Square condenser apertures for square cameras in low-dose transmission electron microscopy.

In transmission electron microscopy (TEM), cameras are square or rectangular but beams are round so the circular lobes irradiate adjacent areas, precluding further neighboring acquisition for beam-sensitive samples. We present condenser aperture plates with square and rectangular shapes that improve the efficiency of area usage by 70% and enhance montage imaging for beam-sensitive specimens. We demonstrate the compatibility of these condenser aperture plates with high-resolution cryogenic TEM by reconstructing a 1.8-Å map of equine apo-ferritin.

Some, but not all, cochlear implant users prefer music stimuli with congruent haptic stimulation.

Cochlear implant (CI) users often report being unsatisfied by music listening through their hearing device. Vibrotactile stimulation could help alleviate those challenges. Previous research has shown that musical stimuli was given higher preference ratings by normal-hearing listeners when concurrent vibrotactile stimulation was congruent in intensity and timing with the corresponding auditory signal compared to incongruent. However, it is not known whether this is also the case for CI users. Therefore, in this experiment, we presented 18 CI users and 24 normal-hearing listeners with five melodies and five different audio-to-tactile maps. Each map varied the congruence between the audio and tactile signals related to intensity, fundamental frequency, and timing. Participants were asked to rate the maps from zero to 100, based on preference. It was shown that almost all normal-hearing listeners, as well as a subset of the CI users, preferred tactile stimulation, which was congruent with the audio in intensity and timing. However, many CI users had no difference in preference between timing aligned and timing unaligned stimuli. The results provide evidence that vibrotactile music enjoyment enhancement could be a solution for some CI users; however, more research is needed to understand which CI users can benefit from it most.

Biochemical Characterization of Caenorhabditis elegans Ferritins.

The nematode Caenorhabditis elegans contains genes for two types of ferritin (ftn-1 and ftn-2) that express FTN-1 and FTN-2. We have expressed and purified both proteins and characterized them by X-ray crystallography, cryo-electron microscopy, transmission electron microscopy, dynamic light scattering, and kinetically by oxygen electrode and UV-vis spectroscopy. Both show ferroxidase activity, but although they have identical ferroxidase active sites, FTN-2 is shown to react approximately 10 times faster than FTN-1, with L-type ferritin character over longer time periods. We hypothesize that the large variation in rate may be due to differences in the three- and four-fold channels into the interior of the protein 24-mer. FTN-2 is shown to have a wider entrance into the three-fold channel than FTN-1. Additionally, the charge gradient through the channel of FTN-2 is more pronounced, with Asn and Gln residues in FTN-1 replaced by Asp and Glu residues in FTN-2. Both FTN-1 and FTN-2 have an Asn residue near the ferroxidase active site that is a Val in most other species, including human H ferritin. This Asn residue has been observed before in ferritin from the marine pennate diatom Pseudo-mitzchia multiseries. By replacing this Asn residue with a Val in FTN-2, we show that the reactivity decreases over long time scales. We therefore propose that Asn106 is involved in iron transport from the ferroxidase active site to the central cavity of the protein.

Strain fields in twisted bilayer graphene.

Van der Waals heteroepitaxy allows deterministic control over lattice mismatch or azimuthal orientation between atomic layers to produce long-wavelength superlattices. The resulting electronic phases depend critically on the superlattice periodicity and localized structural deformations that introduce disorder and strain. In this study we used Bragg interferometry to capture atomic displacement fields in twisted bilayer graphene with twist angles <2°. Nanoscale spatial fluctuations in twist angle and uniaxial heterostrain were statistically evaluated, revealing the prevalence of short-range disorder in moiré heterostructures. By quantitatively mapping strain tensor fields, we uncovered two regimes of structural relaxation and disentangled the electronic contributions of constituent rotation modes. Further, we found that applied heterostrain accumulates anisotropically in saddle-point regions, generating distinctive striped strain phases. Our results establish the reconstruction mechanics underpinning the twist-angle-dependent electronic behaviour of twisted bilayer graphene and provide a framework for directly visualizing structural relaxation, disorder and strain in moiré materials.

Simulation of winter wheat response to variable sowing dates and densities in a high-yielding environment.

Crop multi-model ensembles (MME) have proven to be effective in increasing the accuracy of simulations in modelling experiments. However, the ability of MME to capture crop responses to changes in sowing dates and densities has not yet been investigated. These management interventions are some of the main levers for adapting cropping systems to climate change. Here, we explore the performance of a MME of 29 wheat crop models to predict the effect of changing sowing dates and rates on yield and yield components, on two sites located in a high-yielding environment in New Zealand. The experiment was conducted for 6 years and provided 50 combinations of sowing date, sowing density and growing season. We show that the MME simulates seasonal growth of wheat well under standard sowing conditions, but fails under early sowing and high sowing rates. The comparison between observed and simulated in-season fraction of intercepted photosynthetically active radiation (FIPAR) for early sown wheat shows that the MME does not capture the decrease of crop above ground biomass during winter months due to senescence. Models need to better account for tiller competition for light, nutrients, and water during vegetative growth, and early tiller senescence and tiller mortality, which are exacerbated by early sowing, high sowing densities, and warmer winter temperatures.

Unified fast reconstruction algorithm for conventional, phase-contrast, and diffraction tomography.

A unified method for three-dimensional reconstruction of objects from transmission images collected at multiple illumination directions is described. The method may be applicable to experimental conditions relevant to absorption-based, phase-contrast, or diffraction imaging using x rays, electrons, and other forms of penetrating radiation or matter waves. Both the phase retrieval (also known as contrast transfer function correction) and the effect of Ewald sphere curvature (in the cases with a shallow depth of field and significant in-object diffraction) are incorporated in the proposed algorithm and can be taken into account. Multiple scattering is not treated explicitly but can be mitigated as a result of angular averaging that constitutes an essential feature of the method. The corresponding numerical algorithm is based on three-dimensional gridding which allows for fast computational implementation, including a straightforward parallelization. The algorithm can be used with any scanning geometry involving plane-wave illumination. A software code implementing the proposed algorithm has been developed, tested on simulated and experimental image data, and made publicly available.

Association between frailty and clinical outcomes in hospitalised patients requiring Code Blue activation.

BACKGROUND: Code Blues allow a rapid, hospital wide response to acutely deteriorating patients. The concept of frailty is being increasingly recognised as an important element in determining outcomes of critically ill patients. We hypothesised that increasing frailty would be associated with worse outcomes following a Code Blue. AIMS: To investigate the association between increasing frailty and outcomes of Code Blues. METHODS: Single-centre retrospective design of patients admitted to Frankston Hospital in Australia between 1 January 2013 and 31 December 2017 who triggered a Code Blue. Frailty evaluation was made based on electronic medical records as were the details and the outcomes of the Code Blue. The primary outcome measure was a composite of hospital mortality or Cerebral Performance Categories scale ≥3. Secondary outcomes included the immediate outcome of the Code Blue and hospital mortality. RESULTS: One hundred and forty-eight of 911 screened patients were included in the final analysis. Seventy-three were deemed 'frail' and the remainder deemed 'fit'. Seventy-eight percent of frail patients reached the primary outcome, compared with 41% of fit patients (P < 0.001). Multivariable analysis demonstrated frailty to be associated with primary outcome (odds ratio = 2.87; 95% confidence interval (CI) 1.28-6.44; P = 0.01). A cardiac aetiology for the Code Blue was also associated with an increased odds of primary outcome (OR = 3.52; 95% CI 1.51-8.05; P = 0.004). CONCLUSIONS: Frailty is independently associated with the composite outcome of hospital mortality or severe disability following a Code Blue. Frailty is an important tool in prognostication for these patients and might aid in discussions regarding treatment limitations.

Frailty and mortality associations in patients with COVID-19: a systematic review and meta-analysis.

BACKGROUND: Observational data during the pandemic have demonstrated mixed associations between frailty and mortality. AIM: To examine associations between frailty and short-term mortality in patients hospitalised with coronavirus disease 2019 (COVID-19). METHODS: In this systematic review and meta-analysis, we searched PubMed, Embase and the COVID-19 living systematic review from 1 December 2019 to 15 July 2021. Studies reporting mortality and frailty scores in hospitalised patients with COVID-19 (age ≥18 years) were included. Data on patient demographics, short-term mortality (in hospital or within 30 days), intensive care unit (ICU) admission and need for invasive mechanical ventilation (IMV) were extracted. The quality of studies was assessed using the Newcastle-Ottawa Scale. RESULTS: Twenty-five studies reporting 34 628 patients were included. Overall, 26.2% (n = 9061) died. Patients who died were older (76.7 ± 9.6 vs 69.2 ± 13.4), more likely male (risk ratio (RR) = 1.08; 95% confidence interval (CI): 1.06-1.11) and had more comorbidities. Fifty-eight percent of patients were frail. Adjusting for age, there was no difference in short-term mortality between frail and non-frail patients (RR = 1.04; 95% CI: 0.84-1.28). The non-frail patients were commonly admitted to ICU (27.2% (4256/15639) vs 29.1% (3567/12274); P = 0.011) and had a higher mortality risk (RR = 1.63; 95% CI: 1.30-2.03) than frail patients. Among patients receiving IMV, there was no difference in mortality between frail and non-frail (RR = 1.62; 95% CI 0.93-2.77). CONCLUSION: This systematic review did not demonstrate an independent association between frailty status and short-term mortality in patients with COVID-19. Patients with frailty were less commonly admitted to ICU and non-frail patients were more likely to receive IMV and had higher mortality risk. This finding may be related to allocation decisions for patients with frailty amidst the pandemic.

A Method for High-Resolution Three-Dimensional Reconstruction with Ewald Sphere Curvature Correction from Transmission Electron Images.

A method for three-dimensional reconstruction of objects from defocused images collected at multiple illumination directions in high-resolution transmission electron microscopy is presented. The method effectively corrects for the Ewald sphere curvature by taking into account the in-particle propagation of the electron beam. Numerical simulations demonstrate that the proposed method is capable of accurately reconstructing biological molecules or nanoparticles from high-resolution defocused images under conditions achievable in single-particle electron cryo-microscopy or electron tomography with realistic radiation doses, non-trivial aberrations, multiple scattering, and other experimentally relevant factors. The physics of the method is based on the well-known Diffraction Tomography formalism, but with the phase-retrieval step modified to include a conjugation of the phase (i.e., multiplication of the phase by a negative constant). At each illumination direction, numerically backpropagating the beam with the conjugated phase produces maximum contrast at the location of individual atoms in the molecule or nanoparticle. The resultant algorithm, Conjugated Holographic Reconstruction, can potentially be incorporated into established software tools for single-particle analysis, such as, for example, RELION or FREALIGN, in place of the conventional contrast transfer function correction procedure, in order to account for the Ewald sphere curvature and improve the spatial resolution of the three-dimensional reconstruction.

Effect of audio-tactile congruence on vibrotactile music enhancement.

Music listening experiences can be enhanced with tactile vibrations. However, it is not known which parameters of the tactile vibration must be congruent with the music to enhance it. Devices that aim to enhance music with tactile vibrations often require coding an acoustic signal into a congruent vibrotactile signal. Therefore, understanding which of these audio-tactile congruences are important is crucial. Participants were presented with a simple sine wave melody through supra-aural headphones and a haptic actuator held between the thumb and forefinger. Incongruent versions of the stimuli were made by randomizing physical parameters of the tactile stimulus independently of the auditory stimulus. Participants were instructed to rate the stimuli against the incongruent stimuli based on preference. It was found making the intensity of the tactile stimulus incongruent with the intensity of the auditory stimulus, as well as misaligning the two modalities in time, had the biggest negative effect on ratings for the melody used. Future vibrotactile music enhancement devices can use time alignment and intensity congruence as a baseline coding strategy, which improved strategies can be tested against.

Development of an Australian behavioural method for assessing listening task difficulty at high speech intelligibility levels.

OBJECTIVE: To develop and validate an Australian version of a behavioural test for assessing listening task difficulty at high speech intelligibility levels. DESIGN: In the SWIR-Aus test, listeners perform two tasks: identify the last word of each of seven sentences in a list and recall the identified words after each list. First, the test material was developed by creating seven-sentence lists with similar final-word features. Then, for the validation, participant's performance on the SWIR-Aus test was compared when a binary mask noise reduction algorithm was on and off. STUDY SAMPLE: All participants in this study had normal hearing thresholds. Nine participants (23.8-56.0 years) participated in the characterisation of the speech material. Another thirteen participants (18.4-59.1 years) participated in a pilot test to determine the SNR to use at the validation stage. Finally, twenty-four new participants (20.0-56.9 years) participated in the validation of the test. RESULTS: The results of the validation of the test showed that recall and identification scores were significantly better when the binary mask noise reduction algorithm was on compared to off. CONCLUSIONS: The SWIR-Aus test was developed using Australian speech material and can be used for assessing task difficulty at high speech intelligibility levels.

Scattering Matrix Determination in Crystalline Materials from 4D Scanning Transmission Electron Microscopy at a Single Defocus Value.

Recent work has revived interest in the scattering matrix formulation of electron scattering in transmission electron microscopy as a stepping stone toward atomic-resolution structure determination in the presence of multiple scattering. We discuss ways of visualizing the scattering matrix that make its properties clear. Through a simulation-based case study incorporating shot noise, we shown how regularizing on this continuity enables the scattering matrix to be reconstructed from 4D scanning transmission electron microscopy (STEM) measurements from a single defocus value. Intriguingly, for crystalline samples, this process also yields the sample thickness to nanometer accuracy with no a priori knowledge about the sample structure. The reconstruction quality is gauged by using the reconstructed scattering matrix to simulate STEM images at defocus values different from that of the data from which it was reconstructed.

Optimizing Experimental Conditions for Accurate Quantitative Energy-Dispersive X-ray Analysis of Interfaces at the Atomic Scale.

The invention of silicon drift detectors has resulted in an unprecedented improvement in detection efficiency for energy-dispersive X-ray (EDX) spectroscopy in the scanning transmission electron microscope. The result is numerous beautiful atomic-scale maps, which provide insights into the internal structure of a variety of materials. However, the task still remains to understand exactly where the X-ray signal comes from and how accurately it can be quantified. Unfortunately, when crystals are aligned with a low-order zone axis parallel to the incident beam direction, as is necessary for atomic-resolution imaging, the electron beam channels. When the beam becomes localized in this way, the relationship between the concentration of a particular element and its spectroscopic X-ray signal is generally nonlinear. Here, we discuss the combined effect of both spatial integration and sample tilt for ameliorating the effects of channeling and improving the accuracy of EDX quantification. Both simulations and experimental results will be presented for a perovskite-based oxide interface. We examine how the scattering and spreading of the electron beam can lead to erroneous interpretation of interface compositions, and what approaches can be made to improve our understanding of the underlying atomic structure.

py4DSTEM: A Software Package for Four-Dimensional Scanning Transmission Electron Microscopy Data Analysis.

Scanning transmission electron microscopy (STEM) allows for imaging, diffraction, and spectroscopy of materials on length scales ranging from microns to atoms. By using a high-speed, direct electron detector, it is now possible to record a full two-dimensional (2D) image of the diffracted electron beam at each probe position, typically a 2D grid of probe positions. These 4D-STEM datasets are rich in information, including signatures of the local structure, orientation, deformation, electromagnetic fields, and other sample-dependent properties. However, extracting this information requires complex analysis pipelines that include data wrangling, calibration, analysis, and visualization, all while maintaining robustness against imaging distortions and artifacts. In this paper, we present py4DSTEM, an analysis toolkit for measuring material properties from 4D-STEM datasets, written in the Python language and released with an open-source license. We describe the algorithmic steps for dataset calibration and various 4D-STEM property measurements in detail and present results from several experimental datasets. We also implement a simple and universal file format appropriate for electron microscopy data in py4DSTEM, which uses the open-source HDF5 standard. We hope this tool will benefit the research community and help improve the standards for data and computational methods in electron microscopy, and we invite the community to contribute to this ongoing project.

Cortical fNIRS Responses Can Be Better Explained by Loudness Percept than Sound Intensity.

OBJECTIVES: Functional near-infrared spectroscopy (fNIRS) is a brain imaging technique particularly suitable for hearing studies. However, the nature of fNIRS responses to auditory stimuli presented at different stimulus intensities is not well understood. In this study, we investigated whether fNIRS response amplitude was better predicted by stimulus properties (intensity) or individually perceived attributes (loudness). DESIGN: Twenty-two young adults were included in this experimental study. Four different stimulus intensities of a broadband noise were used as stimuli. First, loudness estimates for each stimulus intensity were measured for each participant. Then, the 4 stimulation intensities were presented in counterbalanced order while recording hemoglobin saturation changes from cortical auditory brain areas. The fNIRS response was analyzed in a general linear model design, using 3 different regressors: a non-modulated, an intensity-modulated, and a loudness-modulated regressor. RESULTS: Higher intensity stimuli resulted in higher amplitude fNIRS responses. The relationship between stimulus intensity and fNIRS response amplitude was better explained using a regressor based on individually estimated loudness estimates compared with a regressor modulated by stimulus intensity alone. CONCLUSIONS: Brain activation in response to different stimulus intensities is more reliant upon individual loudness sensation than physical stimulus properties. Therefore, in measurements using different auditory stimulus intensities or subjective hearing parameters, loudness estimates should be examined when interpreting results.

Atomic Resolution Imaging of Light Elements in a Crystalline Environment using Dynamic Hollow-Cone Illumination Transmission Electron Microscopy.

Multiple electron scattering and the nonintuitive nature of image formation with coherent radiation complicate the interpretation of conventional transmission electron microscopy images. Precession of the illuminating beam in transmission electron microscopy (TEM) can lead to more robust and interpretable images with some penalty to image contrast, a technique known as dynamic hollow-cone illumination TEM. We demonstrate direct and robust imaging of light and heavy atoms in a crystalline environment with this technique. This method is similar to the annular bright-field technique in scanning transmission electron microscopy, via the principle of reciprocity. Dynamic hollow-cone illumination TEM is challenging in practice due to sensitivity to the misalignment of the precession axis, microscope objective aperture, and crystal zone axis.

Improving process-based crop models to better capture genotype×environment×management interactions.

In spite of the increasing expectation for process-based crop modelling to capture genotype (G) by environment (E) by management (M) interactions to support breeding selections, it remains a challenge to use current crop models to accurately predict phenotypes from genotypes or from candidate genes. We use wheat as a target crop and the APSIM farming systems model (Holzworth et al., 2014) as an example to analyse the current status of process-based crop models with a major focus on need to improve simulation of specific eco-physiological processes and their linkage to underlying genetic controls. For challenging production environments in Australia, we examine the potential opportunities to capture physiological traits, and to integrate genetic and molecular approaches for future model development and applications. Model improvement will require both reducing the uncertainty in simulating key physiological processes and enhancing the capture of key observable traits and underlying genetic control of key physiological responses to environment. An approach consisting of three interactive stages is outlined to (i) improve modelling of crop physiology, (ii) develop linkage from model parameter to genotypes and further to loci or alleles, and (iii) further link to gene expression pathways. This helps to facilitate the integration of modelling, phenotyping, and functional gene detection and to effectively advance modelling of G×E×M interactions. While gene-based modelling is not always needed to simulate G×E×M, including well-understood gene effects can improve the estimation of genotype effects and prediction of phenotypes. Specific examples are given for enhanced modelling of wheat in the APSIM framework.

Experimental and modeling evidence of carbon limitation of leaf appearance rate for spring and winter wheat.

Accurate predictions of the timing of physiological stages and the development rate are crucial for predicting crop performance under field conditions. Plant development is controlled by the leaf appearance rate (LAR) and our understanding of how LAR responds to environmental factors is still limited. Here, we tested the hypothesis that carbon availability may account for the effects of irradiance, photoperiod, atmospheric CO2 concentration, and ontogeny on LAR. We conducted three experiments in growth chambers to quantify and disentangle these effects for both winter and spring wheat cultivars. Variations of LAR observed between environmental scenarios were well explained by the supply/demand ratio for carbon, quantified using the photothermal quotient. We therefore developed an ecophysiological model based on the photothermal quotient that accounts for the effects of temperature, irradiance, photoperiod, and ontogeny on LAR. Comparisons of observed leaf stages and LAR with simulations from our model, from a linear thermal-time model, and from a segmented linear thermal-time model corrected for sowing date showed that our model can simulate the observed changes in LAR in the field with the lowest error. Our findings demonstrate that a hypothesis-driven approach that incorporates more physiology in specific processes of crop models can increase their predictive power under variable environments.

Raising genetic yield potential in high productive countries: Designing wheat ideotypes under climate change.

Designing crop ideotype is an important step to raise genetic yield potential in a target environment. In the present study, we designed wheat ideotypes based on the state-of-the-art knowledge in crop physiology to increase genetic yield potential for the 2050-climate, as projected by the HadGEM2 global climate model for the RCP8.5 emission scenario, in two high-wheat-productive countries, viz. the United Kingdom (UK) and New Zealand (NZ). Wheat ideotypes were optimized to maximize yield potential for both water-limited (IW2050 ) and potential (IP2050 ) conditions by using Sirius model and exploring the full range of cultivar parameters. On average, a 43-51% greater yield potential over the present winter wheat cv. Claire was achieved for IW2050 in the UK and NZ, whereas a 51-62% increase was obtained for IP2050 . Yield benefits due to the potential condition over water-limitation were small in the UK, but 13% in NZ. The yield potentials of wheat were 16% (2.6 t ha-1) and 31% (5 t ha-1) greater in NZ than in the UK under 2050-climate in water-limited and potential conditions respectively. Modelling predicts the possibility of substantial increase in genetic yield potential of winter wheat under climate change in high productive countries. Wheat ideotypes optimized for future climate could provide plant scientists and breeders with a road map for selection of the target traits and their optimal combinations for wheat improvement and genetic adaptation to raise the yield potential.

Audio-visual integration in cochlear implant listeners and the effect of age difference.

This study aimed to investigate differences in audio-visual (AV) integration between cochlear implant (CI) listeners and normal-hearing (NH) adults. A secondary aim was to investigate the effect of age differences by examining AV integration in groups of older and younger NH adults. Seventeen CI listeners, 13 similarly aged NH adults, and 16 younger NH adults were recruited. Two speech identification experiments were conducted to evaluate AV integration of speech cues. In the first experiment, reaction times in audio-alone (A-alone), visual-alone (V-alone), and AV conditions were measured during a speeded task in which participants were asked to identify a target sound /aSa/ among 11 alternatives. A race model was applied to evaluate AV integration. In the second experiment, identification accuracies were measured using a closed set of consonants and an open set of consonant-nucleus-consonant words. The authors quantified AV integration using a combination of a probability model and a cue integration model (which model participants' AV accuracy by assuming no or optimal integration, respectively). The results found that experienced CI listeners showed no better AV integration than their similarly aged NH adults. Further, there was no significant difference in AV integration between the younger and older NH adults.