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At least 1,009 records · Page 56

ZIKV – CDB: A Collaborative Database to Guide Research Linking SncRNAs and ZIKA Virus Disease Symptoms

Background In early 2015, a ZIKA Virus (ZIKV) infection outbreak was recognized in northeast Brazil, where concerns over its possible links with infant microcephaly have been discussed. Providing a causal link between ZIKV infection and birth defects is still a challenge. MicroRNAs (miRNAs) are small noncoding RNAs (sncRNAs) that regulate post-transcriptional gene expression by translational repression, and play important roles in viral pathogenesis and brain development. The potential for flavivirus-mediated miRNA signalling dysfunction in brain-tissue development provides a compelling hypothesis to test the perceived link between ZIKV and microcephaly. Methodology/Principal Findings Here, we applied in silico analyses to provide novel insights to understand how Congenital ZIKA Syndrome symptoms may be related to an imbalance in miRNAs function. Moreover, following World Health Organization (WHO) recommendations, we have assembled a database to help target investigations of the possible relationship between ZIKV symptoms and miRNA-mediated human gene expression. Conclusions/Significance We have computationally predicted both miRNAs encoded by ZIKV able to target genes in the human genome and cellular (human) miRNAs capable of interacting with ZIKV genomes. Our results represent a step forward in the ZIKV studies, providing new insights to support research in this field and identify potential targets for therapy.

59 BASIC BIOLOGICAL SCIENCES↗

The collaborative effects of intrinsic and extrinsic impurities in low RRR SRF cavities

The superconducting radio-frequency (SRF) community has shown that introducing certain impurities into high-purity niobium can improve quality factors and accelerating gradients. We question why some impurities improve RF performance while others hinder it. The purpose of this study is to characterize the impurity profile of niobium with a low residual resistance ratio (RRR) and correlate these impurities with the RF performance of low RRR cavities so that the mechanism of impurity-based improvements can be better understood and improved upon. The combination of RF testing and material analysis reveals a microscopic picture of why low RRR cavities experience low temperature-dependent BCS resistance behavior more prominently than their high RRR counterparts. We performed surface treatments, low temperature baking and nitrogen-doping, on low RRR cavities to evaluate how the intentional addition of oxygen and nitrogen to the RF layer further improves performance through changes in the mean free path and impurity profile. The results of this study have the potential to unlock a new understanding on SRF materials and enable the next generation of SRF surface treatments.

43 PARTICLE ACCELERATORS↗

Neutron Detection in the A2 Collaboration Experiment on Neutral Pion Photo-production on Neutron

Neutron detection is of crucial importance for the neutral pion photo-production study on a neutron target that now is in progress at MAMI. Two electro-magnetic calorimeters, based on NaI and BaF 2 crystals, are used in the A2 experiment. While these calorimeters are optimized for pion decay photon detection, they have a reason able efficiency for neutron detection also. The paper describes the method, which has been used to measure this efficiency using the same data taken for pion photo-production study on deuterium target with tagged photon been of 800 MeV maximal energy. As a result, the detection efficiency is a rising function of neutron momentum that reaches 40% near 1 GeV/c.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Collaborative Research: Towards Advanced Understanding and Predictive Capability of Climate Change in the Arctic Using a High-Resolution Regional Arctic Climate Model

The primary research task completed for this project was the development of the Regional Arctic Climate Model (RACM). This involved coupling existing atmosphere, ocean, sea ice, and land models using the National Center for Atmospheric Research (NCAR) Community Climate System Model (CCSM) coupler (CPL7). RACM is based on the Weather Research and Forecasting (WRF) atmospheric model, the Parallel Ocean Program (POP) ocean model, the CICE sea ice model, and the Variable Infiltration Capacity (VIC) land model. A secondary research task for this project was testing and evaluation of WRF for climate-scale simulations on the large pan-Arctic model domain used in RACM. This involved identification of a preferred set of model physical parameterizations for use in our coupled RACM simulations and documenting any atmospheric biases present in RACM.

54 ENVIRONMENTAL SCIENCES↗

Collaborative Research: Regional climate-change projections through next-generation empirical and dynamical models (Final Technical Report)

This is the final report for a DOE-funded research project describing the outcome of research on non-homogeneous hidden Markov models (NHMMs) and coupled ocean-atmosphere (O-A) intermediate-complexity models (ICMs) to identify the potentially predictable modes of climate variability, and to investigate their impacts on the regional-scale. The main results consist of extensive development of the hidden Markov models for rainfall simulation and downscaling specifically within the non-stationary climate change context together with the development of parallelized software; application of NHMMs to downscaling of rainfall projections over India; identification and analysis of decadal climate signals in data and models; and, studies of climate variability in terms of the dynamics of atmospheric flow regimes.

58 GEOSCIENCES↗

Collaborative Research: Neutrinos & Nucleosynthesis in Hot Dense Matter

It is now firmly established that neutrinos, which are copiously produced in the hot and dense core of the supernova, play a role in the supernova explosion mechanism and in the synthesis of heavy elements through a phenomena known as r-process nucleosynthesis. They are also detectable in terrestrial neutrino experiments, and serve as a probe of the extreme environment and complex dynamics encountered in the supernova. The major goal of the UW research activity relevant to this project was to calculate the neutrino interaction rates in hot and dense matter of relevance to core collapse supernova. These serve as key input physics in large scale computer simulations of the supernova dynamics and nucleosynthesis being pursued at national laboratories here in the United States and by other groups in Europe and Japan. Our calculations show that neutrino production and scattering rate are altered by the nuclear interactions and that these modifications have important implications for nucleosynthesis and terrestrial neutrino detection. The calculation of neutrino rates in dense matter are difficult because nucleons in the dense matter are strongly coupled. A neutrino interacts with several nucleons and the quantum interference between scattering off different nucleons depends on the nature of correlations between them in dense matter. To describe these correlations we used analytic methods based on mean field theory and hydrodynamics, and computational methods such as Quantum Monte Carlo. We found that due to nuclear effects neutrino production rates at relevant temperatures are enhanced, and that electron neutrinos are more easily absorbed than anti-electron neutrinos in dense matter. The latter, was shown to favor synthesis of heavy neutron-rich elements in the supernova.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Aspen Code Development Collaboration

Wyoming has a wealth of primary energy resources in the forms of coal, natural gas, wind, uranium, and oil shale. Most of Wyoming’s coal and gas resources are exported from the state in unprocessed form rather than as refined higher value products. Wyoming’s leadership recognizes the opportunity to broaden the state’s economic base energy resources to make value-added products such as synthetic vehicle fuels and commodity chemicals. Producing these higher value products in an environmentally responsible manner can benefit from the use of clean energy technologies including Wyoming’s abundant wind energy and nuclear energy such as new generation small modular reactors including the high temperature gas-cooled reactors.

99 GENERAL AND MISCELLANEOUS↗

Milestone M4FT-13LL0807071: International Collaboration - Radionuclide Interactions and Transport in Geologic Repository Environments - Pu Interaction with Bentonite

The focus of this project is to investigate radionuclide interactions with natural and engineered materials, specifically the mineral bentonite that will be used in EU repositories and possibly in US high-level waste repository designs. These experiments are designed to develop a mechanistic understanding of Pu interactions with representative mineral substrates under granitic chemical conditions. The sorption/desorption experiments cover a large range of Pu concentrations and will be compared to sorption/desorption experiment with montmorillonite. The experiments are being coordinated with the Colloid Formation and Migration (CFM) international project led by Karlsruhe Institute of Technology and located at the Grimsel Test Site underground research laboratory in Switzerland. Experiments will be completed by 8/15/2014. Milestone M4FT-13LL0807071 is a progress report on this effort. The research is addressing the following FEPs/needs identified in the R&D Roadmap: 2.2.09.05 - radionuclide speciation and solubility in host rock; 2.2.09.55 - sorption of dissolved radionuclides in host rock; 2.2.09.59 - colloidal transport in host rock.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

Collaborative research: Dynamics of electrostatic solitary waves and their effects on current layers

The project has accomplished the following achievements including the goals outlined in the original proposal. Generation and measurements of Debye-scale electron holes in laboratory: We have generated by beam injections electron solitary waves in the LAPD experiments. The measurements were made possible by the fabrication of the state-of-the-art microprobes at UCLA to measure Debye-scale electric fields [Chiang et al., 2011]. We obtained a result that challenged the state of knowledge about electron hole generation. We found that the electron holes were not due to two-stream instability, but generated by a current-driven instability that also generated whistler-mode waves [Lefebvre et al., 2011, 2010b]. Most of the grant supported a young research scientist Bertrand Lefebvre who led the dissemination of the laboratory experimental results. In addition to two publications, our work relevant to the laboratory experiments on electron holes has resulted in 7 invited talks [Chen, 2007, 2009; Pickett et al., 2009a; Lefebvre et al., 2010a; Pickett et al., 2010; Chen et al., 2011c, b] (including those given by the co-I Jolene Pickett) and 2 contributed talks [Lefebvre et al., 2009b, a]. Discovery of elecctron phase-space-hole structure in the reconnection electron layer: Our theoretical analyses and simulations under this project led to the discovery of an inversion electric field layer whose phase-space signature is an electron hole within the electron diffusion layer in 2D anti-parallel reconnection [Chen et al., 2011a]. We carried out particle tracing studies to understand the electron orbits that result in the phase-space hole structure. Most importantly, we showed that the current density in the electron layer is limited in collisionless reconnection with negligible guide field by the cyclotron turning of meandering electrons. Comparison of electrostatic solitary waves in current layers observed by Cluster and in LAPD: We compared the ESWs observed in a supersubstorm by the Cluster spacecraft and those measured in LAPD. One of the similarities in the characteristics of ESWs observed in space and in LAPD is that the time duration tends to be approximately the inverse of the electron plasma frequency [Pickett et al., 2009b]. Discovery of suprathermal electron bursts inside a series of magnetic islands: Our effort in examining the roles of ESWs in reconnection current layers resulted in the serendipitous discovery that was published in Nature Physics. In earth’s magnetosphere, we observed through the measurements from the four Cluster spacecraft, a series of magnetic islands and suprathermal electron bursts within the islands. The islands were identified to be effectively acceleration sites for electrons [Chen et al., 2008, 2009].

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Final Report for UW-Madison Portion of DE-SC0005301, "Collaborative Project: Pacific Decadal Variability and Central Pacific Warming El Niño in a Changing Climate"

This project funded two efforts at understanding the interactions between Central Pacific ENSO events, the mid-latitude atmosphere, and decadal variability in the Pacific. The first was an investigation of conditions that lead to Central Pacific (CP) and East Pacific (EP) ENSO events through the use of linear inverse modeling with defined norms. The second effort was a modeling study that combined output from the National Center for Atmospheric Research (NCAR) Community Atmospheric Model (CAM4) with the Battisti (1988) intermediate coupled model. The intent of the second activity was to investigate the relationship between the atmospheric North Pacific Oscillation (NPO), the Pacific Meridional Mode (PMM), and ENSO. These two activities are described herein.

54 ENVIRONMENTAL SCIENCES↗

Report: Update of chemical analysis results for the Japan Atomic Energy Agency (JAEA) collaboration study sample (CRM 124-3)

Additional measurement data for collected by the Actinide Analytical Chemistry group at Los Alamos National Laboratory is provided in this report. Initial data was provided in April 2014 (LA-UR-14-22300) on the same sample material. That earlier document also contained procedure references for all the utilized techniques including those used to generate the data in this document. The Measurement Protocol table below summarizes the characterization that was planned for this sample material.

07 ISOTOPE AND RADIATION SOURCES↗

COLLABORATIVE RESEARCH: Study of Aerosol Sources and Processing at the GVAX Pantnagar Supersite

This project funded the participation of scientists from seven research groups, running more than thirty instruments, in the Winter Intensive Operating Period (January-February 2012) of the Clean Air for London (ClearfLo) campaign at a rural site in Detling, UK, 45 km southeast of central London. The primary science questions for the ClearfLo Winter IOP were, 1) what is the urban increment of particulate matter (PM) and other pollutants in the greater London area, and, 2) what is the contribution of solid fuel use for home heating to wintertime PM? An additional motivation for the Detling measurements was the question of whether coatings on black carbon particles enhance absorption. The following four key accomplishments have been identified so far: 1) Chemical, physical and optical characterization of PM from local and regional sources (Figures 2, 4, 5 and 6). 2) Measurement of urban increment in particulate matter and gases in London (Figure 3). 3) Measurement of optical properties and chemical composition of coatings on black carbon containing particles indicates absorption enhancement. 4) First deployment of chemical ionization instrument (MOVI-CI-TOFMS) to measure both particle-phase and gas-phase organic acids. (See final report from Joel Thornton, University of Washington, for details.) Analysis of the large dataset acquired in Detling is ongoing and will yield further key accomplishments. These measurements of urban and rural aerosol properties will contribute to improved modeling of regional aerosol emissions, and of atmospheric aging and removal. The measurement of absorption enhancement by coatings on black carbon will contribute to improved modeling of the direct radiative properties of PM.

54 ENVIRONMENTAL SCIENCES↗

Collaborative Project: The problem of bias in defining uncertainty in computationally enabled strategies for data-driven climate model development

The objective of the project is to develop strategies for better representing scientific sensibilities within statistical measures of model skill that then can be used within a Bayesian statistical framework for data-driven climate model development and improved measures of model scientific uncertainty. One of the thorny issues in model evaluation is quantifying the effect of biases on climate projections. While any bias is not desirable, only those biases that affect feedbacks affect scatter in climate projections. The effort at the University of Texas is to analyze previously calculated ensembles of CAM3.1 with perturbed parameters to discover how biases affect projections of global warming. The hypothesis is that compensating errors in the control model can be identified by their effect on a combination of processes and that developing metrics that are sensitive to dependencies among state variables would provide a way to select version of climate models that may reduce scatter in climate projections. Gabriel Huerta was responsible for leading the effort to develop statistical methods for evaluating these field dependencies. The UT effort will incorporate these developments into MECS, which is a set of python scripts being developed at the University of Texas for managing the workflow associated with data-driven climate model development over HPC resources. We regularly consult with Peter Gleckler (LLNL), Mark Taylor (SNL), and Rich Neale (NCAR) to provide additional insight into issues concerning CAM5 model development and multi-model evaluation of the AR5 archive. This grant was originally assigned to Indiana University where both the PI (Huerta) and the Postdoc (Nosedal) worked on the project from March 1, 2012-March 31, 2013.

97 MATHEMATICS AND COMPUTING↗