Quantitative Imaging of Single, Unstained Viruses with Coherent X-rays

Since Perutz, Kendrew and colleagues unveiled the structure of hemoglobin and myoglobin based on X-ray diffraction analysis in the 1950s, X-ray crystallography has become the primary methodology used to determine the 3D structure of macromolecules. However, biological specimens such as cells, organelles, viruses and many important macromolecules are difficult or impossible to crystallize, and hence their structures are not accessible by crystallography. Here we report, for the first time, the recording and reconstruction of X-ray diffraction patterns from single, unstained viruses. The structure of the viral capsid inside a virion was visualized. This work opens the door for quantitative X-ray imaging of a broad range of specimens from protein machineries, viruses and organelles to whole cells. Moreover, our experiment is directly transferable to the use of X-ray free electron lasers, and represents a major experimental milestone towards the X-ray imaging of single macromolecules.Comment: 16 pages, 5 figure

Advanced machine learning optimized by the genetic algorithm in ionospheric models using long-term multi-instrument observations

The ionospheric delay is of paramount importance to radio communication, satellite navigation and positioning. It is necessary to predict high-accuracy ionospheric peak parameters for single frequency receivers. In this study, the state-of-the-art artificial neural network (ANN) technique optimized by the genetic algorithm is used to develop global ionospheric models for predicting foF2 and hmF2. The models are based on long-term multiple measurements including ionospheric peak frequency model (GIPFM) and global ionospheric peak height model (GIPHM). Predictions of the GIPFM and GIPHM are compared with the International Reference Ionosphere (IRI) model in 2009 and 2013 respectively. This comparison shows that the root-mean-square errors (RMSEs) of GIPFM are 0.82 MHz and 0.71 MHz in 2013 and 2009, respectively. This result is about 20%-35% lower than that of IRI. Additionally, the corresponding hmF2 median errors of GIPHM are 20% to 30% smaller than that of IRI. Furthermore, the ANN models present a good capability to capture the global or regional ionospheric spatial-temporal characteristics, e.g., the equatorial ionization anomaly andWeddell Sea anomaly. The study shows that the ANN-based model has a better agreement to reference value than the IRI model, not only along the Greenwich meridian, but also on a global scale. The approach proposed in this study has the potential to be a new three-dimensional electron density model combined with the inclusion of the upcoming Constellation Observing System for Meteorology, Ionosphere and Climate (COSMIC-2) data

In situ defect annealing of swift heavy ion irradiated CeO2 and ThO2 using synchrotron X‐ray diffraction and a hydrothermal diamond anvil cell

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/111991/1/S160057671500477X.pd

Predicting Shielding Effectiveness of Populated Enclosures Using Absorption Cross Section of PCBs

Shielding effectiveness (SE) is an important measure of how well an enclosure reduces the electromagnetic (EM) field incident upon it. Commonly, when the shielding effectiveness of an enclosure is stated it is for the case when the enclosure is empty. Including contents such as printed circuit boards (PCBs) in the enclosure will affect the shielding effectiveness as the PCB absorbs EM energy. One technique of determining how much energy a PCB absorbs is to measure its absorption cross section (ACS) using a reverberation chamber (RC). The measured ACS can be used to predict the shielding effectiveness of an enclosure when the PCB is inside it using power balance techniques. In this paper the ACS of a number of PCBs are measured both individually and in closely stacked groups. This information is then used to show how the ACS can be used to calculate shielding effectiveness and the results are compared to direct measurement of the SE of the enclosure containing a PCB. Knowledge of the ACS of typical or particular PCBs could be used by engineers to estimate the real shielding effectiveness of an enclosure with contents, when designing electronic systems

9G4 Autoreactivity Is Increased in HIV-Infected Patients and Correlates with HIV Broadly Neutralizing Serum Activity

The induction of a broadly neutralizing antibody (BNAb) response against HIV-1 would be a desirable feature of a protective vaccine. Vaccine strategies thus far have failed to elicit broadly neutralizing antibody responses; however a minority of HIV-infected patients do develop circulating BNAbs, from which several potent broadly neutralizing monoclonal antibodies (mAbs) have been isolated. The findings that several BNmAbs exhibit autoreactivity and that autoreactive serum antibodies are observed in some HIV patients have advanced the possibility that enforcement of self-tolerance may contribute to the rarity of BNAbs. To examine the possible breakdown of tolerance in HIV patients, we utilized the 9G4 anti-idiotype antibody system, enabling resolution of both autoreactive VH4-34 gene-expressing B cells and serum antibodies. Compared with healthy controls, HIV patients had significantly elevated 9G4+ serum IgG antibody concentrations and frequencies of 9G4+ B cells, a finding characteristic of systemic lupus erythematosus (SLE) patients, both of which positively correlated with HIV viral load. Compared to the global 9G4−IgD− memory B cell population, the 9G4+IgD− memory fraction in HIV patients was dominated by isotype switched IgG+ B cells, but had a more prominent bias toward “IgM only" memory. HIV envelope reactivity was observed both in the 9G4+ serum antibody and 9G4+ B cell population. 9G4+ IgG serum antibody levels positively correlated (r = 0.403, p = 0.0019) with the serum HIV BNAbs. Interestingly, other serum autoantibodies commonly found in SLE (anti-dsDNA, ANA, anti-CL) did not correlate with serum HIV BNAbs. 9G4-associated autoreactivity is preferentially expanded in chronic HIV infection as compared to other SLE autoreactivities. Therefore, the 9G4 system provides an effective tool to examine autoreactivity in HIV patients. Our results suggest that the development of HIV BNAbs is not merely a consequence of a general breakdown in tolerance, but rather a more intricate expansion of selective autoreactive B cells and antibodies

Single-shot 3D coherent diffractive imaging of core-shell nanoparticles with elemental specificity.

We report 3D coherent diffractive imaging (CDI) of Au/Pd core-shell nanoparticles with 6.1 nm spatial resolution with elemental specificity. We measured single-shot diffraction patterns of the nanoparticles using intense x-ray free electron laser pulses. By exploiting the curvature of the Ewald sphere and the symmetry of the nanoparticle, we reconstructed the 3D electron density of 34 core-shell structures from these diffraction patterns. To extract 3D structural information beyond the diffraction signal, we implemented a super-resolution technique by taking advantage of CDI's quantitative reconstruction capabilities. We used high-resolution model fitting to determine the Au core size and the Pd shell thickness to be 65.0 ± 1.0 nm and 4.0 ± 0.5 nm, respectively. We also identified the 3D elemental distribution inside the nanoparticles with an accuracy of 3%. To further examine the model fitting procedure, we simulated noisy diffraction patterns from a Au/Pd core-shell model and a solid Au model and confirmed the validity of the method. We anticipate this super-resolution CDI method can be generally used for quantitative 3D imaging of symmetrical nanostructures with elemental specificity

Application of a multi-layer artificial neural network in a 3-D global electron density model using the long-term observations of COSMIC, Fengyun-3C, and Digisonde

The ionosphere plays an important role in satellite navigation, radio communication, and space weather prediction. However, it is still a challenging mission to develop a model with high predictability that captures the horizontal-vertical features of ionospheric electrodynamics. In this study, multiple observations during 2005–2019 from space-borne global navigation satellite system (GNSS) radio occultation (RO) systems (COSMIC and FY-3C) and the Digisonde Global Ionosphere Radio Observatory are utilized to develop a completely global ionospheric three-dimensional electron density model based on an artificial neural network, namely ANN-TDD. The correlation coefficients of the predicted profiles all exceed 0.96 for the training, validation and test datasets, and the minimum root-mean-square error of the predicted residuals is 7.8 × 104 el/cm3. Under quiet space weather, the predicted accuracy of the ANN-TDD is 30%–60% higher than the IRI-2016 at the Millstone Hill and Jicamarca incoherent scatter radars. However, the ANN-TDD is less capable of predicting ionospheric dynamic evolution under severe geomagnetic storms compared to the IRI-2016 with the STORM option activated. Additionally, the ANN-TDD successfully reproduces the large-scale horizontal-v

A new method for improving the performance of an ionospheric model developed by multi-instrument measurements based on artificial neural network

There are remarkable ionospheric discrepancies between space-borne (COSMIC) measurements and ground-based (ionosonde) observations, the discrepancies could decrease the accuracies of the ionospheric model developed by multi-source data seriously. To reduce the discrepancies between two observational systems, the peak frequency (foF2) and peak height (hmF2) derived from the COSMIC and ionosonde data are used to develop the ionospheric models by an artificial neural network (ANN) method, respectively. The averaged root-mean-square errors (RMSEs) of COSPF (COSMIC peak frequency model), COSPH (COSMIC peak height model), IONOPF (Ionosonde peak frequency model) and IONOPH (Ionosonde peak height model) are 0.58 MHz, 19.59 km, 0.92 MHz and 23.40 km, respectively. The results indicate that the discrepancies between these models are dependent on universal time, geographic latitude and seasons. The peak frequencies measured by COSMIC are generally larger than ionosonde's observations in the nighttime or middle-latitudes with the amplitude of lower than 25%, while the averaged peak height derived from COSMIC is smaller than ionosonde's data in the polar regions. The differences between ANN-based maps and references show that the d

Coherent diffraction of single Rice Dwarf virus particles using hard X-rays at the Linac Coherent Light Source

Single particle diffractive imaging data from Rice Dwarf Virus (RDV) were recorded using the Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS). RDV was chosen as it is a wellcharacterized model system, useful for proof-of-principle experiments, system optimization and algorithm development. RDV, an icosahedral virus of about 70 nm in diameter, was aerosolized and injected into the approximately 0.1 mu m diameter focused hard X-ray beam at the CXI instrument of LCLS. Diffraction patterns from RDV with signal to 5.9 angstrom ngstrom were recorded. The diffraction data are available through the Coherent X-ray Imaging Data Bank (CXIDB) as a resource for algorithm development, the contents of which are described here.11Ysciescopu

Single-shot 3D coherent diffractive imaging of core-shell nanoparticles with elemental specificity

We report 3D coherent diffractive imaging (CDI) of Au/Pd core-shell nanoparticles with 6.1 nm spatial resolution with elemental specificity. We measured single-shot diffraction patterns of the nanoparticles using intense x-ray free electron laser pulses. By exploiting the curvature of the Ewald sphere and the symmetry of the nanoparticle, we reconstructed the 3D electron density of 34 core-shell structures from these diffraction patterns. To extract 3D structural information beyond the diffraction signal, we implemented a super-resolution technique by taking advantage of CDI's quantitative reconstruction capabilities. We used high-resolution model fitting to determine the Au core size and the Pd shell thickness to be 65.0 +/- 1.0 nm and 4.0 +/- 0.5 nm, respectively. We also identified the 3D elemental distribution inside the nanoparticles with an accuracy of 3%. To further examine the model fitting procedure, we simulated noisy diffraction patterns from a Au/Pd core-shell model and a solid Au model and confirmed the validity of the method. We anticipate this super-resolution CDI method can be generally used for quantitative 3D imaging of symmetrical nanostructures with elemental specificity.111Ysciescopu