Deep generative priors for biomolecular 3D heterogeneous reconstruction from cryo-EM projections.

Cryo-electron microscopy has become a powerful tool to determine three-dimensional (3D) structures of rigid biological macromolecules from noisy micrographs with single-particle reconstruction. Recently, deep neural networks, e.g., CryoDRGN, have demonstrated conformational and compositional heterogeneity of complexes. However, the lack of ground-truth conformations poses a challenge to assess the performance of heterogeneity analysis methods. In this work, variational autoencoders (VAE) with three types of deep generative priors were learned for latent variable inference and heterogeneous 3D reconstruction via Bayesian inference. More specifically, VAEs with "Variational Mixture of Posteriors" priors (VampPrior-SPR), non-parametric exemplar-based priors (ExemplarPrior-SPR) and priors from latent score-based generative models (LSGM-SPR) were quantitatively compared with CryoDRGN. We built four simulated datasets composed of hypothetical continuous conformation or discrete states of the hERG K + channel. Empirical and quantitative comparisons of inferred latent representations were performed with affine-transformation-based metrics. These models with more informative priors gave better regularized, interpretable factorized latent representations with better conserved pairwise distances, less deformed latent distributions and lower within-cluster variances. They were also tested on experimental datasets to resolve compositional and conformational heterogeneity (50S ribosome assembly, cowpea chlorotic mottle virus, and pre-catalytic spliceosome) with comparable high resolution. Codes and data are available: https://github.com/benjamin3344/DGP-SPR.

Fast finite difference solver for optical microscopy in deep biological tissue.

Optical scattering poses a significant challenge to high-resolution microscopy within deep tissue. To accurately predict the performance of various microscopy techniques in thick samples, we present a computational model that efficiently solves Maxwell's equation in highly scattering media. This toolkit simulates the deterioration of the laser beam point spread function (PSF) without making a paraxial approximation, enabling accurate modeling of high-numerical-aperture (NA) objective lenses commonly employed in experiments. Moreover, this framework is applicable to a broad range of scanning microscopy techniques including confocal microscopy, stimulated emission depletion (STED) microscopy, and ground-state depletion microscopy. Notably, the proposed method requires only readily obtainable macroscopic tissue parameters. As a practical demonstration, we investigate the performance of Laguerre-Gaussian (LG) versus Hermite-Gaussian (HG) depletion beams in STED microscopy.

Acoustic analysis of the effect of personal protective equipment on speech understanding: lessons for clinical environments.

OBJECTIVE: The use of various types of filtering facepiece class 3 (FFP3) mask have become commonplace since the Covid-19 outbreak. These have been evaluated in terms of efficacy regarding aerosol filtration but less emphasis has been placed on the acoustic effects of such masks and their consequences for clinical communication. DESIGN: A microphone 65 cm from a sound-producing Head and Torso Simulator (wearing the masks) was used to measure attenuation via a tone sweep. Predicted impact on speech reception in noise was assessed by weighting the attenuations of cochlear excitation patterns by the frequency importance function of the Speech Intelligibility Index. STUDY SAMPLE: We evaluated acoustic attenuation properties of seven FFP3 masks and a Type IIR surgical mask (as a comparator). RESULTS: The Type IIR mask had the smallest impact on SNR (2.6 dB with visor). Most FFP3s with an addition of a visor (if not already face covering) impacted SNR by approximately 6 dB. The 3 M 6000 was significantly worse (15.8 dB). CONCLUSIONS: Mouth-and-nose covering FFP3s masks had similar effects on SNR (≈6.2 dB with visor). The Tecmen TM-H2 had several advantages over other masks evaluated. It was reusable, allowed lipreading clues and the attenuation was similar to other FFP3s.

The SARS-CoV2 envelope differs from host cells, exposes procoagulant lipids, and is disrupted in vivo by oral rinses.

The lipid envelope of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an essential component of the virus; however, its molecular composition is undetermined. Addressing this knowledge gap could support the design of antiviral agents as well as further our understanding of viral-host protein interactions, infectivity, pathogenicity, and innate immune system clearance. Lipidomics revealed that the virus envelope comprised mainly phospholipids (PLs), with some cholesterol and sphingolipids, and with cholesterol/phospholipid ratio similar to lysosomes. Unlike cellular membranes, procoagulant amino-PLs were present on the external side of the viral envelope at levels exceeding those on activated platelets. Accordingly, virions directly promoted blood coagulation. To investigate whether these differences could enable selective targeting of the viral envelope in vivo, we tested whether oral rinses containing lipid-disrupting chemicals could reduce infectivity. Products containing PL-disrupting surfactants (such as cetylpyridinium chloride) met European virucidal standards in vitro; however, components that altered the critical micelle concentration reduced efficacy, and products containing essential oils, povidone-iodine, or chlorhexidine were ineffective. This result was recapitulated in vivo, where a 30-s oral rinse with cetylpyridinium chloride mouthwash eliminated live virus in the oral cavity of patients with coronavirus disease 19 for at least 1 h, whereas povidone-iodine and saline mouthwashes were ineffective. We conclude that the SARS-CoV-2 lipid envelope i) is distinct from the host plasma membrane, which may enable design of selective antiviral approaches; ii) contains exposed phosphatidylethanolamine and phosphatidylserine, which may influence thrombosis, pathogenicity, and inflammation; and iii) can be selectively targeted in vivo by specific oral rinses.

Hydrolytically degradable Poly (ß-amino ester) resins with tunable degradation for 3D printing by projection micro-stereolithography.

Applications of 3D printing that range from temporary medical devices to environmentally responsible manufacturing would benefit from printable resins that yield polymers with controllable material properties and degradation behavior. Towards this goal, poly(ß-amino ester) (PBAE)-diacrylate resins were investigated due to the wide range of available chemistries and tunable material properties. PBAE-diacrylate resins were synthesized from hydrophilic and hydrophobic chemistries and with varying electron densities on the ester bond to provide control over degradation. Hydrophilic PBAE-diacrylates led to degradation behaviors characteristic of bulk degradation while hydrophobic PBAE-diacrylates led to degradation behaviors dominated initially by surface degradation and then transitioned to bulk degradation. Depending on chemistry, the crosslinked PBAE-polymers exhibited a range of degradation times under accelerated conditions, from complete mass loss in 90 min to minimal mass loss at 45 days. Patterned features with 55 µm resolution were achieved across all resins, but their fidelity was dependent on PBAE-diacrylate molecular weight, reactivity, and printing parameters. In summary, simple chemical modifications in the PBAE-diacrylate resins coupled with projection microstereolithography enables high resolution 3D printed parts with similar architectures and initial properties, but widely different degradation rates and behaviors.

Latent image volumetric additive manufacturing.

Volumetric additive manufacturing (VAM) enables rapid printing into a wide range of materials, offering significant advantages over other printing technologies, with a lack of inherent layering of particular note. However, VAM suffers from striations, similar in appearance to layers, and similarly limiting applications due to mechanical and refractive index inhomogeneity, surface roughness, etc. We hypothesize that these striations are caused by a self-written waveguide effect, driven by the gelation material nonlinearity upon which VAM relies, and that they are not a direct recording of non-uniform patterning beams. We demonstrate a simple and effective method of mitigating striations via a uniform optical exposure added to the end of any VAM printing process. We show this step to additionally shorten the period from initial gelation to print completion, mitigating the problem of partially gelled parts sinking before print completion, and expanding the range of resins printable in any VAM printer.

Effects of Kinetic Chain Length on the Degradation of Poly(ß-amino ester)-Based Networks and Use in 3D Printing by Projection Microstereolithography.

Poly(ß-amino ester)-diacrylates (PBAE-dAs) are promising resins for three-dimensional (3D) printing. This study investigated the degradation of two PBAEs with different chemistries and kinetic chain lengths. PBAE-dA monomers were synthesized from benzhydrazide and poly(ethylene glycol) (A6) or butanediol (B6) diacrylate and then photopolymerized with pentaerythritol tetrakis(3-mercaptopropionate), which formed thiol-polyacrylate kinetic chains. This tetrathiol acts as a cross-linker and chain-transfer agent that controls the polyacrylate kinetic chain length. A6 networks exhibited bulk degradation, while B6 networks exhibited surface degradation, which transitioned to a combined surface and bulk degradation. Increasing the tetrathiol concentration shortened the polyacrylate kinetic chain and time-to-reverse gelation but degradation mode was unaffected. Hydrolysis occurred primarily through the ß-amino ester. As network hydrophilicity increased, the slower degrading ester in the thiol-polyacrylate chains contributed to degradation. Overall, this work demonstrates control over network degradation rate, mode of degradation, and time-to-reverse gelation in PBAE networks and their application in 3D printing.

A multi-layered strategy for COVID-19 infection prophylaxis in schools: A review of the evidence for masks, distancing, and ventilation.

Implications for the academic and interpersonal development of children and adolescents underpin a global political consensus to maintain in-classroom teaching during the ongoing COVID-19 pandemic. In support of this aim, the WHO and UNICEF have called for schools around the globe to be made safer from the risk of COVID-19 transmission. Detailed guidance is needed on how this goal can be successfully implemented in a wide variety of educational settings in order to effectively mitigate impacts on the health of students, staff, their families, and society. This review provides a comprehensive synthesis of current scientific evidence and emerging standards in relation to the use of layered prevention strategies (involving masks, distancing, and ventilation), setting out the basis for their implementation in the school environment. In the presence of increasingly infectious SARS-Cov-2 variants, in-classroom teaching can only be safely maintained through a layered strategy combining multiple protective measures. The precise measures that are needed at any point in time depend upon a number of dynamic factors, including the specific threat-level posed by the circulating variant, the level of community infection, and the political acceptability of the resultant risk. By consistently implementing appropriate prophylaxis measures, evidence shows that the risk of infection from in-classroom teaching can be dramatically reduced. Current studies indicate that wearing high-quality masks and regular testing are amongst the most important measures in preventing infection transmission; whilst effective natural and mechanical ventilation systems have been shown to reduce infection risks in classrooms by over 80%.

Structure of a zosuquidar and UIC2-bound human-mouse chimeric ABCB1.

The multidrug transporter ABCB1 (P-glycoprotein) is an ATP-binding cassette transporter that has a key role in protecting tissues from toxic insult and contributes to multidrug extrusion from cancer cells. Here, we report the near-atomic resolution cryo-EM structure of nucleotide-free ABCB1 trapped by an engineered disulfide cross-link between the nucleotide-binding domains (NBDs) and bound to the antigen-binding fragment of the human-specific inhibitory antibody UIC2 and to the third-generation ABCB1 inhibitor zosuquidar. Our structure reveals the transporter in an occluded conformation with a central, enclosed, inhibitor-binding pocket lined by residues from all transmembrane (TM) helices of ABCB1. The pocket spans almost the entire width of the lipid membrane and is occupied exclusively by two closely interacting zosuquidar molecules. The external, conformational epitope facilitating UIC2 binding is also visualized, providing a basis for its inhibition of substrate efflux. Additional cryo-EM structures suggest concerted movement of TM helices from both halves of the transporters associated with closing the NBD gap, as well as zosuquidar binding. Our results define distinct recognition interfaces of ABCB1 inhibitory agents, which may be exploited for therapeutic purposes.

Photo-tunable hydrogel mechanical heterogeneity informed by predictive transport kinetics model.

Understanding the three-dimensional (3D) mechanical and chemical properties of distinctly different, adjacent biological tissues is crucial to mimicking their complex properties with materials. 3D printing is a technique often employed to spatially control the distribution of the biomaterials, such as hydrogels, of interest, but it is difficult to print both mechanically robust (high modulus and toughness) and biocompatible (low modulus) hydrogels in a single structure. Moreover, due to the fast diffusion of mobile species during printing and nonequilibrium swelling conditions of low-solids-content hydrogels, it is challenging to form the high-fidelity structures required to mimic tissues. Here a predictive transport and swelling model is presented to model these effects and then is used to compensate for these effects during printing. This model is validated experimentally by photopatterning spatially distinct hydrogel elastic moduli using a single photo-tunable poly(ethylene glycol) (PEG) pre-polymer solution by sequentially patterning and in-diffusing fresh pre-polymer for further polymerization.

Unilateral crosstalk cancellation in normal hearing participants using bilateral bone transducers.

It is possible to psychophysically measure the phase and level of bone conducted sound at the cochleae using two bone transducers (BTs) [Mcleod and Culling (2019). J. Acoust Soc. Am. 146, 3295 - 3301]. The present work uses such measurements to improve masked thresholds by using the phase and level values to create a unilateral crosstalk cancellation system. To avoid changes in the coupling of the BT to the head, testing of tone and speech reception thresholds with and without crosstalk cancellation had to be performed immediately following the measurements without adjustment of the BT. To achieve this, a faster measurement method was created. Previously measured phase and level results were interpolated to predict likely results for new test frequencies. Testing time to collect the necessary phase and level values was reduced to approximately 15 min by exploiting listeners' previous measurements. The inter-cochlear phase difference and inter-cochlear level difference were consistent between experimental sittings in the same participant but different between participants. Addition of a crosstalk cancellation signal improved tone and speech reception thresholds for tones/speech presented with one BT and noise presented on the other by an average of 12.1 dB for tones and 13.67 dB for speech.

Reflection suppression via elastomeric films.

Transparent substrates introduce challenges in optical metrology, recording, and microscopy. Backside reflections reduce signal to noise, are recorded as artifacts, or introduce spurious signals. These reflections often need to be suppressed, but large angular and spectral bandwidths preclude the use of anti-reflection (AR) coatings. Using elastomeric materials doped with optical absorbers, we detail a method and a materials set for temporary suppression of Fresnel reflections for multiple substrates spanning wide spectral and angular bandwidths. Tuning the refractive index of the elastomer to match a substrate minimizes reflection and the addition of different absorptive dopants allow for either broadband or wavelength-selective reflection suppression. As performance is limited only by the index mismatch, both spectral and angular performances significantly exceed those of AR coatings. We demonstrate reflection suppression in excess of 30 dB spanning a bandwidth over 500 nm. After use, these light traps may be removed and reused without damaging the substrate.

High efficiency Fresnel lens design and fabrication in a two-stage photopolymer.

We show the design and fabrication of high diffraction efficiency, optically recorded gradient-index Fresnel lenses in a two-stage photopolymer. A design analysis reveals that lens f/# is limited by the material refractive index contrast, motivating use of recent high-contrast polymers. The number of pixels required for the optical exposure is typically well beyond available spatial light-modulator resolutions, motivating the use of a photolithographic mask. We use a dithered binary chrome mask with 9000×9000 pixels of 2.5 µm diameter to write lenses up to 23 mm in diameter. Lenses down to f/44 with 76% diffraction efficiency and f/79 with 83% diffraction efficiency are demonstrated.

Psychoacoustic measurement of phase and level for cross-talk cancellation using bilateral bone transducers: Comparison of methods.

Two bone-conduction hearing aids (BCHAs) could deliver improved stereo separation using cross-talk cancellation. Sound vibrations from each BCHA would be cancelled at the contralateral cochlea by an out-of-phase signal of the same level from the ipsilateral BCHA. A method to measure the level and phase required for these cancellation signals was developed and cross-validated with an established technique that combines air- and bone-conducted sound. Three participants with normal hearing wore bone transducers (BTs) on each mastoid and insert earphones. Both BTs produced a pure tone and the level and phase were adjusted in the right BT in order to cancel all perceived sound at that ear. To cross-validate, one BT was stimulated with a pure tone and participants cancelled the resultant signal at both cochleae via adjustment of the phase and level of signals from the earphones. Participants achieved cancellation using both methods between 1.5 and 8 kHz. Levels measured with each method differed by <1 dB between 3 and 5 kHz. The phase results also corresponded well for the cancelled ear (11° mean difference) but poorly for the contralateral ear (38.4° mean difference). The first method is transferable to patients with middle-ear dysfunction, but covers a limited frequency range.

MRCZ - A file format for cryo-TEM data with fast compression.

The introduction of fast CMOS detectors is moving the field of transmission electron microscopy into the computer science field of big data. Automated data pipelines control the instrument and initial processing steps which imposes more onerous data transfer and archiving requirements. Here we conduct a technical demonstration whereby storage and read/write times are improved 10× at a dose rate of 1 e-/pix/frame for data from a Gatan K2 direct-detection device by combination of integer decimation and lossless compression. The example project is hosted at github.com/em-MRCZ and released under the BSD license.

A phase I trial of the γ-secretase inhibitor MK-0752 in combination with gemcitabine in patients with pancreatic ductal adenocarcinoma.

BACKGROUND: The Notch pathway is frequently activated in cancer. Pathway inhibition by γ-secretase inhibitors has been shown to be effective in pre-clinical models of pancreatic cancer, in combination with gemcitabine. METHODS: A multi-centre, non-randomised Bayesian adaptive design study of MK-0752, administered per os weekly, in combination with gemcitabine administered intravenously on days 1, 8 and 15 (28 day cycle) at 800 or 1000 mg m-2, was performed to determine the safety of combination treatment and the recommended phase 2 dose (RP2D). Secondary and tertiary objectives included tumour response, plasma and tumour MK-0752 concentration, and inhibition of the Notch pathway in hair follicles and tumour. RESULTS: Overall, 44 eligible patients (performance status 0 or 1 with adequate organ function) received gemcitabine and MK-0752 as first or second line treatment for pancreatic cancer. RP2Ds of MK-0752 and gemcitabine as single agents could be combined safely. The Bayesian algorithm allowed further dose escalation, but pharmacokinetic analysis showed no increase in MK-0752 AUC (area under the curve) beyond 1800 mg once weekly. Tumour response evaluation was available in 19 patients; 13 achieved stable disease and 1 patient achieved a confirmed partial response. CONCLUSIONS: Gemcitabine and a γ-secretase inhibitor (MK-0752) can be combined at their full, single-agent RP2Ds.

Transport-of-intensity-based phase imaging to quantify the refractive index response of 3D direct-write lithography.

Precise direct-write lithography of 3D waveguides or diffractive structures within the volume of a photosensitive material is hindered by the lack of metrology that can yield predictive models for the micron-scale refractive index profile in response to a range of exposure conditions. We apply the transport of intensity equation in conjunction with confocal reflection microscopy to capture the complete spatial frequency spectrum of isolated 10 µm-scale gradient-refractive index structures written by single-photon direct-write laser lithography. The model material, a high-performance two-component photopolymer, is found to be linear, integrating, and described by a single master dose response function. The sharp saturation of this function is used to demonstrate nearly binary, flat-topped waveguide profiles in response to a Gaussian focus.

Multiple patterning of holographic photopolymers for increased refractive index contrast.

We demonstrate that multiple exposures of a two-component holographic photopolymer can quadruple the refractive index contrast of the material beyond the single-exposure saturation limit. Quantitative phase microscopy of isolated structures written by laser direct-write lithography is used to characterize the process. This technique reveals that multiple exposures are made possible by diffusion of the chemical components consumed during writing into the previously exposed regions. The ultimate index contrast is shown to be limited by the solubility of fresh components into the multiply exposed region.

In situ biasing and off-axis electron holography of a ZnO nanowire.

Quantitative characterization of electrically active dopants and surface charges in nano-objects is challenging, since most characterization techniques using electrons [1-3], ions [4] or field ionization effects [5-7] study the chemical presence of dopants, which are not necessarily electrically active. We perform cathodoluminescence and voltage contrast experiments on a contacted and biased ZnO nanowire with a Schottky contact and measure the depletion length as a function of reverse bias. We compare these results with state-of-the-art off-axis electron holography in combination with electrical in situ biasing on the same nanowire. The extension of the depletion length under bias observed in scanning electron microscopy based techniques is unusual as it follows a linear rather than square root dependence, and is therefore difficult to model by bulk equations or finite element simulations. In contrast, the analysis of the axial depletion length observed by holography may be compared with three-dimensional simulations, which allows estimating an n-doping level of 1 × 1018 cm-3 and negative sidewall surface charge of 2.5 × 1012 cm-2 of the nanowire, resulting in a radial surface depletion to a depth of 36 nm. We found excellent agreement between the simulated diameter of the undepleted core and the active thickness observed in the experimental data. By combining TEM holography experiments and finite element simulation of the NW electrostatics, the bulk-like character of the nanowire core is revealed.