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  • 05. General::05.07. Space and Planetary sciences::05.07.02. Space weather
  • Bayesian particle polishingbeam-induced motion correctioncryo-EMsingle-particle analysiselectron cryo-microscopy
  • in-cell NMRnuclear magnetic resonancecellular structural biologycellular environmentprotein interactions
  • AGU  (6)
  • International Union of Crystallography (IUCr)  (3)
  • American Institute of Physics  (1)
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  • 1
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    A Bayesian approach to beam-induced motion correction in cryo-EM single-particle analysis (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2018-11-09
    Description: A new method to estimate the trajectories of particle motion and the amount of cumulative beam damage in electron cryo-microscopy (cryo-EM) single-particle analysis is presented. The motion within the sample is modelled through the use of Gaussian process regression. This allows a prior likelihood that favours spatially and temporally smooth motion to be associated with each hypothetical set of particle trajectories without imposing hard constraints. This formulation enables the a posteriori likelihood of a set of particle trajectories to be expressed as a product of that prior likelihood and an observation likelihood given by the data, and this a posteriori likelihood to then be maximized. Since the smoothness prior requires three parameters that describe the statistics of the observed motion, an efficient stochastic method to estimate these parameters is also proposed. Finally, a practical algorithm is proposed that estimates the average amount of cumulative radiation damage as a function of radiation dose and spatial frequency, and then fits relative B factors to that damage in a robust way. The method is evaluated on three publicly available data sets, and its usefulness is illustrated by comparison with state-of-the-art methods and previously published results. The new method has been implemented as Bayesian polishing in RELION-3, where it replaces the existing particle-polishing method, as it outperforms the latter in all tests conducted.
    Keywords: Bayesian particle polishingbeam-induced motion correctioncryo-EMsingle-particle analysiselectron cryo-microscopy
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
    Published by International Union of Crystallography (IUCr)
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  • 2
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    In-cell NMR: a topical review (2017)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2017-02-15
    Description: Classical structural biology approaches allow structural characterization of biological macromolecules in vitro, far from their physiological context. Nowadays, thanks to the wealth of structural data available and to technological and methodological advances, the interest of the research community is gradually shifting from pure structural determination towards the study of functional aspects of biomolecules. Therefore, a cellular structural approach is ideally needed to characterize biological molecules, such as proteins, in their native cellular environment and the functional processes that they are involved in. In-cell NMR is a new application of high-resolution nuclear magnetic resonance spectroscopy that allows structural and dynamical features of proteins and other macromolecules to be analyzed directly in living cells. Owing to its challenging nature, this methodology has shown slow, but steady, development over the past 15 years. To date, several in-cell NMR approaches have been successfully applied to both bacterial and eukaryotic cells, including several human cell lines, and important structural and functional aspects have been elucidated. In this topical review, the major advances of in-cell NMR are summarized, with a special focus on recent developments in eukaryotic and mammalian cells.
    Keywords: in-cell NMRnuclear magnetic resonancecellular structural biologycellular environmentprotein interactions
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
    Published by International Union of Crystallography (IUCr)
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  • 3
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    High-resolution NMR in the native state (2017)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2017-02-24
    Keywords: in-cell NMRnuclear magnetic resonancecellular structural biologycellular environmentprotein interactions
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
    Published by International Union of Crystallography (IUCr)
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  • 4
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    Correlation between scintillation indices and gradient drift wave amplitudes in the northern polar ionosphere (2009)
    AGU
    Details
    Publication Date: 2020-12-03
    Description: A model is developed of the gradient drift instability growth rate in the north polar cap ionosphere, utilizing a novel approach employing an ionospheric imaging algorithm. The growth rate values calculated by this model are in turn used to estimate how the amplitudes of actual gradient drift waves vary over time as the plasma drifts and the growth rates change with time. Ionospheric imaging is again used in order to determine plasma drift velocities. The final output from the model is in turn used to assess the linear correlation between the scintillation indices S4 and σØ recorded by several GPS L1 band scintillation receivers stationed in the north polar cap and mean gradient drift wave amplitudes. Four separate magnetic storm periods, totaling 13 days, are analyzed in this way. The results show weak but significant linear correlations between the mean wave amplitudes calculated and the observed scintillation indices at F layer altitudes.
    Description: Published
    Description: A07309
    Description: 1.7. Osservazioni di alta e media atmosfera
    Description: 3.9. Fisica della magnetosfera, ionosfera e meteorologia spaziale
    Description: JCR Journal
    Description: reserved
    Keywords: scintillations ; polar ionosphere ; gradient drift ; instability ; 01. Atmosphere::01.02. Ionosphere::01.02.04. Plasma Physics ; 01. Atmosphere::01.02. Ionosphere::01.02.07. Scintillations ; 03. Hydrosphere::03.03. Physical::03.03.05. Instruments and techniques ; 05. General::05.07. Space and Planetary sciences::05.07.01. Solar-terrestrial interaction ; 05. General::05.07. Space and Planetary sciences::05.07.02. Space weather
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 5
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    Unusual nighttime impulsive foF2 enhancement below the southern anomaly crest under geomagnetically quiet conditions (2011)
    AGU
    Details
    Publication Date: 2020-12-14
    Description: An unusual nighttime impulsive electron density enhancement was observed on 6 March 2010 over a wide region of South America, below the southern crest of the equatorial anomaly, under low solar activity and quiet geomagnetic conditions. The phenomenon was observed almost simultaneously by the F2 layer critical frequency ( foF2) recorded at three ionospheric stations which are widely distributed in space, namely Cachoeira Paulista (22.4°S, 44.6°W, magnetic latitude 13.4°S), São José dos Campos (23.2°S, 45.9°W, magnetic latitude 14.1°S), Brazil, and Tucumán (26.9°S, 65.4°W, magnetic latitude 16.8°S), Argentina. Although in a more restricted region over Tucumán, the phenomenon was also observed by the total electron content (TEC) maps computed by usingmeasurements from 12 GPS receivers. The investigated phenomenon is very particular because besides being of brief duration, it is characterized by a pronounced compression of the ionosphere. This compression was clearly visible both by the virtual height of the base of the F region (h′F) recorded at the aforementioned ionospheric stations, and by both the vertical electron density profiles and the slab thickness computed over Tucumán. Consequently, neither an enhanced fountain effect nor plasma diffusion from the plasmasphere can be considered as the single cause of this unusual event. A thorough analysis of isoheight and isofrequency ionosonde plots suggest that traveling ionospheric disturbances (TIDs) caused by gravity wave (GW) propagation could have likely played a significant role in causing the phenomenon.
    Description: Published
    Description: A12314
    Description: 1.6. Osservazioni di geomagnetismo
    Description: 1.7. Osservazioni di alta e media atmosfera
    Description: 3.9. Fisica della magnetosfera, ionosfera e meteorologia spaziale
    Description: 5.4. Banche dati di geomagnetismo, aeronomia, clima e ambiente
    Description: JCR Journal
    Description: open
    Keywords: equatorial ionosphere ; travelling ionospheric disturbance ; ionosphere-atmosphere interactions ; instrument and techniques ; 01. Atmosphere::01.02. Ionosphere::01.02.99. General or miscellaneous ; 01. Atmosphere::01.02. Ionosphere::01.02.02. Dynamics ; 01. Atmosphere::01.02. Ionosphere::01.02.04. Plasma Physics ; 01. Atmosphere::01.02. Ionosphere::01.02.05. Wave propagation ; 01. Atmosphere::01.02. Ionosphere::01.02.06. Instruments and techniques ; 05. General::05.07. Space and Planetary sciences::05.07.99. General or miscellaneous ; 05. General::05.07. Space and Planetary sciences::05.07.01. Solar-terrestrial interaction ; 05. General::05.07. Space and Planetary sciences::05.07.02. Space weather
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 6
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    From COST 238 To COST 296: Four European COST Actions On Ionospheric Physics And Radio Propagation (2008)
    American Institute of Physics
    Details
    Publication Date: 2017-04-04
    Description: COST (Co-operation in the field of Scientific and Technical Research) is an important instrument supporting co-operation among scientists and researchers across Europe now joining 35 member countries. Scientific projects in the COST framework are called COST Actions and have the objectives embodied in their respective Memorandum of Understanding (MoU). The main objectives of the COST Actions within the European ionospheric and radio propagation community have been: to study the influence of upper atmospheric conditions on terrestrial and Earthspace communications, to develop methods and techniques to improve existing and generate new ionospheric and propagation models over Europe for telecommunication and navigation applications and to transfer the results to the appropriate national and international organizations, institutions and industry dealing with the modern communication systems. This paper summarises in brief the background and historical context of four ionospheric COST Actions and outlines their main objectives and results. In addition, the paper discusses the dissemination of the results and the collaboration among the participating institutions and researchers.
    Description: DRS Codem Systems Ball Aerospace Corporation University of Massachusetts Lowell
    Description: Published
    Description: Lowell, Massachusetts, U.S.A., April 29, 2007
    Description: 3.9. Fisica della magnetosfera, ionosfera e meteorologia spaziale
    Description: open
    Keywords: Physics of the Ionosphere ; 01. Atmosphere::01.02. Ionosphere::01.02.99. General or miscellaneous ; 05. General::05.07. Space and Planetary sciences::05.07.02. Space weather
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: Conference paper
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  • 7
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    Turbulent Times in the Northern Polar Ionosphere? (2010)
    AGU
    Details
    Publication Date: 2017-04-04
    Description: A model is presented of the growth rate of turbulently generated irregularities in the electron concentration of northern polar cap plasma patches. The turbulence is generated by the short-term fluctuations in the electric field imposed on the polar-cap ionosphere by electric field mapping from the magnetosphere. The model uses an ionospheric imaging algorithm to specify the state of the ionosphere, throughout. The growth rates are used to estimate mean amplitudes for the irregularities and these mean amplitudes are compared with observations of the scintillation indices, S4 and бø, by calculating the linear correlation co-efficients between them. The scintillation data are recorded by GPS L1 band receivers stationed at high northern latitudes. A total of 13 days are analysed, covering four separate magnetic storm periods. These results are compared with those from a similar model of the Gradient Drift Instability (GDI) growth rate. Over-all, the results show better correlation between the GDI process and the scintillation indices than for the turbulence process and the scintillation indices. Two storms, however, show approximately equally good correlations for both processes, indicating that there might be times when the turbulence process of irregularity formation on plasma patches may be the controlling one.
    Description: In press
    Description: 1.7. Osservazioni di alta e media atmosfera
    Description: 3.9. Fisica della magnetosfera, ionosfera e meteorologia spaziale
    Description: JCR Journal
    Description: open
    Keywords: polar cap patches ; turbulence ; scintillations ; 01. Atmosphere::01.02. Ionosphere::01.02.04. Plasma Physics ; 05. General::05.07. Space and Planetary sciences::05.07.02. Space weather
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 8
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    Scintillation modeling using in situ data (2007)
    AGU
    Details
    Publication Date: 2017-04-03
    Description: Satellite in situ measurements of plasma (electron) density fluctuations provide direct information about the structure and morphology of irregularities that are responsible for scintillation of radio waves on transionospheric links. When supplemented with the ionosphere model and irregularity anisotropy model, they can be applied to model morphology of scintillation provided a suitable propagation model is used. In this paper we present a scintillation climatological model for the Northern Hemisphere high-latitude ionosphere, which makes use of the Dynamics Explorer 2 retarding potential analyzer plasma density data, IRI ionosphere model, and the phase screen propagation model. An important aspect of our work is that we derived from the satellite data not just the turbulence strength parameter Cs but also the spectral index p, which influences the scintillation level as well. We discuss the magnetic activity, season, magnetic time, and latitude dependence of these parameters. We were able to reproduce successfully the observed scintillation intensity diurnal and seasonal variations. The model satisfactorily describes the expansion of the scintillation zone under magnetically disturbed conditions and reproduces the dawn-dusk asymmetry in the scintillation intensity. The results demonstrate the usefulness of the proposed approach.
    Description: Published
    Description: RS1002
    Description: 3.9. Fisica della magnetosfera, ionosfera e meteorologia spaziale
    Description: JCR Journal
    Description: reserved
    Keywords: scintillations modeling ; 01. Atmosphere::01.02. Ionosphere::01.02.99. General or miscellaneous ; 05. General::05.07. Space and Planetary sciences::05.07.01. Solar-terrestrial interaction ; 05. General::05.07. Space and Planetary sciences::05.07.02. Space weather
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 9
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    The DIAS Project: Monitoring and Forecasting the Ionosphere Over Europe (2007)
    AGU
    Details
    Publication Date: 2017-04-04
    Description: Knowledge of the state of the upper atmosphere, and in particular its ionospheric part, is very important in several applications affected by space weather, especially the communications and navigation systems that rely on radio transmission. To better classify the ionosphere and forecast its disturbances over Europe, a data collection endeavour called the European Digital Upper Atmosphere Server (DIAS) was initiated in 2004 by a consortium formed around several European ionospheric stations that transmit in real-time ionospheric parameters automatically scaled. The DIAS project is a collaborative venture of eight institutions funded by the European Commission eContent Programme. The project seeks to improve access to digital information collected by public European institutes and to expand its use. The main objective of the DIAS project is to develop a pan-European digital data collection describing the state of the upper atmosphere, based on real-time information and historical data collections provided by most of the operating ionospheric stations in Europe. Various groups of users require data specifying upper atmospheric conditions over Europe for nowcasting and forecasting purposes. The DIAS system is designed to distribute such information. The successful operation of DIAS is based on the effective use of observational data in operational applications through the development of new added-value ionospheric products and services that best fit the needs of the market. DIAS is a unique European system, and its continuous operation will efficiently support radio propagation services with the most reliable information. DIAS began providing services to users in August 2006.
    Description: Published
    Description: 10-13
    Description: 1.7. Osservazioni di alta e media atmosfera
    Description: JCR Journal
    Description: reserved
    Keywords: Ionospheric monitoring and forecasting ; space weather ; upper atmosphere digital data collection ; 01. Atmosphere::01.02. Ionosphere::01.02.03. Forecasts ; 05. General::05.07. Space and Planetary sciences::05.07.02. Space weather
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 10
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    GPS TEC and scintillation measurements from the polar ionosphere during the October 2003 storm (2008)
    AGU
    Details
    Publication Date: 2017-04-04
    Description: Severe ionospheric storms occurred at the end of October 2003. During the evening of 30 October a narrow stream of high electron concentration plasma crossed the polar cap in the antisunward ionospheric convection. A GPS scintillation receiver in the European high arctic, operating at 1.575 GHz, experienced both phase and amplitude scintillation on several satellite-to-ground links during this period. Close examination of the GPS signals revealed the scintillation to be co-located with strong gradients in Total Electron Content (TEC) at the edge of the plasma stream. The gradient-drift instability is a likely mechanism for the generation of the irregularities causing some of the scintillation at L band frequencies during this storm. The origin of the high TEC is explored and the possible implications of the work for scintillation forecasting are noted. The results indicate that the GPS scintillation over Svalbard can originate from traceable ionospheric plasma structures convecting from the American sector.
    Description: Published
    Description: L12S03
    Description: 3.9. Fisica della magnetosfera, ionosfera e meteorologia spaziale
    Description: JCR Journal
    Description: reserved
    Keywords: Ionosphere ; Ionospheric storms ; GPS scintillation measurements ; Total Electron Content (TEC) ; Gradient-drift instability ; 01. Atmosphere::01.02. Ionosphere::01.02.04. Plasma Physics ; 05. General::05.07. Space and Planetary sciences::05.07.02. Space weather
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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