Single B cell transcriptomics identifies multiple isotypes of broadly neutralizing antibodies against flaviviruses.

Sequential dengue virus (DENV) infections often generate neutralizing antibodies against all four DENV serotypes and sometimes, Zika virus. Characterizing cross-flavivirus broadly neutralizing antibody (bnAb) responses can inform countermeasures that avoid enhancement of infection associated with non-neutralizing antibodies. Here, we used single cell transcriptomics to mine the bnAb repertoire following repeated DENV infections. We identified several new bnAbs with comparable or superior breadth and potency to known bnAbs, and with distinct recognition determinants. Unlike all known flavivirus bnAbs, which are IgG1, one newly identified cross-flavivirus bnAb (F25.S02) was derived from IgA1. Both IgG1 and IgA1 versions of F25.S02 and known bnAbs displayed neutralizing activity, but only IgG1 enhanced infection in monocytes expressing IgG and IgA Fc receptors. Moreover, IgG-mediated enhancement of infection was inhibited by IgA1 versions of bnAbs. We demonstrate a role for IgA in flavivirus infection and immunity with implications for vaccine and therapeutic strategies.

Bright Excitonic Fine Structure in Metal-Halide Perovskites: From Two-Dimensional to Bulk.

The optical response of two-dimensional (2D) perovskites, often referred to as natural quantum wells, is primarily governed by excitons, whose properties can be readily tuned by adjusting the perovskite layer thickness. We have investigated the exciton fine structure splitting in the archetypal 2D perovskite (PEA)2(MA)n-1PbnI3n+1 with varying numbers of inorganic octahedral layers n = 1, 2, 3, and 4. We demonstrate that the in-plane excitonic states exhibit splitting and orthogonally oriented dipoles for all confinement regimes. The evolution of the exciton states in an external magnetic field provides further insights into the g-factors and diamagnetic coefficients. With increasing n, we observe a gradual evolution of the excitonic parameters characteristic of a 2D to three-dimensional transition. Our results provide valuable information concerning the evolution of the optoelectronic properties of 2D perovskites with the changing confinement strength.

Leveraging Pyrazolium Ylide Reactivity to Access Indolizine and 1,2-Dihydropyrimidine Derivatives.

N-Heterocyclic ylides are important synthetic precursors to rapidly build molecular complexity. Pyrazolium ylides have largely been unexplored, and we demonstrate their diverse utility in this report. We show that these readily accessible building blocks can be used to construct different heterocyclic skeletons by varying the coupling partner. Indolizines can be formed via an N-deletion type mechanism when reacting pyrazolium salts with electron deficient alkynes. 1,2-Dihydropyrimidines can be formed via a rearrangement mechanism when reacting pyrazolium ylides with isocyanates. These reactions enable access to valuable heteroarenes without the need for transition metal catalysis, high temperatures, or strong bases.

Approaching the Intrinsic Properties of Moiré Structures Using Atomic Force Microscopy Ironing.

Stacking monolayers of transition metal dichalcogenides (TMDs) has led to the discovery of a plethora of new exotic phenomena, resulting from moiré pattern formation. Due to the atomic thickness and high surface-to-volume ratio of heterostructures, the interfaces play a crucial role. Fluctuations in the interlayer distance affect interlayer coupling and moiré effects. Therefore, to access the intrinsic properties of the TMD stack, it is essential to obtain a clean and uniform interface between the layers. Here, we show that this is achieved by ironing with the tip of an atomic force microscope. This post-stacking procedure dramatically improves the homogeneity of the interfaces, which is reflected in the optical response of the interlayer exciton. We demonstrate that ironing improves the layer coupling, enhancing moiré effects and reducing disorder. This is crucial for the investigation of TMD heterostructure physics, which currently suffers from low reproducibility.

Homologation of Alkenyl Carbonyls via a Cyclopropanation/Light-Mediated Selective C-C Cleavage Strategy.

We report herein our studies on the direct photoactivation of carbonyl cyclopropanes to give biradical intermediates, leading to selective cleavage of the more substituted carbon-carbon bond. Depending on the substrate structure, extended alkenes were isolated or directly reacted in a photo-Nazarov process to give bicyclic products. Based on these results, a unified reductive ring-opening reaction was developed by using diphenyl disulfide as a HAT reagent. By performing a sequential cyclopropanation/selective ring opening reaction, we achieved a CH2 insertion into the α,ß bond of both acyclic and cyclic unsaturated carbonyl compounds. Our protocol provides a further tool for the modification of the carbon framework of organic compounds, complementing the recent progress in "skeletal editing".

Inference of B cell clonal families using heavy/light chain pairing information.

Next generation sequencing of B cell receptor (BCR) repertoires has become a ubiquitous tool for understanding the antibody-mediated immune response: it is now common to have large volumes of sequence data coding for both the heavy and light chain subunits of the BCR. However, until the recent development of high throughput methods of preserving heavy/light chain pairing information, these samples contained no explicit information on which heavy chain sequence pairs with which light chain sequence. One of the first steps in analyzing such BCR repertoire samples is grouping sequences into clonally related families, where each stems from a single rearrangement event. Many methods of accomplishing this have been developed, however, none so far has taken full advantage of the newly-available pairing information. This information can dramatically improve clustering performance, especially for the light chain. The light chain has traditionally been challenging for clonal family inference because of its low diversity and consequent abundance of non-clonal families with indistinguishable naive rearrangements. Here we present a method of incorporating this pairing information into the clustering process in order to arrive at a more accurate partition of the data into clonally related families. We also demonstrate two methods of fixing imperfect pairing information, which may allow for simplified sample preparation and increased sequencing depth. Finally, we describe several other improvements to the partis software package.

Evaluating insecticide resistance across African districts to aid malaria control decisions.

Malaria vector control may be compromised by resistance to insecticides in vector populations. Actions to mitigate against resistance rely on surveillance using standard susceptibility tests, but there are large gaps in the monitoring data across Africa. Using a published geostatistical ensemble model, we have generated maps that bridge these gaps and consider the likelihood that resistance exceeds recommended thresholds. Our results show that this model provides more accurate next-year predictions than two simpler approaches. We have used the model to generate district-level maps for the probability that pyrethroid resistance in Anopheles gambiae s.l. exceeds the World Health Organization thresholds for susceptibility and confirmed resistance. In addition, we have mapped the three criteria for the deployment of piperonyl butoxide-treated nets that mitigate against the effects of metabolic resistance to pyrethroids. This includes a critical review of the evidence for presence of cytochrome P450-mediated metabolic resistance mechanisms across Africa. The maps for pyrethroid resistance are available on the IR Mapper website, where they can be viewed alongside the latest survey data.

Thickness-Dependent Dark-Bright Exciton Splitting and Phonon Bottleneck in CsPbBr3-Based Nanoplatelets Revealed via Magneto-Optical Spectroscopy.

The optimized exploitation of perovskite nanocrystals and nanoplatelets as highly efficient light sources requires a detailed understanding of the energy spacing within the exciton manifold. Dark exciton states are particularly relevant because they represent a channel that reduces radiative efficiency. Here, we apply large in-plane magnetic fields to brighten optically inactive states of CsPbBr3-based nanoplatelets for the first time. This approach allows us to access the dark states and directly determine the dark-bright splitting, which reaches 22 meV for the thinnest nanoplatelets. The splitting is significantly less for thicker nanoplatelets due to reduced exciton confinement. Additionally, the form of the magneto-PL spectrum suggests that dark and bright state populations are nonthermalized, which is indicative of a phonon bottleneck in the exciton relaxation process.

Regioselective Synthesis of C3-Hydroxyarylated Pyrazoles.

Pyrazoles are ubiquitous structures in medicinal chemistry. We report the first regioselective route to C3-hydroxyarylated pyrazoles obtained through reaction of pyrazole N-oxides with arynes using mild conditions. Importantly, this method does not require the C4 and C5 positions of the pyrazole to be functionalized to observe regioselectivity. Using this method, we completed the synthesis of a recently reported JAK 1/2 inhibitor. Our synthesis produces the desired product in 4 steps from commercially available starting materials.

Linkage to Care Intervention to Improve Post-Hospital Outcomes Among Children with Sickle Cell Disease in Tanzania: A Pilot Study.

We conducted a pilot study to determine the effectiveness of a linkage to care intervention with social workers to improve 12-month post-hospital mortality for children in Tanzania with sickle cell disease. Comparison was done with a historical cohort. Mortality was 6.7% in the interventional cohort compared with 19.2% (adjusted Hazard Ratio, 0.26; 95% CI, 0.08-0.83).

Using B cell receptor lineage structures to predict affinity.

We are frequently faced with a large collection of antibodies, and want to select those with highest affinity for their cognate antigen. When developing a first-line therapeutic for a novel pathogen, for instance, we might look for such antibodies in patients that have recovered. There exist effective experimental methods of accomplishing this, such as cell sorting and baiting; however they are time consuming and expensive. Next generation sequencing of B cell receptor (BCR) repertoires offers an additional source of sequences that could be tapped if we had a reliable method of selecting those coding for the best antibodies. In this paper we introduce a method that uses evolutionary information from the family of related sequences that share a naive ancestor to predict the affinity of each resulting antibody for its antigen. When combined with information on the identity of the antigen, this method should provide a source of effective new antibodies. We also introduce a method for a related task: given an antibody of interest and its inferred ancestral lineage, which branches in the tree are likely to harbor key affinity-increasing mutations? We evaluate the performance of these methods on a wide variety of simulated samples, as well as two real data samples. These methods are implemented as part of continuing development of the partis BCR inference package, available at https://github.com/psathyrella/partis. Comments Please post comments or questions on this paper as new issues at https://git.io/Jvxkn.

A Bayesian phylogenetic hidden Markov model for B cell receptor sequence analysis.

The human body generates a diverse set of high affinity antibodies, the soluble form of B cell receptors (BCRs), that bind to and neutralize invading pathogens. The natural development of BCRs must be understood in order to design vaccines for highly mutable pathogens such as influenza and HIV. BCR diversity is induced by naturally occurring combinatorial "V(D)J" rearrangement, mutation, and selection processes. Most current methods for BCR sequence analysis focus on separately modeling the above processes. Statistical phylogenetic methods are often used to model the mutational dynamics of BCR sequence data, but these techniques do not consider all the complexities associated with B cell diversification such as the V(D)J rearrangement process. In particular, standard phylogenetic approaches assume the DNA bases of the progenitor (or "naive") sequence arise independently and according to the same distribution, ignoring the complexities of V(D)J rearrangement. In this paper, we introduce a novel approach to Bayesian phylogenetic inference for BCR sequences that is based on a phylogenetic hidden Markov model (phylo-HMM). This technique not only integrates a naive rearrangement model with a phylogenetic model for BCR sequence evolution but also naturally accounts for uncertainty in all unobserved variables, including the phylogenetic tree, via posterior distribution sampling.

Symmetry Breakdown in Franckeite: Spontaneous Strain, Rippling, and Interlayer Moiré.

Franckeite is a naturally occurring layered mineral with a structure composed of alternating stacks of SnS2-like and PbS-like layers. Although this superlattice is composed of a sequence of isotropic two-dimensional layers, it exhibits a spontaneous rippling that makes the material structurally anisotropic. We demonstrate that this rippling comes hand in hand with an inhomogeneous in-plane strain profile and anisotropic electrical, vibrational, and optical properties. We argue that this symmetry breakdown results from a spatial modulation of the van der Waals interaction between layers due to the SnS2-like and PbS-like lattices incommensurability.

Per-sample immunoglobulin germline inference from B cell receptor deep sequencing data.

The collection of immunoglobulin genes in an individual's germline, which gives rise to B cell receptors via recombination, is known to vary significantly across individuals. In humans, for example, each individual has only a fraction of the several hundred known V alleles. Furthermore, the currently-accepted set of known V alleles is both incomplete (particularly for non-European samples), and contains a significant number of spurious alleles. The resulting uncertainty as to which immunoglobulin alleles are present in any given sample results in inaccurate B cell receptor sequence annotations, and in particular inaccurate inferred naive ancestors. In this paper we first show that the currently widespread practice of aligning each sequence to its closest match in the full set of IMGT alleles results in a very large number of spurious alleles that are not in the sample's true set of germline V alleles. We then describe a new method for inferring each individual's germline gene set from deep sequencing data, and show that it improves upon existing methods by making a detailed comparison on a variety of simulated and real data samples. This new method has been integrated into the partis annotation and clonal family inference package, available at https://github.com/psathyrella/partis, and is run by default without affecting overall run time.

Demonstrating the Use of Optical Fibres in Biomedical Sensing: A Collaborative Approach for Engagement and Education.

This paper demonstrates how research at the intersection of physics, engineering, biology and medicine can be presented in an interactive and educational way to a non-scientific audience. Interdisciplinary research with a focus on prevalent diseases provides a relatable context that can be used to engage with the public. Respiratory diseases are significant contributors to avoidable morbidity and mortality and have a growing social and economic impact. With the aim of improving lung disease understanding, new techniques in fibre-based optical endomicroscopy have been recently developed. Here, we present a novel engagement activity that resembles a bench-to-bedside pathway. The activity comprises an inexpensive educational tool (<$70) adapted from a clinical optical endomicroscopy system and tutorials that cover state-of-the-art research. The activity was co-created by high school science teachers and researchers in a collaborative way that can be implemented into any engagement development process.

Determining Interaction Enhanced Valley Susceptibility in Spin-Valley-Locked MoS2.

Two-dimensional transition metal dichalcogenides (TMDCs) are recently emerged electronic systems with various novel properties, such as spin-valley locking, circular dichroism, valley Hall effect, and superconductivity. The reduced dimensionality and large effective masses further produce unconventional many-body interaction effects. Here we reveal strong interaction effects in the conduction band of MoS2 by transport experiment. We study the massive Dirac electron Landau levels (LL) in high-quality MoS2 samples with field-effect mobilities of 24 000 cm2/(V·s) at 1.2 K. We identify the valley-resolved LLs and low-lying polarized LLs using the Lifshitz-Kosevitch formula. By further tracing the LL crossings in the Landau fan diagram, we unambiguously determine the density-dependent valley susceptibility and the interaction enhanced g-factor from 12.7 to 23.6. Near integer ratios of Zeeman-to-cyclotron energies, we discover LL anticrossings due to the formation of quantum Hall Ising ferromagnets, the valley polarizations of which appear to be reversible by tuning the density or an in-plane magnetic field. Our results provide evidence for many-body interaction effects in the conduction band of MoS2 and establish a fertile ground for exploring strongly correlated phenomena of massive Dirac electrons.

The impact of hexagonal boron nitride encapsulation on the structural and vibrational properties of few layer black phosphorus.

The encapsulation of two-dimensional layered materials such as black phosphorus is of paramount importance for their stability in air. However, the encapsulation poses several questions, namely, how it affects, via the weak van der Waals forces, the properties of the black phosphorus and whether these properties can be tuned on demand. Prompted by these questions, we have investigated the impact of hexagonal boron nitride encapsulation on the structural and vibrational properties of few layer black phosphorus, using a first-principles method in the framework of density functional theory. We demonstrate that the encapsulation with hexagonal boron nitride imposes biaxial strain on the black phosphorus material, flattening its puckered structure, by decreasing the thickness of the layers via the increase of the puckered angle and the intra-layer P-P bonds. This work exemplifies the evolution of structural parameters in layered materials after the encapsulation process. We find that after encapsulation, phosphorene (single layer black phosphorous) contracts by 1.1% in the armchair direction and stretches by 1.3% in the zigzag direction, whereas few layer black phosphorus mainly expands by up to 3% in the armchair direction. However, these relatively small strains induced by the hexagonal BN, lead to significant changes in the vibrational properties of black phosphorus, with the redshifts of up to 10 cm-1 of the high frequency optical mode A g 1. In general, structural changes induced by the encapsulation process open the door to substrate controlled strain engineering in two-dimensional crystals.

Moiré Intralayer Excitons in a MoSe2/MoS2 Heterostructure.

Spatially periodic structures with a long-range period, referred to as a moiré pattern, can be obtained in van der Waals bilayers in the presence of a small stacking angle or of lattice mismatch between the monolayers. Theoretical predictions suggest that the resulting spatially periodic variation of the band structure modifies the optical properties of both intra- and interlayer excitons of transition metal dichalcogenide heterostructures. Here, we report on the impact of the moiré pattern formed in a MoSe2/MoS2 heterobilayer encapsulated in hexagonal boron nitride. The periodic in-plane potential results in a splitting of the MoSe2 exciton and trion in emission and (for the exciton) absorption spectra. The observed energy difference between the split peaks is fully consistent with theoretical predictions.

Intervalley Scattering of Interlayer Excitons in a MoS2/MoSe2/MoS2 Heterostructure in High Magnetic Field.

Degenerate extrema in the energy dispersion of charge carriers in solids, also referred to as valleys, can be regarded as a binary quantum degree of freedom, which can potentially be used to implement valleytronic concepts in van der Waals heterostructures based on transition metal dichalcogenides. Using magneto-photoluminescence spectroscopy, we achieve a deeper insight into the valley polarization and depolarization mechanisms of interlayer excitons formed across a MoS2/MoSe2/MoS2 heterostructure. We account for the nontrivial behavior of the valley polarization as a function of the magnetic field by considering the interplay between exchange interaction and phonon-mediated intervalley scattering in a system consisting of Zeeman-split energy levels. Our results represent a crucial step toward the understanding of the properties of interlayer excitons with strong implications for the implementation of atomically thin valleytronic devices.

Beyond geminal diesters: increasing the scope of metal-mediated vinylcyclopropane annulations while decreasing pre-activation.

The utilization of unactivated substrates in annulation reactions provides access to complex products without the need for subsequent removal of the activating group. Vinylcyclopropanes (VCPs), occurring naturally in several monoterpene natural products, are an important building block for organic chemistry, and can be activated by electron withdrawing substituents directly on the cyclopropane to facilitate ring opening reactions. However, many VCPs that lack these activated groups remain reactive with several group 8, 9 and 10 transition metals, by alternative modes of activation, forming metallacycles. These useful intermediates produce annulation products in reactions with unsaturated π-units, providing rapid access to new carbocycles. Several formal cycloadditions that incorporate unactivated VCPs as substrates have been developed, including [5 + 2], [5 + 2 + 1], [5 + 1 + 2 + 1], [3 + 2], [3 + 2 + 1], [5 + 1], and others, using Rh, Ni, Ru, Ir, Fe and Co based catalysts. Mono- and polycyclic ring systems have been made using these methods with their utility demonstrated through the synthesis of complex natural products. This review will summarize the annulations of VCPs that lack geminal diesters, but retain reactivity via transition metal catalysts.