SARS-CoV-2 prevalence and immunity: a hospital-based study from Malawi.

BACKGROUND: COVID-19 transmission and disease dynamics in sub-Saharan Africa are not well understood. Our study aims to provide insight into COVID-19 epidemiology in Malawi by estimating SARS-CoV-2 prevalence and immunity after SARS-CoV-2 infection in a hospital-based setting. METHODS: We conducted a hospital-based, convenience sampling, cross-sectional survey for SARS-CoV-2 in Lilongwe, Malawi. Participants answered a questionnaire and were tested for SARS-CoV-2 by enzyme-linked immunosorbent assay and real-time reverse-transcription polymerase chain reaction (RT-PCR). A surrogate virus neutralization test (sVNT) was performed in seropositive samples to estimate immunity. Poisson regression was used to assess SARS-CoV-2 point prevalence association with demographic and behavioral variables. FINDINGS: The study included 930 participants. We found a combined point prevalence of 10.1%. Separately analyzed, RT-PCR positivity was 2.0%, and seropositivity was 9.3%. Of tested seropositive samples, 90.1% were sVNT positive. We found a high rate (45.7%) of asymptomatic SARS-CoV-2 infection. SARS-CoV-2 point prevalence was significantly associated with being a healthcare worker. INTERPRETATION: Our study suggests that official data underestimate COVID-19 transmission. Using sVNTs to estimate immunity in Malawi is feasible and revealed considerable post-infection immunity in our cohort. Subclinical infection and transmission are probably a game-changer in surveillance, mitigation and vaccination strategies.

Response of free-standing graphene monolayer exposed to ultrashort intense XUV pulse from free-electron laser.

The response of a free-standing graphene monolayer exposed to a few tens of femtoseconds long extreme ultraviolet (XUV) pulse was studied theoretically in order to analyze and compare contributions of various mechanisms to the graphene damage, understood here as a global atomic disintegration. Our simulation results indicate that nonthermal disintegration of the atomic structure is the predominant damage mechanism for a free-standing graphene layer. Only at high absorbed doses, charge-induced disintegration of the graphene structure prevails. We also demonstrate that the progressing damage can be probed by femtosecond optical pulses in the soft UV regime (4 eV photon energy). The achieved quantitative understanding of the damage mechanisms may enable a better control of graphene-based devices when they are exposed to x-ray radiation, as well as an efficient processing of graphene layers with ultrashort intense XUV pulses.

Nanoplasma Formation by High Intensity Hard X-rays.

Using electron spectroscopy, we have investigated nanoplasma formation from noble gas clusters exposed to high-intensity hard-x-ray pulses at ~5 keV. Our experiment was carried out at the SPring-8 Angstrom Compact free electron LAser (SACLA) facility in Japan. Dedicated theoretical simulations were performed with the molecular dynamics tool XMDYN. We found that in this unprecedented wavelength regime nanoplasma formation is a highly indirect process. In the argon clusters investigated, nanoplasma is mainly formed through secondary electron cascading initiated by slow Auger electrons. Energy is distributed within the sample entirely through Auger processes and secondary electron cascading following photoabsorption, as in the hard x-ray regime there is no direct energy transfer from the field to the plasma. This plasma formation mechanism is specific to the hard-x-ray regime and may, thus, also be important for XFEL-based molecular imaging studies. In xenon clusters, photo- and Auger electrons contribute more significantly to the nanoplasma formation. Good agreement between experiment and simulations validates our modelling approach. This has wide-ranging implications for our ability to quantitatively predict the behavior of complex molecular systems irradiated by high-intensity hard x-rays.

Single-shot pulse duration monitor for extreme ultraviolet and X-ray free-electron lasers.

The resolution of ultrafast studies performed at extreme ultraviolet and X-ray free-electron lasers is still limited by shot-to-shot variations of the temporal pulse characteristics. Here we show a versatile single-shot temporal diagnostic tool that allows the determination of the extreme ultraviolet pulse duration and the relative arrival time with respect to an external pump-probe laser pulse. This method is based on time-resolved optical probing of the transient reflectivity change due to linear absorption of the extreme ultraviolet pulse within a solid material. In this work, we present measurements performed at the FLASH free-electron laser. We determine the pulse duration at two distinct wavelengths, yielding (184±14) fs at 41.5 nm and (21±19) fs at 5.5 nm. Furthermore, we demonstrate the feasibility to operate the tool as an online diagnostic by using a 20-nm-thin Si3N4 membrane as target. Our results are supported by detailed numerical and analytical investigations.

Breakdown of the x-ray resonant magnetic scattering signal during intense pulses of extreme ultraviolet free-electron-laser radiation.

We present results of single-shot resonant magnetic scattering experiments of Co/Pt multilayer systems using 100 fs long ultraintense pulses from an extreme ultraviolet (XUV) free-electron laser. An x-ray-induced breakdown of the resonant magnetic scattering channel during the pulse duration is observed at fluences of 5 J/cm(2). Simultaneously, the speckle contrast of the high-fluence scattering pattern is significantly reduced. We performed simulations of the nonequilibrium evolution of the Co/Pt multilayer system during the XUV pulse duration. We find that the electronic state of the sample is strongly perturbed during the first few femtoseconds of exposure leading to an ultrafast quenching of the resonant magnetic scattering mechanism.

Coherent diffraction of a single virus particle: the impact of a water layer on the available orientational information.

Coherent diffractive imaging using x-ray free-electron lasers (XFELs) may provide a unique opportunity for high-resolution structural analysis of single particles sprayed from an aqueous solution into the laser beam. As a result, diffraction images are measured from randomly oriented objects covered by a water layer. We analyze theoretically how the thickness of the covering water layer influences the structural and orientational information contained in the recorded diffraction images. This study has implications for planned experiments on single-particle imaging with XFELs.

Theoretical estimation for correlations of diffraction patterns from objects differently oriented in space.

Coherent diffraction imaging of single biomolecules is expected to open unique opportunities for studies of non-crystalline samples. There are, however, still many technical and physical issues that need to be resolved in a more quantitative manner, especially if one aims for structural information at high resolution. Signal recorded from an object after a single shot is low. As primarily proposed in Spence and Doak (2004) and Huldt et al. (2003), averaging over the diffraction patterns from many different shots is necessary, in order to achieve a signal-to-noise ratio sufficient for image reconstruction. The images of the randomly oriented molecules have to be sorted out in order to identify those corresponding to the similar spatial orientations of the objects. This procedure is called the classification of diffraction images. Here we approach the classification in the framework of pattern-to-pattern correlations, and analyse theoretically the correlations between diffraction images of differently oriented objects.

Observation of ultrafast nonequilibrium collective dynamics in warm dense hydrogen.

We investigate ultrafast (fs) electron dynamics in a liquid hydrogen sample, isochorically and volumetrically heated to a moderately coupled plasma state. Thomson scattering measurements using 91.8 eV photons from the free-electron laser in Hamburg (FLASH at DESY) show that the hydrogen plasma has been driven to a nonthermal state with an electron temperature of 13 eV and an ion temperature below 0.1 eV, while the free-electron density is 2.8x10{20} cm{-3}. For dense plasmas, our experimental data strongly support a nonequilibrium kinetics model that uses impact ionization cross sections based on classical free-electron collisions.

Energetics, ionization, and expansion dynamics of atomic clusters irradiated with short intense vacuum-ultraviolet pulses.

Kinetic equations are used to model the dynamics of Xe clusters irradiated with short, intense vacuum-ultraviolet pulses. Various cluster size and pulse fluences are considered. It is found that the highly charged ions observed in the experiments are mainly due to Coulomb explosion of the outer cluster shell. Ions within the cluster core predominantly recombine with plasma electrons, forming a large fraction of neutral atoms. To our knowledge, our model is the first and only one that gives an accurate description of all of the experimental data collected from atomic clusters at 100 nm photon wavelength.

Shake-up and shake-off excitations with associated electron losses in X-ray studies of proteins.

Photoionization of an atom by X-rays usually removes an inner shell electron from the atom, leaving behind a perturbed "hollow ion" whose relaxation may take different routes. In light elements, emission of an Auger electron is common. However, the energy and the total number of electrons released from the atom may be modulated by shake-up and shake-off effects. When the inner shell electron leaves, the outer shell electrons may find themselves in a state that is not an eigen-state of the atom in its surroundings. The resulting collective excitation is called shake-up. If this process also involves the release of low energy electrons from the outer shell, then the process is called shake-off. It is not clear how significant shake-up and shake-off contributions are to the overall ionization of biological materials like proteins. In particular, the interaction between the outgoing electron and the remaining system depends on the chemical environment of the atom, which can be studied by quantum chemical methods. Here we present calculations on model compounds to represent the most common chemical environments in proteins. The results show that the shake-up and shake-off processes affect approximately 20% of all emissions from nitrogen, 30% from carbon, 40% from oxygen, and 23% from sulfur. Triple and higher ionizations are rare for carbon, nitrogen, and oxygen, but are frequent for sulfur. The findings are relevant to the design of biological experiments at emerging X-ray free-electron lasers.

A chemiluminescence detection method of hantaviral antigens in neutralisation assays and inhibitor studies.

A protocol for chemiluminescence detection of hantaviral antigens in infected cell foci is described. This focus detection is based on the conversion of a substrate into a luminescent product by peroxidase-antibody conjugates; the emitted light of infected cell foci can easily be recorded by autoradiography or video imaging providing a hard copy for documentation. The main advantage of this method as compared to conventional immunochemical staining is a higher detection sensitivity due to the inherent magnification effect of luminescence causing an obvious boost in focal image and intensity. This enables reduction of (i) incubation time of virus-infected cells and (ii) amount of needed antibody for antigen detection in foci. This method is applied to a chemiluminescence focus reduction assay for the serotyping of hantavirus-specific neutralising antibodies in infected persons and for the determination of activity of antiviral agents against hantavirus.