Single molecule light field microscopy

We introduce single molecule light field microscopy (SMLFM), a new class of three-dimensional (3D) single molecule localization microscopy. By segmenting the back focal plane of a microscope objective with an array of microlenses to generate multiple 2D perspective views, the same single fluorophore can be imaged from different angles. These views, in combination with a bespoke fitting algorithm, enable the 3D positions of single fluorophores to be determined from parallax. SMLFM achieves up to 20 nm localization precision throughout an extended 6 µ m depth of field. The capabilities of SMLFM are showcased by imaging membranes of fixed eukaryotic cells and DNA nanostructures below the optical diffraction limit.</jats:p

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Dependence of cuprous oxide conductivity on metal doping: a hybrid density functional simulation

Multiple metallic elements were screened as doping agents to alternate conductivity in cuprous oxide (Cu2O). Energetic, charge transition levels and optical properties of Be, Mg, Ca, Sr, Zn, Cd, Hg, Al, Ga, and In substitutionally doped Cu2O systems were investigated based on first principles methods. Results of formation energy calculation under both Cu-rich and Cu-poor conditions indicate the easy incorporation of 2A (Be, Mg, Ca, and Sr) group impurities into the crystal lattice of Cu2O under both conditions. However, 3A (Al, Ga, and In) group impurities could be incorporated only under Cu-poor conditions. While, the incorporation of Zn, Cd, and Hg in Cu2O is energetically less favorable under both conditions. The calculated charge transition levels of these dopants revealed an n-type conductivity. The calculated work functions show n-type to p-type surface inversion behavior for some doped systems. This can explain the p-type conductivity of Mg-doped Cu2O found experimentally. Furthermore, the optical properties of each system are calculated to investigate the effect of the introduced impurity on Cu2O. This study can help identify potential dopants to use for solar cell fabrication

Insight into the electronic, magnetic and optical properties of orthorhombic perovskite PrMn

Structural, electronic, magnetic and optical properties of orthorhombic perovskite PrMn1-xFexO3 (0 ≤ x ≤ 1) have been performed using first-principles density functional calculations. We focused on Mn-rich, Fe-rich and intermediate compounds in ferromagnetic and antiferromagnetic spin ordering. Our results show the ferromagnetic semiconductor behavior in PrMn0.5Fe0.5O3 due to the Fe3+–O–Mn3+ ferromagnetic super-exchange interaction, while half-metallic antiferromagnetic behavior in Mn-rich and Fe-rich compounds due to the Mn–O–Mn and Fe–O–Fe interactions. The absorption coefficient $$\alpha \left(\omega \right)$$, reflectivity $$R\left(\omega \right)$$ and the refractive index $$n\left(\omega \right)$$ of pure and mixed PrMn1-xFexO3 perovskites are also discussed

Ab initio comparative study of B2–MnX intermetallics with

Energetic, structural, electronic, mechanical and thermodynamic properties of B2–MnX intermetallics with X = V, Nb, and Ta have been investigated using first-principles calculations. The results show that MnV, MnNb, and MnTa compounds are thermodynamically and mechanically stable in the B2 structure. Mechanical property analysis indicates that the MnX intermetallics have remarkable ductility in the order $${\mathrm{MnNb}} > {\mathrm{MnTa}}> {\mathrm{MnV}}$$, which are part of the unusual category of intrinsic ductile B2 intermetallics

Mechanical and thermodynamic properties of rare-earth-based Ni intermetallic compounds crystallized in the C15b structure: an Ab-initio study

International audienceThis study investigates the mechanical properties and structural and thermodynamic stabilities of RENi5 compounds (RE: rare earth metals, with RE = Y, La, and Gd) in the AuBe5 (C15b) structure. Intermetallics of this type have potential applications in hydrogen battery technology, but their properties are not well understood. Using first-principles calculations, we calculated the mechanical properties, including the shear modulus, Young&#039;s modulus, bulk modulus, Poisson&#039;s ratio, Vickers hardness, and ductility of these compounds. Our calculations revealed that these compounds are both mechanically and thermodynamically stable. Additionally, our results suggest that all compounds are ductile. The YNi5 compound has the highest Debye temperature, indicating greater covalent Y-Ni bonds and greater hardness. We analyzed these findings with respect to the electronic structure of the compounds by calculating the density of states (DOS) and charge density distribution. These insights into the mechanical, thermodynamic, and electronic properties of RENi5 intermetallics can inform the design and development of novel materials with improved properties in hydrogen batteries, mechanical applications or other related fields

Unveiling ductile, rare-earth-free structural materials: A DFT exploration of MnTi and MnZr

International audienceThis paper presents a theoretical exploration of the electronic, structural, and mechanical attributes inherent in three rare-earth-free intermetallic compounds, namely, MnTi, MnZr, and MnHf. Employing density functional theory (DFT) calculations with the Implementation of projector augmented wave (PAW); our investigation adopts the supercell approach to meticulously determine the structural and mechanical properties of these materials. The findings reveal that MnTi and MnZr exhibit intrinsic ductility, positioning them as viable contenders for applications demanding high-strength structures. In contrast, MnHf demonstrates mechanical instability. This study provides promising insights into the mechanical characteristics of MnTi and MnZr, underscoring their potential as sustainable structural materials, given the abundance and non-toxic nature of their constituents. The research findings presented herein contribute to the understanding of rare-earth-free intermetallics, offering valuable information for applications in materials science and engineering

Single molecule light field microscopy

We introduce single molecule light field microscopy (SMLFM), a new class of three-dimensional (3D) single molecule localization microscopy. By segmenting the back focal plane of a microscope objective with an array of microlenses to generate multiple 2D perspective views, the same single fluorophore can be imaged from different angles. These views, in combination with a bespoke fitting algorithm, enable the 3D positions of single fluorophores to be determined from parallax. SMLFM achieves up to 20 nm localization precision throughout an extended 6µm depth of field. The capabilities of SMLFM are showcased by imaging membranes of fixed eukaryotic cells and DNA nanostructures below the optical diffraction limit

resPAINT: Accelerating volumetric super‐resolution localisation microscopy by active control of probe emission

Points for accumulation in nanoscale topography (PAINT) allows practically unlimited measurements in localisation microscopy but is limited by background fluorescence at high probe concentrations, especially in volumetric imaging. We present reservoir-PAINT (resPAINT), which combines PAINT and active control of probe photophysics. In resPAINT, an activatable probe ‘reservoir’ accumulates on target, enabling a 50-fold increase in localisation rate versus conventional PAINT, without compromising contrast. By combining resPAINT with large depth-of-field microscopy, we demonstrate super-resolution imaging of entire cell surfaces. We generalise the approach by implementing various switching strategies and 3D imaging techniques. Finally, we use resPAINT with a Fab to image membrane proteins, extending the operating regime of PAINT to include a wider range of biological interactions