Classification images for aerial images capture visual expertise for binocular disparity and a prior for lighting from above.

Using a novel approach to classification images (CIs), we investigated the visual expertise of surveyors for luminance and binocular disparity cues simultaneously after screening for stereoacuity. Stereoscopic aerial images of hedges and ditches were classified in 10,000 trials by six trained remote sensing surveyors and six novices. Images were heavily masked with luminance and disparity noise simultaneously. Hedge and ditch images had reversed disparity on around half the trials meaning hedges became ditch-like and vice versa. The hedge and ditch images were also flipped vertically on around half the trials, changing the direction of the light source and completing a 2 × 2 × 2 stimulus design. CIs were generated by accumulating the noise textures associated with "hedge" and "ditch" classifications, respectively, and subtracting one from the other. Typical CIs had a central peak with one or two negative side-lobes. We found clear differences in the amplitudes and shapes of perceptual templates across groups and noise-type, with experts prioritizing binocular disparity and using this more effectively. Contrariwise, novices used luminance cues more than experts meaning that task motivation alone could not explain group differences. Asymmetries in the luminance CIs revealed individual differences for lighting interpretation, with experts less prone to assume lighting from above, consistent with their training on aerial images of UK scenes lit by a southerly sun. Our results show that (i) dual noise in images can be used to produce simultaneous CI pairs, (ii) expertise for disparity cues does not depend on stereoacuity, (iii) CIs reveal the visual strategies developed by experts, (iv) top-down perceptual biases can be overcome with long-term learning effects, and (v) CIs have practical potential for directing visual training.

Support for the Time-Varying Drift Rate Model of Perceptual Discrimination in Dynamic and Static Noise Using Bayesian Model-Fitting Methodology.

The drift-diffusion model (DDM) is a common approach to understanding human decision making. It considers decision making as accumulation of evidence about visual stimuli until sufficient evidence is reached to make a decision (decision boundary). Recently, Smith and colleagues proposed an extension of DDM, the time-varying DDM (TV-DDM). Here, the standard simplification that evidence accumulation operates on a fully formed representation of perceptual information is replaced with a perceptual integration stage modulating evidence accumulation. They suggested that this model particularly captures decision making regarding stimuli with dynamic noise. We tested this new model in two studies by using Bayesian parameter estimation and model comparison with marginal likelihoods. The first study replicated Smith and colleagues' findings by utilizing the classical random-dot kinomatogram (RDK) task, which requires judging the motion direction of randomly moving dots (motion discrimination task). In the second study, we used a novel type of stimulus designed to be like RDKs but with randomized hue of stationary dots (color discrimination task). This study also found TV-DDM to be superior, suggesting that perceptual integration is also relevant for static noise possibly where integration over space is required. We also found support for within-trial changes in decision boundaries ("collapsing boundaries"). Interestingly, and in contrast to most studies, the boundaries increased with increasing task difficulty (amount of noise). Future studies will need to test this finding in a formal model.

Accuracy and Precision of a Novel Photogate System to Measure Toe Clearance on Stairs.

Background: Toe clearance on stairs is typically measured using optoelectronic systems, though these are often constrained to the laboratory, due to their complex setups. Here we measured stair toe clearance through a novel prototype photogate setup and compared this to optoelectronic measurements. Methods: Twelve participants (age 22 ± 3 years) completed 25 stair ascent trials, each on a seven-step staircase. Toe clearance over the fifth step edge was measured using Vicon and the photogates. Twenty-two photogates were created in rows through laser diodes and phototransistors. The height of the lowest photogate broken at step-edge crossing was used to determine photogate toe clearance. A limits of agreement analysis and Pearson's correlation coefficient compared the accuracy, precision and relationship between systems. Results: We found a mean difference of -1.5 mm (accuracy) between the two measurement systems, with upper and lower limits (precision) of 10.7 mm and -13.8 mm, respectively. A strong positive correlation was also found (r = 70, n = 12, p = 0.009) between the systems. Discussion: The results suggest that photogates could be an option for measuring real-world stair toe clearances, where optoelectronic systems are not routinely used. Improvements to the design and measurement factors may help to improve the precision of the photogates.

A novel method for identifying coded tags recorded on aquatic acoustic monitoring systems.

Aquatic biotelemetry increasingly relies on using acoustic transmitters ('tags') that enable passive detection of tagged animals using fixed or mobile receivers. Both tracking methods are resource-limited, restricting the spatial area in which movements of highly mobile animals can be measured using proprietary detection systems. Transmissions from tags are recorded by underwater noise monitoring systems designed for other purposes, such as cetacean monitoring devices, which have been widely deployed in the marine environment; however, no tools currently exist to decode these detections, and thus valuable additional information on animal movements may be missed. Here, we describe simple hybrid methods, with potentially wide application, for obtaining information from otherwise unused data sources. The methods were developed using data from moored, acoustic cetacean detectors (C-PODs) and towed passive receiver arrays, often deployed to monitor the vocalisations of cetaceans, but any similarly formatted data source could be used. The method was applied to decode tag detections that were found to have come from two highly mobile fish species, bass (Dicentrarchus labrax) and Twaite shad (Alosa fallax), that had been tagged in other studies. Decoding results were validated using test tags; range testing data were used to demonstrate the relative efficiency of these receiver methods in detecting tags. This approach broadens the range of equipment from which acoustic tag detections can be decoded. Novel detections derived from the method could add significant value to past and present tracking studies at little additional cost, by providing new insights into the movement of mobile animals at sea.

Arabidopsis RING-type E3 ubiquitin ligase XBAT35.2 promotes proteasome-dependent degradation of ACD11 to attenuate abiotic stress tolerance.

Plants employ multiple mechanisms to cope with a constantly changing and challenging environment, including using the ubiquitin proteasome system (UPS) to alter their proteome to assist in initiating, modulating and terminating responses to stress. We previously reported that the ubiquitin ligase XBAT35.2 mediates the proteasome-dependent degradation of Accelerated Cell Death 11 (ACD11) to promote pathogen defense. Here, we demonstrate roles for XBAT35.2 and ACD11 in abiotic stress tolerance. As seen in response to pathogen infection, abiotic stress stabilizes XBAT35.2 and the abundance of ACD11 rose consistently with increasing concentrations of abscisic acid (ABA) and salt. Surprisingly, exposure to ABA and salt increased the stability of ACD11, and the overexpression of ACD11 improves plant survival of salt and drought stress, suggesting a role for ACD11 in promoting tolerance. Prolonged exposure to high concentrations of ABA or salt resulted in ubiquitination and the proteasome-dependent degradation of ACD11, however. The stress-induced turnover of ACD11 requires XBAT35.2, as degradation is slowed in the absence of the E3 ubiquitin ligase. Consistent with XBAT35.2 mediating the proteasome-dependent degradation of ACD11, the loss of E3 ubiquitin ligase function enhances the tolerance of salt and drought stress, whereas overexpression increases sensitivity. A model is presented where, upon the perception of abiotic stress, ACD11 abundance increases to promote tolerance. Meanwhile, XBAT35.2 accumulates and in turn promotes the degradation of ACD11 to attenuate the stress response. The results characterize XBAT35.2 as an E3 ubiquitin ligase with opposing roles in abiotic and biotic stress.

The missing N1 or jittered P2: Electrophysiological correlates of pattern glare in the time and frequency domain.

Excessive sensitivity to certain visual stimuli (cortical hyperexcitability) is associated with a number of neurological disorders including migraine, epilepsy, multiple sclerosis, autism and possibly dyslexia. Others show disruptive sensitivity to visual stimuli with no other obvious pathology or symptom profile (visual stress) which can extend to discomfort and nausea. We used event-related potentials (ERPs) to explore the neural correlates of visual stress and headache proneness. We analysed ERPs in response to thick (0.37 cycles per degree [c/deg]), medium (3 c/deg) and thin (12 c/deg) gratings, using mass univariate analysis, considering three factors in the general population: headache proneness, visual stress and discomfort. We found relationships between ERP features and the headache and discomfort factors. Stimulus main effects were driven by the medium stimulus regardless of participant characteristics. Participants with high discomfort ratings had larger P1 components for the initial presentation of medium stimuli, suggesting initial cortical hyperexcitability that is later suppressed. The participants with high headache ratings showed atypical N1-P2 components for medium stripes relative to the other stimuli. This effect was present only after repeated stimulus presentation. These effects were also explored in the frequency domain, suggesting variations in intertrial theta band phase coherence. Our results suggest that discomfort and headache in response to striped stimuli are related to different neural processes; however, more exploration is needed to determine whether the results translate to a clinical migraine population.

Complex High-Internal Phase Emulsions that can Form Interfacial Films with Tunable Morphologies.

High-internal phase emulsions (HIPEs) were considered as an important functional material and have been the focus of intense development effort, but their fundamental attributes have hardly been altered at either the microcosmic or macroscopic level, which severely limits their practical applications in various areas. In this work, we report a general strategy for creating complex HIPEs that can form interfacial films at liquid interfaces. Double HIPEs and Janus HIPEs are both realized for the first time. They feature complex microscopic patterns with short-range anisotropy and exhibit non-Newtonian pseudoplastic flow behavior. By taking advantage of their response to a high-pH subphase, interfacial films can be successfully obtained, which are tunable in thickness and morphologies under compression. Complex HIPEs can greatly expand the applications of liquid materials, and the interfacial films of droplets represent an important step toward producing 2D soft materials with a unique functionality that can be broadly applied to biological processes.

Precise Self-Positioning of Colloidal Particles on Liquid Emulsion Droplets.

Decorating emulsion droplets by particles stabilizes foodstuff and pharmaceuticals. Interfacial particles also influence aerosol formation, thus impacting atmospheric CO2 exchange. While studies of particles at disordered droplet interfaces abound in the literature, such studies for ubiquitous ordered interfaces are not available. Here, we report such an experimental study, showing that particles residing at crystalline interfaces of liquid droplets spontaneously self-position to specific surface locations, identified as structural topological defects in the crystalline surface monolayer. This monolayer forms at temperature T = Ts, leaving the droplet liquid and driving at Td < Ts a spontaneous shape-change transition of the droplet from spherical to icosahedral. The particle's surface position remains unchanged in the transition, demonstrating these positions to coincide with the vertices of the sphere-inscribed icosahedron. Upon further cooling, droplet shape-changes to other polyhedra occur, with the particles remaining invariably at the polyhedra's vertices. At still lower temperatures, the particles are spontaneously expelled from the droplets. Our results probe the molecular-scale elasticity of quasi-two-dimensional curved crystals, impacting also other fields, such as protein positioning on cell membranes, controlling essential biological functions. Using ligand-decorated particles, and the precise temperature-tunable surface position control found here, may also allow using these droplets for directed supra-droplet self-assembly into larger structures, with a possible post-assembly structure fixation by UV polymerization of the droplet's liquid.

Periodic buckling and grain boundary slips in a colloidal model of solid friction.

The intermittent 'stick-slip' dynamics in frictional sliding of solid bodies is common in everyday life and technology. This dynamics has been widely studied on a macroscopic scale, where the thermal motion can usually be neglected. However, the microscopic mechanisms behind the periodic stick-slip events are yet unclear. We employ confocal microscopy of colloidal spheres, to study the frictional dynamics at the boundary between two quasi-two-dimensional (2D) crystalline grains, with a single particle resolution. Such unprecedentedly-detailed observations of the microscopic-scale frictional solid-on-solid sliding have never been previously carried out. At this scale, the particles undergo an intense thermal motion, which masks the avalanche-like nature of the underlying frictional dynamics. We demonstrate that the underlying sliding dynamics involving out-of-plane buckling events, is intermittent and periodic, like in macroscopic friction. However, unlike in the common models of friction, the observed periodic frictional dynamics is promoted, rather than just suppressed, by the thermal noise, which maximizes the entropy of the system.

Degradation of the stress-responsive enzyme formate dehydrogenase by the RING-type E3 ligase Keep on Going and the ubiquitin 26S proteasome system.

KEY MESSAGE: KEG is involved in mediating the proteasome-dependent degradation of FDH, a stress-responsive enzyme. The UPS may function to suppress FDH mediated stress responses under favorable growth conditions. Formate dehydrogenase (FDH) has been studied in bacteria and yeasts for the purpose of industrial application of NADH co-factor regeneration. In plants, FDH is regarded as a universal stress protein involved in responses to various abiotic and biotic stresses. Here we show that FDH abundance is regulated by the ubiquitin proteasome system (UPS). FDH is ubiquitinated in planta and degraded by the 26S proteasome. Interaction assays identified FDH as a potential substrate for the RING-type ubiquitin ligase Keep on Going (KEG). KEG is capable of attaching ubiquitin to FDH in in vitro assays and the turnover of FDH was increased when co-expressed with a functional KEG in planta, suggesting that KEG contributes to FDH degradation. Consistent with a role in regulating FDH abundance, transgenic plants overexpressing KEG were more sensitive to the inhibitory effects of formate. In addition, FDH is a phosphoprotein and dephosphorylation was found to increase the stability of FDH in degradation assays. Based on results from this and previous studies, we propose a model where KEG mediates the ubiquitination and subsequent degradation of phosphorylated FDH and, in response to unfavourable growth conditions, reduction in FDH phosphorylation levels may prohibit turnover allowing the stabilized FDH to facilitate stress responses.

Interfacial Rheology of Sterically Stabilized Colloids at Liquid Interfaces and Its Effect on the Stability of Pickering Emulsions.

Particle-laden interfaces can be used to stabilize a variety of high-interface systems, from foams over emulsions to polymer blends. The relation between the particle interactions, the structure and rheology of the interface, and the stability of the system remains unclear. In the present work, we experimentally investigate how micron-sized, near-hard-sphere-like particles affect the mechanical properties of liquid interfaces. In particular, by comparing dried and undried samples, we investigate the effect of aggregation state on the properties of the particle-laden liquid interface and its relation to the stability of the corresponding Pickering emulsions. Partially aggregated suspensions give rise to a soft-solid-like response under shear, whereas for stable PMMA particulate layers a liquid-like behavior is observed. For interfacial creep-recovery measurements, we present an empirical method to correct for the combined effect of the subphase drag and the compliance of the double-wall ring geometry, which makes a significant contribution to the apparent elasticity of weak interfaces. We further demonstrate that both undried and dried PMMA particles can stabilize emulsions for months, dispelling the notion that particle aggregation, in bulk or at the interface, is required to create stable Pickering emulsions. Our results indicate that shear rheology is a sensitive probe of colloidal interactions but is not necessarily a predictor of the stability of interfaces, e.g., in quiescent Pickering emulsions, as in the latter the response to dilatational deformations can be of prime importance.

Axial Confocal Tomography of Capillary-Contained Colloidal Structures.

Confocal microscopy is widely used for three-dimensional (3D) sample reconstructions. Arguably, the most significant challenge in such reconstructions is posed by the resolution along the optical axis being significantly lower than in the lateral directions. In addition, the imaging rate is lower along the optical axis in most confocal architectures, prohibiting reliable 3D reconstruction of dynamic samples. Here, we demonstrate a very simple, cheap, and generic method of multiangle microscopy, allowing high-resolution high-rate confocal slice collection to be carried out with capillary-contained colloidal samples in a wide range of slice orientations. This method, realizable with any common confocal architecture and recently implemented with macroscopic specimens enclosed in rotatable cylindrical capillaries, allows 3D reconstructions of colloidal structures to be verified by direct experiments and provides a solid testing ground for complex reconstruction algorithms. In this paper, we focus on the implementation of this method for dense nonrotatable colloidal samples, contained in complex-shaped capillaries. Additionally, we discuss strategies to minimize potential pitfalls of this method, such as the artificial appearance of chain-like particle structures.

Reduced sensitivity for visual textures affects judgments of shape-from-shading and step-climbing behaviour in older adults.

Falls on stairs are a major hazard for older adults. Visual decline in normal ageing can affect step-climbing ability, altering gait and reducing toe clearance. Here we show that a loss of fine-grained visual information associated with age can affect the perception of surface undulations in patterned surfaces. We go on to show that such cues affect the limb trajectories of young adults, but due to their lack of sensitivity, not that of older adults. Interestingly neither the perceived height of a step nor conscious awareness is altered by our visual manipulation, but stepping behaviour is, suggesting that the influence of shape perception on stepping behaviour is via the unconscious, action-centred, dorsal visual pathway.

Compressing a spinodal surface at fixed area: bijels in a centrifuge.

Bicontinuous interfacially jammed emulsion gels (bijels) are solid-stabilised emulsions with two inter-penetrating continuous phases. Employing the method of centrifugal compression we find that macroscopically the bijel yields at relatively low angular acceleration. Both continuous phases escape from the top of the structure, making any compression immediately irreversible. Microscopically, the bijel becomes anisotropic with the domains aligned perpendicular to the compression direction which inhibits further liquid expulsion; this contrasts strongly with the sedimentation behaviour of colloidal gels. The original structure can, however, be preserved close to the top of the sample and thus the change to an anisotropic structure suggests internal yielding. Any air bubbles trapped in the bijel are found to aid compression by forming channels aligned parallel to the compression direction which provide a route for liquid to escape.

Dense colloidal fluids form denser amorphous sediments.

We relate, by simple analytical centrifugation experiments, the density of colloidal fluids with the nature of their randomly packed solid sediments. We demonstrate that the most dilute fluids of colloidal hard spheres form loosely packed sediments, where the volume fraction of the particles approaches in frictional systems the random loose packing limit, ϕRLP = 0.55. The dense fluids of the same spheres form denser sediments, approaching the so-called random close packing limit, ϕRCP = 0.64. Our experiments, where particle sedimentation in a centrifuge is sufficiently rapid to avoid crystallization, demonstrate that the density of the sediments varies monotonically with the volume fraction of the initial suspension. We reproduce our experimental data by simple computer simulations, where structural reorganizations are prohibited, such that the rate of sedimentation is irrelevant. This suggests that in colloidal systems, where viscous forces dominate, the structure of randomly close-packed and randomly loose-packed sediments is determined by the well-known structure of the initial fluids of simple hard spheres, provided that the crystallization is fully suppressed.

Gelation of particles with short-range attraction.

Nanoscale or colloidal particles are important in many realms of science and technology. They can dramatically change the properties of materials, imparting solid-like behaviour to a wide variety of complex fluids. This behaviour arises when particles aggregate to form mesoscopic clusters and networks. The essential component leading to aggregation is an interparticle attraction, which can be generated by many physical and chemical mechanisms. In the limit of irreversible aggregation, infinitely strong interparticle bonds lead to diffusion-limited cluster aggregation (DLCA). This is understood as a purely kinetic phenomenon that can form solid-like gels at arbitrarily low particle volume fraction. Far more important technologically are systems with weaker attractions, where gel formation requires higher volume fractions. Numerous scenarios for gelation have been proposed, including DLCA, kinetic or dynamic arrest, phase separation, percolation and jamming. No consensus has emerged and, despite its ubiquity and significance, gelation is far from understood-even the location of the gelation phase boundary is not agreed on. Here we report experiments showing that gelation of spherical particles with isotropic, short-range attractions is initiated by spinodal decomposition; this thermodynamic instability triggers the formation of density fluctuations, leading to spanning clusters that dynamically arrest to create a gel. This simple picture of gelation does not depend on microscopic system-specific details, and should thus apply broadly to any particle system with short-range attractions. Our results suggest that gelation-often considered a purely kinetic phenomenon-is in fact a direct consequence of equilibrium liquid-gas phase separation. Without exception, we observe gelation in all of our samples predicted by theory and simulation to phase-separate; this suggests that it is phase separation, not percolation, that corresponds to gelation in models for attractive spheres.

Deductive machine learning models for product identification.

Deductive solution strategies are required in prediction scenarios that are under determined, when contradictory information is available, or more generally wherever one-to-many non-functional mappings occur. In contrast, most contemporary machine learning (ML) in the chemical sciences is inductive learning from example, with a fixed set of features. Chemical workflows are replete with situations requiring deduction, including many aspects of lab automation and spectral interpretation. Here, a general strategy is described for designing and training machine learning models capable of deduction that consists of combining individual inductive models into a larger deductive network. The training and testing of these models is demonstrated on the task of deducing reaction products from a mixture of spectral sources. The resulting models can distinguish between intended and unintended reaction outcomes and identify starting material based on a mixture of spectral sources. The models also perform well on tasks that they were not directly trained on, like performing structural inference using real rather than simulated spectral inputs, predicting minor products from named organic chemistry reactions, identifying reagents and isomers as plausible impurities, and handling missing or conflicting information. A new dataset of 1 124 043 simulated spectra that were generated to train these models is also distributed with this work. These findings demonstrate that deductive bottlenecks for chemical problems are not fundamentally insuperable for ML models.

Five draft genome assemblies from Bacillaceae isolated from a degraded wetland environment.

We isolated five Bacillaceae from a degraded wetland environment and sequenced their genomes using Illumina NextSeq. Here, we report draft genome sequences of Bacillus velezensus-SC119, Priestia megaterium strain SC120, Bacillus zhangzhouensis strain SC123, Bacillus pumilis strain SC124, and Bacillus idriensis strain SC127. The genomes range between 3,657,353 and 5,772,725 bp with % GC between 37.62% and 46.38%.

Perceptual integration for qualitatively different 3-D cues in the human brain.

The visual system's flexibility in estimating depth is remarkable: We readily perceive 3-D structure under diverse conditions from the seemingly random dots of a "magic eye" stereogram to the aesthetically beautiful, but obviously flat, canvasses of the Old Masters. Yet, 3-D perception is often enhanced when different cues specify the same depth. This perceptual process is understood as Bayesian inference that improves sensory estimates. Despite considerable behavioral support for this theory, insights into the cortical circuits involved are limited. Moreover, extant work tested quantitatively similar cues, reducing some of the challenges associated with integrating computationally and qualitatively different signals. Here we address this challenge by measuring fMRI responses to depth structures defined by shading, binocular disparity, and their combination. We quantified information about depth configurations (convex "bumps" vs. concave "dimples") in different visual cortical areas using pattern classification analysis. We found that fMRI responses in dorsal visual area V3B/KO were more discriminable when disparity and shading concurrently signaled depth, in line with the predictions of cue integration. Importantly, by relating fMRI and psychophysical tests of integration, we observed a close association between depth judgments and activity in this area. Finally, using a cross-cue transfer test, we found that fMRI responses evoked by one cue afford classification of responses evoked by the other. This reveals a generalized depth representation in dorsal visual cortex that combines qualitatively different information in line with 3-D perception.

Arabidopsis CIPK26 interacts with KEG, components of the ABA signalling network and is degraded by the ubiquitin-proteasome system.

The RING-type E3 ligase, Keep on Going (KEG), is required for early seedling establishment in Arabidopsis thaliana. Post-germination, KEG negatively regulates abscisic acid (ABA) signalling by targeting Abscisic Acid Insensitive 5 (ABI5) for ubiquitination and subsequent degradation. Previous reports suggest that the role of KEG during early seedling development is not limited to regulation of ABI5 abundance. Using a yeast two-hybrid screen, this study identified Calcineurin B-like Interacting Protein Kinase (CIPK) 26 as a KEG-interacting protein. In vitro pull-down and in planta bimolecular fluorescence complementation assays confirmed the interactions between CIPK26 and KEG. In planta experiments demonstrated that CIPK26 was ubiquitinated and degraded via the 26S proteasome. It was also found that turnover of CIPK26 was increased when KEG protein levels were elevated, suggesting that the RING-type E3 ligase is involved in targeting CIPK26 for degradation. CIPK26 was found to interact with the ABA signalling components ABI1, ABI2, and ABI5. In addition, CIPK26 was capable of phosphorylating ABI5 in vitro. Consistent with a role in ABA signalling, overexpression of CIPK26 increased the sensitivity of germinating seeds to the inhibitory effects of ABA. The data presented in this report suggest that KEG mediates the proteasomal degradation of CIPK26 and that CIPK26 is part of the ABA signalling network.