Cryo-electron ptychography: Applications and potential in biological characterisation.

There is a clear need for developments in characterisation techniques that provide detailed information about structure-function relationships in biology. Using electron microscopy to achieve high resolution while maintaining a broad field of view remains a challenge, particularly for radiation-sensitive specimens where the signal-to-noise ratio required to maintain structural integrity is limited by low electron fluence. In this review, we explore the potential of cryogenic electron ptychography as an alternative method for characterising biological systems under low-fluence conditions. Using this method with increased information content from multiple sampled regions of interest potentially allows 3D reconstruction with far fewer particles than required in conventional cryo-electron microscopy. This is important for achieving higher resolution in systems where distributions of homogeneous single particles are difficult to obtain. We discuss the progress, limitations, and potential areas for future development of this approach for both single particle analysis and applications to heterogeneous large objects.

Cryogenic electron ptychographic single particle analysis with wide bandwidth information transfer.

Advances in cryogenic transmission electron microscopy have revolutionised the determination of many macromolecular structures at atomic or near-atomic resolution. This method is based on conventional defocused phase contrast imaging. However, it has limitations of weaker contrast for small biological molecules embedded in vitreous ice, in comparison with cryo-ptychography, which shows increased contrast. Here we report a single-particle analysis based on the use of ptychographic reconstruction data, demonstrating that three dimensional reconstructions with a wide information transfer bandwidth can be recovered by Fourier domain synthesis. Our work suggests future applications in otherwise challenging single particle analyses, including small macromolecules and heterogeneous or flexible particles. In addition structure determination in situ within cells without the requirement for protein purification and expression may be possible.

From Puzzle to Progress: How Engaging With Neurodiversity Can Improve Cognitive Science.

In cognitive science, there is a tacit norm that phenomena such as cultural variation or synaesthesia are worthy examples of cognitive diversity that contribute to a better understanding of cognition, but that other forms of cognitive diversity (e.g., autism, attention deficit hyperactivity disorder/ADHD, and dyslexia) are primarily interesting only as examples of deficit, dysfunction, or impairment. This status quo is dehumanizing and holds back much-needed research. In contrast, the neurodiversity paradigm argues that such experiences are not necessarily deficits but rather are natural reflections of biodiversity. Here, we propose that neurodiversity is an important topic for future research in cognitive science. We discuss why cognitive science has thus far failed to engage with neurodiversity, why this gap presents both ethical and scientific challenges for the field, and, crucially, why cognitive science will produce better theories of human cognition if the field engages with neurodiversity in the same way that it values other forms of cognitive diversity. Doing so will not only empower marginalized researchers but will also present an opportunity for cognitive science to benefit from the unique contributions of neurodivergent researchers and communities.

Sensory modality and spoken language shape reading network in blind readers of Braille.

The neural basis of reading is highly consistent across many languages and scripts. Are there alternative neural routes to reading? How does the sensory modality of symbols (tactile vs. visual) influence their neural representations? We examined these questions by comparing reading of visual print (sighted group, n = 19) and tactile Braille (congenitally blind group, n = 19). Blind and sighted readers were presented with written (words, consonant strings, non-letter shapes) and spoken stimuli (words, backward speech) that varied in word-likeness. Consistent with prior work, the ventral occipitotemporal cortex (vOTC) was active during Braille and visual reading. A posterior/anterior vOTC word-form gradient was observed only in sighted readers with more anterior regions preferring larger orthographic units (words). No such gradient was observed in blind readers. Consistent with connectivity predictions, in blind compared to sighted readers, posterior parietal cortices were recruited to a greater degree and contained word-preferring patches. Lateralization of Braille in blind readers was predicted by laterality of spoken language and reading hand. The effect of spoken language increased along a cortical hierarchy, whereas effect of reading hand waned. These results suggested that the neural basis of reading is influenced by symbol modality and spoken language and support connectivity-based views of cortical function.

Trainable segmentation for transmission electron microscope images of inorganic nanoparticles.

We present a trainable segmentation method implemented within the python package ParticleSpy. The method takes user labelled pixels, which are used to train a classifier and segment images of inorganic nanoparticles from transmission electron microscope images. This implementation is based on the trainable Waikato Environment for Knowledge Analysis (WEKA) segmentation, but is written in python, allowing a large degree of flexibility and meaning it can be easily expanded using other python packages. We find that trainable segmentation offers better accuracy than global or local thresholding methods and requires as few as 100 user-labelled pixels to produce an accurate segmentation. Trainable segmentation presents a balance of accuracy and training time between global/local thresholding and neural networks, when used on transmission electron microscope images of nanoparticles. We also quantitatively investigate the effectiveness of the components of trainable segmentation, its filter kernels and classifiers, in order to demonstrate the use cases for the different filter kernels in ParticleSpy and the most accurate classifiers for different data types. A set of filter kernels is identified that are effective in distinguishing particles from background but that retain dissimilar features. In terms of classifiers, we find that different classifiers perform optimally for different image contrast; specifically, a random forest classifier performs best for high-contrast ADF images, but that QDA and Gaussian Naïve Bayes classifiers perform better for low-contrast TEM images.

Measurement of the size, shape and composition of nanoparticles is routinely performed using transmission electron microscopy and related techniques. Typically, distinguishing particles from the background in an image is performed using the intensity of each pixel, creating two sets of pixels to separate particles from background. However, this separation of intensity can be difficult if the contrast in an image is low, or if the intensity of the background varies significantly. In this study, an approach that takes into account additional image features (such as boundaries and texture) was investigated to study electron microscope images of metallic nanoparticles. In this 'trainable segmentation' approach, the user labels examples of particle and background pixels in order to train a machine learning algorithm to distinguish between particles and background. The performance of different machine learning algorithms was investigated, in addition to the effect of using different features to aid the segmentation. Overall, a trainable segmentation approach was found to perform better than use of an intensity threshold to distinguish between particles and background in electron microscope images.

Applications of deep learning in electron microscopy.

We review the growing use of machine learning in electron microscopy (EM) driven in part by the availability of fast detectors operating at kiloHertz frame rates leading to large data sets that cannot be processed using manually implemented algorithms. We summarize the various network architectures and error metrics that have been applied to a range of EM-related problems including denoising and inpainting. We then provide a review of the application of these in both physical and life sciences, highlighting how conventional networks and training data have been specifically modified for EM.

Moral dilemmas and trust in leaders during a global health crisis.

Trust in leaders is central to citizen compliance with public policies. One potential determinant of trust is how leaders resolve conflicts between utilitarian and non-utilitarian ethical principles in moral dilemmas. Past research suggests that utilitarian responses to dilemmas can both erode and enhance trust in leaders: sacrificing some people to save many others ('instrumental harm') reduces trust, while maximizing the welfare of everyone equally ('impartial beneficence') may increase trust. In a multi-site experiment spanning 22 countries on six continents, participants (N = 23,929) completed self-report (N = 17,591) and behavioural (N = 12,638) measures of trust in leaders who endorsed utilitarian or non-utilitarian principles in dilemmas concerning the COVID-19 pandemic. Across both the self-report and behavioural measures, endorsement of instrumental harm decreased trust, while endorsement of impartial beneficence increased trust. These results show how support for different ethical principles can impact trust in leaders, and inform effective public communication during times of global crisis. PROTOCOL REGISTRATION STATEMENT: The Stage 1 protocol for this Registered Report was accepted in principle on 13 November 2020. The protocol, as accepted by the journal, can be found at https://doi.org/10.6084/m9.figshare.13247315.v1 .

Antimony thin films demonstrate programmable optical nonlinearity.

The use of metals of nanometer dimensions to enhance and manipulate light-matter interactions for emerging plasmonics-enabled nanophotonic and optoelectronic applications is an interesting yet not highly explored area of research beyond plasmonics. Even more importantly, the concept of an active metal that can undergo an optical nonvolatile transition has not been explored. Here, we demonstrate that antimony (Sb), a pure metal, is optically distinguishable between two programmable states as nanoscale thin films. We show that these states, corresponding to the crystalline and amorphous phases of the metal, are stable at room temperature. Crucially from an application standpoint, we demonstrate both its optoelectronic modulation capabilities and switching speed using single subpicosecond pulses. The simplicity of depositing a single metal portends its potential for use in any optoelectronic application where metallic conductors with an actively tunable state are important.

Atomic-scale microstructure of metal halide perovskite.

Hybrid organic-inorganic perovskites have high potential as materials for solar energy applications, but their microscopic properties are still not well understood. Atomic-resolution scanning transmission electron microscopy has provided invaluable insights for many crystalline solar cell materials, and we used this method to successfully image formamidinium lead triiodide [CH(NH2)2PbI3] thin films with a low dose of electron irradiation. Such images reveal a highly ordered atomic arrangement of sharp grain boundaries and coherent perovskite/PbI2 interfaces, with a striking absence of long-range disorder in the crystal. We found that beam-induced degradation of the perovskite leads to an initial loss of formamidinium [CH(NH2)2 +] ions, leaving behind a partially unoccupied perovskite lattice, which explains the unusual regenerative properties of these materials. We further observed aligned point defects and climb-dissociated dislocations. Our findings thus provide an atomic-level understanding of technologically important lead halide perovskites.

From shape to meaning: Evidence for multiple fast feedforward hierarchies of concept processing in the human brain.

A number of fMRI studies have provided support for the existence of multiple concept representations in areas of the brain such as the anterior temporal lobe (ATL) and inferior parietal lobule (IPL). However, the interaction among different conceptual representations remains unclear. To better understand the dynamics of how the brain extracts meaning from sensory stimuli, we conducted a human high-density electroencephalography (EEG) study in which we first trained participants to associate pseudowords with various animal and tool concepts. After training, multivariate pattern classification of EEG signals in sensor and source space revealed the representation of both animal and tool concepts in the left ATL and tool concepts within the left IPL within 250 â€‹ms. Finally, we used Granger Causality analyses to show that orthography-selective sensors directly modulated activity in the parietal-tool selective cluster. Together, our results provide evidence for distinct but parallel "perceptual-to-conceptual" feedforward hierarchies in the brain.

Low-dose phase retrieval of biological specimens using cryo-electron ptychography.

Cryo-electron microscopy is an essential tool for high-resolution structural studies of biological systems. This method relies on the use of phase contrast imaging at high defocus to improve information transfer at low spatial frequencies at the expense of higher spatial frequencies. Here we demonstrate that electron ptychography can recover the phase of the specimen with continuous information transfer across a wide range of the spatial frequency spectrum, with improved transfer at lower spatial frequencies, and as such is more efficient for phase recovery than conventional phase contrast imaging. We further show that the method can be used to study frozen-hydrated specimens of rotavirus double-layered particles and HIV-1 virus-like particles under low-dose conditions (5.7 e/Å2) and heterogeneous objects in an Adenovirus-infected cell over large fields of view (1.14 × 1.14 µm), thus making it suitable for studies of many biologically important structures.

Filamentary High-Resolution Electrical Probes for Nanoengineering.

Confining electric fields to a nanoscale region is challenging yet crucial for applications such as high-resolution probing of electrical properties of materials and electric-field manipulation of nanoparticles. State-of-the-art techniques involving atomic force microscopy typically have a lateral resolution limit of tens of nanometers due to limitations in the probe geometry and stray electric fields that extend over space. Engineering the probes is the most direct approach to improving this resolution limit. However, current methods to fabricate high-resolution probes, which can effectively confine the electric fields laterally, involve expensive and sophisticated probe manipulation, which has limited the use of this approach. Here, we demonstrate that nanoscale phase switching of configurable thin films on probes can result in high-resolution electrical probes. These configurable coatings can be both germanium-antimony-tellurium (GST) as well as amorphous-carbon, materials known to undergo electric field-induced nonvolatile, yet reversible switching. By forming a localized conductive filament through phase transition, we demonstrate a spatial resolution of electrical field beyond the geometrical limitations of commercial platinum probes (i.e., an improvement of ∼48%). We then utilize these confined electric fields to manipulate nanoparticles with single nanoparticle precision via dielectrophoresis. Our results advance the field of nanomanufacturing and metrology with direct applications for pick and place assembly at the nanoscale.

Knowledge of animal appearance among sighted and blind adults.

How does first-person sensory experience contribute to knowledge? Contrary to the suppositions of early empiricist philosophers, people who are born blind know about phenomena that cannot be perceived directly, such as color and light. Exactly what is learned and how remains an open question. We compared knowledge of animal appearance across congenitally blind (n = 20) and sighted individuals (two groups, n = 20 and n = 35) using a battery of tasks, including ordering (size and height), sorting (shape, skin texture, and color), odd-one-out (shape), and feature choice (texture). On all tested dimensions apart from color, sighted and blind individuals showed substantial albeit imperfect agreement, suggesting that linguistic communication and visual perception convey partially redundant appearance information. To test the hypothesis that blind individuals learn about appearance primarily by remembering sighted people's descriptions of what they see (e.g., "elephants are gray"), we measured verbalizability of animal shape, texture, and color in the sighted. Contrary to the learn-from-description hypothesis, blind and sighted groups disagreed most about the appearance dimension that was easiest for sighted people to verbalize: color. Analysis of disagreement patterns across all tasks suggest that blind individuals infer physical features from non-appearance properties of animals such as folk taxonomy and habitat (e.g., bats are textured like mammals but shaped like birds). These findings suggest that in the absence of sensory access, structured appearance knowledge is acquired through inference from ontological kind.

Development of the Visual Word Form Area Requires Visual Experience: Evidence from Blind Braille Readers.

Learning to read causes the development of a letter- and word-selective region known as the visual word form area (VWFA) within the human ventral visual object stream. Why does a reading-selective region develop at this anatomical location? According to one hypothesis, the VWFA develops at the nexus of visual inputs from retinotopic cortices and linguistic input from the frontotemporal language network because reading involves extracting linguistic information from visual symbols. Surprisingly, the anatomical location of the VWFA is also active when blind individuals read Braille by touch, suggesting that vision is not required for the development of the VWFA. In this study, we tested the alternative prediction that VWFA development is in fact influenced by visual experience. We predicted that in the absence of vision, the "VWFA" is incorporated into the frontotemporal language network and participates in high-level language processing. Congenitally blind (n = 10, 9 female, 1 male) and sighted control (n = 15, 9 female, 6 male), male and female participants each took part in two functional magnetic resonance imaging experiments: (1) word reading (Braille for blind and print for sighted participants), and (2) listening to spoken sentences of different grammatical complexity (both groups). We find that in blind, but not sighted participants, the anatomical location of the VWFA responds both to written words and to the grammatical complexity of spoken sentences. This suggests that in blindness, this region takes on high-level linguistic functions, becoming less selective for reading. More generally, the current findings suggest that experience during development has a major effect on functional specialization in the human cortex.SIGNIFICANCE STATEMENT The visual word form area (VWFA) is a region in the human cortex that becomes specialized for the recognition of written letters and words. Why does this particular brain region become specialized for reading? We tested the hypothesis that the VWFA develops within the ventral visual stream because reading involves extracting linguistic information from visual symbols. Consistent with this hypothesis, we find that in congenitally blind Braille readers, but not sighted readers of print, the VWFA region is active during grammatical processing of spoken sentences. These results suggest that visual experience contributes to VWFA specialization, and that different neural implementations of reading are possible.

Formation of Klein Edge Doublets from Graphene Monolayers.

With increasing possibilities for applications of graphene, it is essential to fully characterize the rich topological variations in graphene edge structures. Using aberration-corrected transmission electron microscopy, dangling carbon doublets at the edge of monolayer graphene crystals have been observed. Unlike the single-atom Klein edge often found at zigzag edges, these carbon dimers were observed in various edge structure environments, but most frequently on the more stable armchair edges. Observation of this Klein edge doublet over time reveals that its existence enhances the stability of armchair edges and is a route to atom abstraction on zigzag edges.

The development of a 200 kV monochromated field emission electron source.

We report the development of a monochromator for an intermediate-voltage aberration-corrected electron microscope suitable for operation in both STEM and TEM imaging modes. The monochromator consists of two Wien filters with a variable energy selecting slit located between them and is located prior to the accelerator. The second filter cancels the energy dispersion produced by the first filter and after energy selection forms a round monochromated, achromatic probe at the specimen plane. The ultimate achievable energy resolution has been measured as 36 meV at 200 kV and 26 meV at 80 kV. High-resolution Annular Dark Field STEM images recorded using a monochromated probe resolve Si-Si spacings of 135.8 pm using energy spreads of 218 meV at 200 kV and 217 meV at 80 kV respectively. In TEM mode an improvement in non-linear spatial resolution to 64 pm due to the reduction in the effects of partial temporal coherence has been demonstrated using broad beam illumination with an energy spread of 134 meV at 200 kV.

Unusual stacking variations in liquid-phase exfoliated transition metal dichalcogenides.

Liquid-phase exfoliation of layered materials offers a large-scale approach toward the synthesis of 2D nanostructures. Structural properties of materials can however change during transition from bulk to the 2D state. Any such changes must be examined and understood for successful implementation of 2D nanostructures. In this work, we demonstrate nonbulk stacking sequences in the few-layer MoS2 and WS2 nanoflakes produced by liquid-phase exfoliation. Our analysis shows that nonbulk stacking sequences can be derived from its bulk counterparts by translational shifts of the layers. No structural changes within the layers were observed. Twenty-seven MoS2 and five WS2 nanoflakes were imaged and analyzed. Nine MoS2 and four WS2 nanoflakes displayed nonbulk stacking. Such dominance of the nonbulk stacking suggests high possibility of unusual stacking sequences in other 2D nanostructures. Notably, the electronic structure of some non bulk stacked bilayers presents characteristics which are uncommon to either the bulk phase or the single monolayer, for instance, a spin-split conduction band bottom. Our main characterization technique was annular dark-field scanning transmission electron microscopy, which offers direct and reliable imaging of atomic columns. The stacking characterization approach employed here can be readily applied toward other few-layer transition metal chalcogenides and oxides.

Impurity induced non-bulk stacking in chemically exfoliated h-BN nanosheets.

Structural characterization of 2D nanomaterials is an important step towards their future applications. In this work we carried out imaging and structural analysis of 2D h-BN produced by chemical-exfoliation, emphasizing the stacking order in few-layer sheets. Our analysis, for the first time has shown conclusively that non-bulk stacking can exist in 2D h-BN.