonstrated in four commonly used ionic liquids. PAL forward reaction was carried out in 1-butyl-3-methylimidazolium methyl sulfate ([BMIM][MeSO 4 ]), 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF 4 ]), 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF 6 ]) and 1-butyl-3-methylimidazolium lactate ([BMIM][lactate]). Our experiments have revealed that PAL is catalytically active in ionic liquids and the enzyme activity in ([BMIM][PF 6 ]) is comparable to that obtained in aqueous buffer medium. Different conditions were optimized for maximal PAL forward activity including time of incubation (30.0min) L -phenylalanine substrate concentration (30.0mM), nature of buffer (50.0mM Tris-HCl), pH (9.0), temperature (37°C), and speed of agitation (100 rev min -1 ). Under these optimized conditions, about 83% conversion of substrate to product was obtained for the PAL forward reaction that was determined using UV spectroscopy at 290nm. PAL reverse reaction in ([BMIM][PF 6 ]) was determined spectrophotometrically at 520nm; and about 59% substrate conversion was obtained. This data provides further knowledge in enzyme biocatalysis in non-aqueous media, and may be of importance when studying the function of other oligomeric/multimeric proteins and enzymes in ionic liquids. Copyright © 2016 Elsevier Inc. All rights reserved.

Quantum Phases of Matter in Optical Lattices

DTIC Science & Technology

2015-06-30

doi: 10.1103/PhysRevA.89.013625 Hyungwon Kim, David A. Huse. Ballistic Spreading of Entanglement in a Diffusive Nonintegrable System, Physical...Review B, (07 2013): 0. doi: 10.1103/PhysRevB.88.014206 Lin Dong, Lei Jiang, Han Pu. Fulde–Ferrell pairing instability in spin–orbit coupled Fermi...PhysRevA.87.051603 Kuei Sun, C. J. Bolech. Pair tunneling, phase separation, and dimensional crossover in imbalanced fermionic superfluids in a coupled

Proposed Experiment in Two-Qubit Linear Optical Photonic Gates for Maximal Success Rates

DTIC Science & Technology

2012-01-01

Phys. Rev. A 72 032307 [10] Kwiat P G, Waks E White A G, Applebaum I and Eberhaard P E 1999 Phys. Rev. A 60 R773–6 [11] Barz S, Cronenberg G, Zeilinger ...17] Reck M, Zeilinger A, Bernstein H J and Bertani P 1994 Phys. Rev. Lett. 73 58 [18] Thompson M G, Politi A, Matthews J C F and O’Brien J L 2011 IET

Comment on "Comparative study of ab initio nonradiative recombination rate calculations under different formalisms"

NASA Astrophysics Data System (ADS)

Wickramaratne, Darshana; Shen, Jimmy-Xuan; Alkauskas, Audrius; Van de Walle, Chris G.

2018-02-01

In a recent article [Phys. Rev. B 91, 205315 (2015), 10.1103/PhysRevB.91.205315] Shi, Xu, and Wang presented a comparison of several formalisms to calculate nonradiative recombination rates and concluded the "one-dimensional (1D) quantum formula" that was used by Alkauskas et al. [Phys. Rev. B 90, 075202 (2014), 10.1103/PhysRevB.90.075202] is insufficient to accurately describe nonradiative capture rates. Our analysis of the results of Shi, Xu, and Wang indicates that their conclusions about the 1D quantum formula are unfounded and stem from an error in their calculations. Our own calculations demonstrate that the 1D quantum formula approach yields reliable and accurate results for nonradiative recombination rates.

Addendum: New approach to the resummation of logarithms in Higgs-boson decays to a vector quarkonium plus a photon [Phys. Rev. D 95, 054018 (2017)

DOE PAGES

Bodwin, Geoffrey T.; Chung, Hee Sok; Ee, June-Haak; ...

2017-12-20

In this addendum to Phys. Rev. D 95, 054018 (2017) we recompute the rates for the decays of the Higgs boson to a vector quarkonium plus a photon, where the vector quarkonium is J/psi, Upsilon(1S) Upsilon(2S). We correct an error in the Abel-Pad'e summation formula that was used to carry out the evolution of the quarkonium light-cone distribution amplitude in Phys. Rev. D 95, 054018 (2017). We also correct an error in the scale of quarkonium wave function at the origin in Phys. Rev. D 95, 054018 (2017) and introduce several additional refinements in the calculation.

Addendum: New approach to the resummation of logarithms in Higgs-boson decays to a vector quarkonium plus a photon [Phys. Rev. D 95, 054018 (2017)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bodwin, Geoffrey T.; Chung, Hee Sok; Ee, June-Haak

In this addendum to Phys. Rev. D 95, 054018 (2017) we recompute the rates for the decays of the Higgs boson to a vector quarkonium plus a photon, where the vector quarkonium is J/psi, Upsilon(1S) Upsilon(2S). We correct an error in the Abel-Pad'e summation formula that was used to carry out the evolution of the quarkonium light-cone distribution amplitude in Phys. Rev. D 95, 054018 (2017). We also correct an error in the scale of quarkonium wave function at the origin in Phys. Rev. D 95, 054018 (2017) and introduce several additional refinements in the calculation.

The Impact of ENSO on Extratropical Low Frequency Noise in Seasonal Forecasts

NASA Technical Reports Server (NTRS)

Schubert, Siegfried D.; Suarez, Max J.; Chang, Yehui; Branstator, Grant

2000-01-01

This study examines the uncertainty in forecasts of the January-February-March (JFM) mean extratropical circulation, and how that uncertainty is modulated by the El Nino/Southern Oscillation (ENSO). The analysis is based on ensembles of hindcasts made with an Atmospheric General Circulation Model (AGCM) forced with sea surface temperatures observed during; the 1983 El Nino and 1989 La Nina events. The AGCM produces pronounced interannual differences in the magnitude of the extratropical seasonal mean noise (intra-ensemble variability). The North Pacific, in particular, shows extensive regions where the 1989 seasonal mean noise kinetic energy (SKE), which is dominated by a "PNA-like" spatial structure, is more than twice that of the 1983 forecasts. The larger SKE in 1989 is associated with a larger than normal barotropic conversion of kinetic energy from the mean Pacific jet to the seasonal mean noise. The generation of SKE due to sub-monthly transients also shows substantial interannual differences, though these are much smaller than the differences in the mean flow conversions. An analysis of the Generation of monthly mean noise kinetic energy (NIKE) and its variability suggests that the seasonal mean noise is predominantly a statistical residue of variability resulting from dynamical processes operating on monthly and shorter times scales. A stochastically-forced barotropic model (linearized about the AGCM's 1983 and 1989 base states) is used to further assess the role of the basic state, submonthly transients, and tropical forcing, in modulating the uncertainties in the seasonal AGCM forecasts. When forced globally with spatially-white noise, the linear model generates much larger variance for the 1989 base state, consistent with the AGCM results. The extratropical variability for the 1989 base state is dominanted by a single eigenmode, and is strongly coupled with forcing over tropical western Pacific and the Indian Ocean, again consistent with the AGCM results. Linear calculations that include forcing from the AGCM variance of the tropical forcing and submonthly transients show a small impact on the variability over the Pacific/North American region compared with that of the base state differences.

Bayesian ensemble refinement by replica simulations and reweighting.

PubMed

Hummer, Gerhard; Köfinger, Jürgen

2015-12-28

We describe different Bayesian ensemble refinement methods, examine their interrelation, and discuss their practical application. With ensemble refinement, the properties of dynamic and partially disordered (bio)molecular structures can be characterized by integrating a wide range of experimental data, including measurements of ensemble-averaged observables. We start from a Bayesian formulation in which the posterior is a functional that ranks different configuration space distributions. By maximizing this posterior, we derive an optimal Bayesian ensemble distribution. For discrete configurations, this optimal distribution is identical to that obtained by the maximum entropy "ensemble refinement of SAXS" (EROS) formulation. Bayesian replica ensemble refinement enhances the sampling of relevant configurations by imposing restraints on averages of observables in coupled replica molecular dynamics simulations. We show that the strength of the restraints should scale linearly with the number of replicas to ensure convergence to the optimal Bayesian result in the limit of infinitely many replicas. In the "Bayesian inference of ensembles" method, we combine the replica and EROS approaches to accelerate the convergence. An adaptive algorithm can be used to sample directly from the optimal ensemble, without replicas. We discuss the incorporation of single-molecule measurements and dynamic observables such as relaxation parameters. The theoretical analysis of different Bayesian ensemble refinement approaches provides a basis for practical applications and a starting point for further investigations.

Bayesian ensemble refinement by replica simulations and reweighting

NASA Astrophysics Data System (ADS)

Hummer, Gerhard; Köfinger, Jürgen

2015-12-01

We describe different Bayesian ensemble refinement methods, examine their interrelation, and discuss their practical application. With ensemble refinement, the properties of dynamic and partially disordered (bio)molecular structures can be characterized by integrating a wide range of experimental data, including measurements of ensemble-averaged observables. We start from a Bayesian formulation in which the posterior is a functional that ranks different configuration space distributions. By maximizing this posterior, we derive an optimal Bayesian ensemble distribution. For discrete configurations, this optimal distribution is identical to that obtained by the maximum entropy "ensemble refinement of SAXS" (EROS) formulation. Bayesian replica ensemble refinement enhances the sampling of relevant configurations by imposing restraints on averages of observables in coupled replica molecular dynamics simulations. We show that the strength of the restraints should scale linearly with the number of replicas to ensure convergence to the optimal Bayesian result in the limit of infinitely many replicas. In the "Bayesian inference of ensembles" method, we combine the replica and EROS approaches to accelerate the convergence. An adaptive algorithm can be used to sample directly from the optimal ensemble, without replicas. We discuss the incorporation of single-molecule measurements and dynamic observables such as relaxation parameters. The theoretical analysis of different Bayesian ensemble refinement approaches provides a basis for practical applications and a starting point for further investigations.

A Statistical Description of Neural Ensemble Dynamics

PubMed Central

Long, John D.; Carmena, Jose M.

2011-01-01

The growing use of multi-channel neural recording techniques in behaving animals has produced rich datasets that hold immense potential for advancing our understanding of how the brain mediates behavior. One limitation of these techniques is they do not provide important information about the underlying anatomical connections among the recorded neurons within an ensemble. Inferring these connections is often intractable because the set of possible interactions grows exponentially with ensemble size. This is a fundamental challenge one confronts when interpreting these data. Unfortunately, the combination of expert knowledge and ensemble data is often insufficient for selecting a unique model of these interactions. Our approach shifts away from modeling the network diagram of the ensemble toward analyzing changes in the dynamics of the ensemble as they relate to behavior. Our contribution consists of adapting techniques from signal processing and Bayesian statistics to track the dynamics of ensemble data on time-scales comparable with behavior. We employ a Bayesian estimator to weigh prior information against the available ensemble data, and use an adaptive quantization technique to aggregate poorly estimated regions of the ensemble data space. Importantly, our method is capable of detecting changes in both the magnitude and structure of correlations among neurons missed by firing rate metrics. We show that this method is scalable across a wide range of time-scales and ensemble sizes. Lastly, the performance of this method on both simulated and real ensemble data is used to demonstrate its utility. PMID:22319486

Up-, down-, strange-, charm-, and bottom-quark masses from four-flavor lattice QCD

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bazavov, A.; Bernard, C.; Brambilla, N.

We calculate the up-, down-, strange-, charm-, and bottom-quark masses using the MILC highly improved staggered-quark ensembles with four flavors of dynamical quarks. We use ensembles at six lattice spacings ranging frommore » $$a\\approx0.15~$$fm to $0.03~$fm and with both physical and unphysical values of the two light and the strange sea-quark masses. We use a new method based on heavy-quark effective theory (HQET) to extract quark masses from heavy-light pseudoscalar meson masses. Combining our analysis with our separate determination of ratios of light-quark masses we present masses of the up, down, strange, charm, and bottom quarks. Our results for the $$\\overline{\\text{MS}}$$-renormalized masses are $$m_u(2~\\text{GeV}) = 2.118(38)~$$MeV, $$m_d(2~\\text{GeV}) = 4.690(54)~$$MeV, $$m_s(2~\\text{GeV}) = 92.52(69)~$$MeV, $$m_c(3~\\text{GeV}) = 984.3(5.6)~$$MeV, and $$m_c(m_c) = 1273(10)~$$MeV, with four active flavors; and $$m_b(m_b) = 4197(14)~$$MeV with five active flavors. We also obtain ratios of quark masses $$m_c/m_s = 11.784(22)$$, $$m_b/m_s = 53.93(12)$$, and $$m_b/m_c = 4.577(8)$$. The result for $$m_c$$ matches the precision of the most precise calculation to date, and the other masses and all quoted ratios are the most precise to date. Moreover, these results are the first with a perturbative accuracy of $$\\alpha_s^4$$. As byproducts of our method, we obtain the matrix elements of HQET operators with dimension 4 and 5: $$\\overline{\\Lambda}_\\text{MRS}=552(30)~$$MeV in the minimal renormalon-subtracted (MRS) scheme, $$\\mu_\\pi^2 = 0.06(22)~\\text{GeV}^2$$, and $$\\mu_G^2(m_b)=0.38(2)~\\text{GeV}^2$$. The MRS scheme [Phys. Rev. D97, 034503 (2018), arXiv:1712.04983 [hep-ph

Assessing the hydrological impacts of Tropical Cyclones on the Carolinas: An observational and modeling based investigation

NASA Astrophysics Data System (ADS)

Leeper, R. D.; Prat, O. P.; Blanton, B. O.

2012-12-01

During the warm season, the Carolinas are particularly prone to tropical cyclone (TC) activity and can be impacted in many different ways depending on storm track. The coasts of the Carolinas are the most vulnerable areas, but particular situations (Frances and Ivan 2004) affected communities far from the coasts (Prat and Nelson 2012). Regardless of where landfall occurs, TCs are often associated with intense precipitation and strong winds triggering a variety of natural hazards (storm surge, flooding, landslides). The assessment of societal and environmental impacts of TCs requires a suite of observations. The scarcity of station coverage, sensor limitations, and rainfall retrieval uncertainties are issues limiting the ability to assess accurately the impact of extreme precipitation events. Therefore, numerical models, such as the Weather Research and Forecasting model (WRF), can be valuable tools to investigate those impacts at regional and local scales and bridge the gap between observations. The goal of this study is to investigate the impact of TCs across the Carolinas using both observational and modeling technologies, and explore the usefulness of numerical methods in data-scarce regions. To fully assess TC impacts on the Carolinas inhabitants, storms impacting both coastal and inner communities will be selected and high-resolution WRF ensemble simulations generated from a suite of physic schemes for each TC to investigate their impact at finer scales. The ensemble member performance will be evaluated with respect to ground-based and satellite observations. Furthermore, results from the high-resolution WRF simulations, including the average wind-speed and the sea level pressure, will be used with the ADCIRC storm-surge and wave-model (Westerink et al, 2008) to simulate storm surge and waves along the Carolinas coast for TCs travelling along the coast or making landfall. This work aims to provide an assessment of the various types of impacts TCs can have based on their track and other characteristics. Prat, O.P., and B.R. Nelson, 2012. J. Climate. Conditionally Accepted. Westerink, J., R. Luettich, J. Feyen, et al, 2008. Month. Weather Rev., 136, 833-864.

Ensembl genomes 2016: more genomes, more complexity

USDA-ARS?s Scientific Manuscript database

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent...

New type of chimera and mutual synchronization of spatiotemporal structures in two coupled ensembles of nonlocally interacting chaotic maps

NASA Astrophysics Data System (ADS)

Bukh, Andrei; Rybalova, Elena; Semenova, Nadezhda; Strelkova, Galina; Anishchenko, Vadim

2017-11-01

We study numerically the dynamics of a network made of two coupled one-dimensional ensembles of discrete-time systems. The first ensemble is represented by a ring of nonlocally coupled Henon maps and the second one by a ring of nonlocally coupled Lozi maps. We find that the network of coupled ensembles can realize all the spatio-temporal structures which are observed both in the Henon map ensemble and in the Lozi map ensemble while uncoupled. Moreover, we reveal a new type of spatiotemporal structure, a solitary state chimera, in the considered network. We also establish and describe the effect of mutual synchronization of various complex spatiotemporal patterns in the system of two coupled ensembles of Henon and Lozi maps.

An Improved Ensemble of Random Vector Functional Link Networks Based on Particle Swarm Optimization with Double Optimization Strategy

PubMed Central

Ling, Qing-Hua; Song, Yu-Qing; Han, Fei; Yang, Dan; Huang, De-Shuang

2016-01-01

For ensemble learning, how to select and combine the candidate classifiers are two key issues which influence the performance of the ensemble system dramatically. Random vector functional link networks (RVFL) without direct input-to-output links is one of suitable base-classifiers for ensemble systems because of its fast learning speed, simple structure and good generalization performance. In this paper, to obtain a more compact ensemble system with improved convergence performance, an improved ensemble of RVFL based on attractive and repulsive particle swarm optimization (ARPSO) with double optimization strategy is proposed. In the proposed method, ARPSO is applied to select and combine the candidate RVFL. As for using ARPSO to select the optimal base RVFL, ARPSO considers both the convergence accuracy on the validation data and the diversity of the candidate ensemble system to build the RVFL ensembles. In the process of combining RVFL, the ensemble weights corresponding to the base RVFL are initialized by the minimum norm least-square method and then further optimized by ARPSO. Finally, a few redundant RVFL is pruned, and thus the more compact ensemble of RVFL is obtained. Moreover, in this paper, theoretical analysis and justification on how to prune the base classifiers on classification problem is presented, and a simple and practically feasible strategy for pruning redundant base classifiers on both classification and regression problems is proposed. Since the double optimization is performed on the basis of the single optimization, the ensemble of RVFL built by the proposed method outperforms that built by some single optimization methods. Experiment results on function approximation and classification problems verify that the proposed method could improve its convergence accuracy as well as reduce the complexity of the ensemble system. PMID:27835638

An Improved Ensemble of Random Vector Functional Link Networks Based on Particle Swarm Optimization with Double Optimization Strategy.

PubMed

Ling, Qing-Hua; Song, Yu-Qing; Han, Fei; Yang, Dan; Huang, De-Shuang

2016-01-01

For ensemble learning, how to select and combine the candidate classifiers are two key issues which influence the performance of the ensemble system dramatically. Random vector functional link networks (RVFL) without direct input-to-output links is one of suitable base-classifiers for ensemble systems because of its fast learning speed, simple structure and good generalization performance. In this paper, to obtain a more compact ensemble system with improved convergence performance, an improved ensemble of RVFL based on attractive and repulsive particle swarm optimization (ARPSO) with double optimization strategy is proposed. In the proposed method, ARPSO is applied to select and combine the candidate RVFL. As for using ARPSO to select the optimal base RVFL, ARPSO considers both the convergence accuracy on the validation data and the diversity of the candidate ensemble system to build the RVFL ensembles. In the process of combining RVFL, the ensemble weights corresponding to the base RVFL are initialized by the minimum norm least-square method and then further optimized by ARPSO. Finally, a few redundant RVFL is pruned, and thus the more compact ensemble of RVFL is obtained. Moreover, in this paper, theoretical analysis and justification on how to prune the base classifiers on classification problem is presented, and a simple and practically feasible strategy for pruning redundant base classifiers on both classification and regression problems is proposed. Since the double optimization is performed on the basis of the single optimization, the ensemble of RVFL built by the proposed method outperforms that built by some single optimization methods. Experiment results on function approximation and classification problems verify that the proposed method could improve its convergence accuracy as well as reduce the complexity of the ensemble system.

A comparison between EDA-EnVar and ETKF-EnVar data assimilation techniques using radar observations at convective scales through a case study of Hurricane Ike (2008)

NASA Astrophysics Data System (ADS)

Shen, Feifei; Xu, Dongmei; Xue, Ming; Min, Jinzhong

2017-07-01

This study examines the impacts of assimilating radar radial velocity (Vr) data for the simulation of hurricane Ike (2008) with two different ensemble generation techniques in the framework of the hybrid ensemble-variational (EnVar) data assimilation system of Weather Research and Forecasting model. For the generation of ensemble perturbations we apply two techniques, the ensemble transform Kalman filter (ETKF) and the ensemble of data assimilation (EDA). For the ETKF-EnVar, the forecast ensemble perturbations are updated by the ETKF, while for the EDA-EnVar, the hybrid is employed to update each ensemble member with perturbed observations. The ensemble mean is analyzed by the hybrid method with flow-dependent ensemble covariance for both EnVar. The sensitivity of analyses and forecasts to the two applied ensemble generation techniques is investigated in our current study. It is found that the EnVar system is rather stable with different ensemble update techniques in terms of its skill on improving the analyses and forecasts. The EDA-EnVar-based ensemble perturbations are likely to include slightly less organized spatial structures than those in ETKF-EnVar, and the perturbations of the latter are constructed more dynamically. Detailed diagnostics reveal that both of the EnVar schemes not only produce positive temperature increments around the hurricane center but also systematically adjust the hurricane location with the hurricane-specific error covariance. On average, the analysis and forecast from the ETKF-EnVar have slightly smaller errors than that from the EDA-EnVar in terms of track, intensity, and precipitation forecast. Moreover, ETKF-EnVar yields better forecasts when verified against conventional observations.

Pauci ex tanto numero: reduce redundancy in multi-model ensembles

NASA Astrophysics Data System (ADS)

Solazzo, E.; Riccio, A.; Kioutsioukis, I.; Galmarini, S.

2013-08-01

We explicitly address the fundamental issue of member diversity in multi-model ensembles. To date, no attempts in this direction have been documented within the air quality (AQ) community despite the extensive use of ensembles in this field. Common biases and redundancy are the two issues directly deriving from lack of independence, undermining the significance of a multi-model ensemble, and are the subject of this study. Shared, dependant biases among models do not cancel out but will instead determine a biased ensemble. Redundancy derives from having too large a portion of common variance among the members of the ensemble, producing overconfidence in the predictions and underestimation of the uncertainty. The two issues of common biases and redundancy are analysed in detail using the AQMEII ensemble of AQ model results for four air pollutants in two European regions. We show that models share large portions of bias and variance, extending well beyond those induced by common inputs. We make use of several techniques to further show that subsets of models can explain the same amount of variance as the full ensemble with the advantage of being poorly correlated. Selecting the members for generating skilful, non-redundant ensembles from such subsets proved, however, non-trivial. We propose and discuss various methods of member selection and rate the ensemble performance they produce. In most cases, the full ensemble is outscored by the reduced ones. We conclude that, although independence of outputs may not always guarantee enhancement of scores (but this depends upon the skill being investigated), we discourage selecting the members of the ensemble simply on the basis of scores; that is, independence and skills need to be considered disjointly.

Ensemble Methods

NASA Astrophysics Data System (ADS)

Re, Matteo; Valentini, Giorgio

2012-03-01

Ensemble methods are statistical and computational learning procedures reminiscent of the human social learning behavior of seeking several opinions before making any crucial decision. The idea of combining the opinions of different "experts" to obtain an overall “ensemble” decision is rooted in our culture at least from the classical age of ancient Greece, and it has been formalized during the Enlightenment with the Condorcet Jury Theorem[45]), which proved that the judgment of a committee is superior to those of individuals, provided the individuals have reasonable competence. Ensembles are sets of learning machines that combine in some way their decisions, or their learning algorithms, or different views of data, or other specific characteristics to obtain more reliable and more accurate predictions in supervised and unsupervised learning problems [48,116]. A simple example is represented by the majority vote ensemble, by which the decisions of different learning machines are combined, and the class that receives the majority of “votes” (i.e., the class predicted by the majority of the learning machines) is the class predicted by the overall ensemble [158]. In the literature, a plethora of terms other than ensembles has been used, such as fusion, combination, aggregation, and committee, to indicate sets of learning machines that work together to solve a machine learning problem [19,40,56,66,99,108,123], but in this chapter we maintain the term ensemble in its widest meaning, in order to include the whole range of combination methods. Nowadays, ensemble methods represent one of the main current research lines in machine learning [48,116], and the interest of the research community on ensemble methods is witnessed by conferences and workshops specifically devoted to ensembles, first of all the multiple classifier systems (MCS) conference organized by Roli, Kittler, Windeatt, and other researchers of this area [14,62,85,149,173]. Several theories have been proposed to explain the characteristics and the successful application of ensembles to different application domains. For instance, Allwein, Schapire, and Singer interpreted the improved generalization capabilities of ensembles of learning machines in the framework of large margin classifiers [4,177], Kleinberg in the context of stochastic discrimination theory [112], and Breiman and Friedman in the light of the bias-variance analysis borrowed from classical statistics [21,70]. Empirical studies showed that both in classification and regression problems, ensembles improve on single learning machines, and moreover large experimental studies compared the effectiveness of different ensemble methods on benchmark data sets [10,11,49,188]. The interest in this research area is motivated also by the availability of very fast computers and networks of workstations at a relatively low cost that allow the implementation and the experimentation of complex ensemble methods using off-the-shelf computer platforms. However, as explained in Section 26.2 there are deeper reasons to use ensembles of learning machines, motivated by the intrinsic characteristics of the ensemble methods. The main aim of this chapter is to introduce ensemble methods and to provide an overview and a bibliography of the main areas of research, without pretending to be exhaustive or to explain the detailed characteristics of each ensemble method. The paper is organized as follows. In the next section, the main theoretical and practical reasons for combining multiple learners are introduced. Section 26.3 depicts the main taxonomies on ensemble methods proposed in the literature. In Section 26.4 and 26.5, we present an overview of the main supervised ensemble methods reported in the literature, adopting a simple taxonomy, originally proposed in Ref. [201]. Applications of ensemble methods are only marginally considered, but a specific section on some relevant applications of ensemble methods in astronomy and astrophysics has been added (Section 26.6). The conclusion (Section 26.7) ends this paper and lists some issues not covered in this work.

Ensemble Generation and the Influence of Protein Flexibility on Geometric Tunnel Prediction in Cytochrome P450 Enzymes

PubMed Central

Kingsley, Laura J.; Lill, Markus A.

2014-01-01

Computational prediction of ligand entry and egress paths in proteins has become an emerging topic in computational biology and has proven useful in fields such as protein engineering and drug design. Geometric tunnel prediction programs, such as Caver3.0 and MolAxis, are computationally efficient methods to identify potential ligand entry and egress routes in proteins. Although many geometric tunnel programs are designed to accommodate a single input structure, the increasingly recognized importance of protein flexibility in tunnel formation and behavior has led to the more widespread use of protein ensembles in tunnel prediction. However, there has not yet been an attempt to directly investigate the influence of ensemble size and composition on geometric tunnel prediction. In this study, we compared tunnels found in a single crystal structure to ensembles of various sizes generated using different methods on both the apo and holo forms of cytochrome P450 enzymes CYP119, CYP2C9, and CYP3A4. Several protein structure clustering methods were tested in an attempt to generate smaller ensembles that were capable of reproducing the data from larger ensembles. Ultimately, we found that by including members from both the apo and holo data sets, we could produce ensembles containing less than 15 members that were comparable to apo or holo ensembles containing over 100 members. Furthermore, we found that, in the absence of either apo or holo crystal structure data, pseudo-apo or –holo ensembles (e.g. adding ligand to apo protein throughout MD simulations) could be used to resemble the structural ensembles of the corresponding apo and holo ensembles, respectively. Our findings not only further highlight the importance of including protein flexibility in geometric tunnel prediction, but also suggest that smaller ensembles can be as capable as larger ensembles at capturing many of the protein motions important for tunnel prediction at a lower computational cost. PMID:24956479

The physiological and biomechanical effects of forwards and reverse sports wheelchair propulsion

PubMed Central

Mason, Barry S.; Lenton, John P.; Goosey-Tolfrey, Victoria L.

2015-01-01

Objective To explore the physiological and biomechanical differences between forwards (FOR) and reverse (REV) sports wheelchair propulsion. Design Fourteen able-bodied males with previous wheelchair propulsion experience pushed a sports wheelchair on a single-roller ergometer in a FOR and REV direction at three sub-maximal speeds (4, 6, and 8 km/hour). Each trial lasted 3 minutes, and during the final minute physiological and biomechanical measures was collected. Results The physiological results revealed that oxygen uptake (1.51 ± 0.29 vs. 1.38 ± 0.26 L/minute, P = 0.005) and heart rate (121 ± 19 vs. 109 ± 14 beats/minute, P < 0.0005) were significantly greater during REV than FOR only during the 8 km/hour trials. From a biomechanical perspective, push frequencies were similar between FOR and REV across all speeds (P > 0.05). However, greater mean resultant forces were applied during FOR (P < 0.0005) at 4 km/hour (66.7 ± 19.5 vs. 49.2 ± 10.3 N), 6 km/hour (90.7 ± 21.9 vs. 65.3 ± 18.6 N), and 8 km/hour (102.5 ± 17.6 vs. 68.7 ± 13.5 N) compared to REV. Alternatively, push times and push angles were significantly lower (P ≤ 0.001) during FOR at each speed. Conclusions The current study demonstrated that at higher speeds physiological demand becomes elevated during REV. This was likely to be associated with an inability to apply sufficient force to the wheels, thus requiring kinematic adaptations in order to maintain constant speeds in REV. PMID:24593797

Assessing the impact of land use change on hydrology by ensemble modeling (LUCHEM) III: Scenario analysis

USGS Publications Warehouse

Huisman, J.A.; Breuer, L.; Bormann, H.; Bronstert, A.; Croke, B.F.W.; Frede, H.-G.; Graff, T.; Hubrechts, L.; Jakeman, A.J.; Kite, G.; Lanini, J.; Leavesley, G.; Lettenmaier, D.P.; Lindstrom, G.; Seibert, J.; Sivapalan, M.; Viney, N.R.; Willems, P.

2009-01-01

An ensemble of 10 hydrological models was applied to the same set of land use change scenarios. There was general agreement about the direction of changes in the mean annual discharge and 90% discharge percentile predicted by the ensemble members, although a considerable range in the magnitude of predictions for the scenarios and catchments under consideration was obvious. Differences in the magnitude of the increase were attributed to the different mean annual actual evapotranspiration rates for each land use type. The ensemble of model runs was further analyzed with deterministic and probabilistic ensemble methods. The deterministic ensemble method based on a trimmed mean resulted in a single somewhat more reliable scenario prediction. The probabilistic reliability ensemble averaging (REA) method allowed a quantification of the model structure uncertainty in the scenario predictions. It was concluded that the use of a model ensemble has greatly increased our confidence in the reliability of the model predictions. ?? 2008 Elsevier Ltd.

PSA-Based Screening Outcomes, Dietary Heterocyclic Amine Exposure, and Prostate Cancer Risk in African-Americans

DTIC Science & Technology

2006-01-01

associated micronutrients , and risk of prostate cancer. Epidemiol. Rev. 2001a: 23: 82-86. Chan J., and Giovannucci E. Dairy products, calcium, and...118. Chan J., and Giovannucci E. Vegetables, fruits, associated micronutrients , and risk of prostate cancer. Epidemiol. Rev. 2001a: 23: 82-86...Chan J., and Giovannucci E. Dairy products, calcium, and vitamin D, and risk of prostate cancer. Epidemiol. Rev. 2001b: 23: 87-92. Cohen J.H., Kristal

Orbital Debris: Technical and Legal Issues and Solutions

DTIC Science & Technology

2006-08-01

States will seek to minimize the creation of space debris. NASA, the intelligence community, and DoD, in cooperation with the private sector, will...205 and accompanying text. 388 Raymond T. Swenson, “Pollution of the Extraterrestrial Environment” (1985) 25 A.F. L. Rev. 70 at 79. “Article IX is...Hastings Int’l & Comp. L. Rev. 125. Swenson, Raymond T. “Pollution of the Extraterrestrial Environment” (1985) 25 A.F. L. Rev. 70. Tan, David

Spin squeezing a cold molecule

NASA Astrophysics Data System (ADS)

Bhattacharya, M.

2015-12-01

In this article we present a concrete proposal for spin squeezing the cold ground-state polar paramagnetic molecule OH, a system currently under fine control in the laboratory. In contrast to existing work, we consider a single, noninteracting molecule with angular momentum greater than 1 /2 . Starting from an experimentally relevant effective Hamiltonian, we identify an adiabatic regime where different combinations of static electric and magnetic fields can be used to realize the single-axis twisting Hamiltonian of Kitagawa and Ueda [M. Kitagawa and M. Ueda, Phys. Rev. A 47, 5138 (1993), 10.1103/PhysRevA.47.5138], the uniform field Hamiltonian proposed by Law et al. [C. K. Law, H. T. Ng, and P. T. Leung, Phys. Rev. A 63, 055601 (2001), 10.1103/PhysRevA.63.055601], and a model of field propagation in a Kerr medium considered by Agarwal and Puri [G. S. Agarwal and R. R. Puri, Phys. Rev. A 39, 2969 (1989), 10.1103/PhysRevA.39.2969]. We then consider the situation in which nonadiabatic effects are quite large and show that the effective Hamiltonian supports spin squeezing even in this case. We provide analytical expressions as well as numerical calculations, including optimization of field strengths and accounting for the effects of field misalignment. Our results have consequences for applications such as precision spectroscopy, techniques such as magnetometry, and stereochemical effects such as the orientation-to-alignment transition.

Effect of the forcing term in the pseudopotential lattice Boltzmann modeling of thermal flows

NASA Astrophysics Data System (ADS)

Li, Qing; Luo, K. H.

2014-05-01

The pseudopotential lattice Boltzmann (LB) model is a popular model in the LB community for simulating multiphase flows. Recently, several thermal LB models, which are based on the pseudopotential LB model and constructed within the framework of the double-distribution-function LB method, were proposed to simulate thermal multiphase flows [G. Házi and A. Márkus, Phys. Rev. E 77, 026305 (2008), 10.1103/PhysRevE.77.026305; L. Biferale, P. Perlekar, M. Sbragaglia, and F. Toschi, Phys. Rev. Lett. 108, 104502 (2012), 10.1103/PhysRevLett.108.104502; S. Gong and P. Cheng, Int. J. Heat Mass Transfer 55, 4923 (2012), 10.1016/j.ijheatmasstransfer.2012.04.037; M. R. Kamali et al., Phys. Rev. E 88, 033302 (2013), 10.1103/PhysRevE.88.033302]. The objective of the present paper is to show that the effect of the forcing term on the temperature equation must be eliminated in the pseudopotential LB modeling of thermal flows. First, the effect of the forcing term on the temperature equation is shown via the Chapman-Enskog analysis. For comparison, alternative treatments that are free from the forcing-term effect are provided. Subsequently, numerical investigations are performed for two benchmark tests. The numerical results clearly show that the existence of the forcing-term effect will lead to significant numerical errors in the pseudopotential LB modeling of thermal flows.

Reply to "Comment on 'Origin of tilted-phase generation in systems of ellipsoidal molecules with dipolar interactions' "

NASA Astrophysics Data System (ADS)

Bose, Tushar Kanti; Saha, Jayashree

2014-04-01

In a recent article [T. K. Bose and J. Saha, Phys. Rev. E 86, 050701 (2012), 10.1103/PhysRevE.86.050701], we have presented the results of a Monte Carlo simulation study of the systems of dipolar Gay-Berne ellipsoids where two terminal antiparallel dipoles are placed symmetrically on the long axis of each ellipsoid, and the results revealed the combined contribution of dipolar separation and transverse orientations in controlling the tilt angle in the tilted hexatic smectic phase. The tilt angle changed from zero to a significant value, in the case of transverse dipoles, with a change in the dipolar separation. In the related comment, Madhusudana [preceding Comment, Phys. Rev. E 89, 046501 (2014), 10.1103/PhysRevE.89.046501] has claimed that the physical origin of the molecular tilt in the significantly tilted phases found in the simulations is similar to that proposed by McMillan [Phys. Rev. A 8, 1921 (1973), 10.1103/PhysRevA.8.1921]. Here, we explain that the claim is not correct and make it clear that the two compared pictures are quite different. In the preceding Comment, Madhusudana has also suggested an alternative explanation for tilt generation in the simulations by criticizing the original one proposed by us. We argue here in support of the original explanation and clarify that his explanation does not follow the simulation results.

Non-Abelian fermionization and fractional quantum Hall transitions

NASA Astrophysics Data System (ADS)

Hui, Aaron; Mulligan, Michael; Kim, Eun-Ah

2018-02-01

There has been a recent surge of interest in dualities relating theories of Chern-Simons gauge fields coupled to either bosons or fermions within the condensed matter community, particularly in the context of topological insulators and the half-filled Landau level. Here, we study the application of one such duality to the long-standing problem of quantum Hall interplateaux transitions. The key motivating experimental observations are the anomalously large value of the correlation length exponent ν ≈2.3 and that ν is observed to be superuniversal, i.e., the same in the vicinity of distinct critical points [Sondhi et al., Rev. Mod. Phys. 69, 315 (1997), 10.1103/RevModPhys.69.315]. Duality motivates effective descriptions for a fractional quantum Hall plateau transition involving a Chern-Simons field with U (Nc) gauge group coupled to Nf=1 fermion. We study one class of theories in a controlled limit where Nf≫Nc and calculate ν to leading nontrivial order in the absence of disorder. Although these theories do not yield an anomalously large exponent ν within the large Nf≫Nc expansion, they do offer a new parameter space of theories that is apparently different from prior works involving Abelian Chern-Simons gauge fields [Wen and Wu, Phys. Rev. Lett. 70, 1501 (1993), 10.1103/PhysRevLett.70.1501; Chen et al., Phys. Rev. B 48, 13749 (1993), 10.1103/PhysRevB.48.13749].

Random matrix ensembles for many-body quantum systems

NASA Astrophysics Data System (ADS)

Vyas, Manan; Seligman, Thomas H.

2018-04-01

Classical random matrix ensembles were originally introduced in physics to approximate quantum many-particle nuclear interactions. However, there exists a plethora of quantum systems whose dynamics is explained in terms of few-particle (predom-inantly two-particle) interactions. The random matrix models incorporating the few-particle nature of interactions are known as embedded random matrix ensembles. In the present paper, we provide a brief overview of these two ensembles and illustrate how the embedded ensembles can be successfully used to study decoherence of a qubit interacting with an environment, both for fermionic and bosonic embedded ensembles. Numerical calculations show the dependence of decoherence on the nature of the environment.

On the structure and phase transitions of power-law Poissonian ensembles

NASA Astrophysics Data System (ADS)

Eliazar, Iddo; Oshanin, Gleb

2012-10-01

Power-law Poissonian ensembles are Poisson processes that are defined on the positive half-line, and that are governed by power-law intensities. Power-law Poissonian ensembles are stochastic objects of fundamental significance; they uniquely display an array of fractal features and they uniquely generate a span of important applications. In this paper we apply three different methods—oligarchic analysis, Lorenzian analysis and heterogeneity analysis—to explore power-law Poissonian ensembles. The amalgamation of these analyses, combined with the topology of power-law Poissonian ensembles, establishes a detailed and multi-faceted picture of the statistical structure and the statistical phase transitions of these elemental ensembles.

Molecular activity prediction by means of supervised subspace projection based ensembles of classifiers.

PubMed

Cerruela García, G; García-Pedrajas, N; Luque Ruiz, I; Gómez-Nieto, M Á

2018-03-01

This paper proposes a method for molecular activity prediction in QSAR studies using ensembles of classifiers constructed by means of two supervised subspace projection methods, namely nonparametric discriminant analysis (NDA) and hybrid discriminant analysis (HDA). We studied the performance of the proposed ensembles compared to classical ensemble methods using four molecular datasets and eight different models for the representation of the molecular structure. Using several measures and statistical tests for classifier comparison, we observe that our proposal improves the classification results with respect to classical ensemble methods. Therefore, we show that ensembles constructed using supervised subspace projections offer an effective way of creating classifiers in cheminformatics.

Entropy of network ensembles

NASA Astrophysics Data System (ADS)

Bianconi, Ginestra

2009-03-01

In this paper we generalize the concept of random networks to describe network ensembles with nontrivial features by a statistical mechanics approach. This framework is able to describe undirected and directed network ensembles as well as weighted network ensembles. These networks might have nontrivial community structure or, in the case of networks embedded in a given space, they might have a link probability with a nontrivial dependence on the distance between the nodes. These ensembles are characterized by their entropy, which evaluates the cardinality of networks in the ensemble. In particular, in this paper we define and evaluate the structural entropy, i.e., the entropy of the ensembles of undirected uncorrelated simple networks with given degree sequence. We stress the apparent paradox that scale-free degree distributions are characterized by having small structural entropy while they are so widely encountered in natural, social, and technological complex systems. We propose a solution to the paradox by proving that scale-free degree distributions are the most likely degree distribution with the corresponding value of the structural entropy. Finally, the general framework we present in this paper is able to describe microcanonical ensembles of networks as well as canonical or hidden-variable network ensembles with significant implications for the formulation of network-constructing algorithms.

Constructing better classifier ensemble based on weighted accuracy and diversity measure.

PubMed

Zeng, Xiaodong; Wong, Derek F; Chao, Lidia S

2014-01-01

A weighted accuracy and diversity (WAD) method is presented, a novel measure used to evaluate the quality of the classifier ensemble, assisting in the ensemble selection task. The proposed measure is motivated by a commonly accepted hypothesis; that is, a robust classifier ensemble should not only be accurate but also different from every other member. In fact, accuracy and diversity are mutual restraint factors; that is, an ensemble with high accuracy may have low diversity, and an overly diverse ensemble may negatively affect accuracy. This study proposes a method to find the balance between accuracy and diversity that enhances the predictive ability of an ensemble for unknown data. The quality assessment for an ensemble is performed such that the final score is achieved by computing the harmonic mean of accuracy and diversity, where two weight parameters are used to balance them. The measure is compared to two representative measures, Kappa-Error and GenDiv, and two threshold measures that consider only accuracy or diversity, with two heuristic search algorithms, genetic algorithm, and forward hill-climbing algorithm, in ensemble selection tasks performed on 15 UCI benchmark datasets. The empirical results demonstrate that the WAD measure is superior to others in most cases.

Improving Classification Performance through an Advanced Ensemble Based Heterogeneous Extreme Learning Machines.

PubMed

Abuassba, Adnan O M; Zhang, Dezheng; Luo, Xiong; Shaheryar, Ahmad; Ali, Hazrat

2017-01-01

Extreme Learning Machine (ELM) is a fast-learning algorithm for a single-hidden layer feedforward neural network (SLFN). It often has good generalization performance. However, there are chances that it might overfit the training data due to having more hidden nodes than needed. To address the generalization performance, we use a heterogeneous ensemble approach. We propose an Advanced ELM Ensemble (AELME) for classification, which includes Regularized-ELM, L 2 -norm-optimized ELM (ELML2), and Kernel-ELM. The ensemble is constructed by training a randomly chosen ELM classifier on a subset of training data selected through random resampling. The proposed AELM-Ensemble is evolved by employing an objective function of increasing diversity and accuracy among the final ensemble. Finally, the class label of unseen data is predicted using majority vote approach. Splitting the training data into subsets and incorporation of heterogeneous ELM classifiers result in higher prediction accuracy, better generalization, and a lower number of base classifiers, as compared to other models (Adaboost, Bagging, Dynamic ELM ensemble, data splitting ELM ensemble, and ELM ensemble). The validity of AELME is confirmed through classification on several real-world benchmark datasets.

Improving Classification Performance through an Advanced Ensemble Based Heterogeneous Extreme Learning Machines

PubMed Central

Abuassba, Adnan O. M.; Ali, Hazrat

2017-01-01

Extreme Learning Machine (ELM) is a fast-learning algorithm for a single-hidden layer feedforward neural network (SLFN). It often has good generalization performance. However, there are chances that it might overfit the training data due to having more hidden nodes than needed. To address the generalization performance, we use a heterogeneous ensemble approach. We propose an Advanced ELM Ensemble (AELME) for classification, which includes Regularized-ELM, L2-norm-optimized ELM (ELML2), and Kernel-ELM. The ensemble is constructed by training a randomly chosen ELM classifier on a subset of training data selected through random resampling. The proposed AELM-Ensemble is evolved by employing an objective function of increasing diversity and accuracy among the final ensemble. Finally, the class label of unseen data is predicted using majority vote approach. Splitting the training data into subsets and incorporation of heterogeneous ELM classifiers result in higher prediction accuracy, better generalization, and a lower number of base classifiers, as compared to other models (Adaboost, Bagging, Dynamic ELM ensemble, data splitting ELM ensemble, and ELM ensemble). The validity of AELME is confirmed through classification on several real-world benchmark datasets. PMID:28546808

The development of ensemble theory. A new glimpse at the history of statistical mechanics

NASA Astrophysics Data System (ADS)

Inaba, Hajime

2015-12-01

This paper investigates the history of statistical mechanics from the viewpoint of the development of the ensemble theory from 1871 to 1902. In 1871, Ludwig Boltzmann introduced a prototype model of an ensemble that represents a polyatomic gas. In 1879, James Clerk Maxwell defined an ensemble as copies of systems of the same energy. Inspired by H.W. Watson, he called his approach "statistical". Boltzmann and Maxwell regarded the ensemble theory as a much more general approach than the kinetic theory. In the 1880s, influenced by Hermann von Helmholtz, Boltzmann made use of ensembles to establish thermodynamic relations. In Elementary Principles in Statistical Mechanics of 1902, Josiah Willard Gibbs tried to get his ensemble theory to mirror thermodynamics, including thermodynamic operations in its scope. Thermodynamics played the role of a "blind guide". His theory of ensembles can be characterized as more mathematically oriented than Einstein's theory proposed in the same year. Mechanical, empirical, and statistical approaches to foundations of statistical mechanics are presented. Although it was formulated in classical terms, the ensemble theory provided an infrastructure still valuable in quantum statistics because of its generality.

Constructing Better Classifier Ensemble Based on Weighted Accuracy and Diversity Measure

PubMed Central

Chao, Lidia S.

2014-01-01

A weighted accuracy and diversity (WAD) method is presented, a novel measure used to evaluate the quality of the classifier ensemble, assisting in the ensemble selection task. The proposed measure is motivated by a commonly accepted hypothesis; that is, a robust classifier ensemble should not only be accurate but also different from every other member. In fact, accuracy and diversity are mutual restraint factors; that is, an ensemble with high accuracy may have low diversity, and an overly diverse ensemble may negatively affect accuracy. This study proposes a method to find the balance between accuracy and diversity that enhances the predictive ability of an ensemble for unknown data. The quality assessment for an ensemble is performed such that the final score is achieved by computing the harmonic mean of accuracy and diversity, where two weight parameters are used to balance them. The measure is compared to two representative measures, Kappa-Error and GenDiv, and two threshold measures that consider only accuracy or diversity, with two heuristic search algorithms, genetic algorithm, and forward hill-climbing algorithm, in ensemble selection tasks performed on 15 UCI benchmark datasets. The empirical results demonstrate that the WAD measure is superior to others in most cases. PMID:24672402

Improving land resource evaluation using fuzzy neural network ensembles

USGS Publications Warehouse

Xue, Yue-Ju; HU, Y.-M.; Liu, S.-G.; YANG, J.-F.; CHEN, Q.-C.; BAO, S.-T.

2007-01-01

Land evaluation factors often contain continuous-, discrete- and nominal-valued attributes. In traditional land evaluation, these different attributes are usually graded into categorical indexes by land resource experts, and the evaluation results rely heavily on experts' experiences. In order to overcome the shortcoming, we presented a fuzzy neural network ensemble method that did not require grading the evaluation factors into categorical indexes and could evaluate land resources by using the three kinds of attribute values directly. A fuzzy back propagation neural network (BPNN), a fuzzy radial basis function neural network (RBFNN), a fuzzy BPNN ensemble, and a fuzzy RBFNN ensemble were used to evaluate the land resources in Guangdong Province. The evaluation results by using the fuzzy BPNN ensemble and the fuzzy RBFNN ensemble were much better than those by using the single fuzzy BPNN and the single fuzzy RBFNN, and the error rate of the single fuzzy RBFNN or fuzzy RBFNN ensemble was lower than that of the single fuzzy BPNN or fuzzy BPNN ensemble, respectively. By using the fuzzy neural network ensembles, the validity of land resource evaluation was improved and reliance on land evaluators' experiences was considerably reduced. ?? 2007 Soil Science Society of China.

Ensemble Eclipse: A Process for Prefab Development Environment for the Ensemble Project

NASA Technical Reports Server (NTRS)

Wallick, Michael N.; Mittman, David S.; Shams, Khawaja, S.; Bachmann, Andrew G.; Ludowise, Melissa

2013-01-01

This software simplifies the process of having to set up an Eclipse IDE programming environment for the members of the cross-NASA center project, Ensemble. It achieves this by assembling all the necessary add-ons and custom tools/preferences. This software is unique in that it allows developers in the Ensemble Project (approximately 20 to 40 at any time) across multiple NASA centers to set up a development environment almost instantly and work on Ensemble software. The software automatically has the source code repositories and other vital information and settings included. The Eclipse IDE is an open-source development framework. The NASA (Ensemble-specific) version of the software includes Ensemble-specific plug-ins as well as settings for the Ensemble project. This software saves developers the time and hassle of setting up a programming environment, making sure that everything is set up in the correct manner for Ensemble development. Existing software (i.e., standard Eclipse) requires an intensive setup process that is both time-consuming and error prone. This software is built once by a single user and tested, allowing other developers to simply download and use the software

The converter mechanism of particle acceleration and the maximum energy of cosmic rays

NASA Astrophysics Data System (ADS)

Kocharovsky, Vl. V.; Aharonian, F. A.; Derishev, E. V.; Kocharovsky, V. V.

We consider the fundamental limits on the energy of particles accelerated by electromagnetic forces in various astrophysical objects [1]. We show that accelerator's parameters are strongly limited not only by the particle confinement in large-scale magnetic field or by the difference in electric potentials (generalized Hillas criterion) but also by the curvature and other types of radiative losses of accelerated particles. Optimization of these requirements in terms of accelerator's size and the magnetic field strength results in the ultimate lower limit on the overall source energy budget, which scales as the fifth power of attainable particle energy. It is demonstrated that the curvature gamma-rays accompanying the acceleration gives further restrictions for potential acceleration sites. We compare different acceleration mechanisms and show, that the converter mechanism, which we suggested earlier [2], is the least sensitive to the geometry of the magnetic field in accelerators and allows to reach cosmic-ray energies close to the fundamental limit. The converter mechanism works most efficiently in relativistic shocks or shear flows. It utilizes multiple conversions of charged particles into neutral ones (protons to neutrons and electrons/positrons to photons) and back by means of photon-induced reactions or inelastic nucleon- nucleon collisions. We discuss the properties of gamma-ray radiation, which accompanies acceleration of cosmic rays via the converter mechanism and can provide an evidence for the latter. 1. F.A. Aharonian, A.A. Belyanin, E.V. Derishev, V.V. Kocharovsky, and Vl.V. Kocharovsky, Phys. Rev. D 66, 023005 (2002). 2. E.V. Derishev, F.A. Aharonian, V.V. Kocharovsky, and Vl.V. Kocharovsky, Phys. Rev. D 68, 043003 (2003).

Flow harmonics from self-consistent particlization of a viscous fluid

NASA Astrophysics Data System (ADS)

Wolff, Zack; Molnar, Denes

2017-10-01

The quantitative extraction of quark-gluon plasma (QGP) properties from heavy-ion data, such as its specific shear viscosity η /s , typically requires comparison to viscous hydrodynamic or "hybrid" hydrodynamics + transport simulations. In either case, one has to convert the fluid to hadrons, yet without additional theory input the conversion is ambiguous for dissipative fluids. Here, shear viscous phase-space corrections calculated using linearized transport theory are applied in Cooper-Frye freeze-out to quantify the effects on anisotropic flow coefficients vn(pT) at the energies available at both the BNL Relativistic Heavy Ion Collider and the CERN Large Hadron Collider. Expanding upon our previous flow harmonics studies [D. Molnar and Z. Wolff, Phys. Rev. C 95, 024903 (2017), 10.1103/PhysRevC.95.024903; Z. Wolff and D. Molnar, J. Phys.: Conf. Ser. 535, 012020 (2014), 10.1088/1742-6596/535/1/012020], we calculate pion and proton v2(pT) , v4(pT) , and v6(pT) , but here we incorporate a hadron gas that is chemically frozen below a temperature of 175 MeV and use hypersurfaces from realistic viscous hydrodynamic simulations. For additive quark model cross sections and relative phase-space corrections with p3 /2 momentum dependence rather than the quadratic Grad form, we find at moderately high transverse momentum noticeably higher v4(pT) and v6(pT) for protons than for pions. In addition, the value of η /s deduced from elliptic flow data differs by nearly 50% from the value extracted using the naive "democratic Grad" form of freeze-out distributions. To facilitate the use of the self-consistent viscous corrections calculated here in hydrodynamic and hybrid calculations, we also present convenient parametrizations of the corrections for the various hadron species.

The nodal count {0,1,2,3,…} implies the graph is a tree

PubMed Central

Band, Ram

2014-01-01

Sturm's oscillation theorem states that the nth eigenfunction of a Sturm–Liouville operator on the interval has n−1 zeros (nodes) (Sturm 1836 J. Math. Pures Appl. 1, 106–186; 373–444). This result was generalized for all metric tree graphs (Pokornyĭ et al. 1996 Mat. Zametki 60, 468–470 (doi:10.1007/BF02320380); Schapotschnikow 2006 Waves Random Complex Media 16, 167–178 (doi:10.1080/1745530600702535)) and an analogous theorem was proved for discrete tree graphs (Berkolaiko 2007 Commun. Math. Phys. 278, 803–819 (doi:10.1007/S00220-007-0391-3); Dhar & Ramaswamy 1985 Phys. Rev. Lett. 54, 1346–1349 (doi:10.1103/PhysRevLett.54.1346); Fiedler 1975 Czechoslovak Math. J. 25, 607–618). We prove the converse theorems for both discrete and metric graphs. Namely if for all n, the nth eigenfunction of the graph has n−1 zeros, then the graph is a tree. Our proofs use a recently obtained connection between the graph's nodal count and the magnetic stability of its eigenvalues (Berkolaiko 2013 Anal. PDE 6, 1213–1233 (doi:10.2140/apde.2013.6.1213); Berkolaiko & Weyand 2014 Phil. Trans. R. Soc. A 372, 20120522 (doi:10.1098/rsta.2012.0522); Colin de Verdière 2013 Anal. PDE 6, 1235–1242 (doi:10.2140/apde.2013.6.1235)). In the course of the proof, we show that it is not possible for all (or even almost all, in the metric case) the eigenvalues to exhibit a diamagnetic behaviour. In addition, we develop a notion of ‘discretized’ versions of a metric graph and prove that their nodal counts are related to those of the metric graph. PMID:24344337

A quasi-lentiviral green fluorescent protein reporter exhibits nuclear export features of late human immunodeficiency virus type 1 transcripts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Graf, Marcus; Ludwig, Christine; Kehlenbeck, Sylvia

2006-09-01

We have previously shown that Rev-dependent expression of HIV-1 Gag from CMV immediate early promoter critically depends on the AU-rich codon bias of the gag gene. Here, we demonstrate that adaptation of the green fluorescent protein (GFP) reporter gene to HIV codon bias is sufficient to turn this hivGFP RNA into a quasi-lentiviral message following the rules of late lentiviral gene expression. Accordingly, GFP expression was significantly decreased in transfected cells strictly correlating with reduced RNA levels. In the presence of the HIV 5' major splice donor, the hivGFP RNAs were stabilized in the nucleus and efficiently exported to themore » cytoplasm following fusion of the 3' Rev-responsive element (RRE) and coexpression of HIV-1 Rev. This Rev-dependent translocation was specifically inhibited by leptomycin B suggesting export via the CRM1-dependent pathway used by late lentiviral transcripts. In conclusion, this quasi-lentiviral reporter system may provide a new platform for developing sensitive Rev screening assays.« less

Did Rev-1 small ruminants vaccination helped improve cattle brucellosis prevalence status in Algeria?

PubMed

Kardjadj, Moustafa

2017-12-01

In 2006, the Algerian authorities started the Rev-1 vaccination of sheep and goats; consequently, there was a significant improvement of small ruminant brucellosis sanitary status. In this paper, we attempt to study the effect of Rev-1 small ruminants' vaccination on cattle brucellosis prevalence in Algeria. Our results showed an overall cattle herd seroprevalence of 12% (9 positive herds of 75). The risk factor analysis using a logistic regression model indicated that the presence of small ruminants along with cattle in the herd (mixed herds) decreased the odds for brucellosis seropositivity by 1.69 [95% CI 0.54-2.84; P = 0.042] compared to the cattle herds only. Likewise, the present study showed that the presence of Rev-1 vaccinated small ruminants in the herd decreased also the odds for brucellosis seropositivity by 4.10 [95% CI 3.20-5.00; P = 0.003] compared to other herds. This result lead to the assumption that the small ruminants Rev-1 vaccination diminish Brucella microbisme pressure in the mixed herds and help decrease the cattle brucellosis prevalence in these herds.

Comparative Proteome Analysis of Brucella melitensis Vaccine Strain Rev 1 and a Virulent Strain, 16M

PubMed Central

Eschenbrenner, Michel; Wagner, Mary Ann; Horn, Troy A.; Kraycer, Jo Ann; Mujer, Cesar V.; Hagius, Sue; Elzer, Philip; DelVecchio, Vito G.

2002-01-01

The genus Brucella consists of bacterial pathogens that cause brucellosis, a major zoonotic disease characterized by undulant fever and neurological disorders in humans. Among the different Brucella species, Brucella melitensis is considered the most virulent. Despite successful use in animals, the vaccine strains remain infectious for humans. To understand the mechanism of virulence in B. melitensis, the proteome of vaccine strain Rev 1 was analyzed by two-dimensional gel electrophoresis and compared to that of virulent strain 16M. The two strains were grown under identical laboratory conditions. Computer-assisted analysis of the two B. melitensis proteomes revealed proteins expressed in either 16M or Rev 1, as well as up- or down-regulation of proteins specific for each of these strains. These proteins were identified by peptide mass fingerprinting. It was found that certain metabolic pathways may be deregulated in Rev 1. Expression of an immunogenic 31-kDa outer membrane protein, proteins utilized for iron acquisition, and those that play a role in sugar binding, lipid degradation, and amino acid binding was altered in Rev 1. PMID:12193611

Comparative proteome analysis of Brucella melitensis vaccine strain Rev 1 and a virulent strain, 16M.

PubMed

Eschenbrenner, Michel; Wagner, Mary Ann; Horn, Troy A; Kraycer, Jo Ann; Mujer, Cesar V; Hagius, Sue; Elzer, Philip; DelVecchio, Vito G

2002-09-01

The genus Brucella consists of bacterial pathogens that cause brucellosis, a major zoonotic disease characterized by undulant fever and neurological disorders in humans. Among the different Brucella species, Brucella melitensis is considered the most virulent. Despite successful use in animals, the vaccine strains remain infectious for humans. To understand the mechanism of virulence in B. melitensis, the proteome of vaccine strain Rev 1 was analyzed by two-dimensional gel electrophoresis and compared to that of virulent strain 16M. The two strains were grown under identical laboratory conditions. Computer-assisted analysis of the two B. melitensis proteomes revealed proteins expressed in either 16M or Rev 1, as well as up- or down-regulation of proteins specific for each of these strains. These proteins were identified by peptide mass fingerprinting. It was found that certain metabolic pathways may be deregulated in Rev 1. Expression of an immunogenic 31-kDa outer membrane protein, proteins utilized for iron acquisition, and those that play a role in sugar binding, lipid degradation, and amino acid binding was altered in Rev 1.

Tool feed influence on the machinability of CO(2) laser optics.

PubMed

Arnold, J B; Steger, P J; Saito, T T

1975-08-01

Influence of tool feed on reflectivity of diamond-machined surfaces was evaluated using materials (gold, silver, and copper) from which CO(2) laser optics are primarily produced. Fifteen specimens were machined by holding all machining parameters constant, except tool feed. Tool feed was allowed to vary by controlled amounts from one evaluation zone (or part) to another. Past experience has verified that the quality of a diamond-machined surface is not a function of the cutting velocity; therefore, this experiment was conducted on the basis that a variation in cutting velocity was not an influencing factor on the diamondturning process. Inspection results of the specimens indicated that tool feeds significantly higher than 5.1 micro/rev (200 microin./rev) produced detrimental effects on the machined surfaces. In some cases, at feeds as high as 13 microm/rev (500 microin./rev), visible scoring was evident. Those surfaces produced with tool feeds less than 5.1 microm/rev had little difference in reflectivity. Measurements indicat d that their reflectivity existed in a range from 96.7% to 99.3% at 10.6 microm.

Ensemble data assimilation in the Red Sea: sensitivity to ensemble selection and atmospheric forcing

NASA Astrophysics Data System (ADS)

Toye, Habib; Zhan, Peng; Gopalakrishnan, Ganesh; Kartadikaria, Aditya R.; Huang, Huang; Knio, Omar; Hoteit, Ibrahim

2017-07-01

We present our efforts to build an ensemble data assimilation and forecasting system for the Red Sea. The system consists of the high-resolution Massachusetts Institute of Technology general circulation model (MITgcm) to simulate ocean circulation and of the Data Research Testbed (DART) for ensemble data assimilation. DART has been configured to integrate all members of an ensemble adjustment Kalman filter (EAKF) in parallel, based on which we adapted the ensemble operations in DART to use an invariant ensemble, i.e., an ensemble Optimal Interpolation (EnOI) algorithm. This approach requires only single forward model integration in the forecast step and therefore saves substantial computational cost. To deal with the strong seasonal variability of the Red Sea, the EnOI ensemble is then seasonally selected from a climatology of long-term model outputs. Observations of remote sensing sea surface height (SSH) and sea surface temperature (SST) are assimilated every 3 days. Real-time atmospheric fields from the National Center for Environmental Prediction (NCEP) and the European Center for Medium-Range Weather Forecasts (ECMWF) are used as forcing in different assimilation experiments. We investigate the behaviors of the EAKF and (seasonal-) EnOI and compare their performances for assimilating and forecasting the circulation of the Red Sea. We further assess the sensitivity of the assimilation system to various filtering parameters (ensemble size, inflation) and atmospheric forcing.

Simulation's Ensemble is Better Than Ensemble Simulation

NASA Astrophysics Data System (ADS)

Yan, X.

2017-12-01

Simulation's ensemble is better than ensemble simulation Yan Xiaodong State Key Laboratory of Earth Surface Processes and Resource Ecology (ESPRE) Beijing Normal University,19 Xinjiekouwai Street, Haidian District, Beijing 100875, China Email: yxd@bnu.edu.cnDynamical system is simulated from initial state. However initial state data is of great uncertainty, which leads to uncertainty of simulation. Therefore, multiple possible initial states based simulation has been used widely in atmospheric science, which has indeed been proved to be able to lower the uncertainty, that was named simulation's ensemble because multiple simulation results would be fused . In ecological field, individual based model simulation (forest gap models for example) can be regarded as simulation's ensemble compared with community based simulation (most ecosystem models). In this talk, we will address the advantage of individual based simulation and even their ensembles.

Visualization and classification of physiological failure modes in ensemble hemorrhage simulation

NASA Astrophysics Data System (ADS)

Zhang, Song; Pruett, William Andrew; Hester, Robert

2015-01-01

In an emergency situation such as hemorrhage, doctors need to predict which patients need immediate treatment and care. This task is difficult because of the diverse response to hemorrhage in human population. Ensemble physiological simulations provide a means to sample a diverse range of subjects and may have a better chance of containing the correct solution. However, to reveal the patterns and trends from the ensemble simulation is a challenging task. We have developed a visualization framework for ensemble physiological simulations. The visualization helps users identify trends among ensemble members, classify ensemble member into subpopulations for analysis, and provide prediction to future events by matching a new patient's data to existing ensembles. We demonstrated the effectiveness of the visualization on simulated physiological data. The lessons learned here can be applied to clinically-collected physiological data in the future.

Formation of molecules in an expanding Bose-Einstein condensate

NASA Astrophysics Data System (ADS)

Yurovsky, Vladimir; Ben-Reuven, Abraham

2004-05-01

A mean field theory [1] is extended to an inhomogeneous case of expanding hybrid atom-molecule Bose-Einstein condensates. This theory is applied to the recent MPI experiments [2] on ^87Rb demonstrating the formation of ultracold molecules due to Feshbach resonance. The subsequent dissociation of the molecules is treated using a non-mean-field parametric approximation [3]. The latter method is also used in determining optimal conditions for the formation of molecular BEC. [1] V. A. Yurovsky, A. Ben-Reuven, P. S. Julienne and C. J. Williams, Phys. Rev. A 60, R765 (1999); Phys. Rev. A 62, 043605 (2000). [2] S. Dürr, T. Volz, A. Marte, and G. Rempe, Phys. Rev. Lett. 92, 020406 (2004). [3] V. A. Yurovsky and A. Ben-Reuven, Phys. Rev. A 67, 043611 (2003).

Inclusive breakup calculations in angular momentum basis: Application to 7Li+58Ni

NASA Astrophysics Data System (ADS)

Lei, Jin

2018-03-01

The angular momentum basis method is introduced to solve the inclusive breakup problem within the model proposed by Ichimura, Austern, and Vincent [Phys. Rev. C 32, 431 (1985), 10.1103/PhysRevC.32.431]. This method is based on the geometric transformation between different Jacobi coordinates, in which the particle spins can be included in a natural and efficient way. To test the validity of this partial wave expansion method, a benchmark calculation is done comparing with the one given by Lei and Moro [Phys. Rev. C 92, 044616 (2015), 10.1103/PhysRevC.92.044616]. In addition, using the distorted-wave Born approximation version of the IAV model, applications to 7Li+58Ni reactions at energies around Coulomb barrier are presented and compared with available data.

Reply to "Comment on 'Defocusing complex short-pulse equation and its multi-dark-soliton solution' ".

PubMed

Feng, Bao-Feng; Ling, Liming; Zhu, Zuonong

2017-08-01

Our paper [Phys. Rev. E 93, 052227 (2016)PREHBM2470-004510.1103/PhysRevE.93.052227], proposing an integrable model for the propagation of ultrashort pulses, has recently received a Comment by Youssoufa et al. [Phys. Rev. E 96, 026201 (2017)10.1103/PhysRevE.96.026201] about a possible flaw in its derivation. We point out that their claim is incorrect since we have stated explicitly that a term is neglected to derive our model equation in our paper. Furthermore, the integrable model is validated by comparing with the normalized Maxwell equation and other known integrable models. Moreover, we show that a similar approximation has to be performed in deriving the same integrable equation as explained in the Comment.

Constraining some Horndeski gravity theories

NASA Astrophysics Data System (ADS)

Bhattacharya, Sourav; Chakraborty, Sumanta

2017-02-01

We discuss two spherically symmetric solutions admitted by the Horndeski (or scalar-tensor) theory in the context of Solar System and astrophysical scenarios. One of these solutions is derived for Einstein-Gauss-Bonnet gravity, while the other originates from the coupling of the Gauss-Bonnet invariant with a scalar field. Specifically, we discuss the perihelion precession and the bending angle of light for these two different spherically symmetric spacetimes derived in Maeda and Dadhich [Phys. Rev. D 75, 044007 (2007), 10.1103/PhysRevD.75.044007] and Sotiriou and Zhou [Phys. Rev. D 90, 124063 (2014), 10.1103/PhysRevD.90.124063], respectively. The latter, in particular, applies only to black-hole spacetimes. We further delineate on the numerical bounds of relevant parameters of these theories from such computations.

Calculating work in weakly driven quantum master equations: Backward and forward equations

NASA Astrophysics Data System (ADS)

Liu, Fei

2016-01-01

I present a technical report indicating that the two methods used for calculating characteristic functions for the work distribution in weakly driven quantum master equations are equivalent. One involves applying the notion of quantum jump trajectory [Phys. Rev. E 89, 042122 (2014), 10.1103/PhysRevE.89.042122], while the other is based on two energy measurements on the combined system and reservoir [Silaev et al., Phys. Rev. E 90, 022103 (2014), 10.1103/PhysRevE.90.022103]. These represent backward and forward methods, respectively, which adopt a very similar approach to that of the Kolmogorov backward and forward equations used in classical stochastic theory. The microscopic basis for the former method is also clarified. In addition, a previously unnoticed equality related to the heat is also revealed.

A Simple Ensemble Simulation Technique for Assessment of Future Variations in Specific High-Impact Weather Events

NASA Astrophysics Data System (ADS)

Taniguchi, Kenji

2018-04-01

To investigate future variations in high-impact weather events, numerous samples are required. For the detailed assessment in a specific region, a high spatial resolution is also required. A simple ensemble simulation technique is proposed in this paper. In the proposed technique, new ensemble members were generated from one basic state vector and two perturbation vectors, which were obtained by lagged average forecasting simulations. Sensitivity experiments with different numbers of ensemble members, different simulation lengths, and different perturbation magnitudes were performed. Experimental application to a global warming study was also implemented for a typhoon event. Ensemble-mean results and ensemble spreads of total precipitation, atmospheric conditions showed similar characteristics across the sensitivity experiments. The frequencies of the maximum total and hourly precipitation also showed similar distributions. These results indicate the robustness of the proposed technique. On the other hand, considerable ensemble spread was found in each ensemble experiment. In addition, the results of the application to a global warming study showed possible variations in the future. These results indicate that the proposed technique is useful for investigating various meteorological phenomena and the impacts of global warming. The results of the ensemble simulations also enable the stochastic evaluation of differences in high-impact weather events. In addition, the impacts of a spectral nudging technique were also examined. The tracks of a typhoon were quite different between cases with and without spectral nudging; however, the ranges of the tracks among ensemble members were comparable. It indicates that spectral nudging does not necessarily suppress ensemble spread.

Ensemble flood simulation for a small dam catchment in Japan using 10 and 2 km resolution nonhydrostatic model rainfalls

NASA Astrophysics Data System (ADS)

Kobayashi, Kenichiro; Otsuka, Shigenori; Apip; Saito, Kazuo

2016-08-01

This paper presents a study on short-term ensemble flood forecasting specifically for small dam catchments in Japan. Numerical ensemble simulations of rainfall from the Japan Meteorological Agency nonhydrostatic model (JMA-NHM) are used as the input data to a rainfall-runoff model for predicting river discharge into a dam. The ensemble weather simulations use a conventional 10 km and a high-resolution 2 km spatial resolutions. A distributed rainfall-runoff model is constructed for the Kasahori dam catchment (approx. 70 km2) and applied with the ensemble rainfalls. The results show that the hourly maximum and cumulative catchment-average rainfalls of the 2 km resolution JMA-NHM ensemble simulation are more appropriate than the 10 km resolution rainfalls. All the simulated inflows based on the 2 and 10 km rainfalls become larger than the flood discharge of 140 m3 s-1, a threshold value for flood control. The inflows with the 10 km resolution ensemble rainfall are all considerably smaller than the observations, while at least one simulated discharge out of 11 ensemble members with the 2 km resolution rainfalls reproduces the first peak of the inflow at the Kasahori dam with similar amplitude to observations, although there are spatiotemporal lags between simulation and observation. To take positional lags into account of the ensemble discharge simulation, the rainfall distribution in each ensemble member is shifted so that the catchment-averaged cumulative rainfall of the Kasahori dam maximizes. The runoff simulation with the position-shifted rainfalls shows much better results than the original ensemble discharge simulations.

On averaging aspect ratios and distortion parameters over ice crystal population ensembles for estimating effective scattering asymmetry parameters

PubMed Central

van Diedenhoven, Bastiaan; Ackerman, Andrew S.; Fridlind, Ann M.; Cairns, Brian

2017-01-01

The use of ensemble-average values of aspect ratio and distortion parameter of hexagonal ice prisms for the estimation of ensemble-average scattering asymmetry parameters is evaluated. Using crystal aspect ratios greater than unity generally leads to ensemble-average values of aspect ratio that are inconsistent with the ensemble-average asymmetry parameters. When a definition of aspect ratio is used that limits the aspect ratio to below unity (α≤1) for both hexagonal plates and columns, the effective asymmetry parameters calculated using ensemble-average aspect ratios are generally consistent with ensemble-average asymmetry parameters, especially if aspect ratios are geometrically averaged. Ensemble-average distortion parameters generally also yield effective asymmetry parameters that are largely consistent with ensemble-average asymmetry parameters. In the case of mixtures of plates and columns, it is recommended to geometrically average the α≤1 aspect ratios and to subsequently calculate the effective asymmetry parameter using a column or plate geometry when the contribution by columns to a given mixture’s total projected area is greater or lower than 50%, respectively. In addition, we show that ensemble-average aspect ratios, distortion parameters and asymmetry parameters can generally be retrieved accurately from simulated multi-directional polarization measurements based on mixtures of varying columns and plates. However, such retrievals tend to be somewhat biased toward yielding column-like aspect ratios. Furthermore, generally large retrieval errors can occur for mixtures with approximately equal contributions of columns and plates and for ensembles with strong contributions of thin plates. PMID:28983127

Insight into the Selectivity of Isopropanol Conversion at Strontium Titanate (100) Surfaces: A Combination Kinetic and Spectroscopic Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tan, Shuai; Grey, Matthew B.; Kidder, Michelle

This work aims to better understand the role of interfacial molecular structure that governs selectivity and activity in heterogeneous catalytic reactions. To address this, a comprehensive study of isopropanol conversion over an archetypal perovskite material, strontium titanate (SrTiO 3 or STO), was performed with an array of techniques sensitive to orthogonal aspects of the ensuing chemistry. Cubic-shape STO nanoparticles with only the (100) facet exposed were synthesized and used to study the ensemble kinetic conversion of isopropanol over the surfaces, which showed a remarkable selectivity to form acetone, with minor propylene products appearing at elevated temperatures. These results in combinationmore » with inelastic neutron scattering measurements provide not only new insight into the selectivity and overall activity of the catalysts but also low frequency vibrational signatures of the adsorbed and reacted species. To compliment these measurements, pristine thin films of STO (100) were synthesized and used in combination with vibrational sum frequency generation spectroscopy to extract the absolute molecular orientation of the adsorbed molecules at the interface. It was found that the isopropanol assumes an orientation where the -CH group points towards the STO surface; this pre-reaction geometry offers an obvious pathway to produce acetone by abstracting the alpha-proton and, thus, provides a mechanistic explanation of selectivity at STO (100) surfaces. This new insight opens up pathways to explore and modify surfaces to tune the activity/selectivity though a molecular level understanding of the reactions at the surface.« less

Insight into the Selectivity of Isopropanol Conversion at Strontium Titanate (100) Surfaces: A Combination Kinetic and Spectroscopic Study

DOE PAGES

Tan, Shuai; Grey, Matthew B.; Kidder, Michelle; ...

2017-10-13

This work aims to better understand the role of interfacial molecular structure that governs selectivity and activity in heterogeneous catalytic reactions. To address this, a comprehensive study of isopropanol conversion over an archetypal perovskite material, strontium titanate (SrTiO 3 or STO), was performed with an array of techniques sensitive to orthogonal aspects of the ensuing chemistry. Cubic-shape STO nanoparticles with only the (100) facet exposed were synthesized and used to study the ensemble kinetic conversion of isopropanol over the surfaces, which showed a remarkable selectivity to form acetone, with minor propylene products appearing at elevated temperatures. These results in combinationmore » with inelastic neutron scattering measurements provide not only new insight into the selectivity and overall activity of the catalysts but also low frequency vibrational signatures of the adsorbed and reacted species. To compliment these measurements, pristine thin films of STO (100) were synthesized and used in combination with vibrational sum frequency generation spectroscopy to extract the absolute molecular orientation of the adsorbed molecules at the interface. It was found that the isopropanol assumes an orientation where the -CH group points towards the STO surface; this pre-reaction geometry offers an obvious pathway to produce acetone by abstracting the alpha-proton and, thus, provides a mechanistic explanation of selectivity at STO (100) surfaces. This new insight opens up pathways to explore and modify surfaces to tune the activity/selectivity though a molecular level understanding of the reactions at the surface.« less

Critical Listening in the Ensemble Rehearsal: A Community of Learners

ERIC Educational Resources Information Center

Bell, Cindy L.

2018-01-01

This article explores a strategy for engaging ensemble members in critical listening analysis of performances and presents opportunities for improving ensemble sound through rigorous dialogue, reflection, and attentive rehearsing. Critical listening asks ensemble members to draw on individual playing experience and knowledge to describe what they…

World Music Ensemble: Kulintang

ERIC Educational Resources Information Center

Beegle, Amy C.

2012-01-01

As instrumental world music ensembles such as steel pan, mariachi, gamelan and West African drums are becoming more the norm than the exception in North American school music programs, there are other world music ensembles just starting to gain popularity in particular parts of the United States. The kulintang ensemble, a drum and gong ensemble…

Analyzing the impact of changing size and composition of a crop model ensemble

NASA Astrophysics Data System (ADS)

Rodríguez, Alfredo

2017-04-01

The use of an ensemble of crop growth simulation models is a practice recently adopted in order to quantify aspects of uncertainties in model simulations. Yet, while the climate modelling community has extensively investigated the properties of model ensembles and their implications, this has hardly been investigated for crop model ensembles (Wallach et al., 2016). In their ensemble of 27 wheat models, Martre et al. (2015) found that the accuracy of the multi-model ensemble-average only increases up to an ensemble size of ca. 10, but does not improve when including more models in the analysis. However, even when this number of members is reached, questions about the impact of the addition or removal of a member to/from the ensemble arise. When selecting ensemble members, identifying members with poor performance or giving implausible results can make a large difference on the outcome. The objective of this study is to set up a methodology that defines indicators to show the effects of changing the ensemble composition and size on simulation results, when a selection procedure of ensemble members is applied. Ensemble mean or median, and variance are measures used to depict ensemble results among other indicators. We are utilizing simulations from an ensemble of wheat models that have been used to construct impact response surfaces (Pirttioja et al., 2015) (IRSs). These show the response of an impact variable (e.g., crop yield) to systematic changes in two explanatory variables (e.g., precipitation and temperature). Using these, we compare different sub-ensembles in terms of the mean, median and spread, and also by comparing IRSs. The methodology developed here allows comparing an ensemble before and after applying any procedure that changes the ensemble composition and size by measuring the impact of this decision on the ensemble central tendency measures. The methodology could also be further developed to compare the effect of changing ensemble composition and size on IRS features. References Martre, P., Wallach, D., Asseng, S., Ewert, F., Jones, J.W., Rötter, R.P., Boote, K.J., Ruane, A.C., Thorburn, P.J., Cammarano, D., Hatfield, J.L., Rosenzweig, C., Aggarwal, P.K., Angulo, C., Basso, B., Bertuzzi, P., Biernath, C., Brisson, N., Challinor, A.J., Doltra, J., Gayler, S., Goldberg, R., Grant, R.F., Heng, L., Hooker, J., Hunt, L.A., Ingwersen, J., Izaurralde, R.C., Kersebaum, K.C., Muller, C., Kumar, S.N., Nendel, C., O'Leary, G., Olesen, J.E., Osborne, T.M., Palosuo, T., Priesack, E., Ripoche, D., Semenov, M.A., Shcherbak, I., Steduto, P., Stockle, C.O., Stratonovitch, P., Streck, T., Supit, I., Tao, F.L., Travasso, M., Waha, K., White, J.W., Wolf, J., 2015. Multimodel ensembles of wheat growth: many models are better than one. Glob. Change Biol. 21, 911-925. Pirttioja N., Carter T., Fronzek S., Bindi M., Hoffmann H., Palosuo T., Ruiz-Ramos, M., Tao F., Trnka M., Acutis M., Asseng S., Baranowski P., Basso B., Bodin P., Buis S., Cammarano D., Deligios P., Destain M.-F., Doro L., Dumont B., Ewert F., Ferrise R., Francois L., Gaiser T., Hlavinka P., Jacquemin I., Kersebaum K.-C., Kollas C., Krzyszczak J., Lorite I. J., Minet J., Minguez M. I., Montesion M., Moriondo M., Müller C., Nendel C., Öztürk I., Perego A., Rodriguez, A., Ruane A.C., Ruget F., Sanna M., Semenov M., Slawinski C., Stratonovitch P., Supit I., Waha K., Wang E., Wu L., Zhao Z., Rötter R.P, 2015. A crop model ensemble analysis of temperature and precipitation effects on wheat yield across a European transect using impact response surfaces. Clim. Res., 65:87-105, doi:10.3354/cr01322 Wallach, D., Mearns, L.O. Ruane, A.C., Rötter, R.P., Asseng, S. (2016). Lessons from climate modeling on the design and use of ensembles for crop modeling. Climate Change (in press) doi:10.1007/s10584-016-1803-1.

Energy transduction and signal averaging of fluctuating electric fields by a single protein ion channel.

PubMed

Verdia-Baguena, C; Gomez, V; Cervera, J; Ramirez, P; Mafe, S

2016-12-21

We demonstrate the electrical rectification and signal averaging of fluctuating signals using a biological nanostructure in aqueous solution: a single protein ion channel inserted in the lipid bilayer characteristic of cell membranes. The conversion of oscillating, zero time-average potentials into directional currents permits charging of a load capacitor to significant steady-state voltages within a few minutes in the case of the outer membrane porin F (OmpF) protein, a bacterial channel of Escherichia coli. The experiments and simulations show signal averaging effects at a more fundamental level than the traditional cell and tissue scales, which are characterized by ensembles of many ion channels operating simultaneously. The results also suggest signal transduction schemes with bio-electronic interfaces and ionic circuits where soft matter nanodiodes can be coupled to conventional electronic elements.