High-speed 4-dimensional scanning transmission electron microscopy using compressive sensing techniques.

Here we show that compressive sensing allows 4-dimensional (4-D) STEM data to be obtained and accurately reconstructed with both high-speed and reduced electron fluence. The methodology needed to achieve these results compared to conventional 4-D approaches requires only that a random subset of probe locations is acquired from the typical regular scanning grid, which immediately generates both higher speed and the lower fluence experimentally. We also consider downsampling of the detector, showing that oversampling is inherent within convergent beam electron diffraction (CBED) patterns and that detector downsampling does not reduce precision but allows faster experimental data acquisition. Analysis of an experimental atomic resolution yttrium silicide dataset shows that it is possible to recover over 25 dB peak signal-to-noise ratio in the recovered phase using 0.3% of the total data. Lay abstract: Four-dimensional scanning transmission electron microscopy (4-D STEM) is a powerful technique for characterizing complex nanoscale structures. In this method, a convergent beam electron diffraction pattern (CBED) is acquired at each probe location during the scan of the sample. This means that a 2-dimensional signal is acquired at each 2-D probe location, equating to a 4-D dataset. Despite the recent development of fast direct electron detectors, some capable of 100kHz frame rates, the limiting factor for 4-D STEM is acquisition times in the majority of cases, where cameras will typically operate on the order of 2kHz. This means that a raster scan containing 256^2 probe locations can take on the order of 30s, approximately 100-1000 times longer than a conventional STEM imaging technique using monolithic radial detectors. As a result, 4-D STEM acquisitions can be subject to adverse effects such as drift, beam damage, and sample contamination. Recent advances in computational imaging techniques for STEM have allowed for faster acquisition speeds by way of acquiring only a random subset of probe locations from the field of view. By doing this, the acquisition time is significantly reduced, in some cases by a factor of 10-100 times. The acquired data is then processed to fill-in or inpaint the missing data, taking advantage of the inherently low-complex signals which can be linearly combined to recover the information. In this work, similar methods are demonstrated for the acquisition of 4-D STEM data, where only a random subset of CBED patterns are acquired over the raster scan. We simulate the compressive sensing acquisition method for 4-D STEM and present our findings for a variety of analysis techniques such as ptychography and differential phase contrast. Our results show that acquisition times can be significantly reduced on the order of 100-300 times, therefore improving existing frame rates, as well as further reducing the electron fluence beyond just using a faster camera.

Model-based and model-free mechanisms in methamphetamine use disorder.

People with methamphetamine use disorder (MUD) struggle to shift their behaviour from methamphetamine-orientated habits to goal-oriented choices. The model-based/model-free framework is well suited to understand this difficulty by unpacking the computational mechanisms that support experienced-based (model-free) and goal-directed (model-based) choices. We aimed to examine whether 1) participants with MUD differed from controls on behavioural proxies and/or computational mechanisms of model-based/model-free choices; 2) model-based/model-free decision-making correlated with MUD symptoms; and 3) model-based/model-free deficits improved over six weeks in the group with MUD. Participants with MUD and controls with similar age, IQ and socioeconomic status completed the Two-Step Task at treatment commencement (MUD n = 30, Controls n = 31) and six weeks later (MUD n = 23, Controls n = 26). We examined behavioural proxies of model-based/model-free decisions using mixed logistic regression, and their underlying mechanisms using computational modelling. At a behavioural level, participants with MUD were more likely to switch their choices following rewarded actions, although this pattern improved at follow up. At a computational level, groups were similar in their use of model-based mechanisms, but participants with MUD were less likely to apply model-free mechanisms and less likely to repeat rewarded actions. We did not find evidence that individual differences in model-based or model-free parameters were associated with greater severity of methamphetamine dependence, nor did we find that group differences in computational parameters changed between baseline and follow-up assessment. Decision-making challenges in people with MUD are likely related to difficulties in pursuing choices previously associated with positive outcomes.

The Potential of Subsampling and Inpainting for Fast Low-Dose Cryo FIB-SEM Imaging.

Traditional image acquisition for cryo focused ion-beam scanning electron microscopy (FIB-SEM) tomography often sees thousands of images being captured over a period of many hours, with immense data sets being produced. When imaging beam sensitive materials, these images are often compromised by additional constraints related to beam damage and the devitrification of the material during imaging, which renders data acquisition both costly and unreliable. Subsampling and inpainting are proposed as solutions for both of these aspects, allowing fast and low-dose imaging to take place in the Focused ion-beam scanning electron microscopy FIB-SEM without an appreciable loss in image quality. In this work, experimental data are presented which validate subsampling and inpainting as a useful tool for convenient and reliable data acquisition in a FIB-SEM, with new methods of handling three-dimensional data being employed in the context of dictionary learning and inpainting algorithms using a newly developed microscope control software and data recovery algorithm.

Towards real-time STEM simulations through targeted subsampling strategies.

Scanning transmission electron microscopy images can be complex to interpret on the atomic scale as the contrast is sensitive to multiple factors such as sample thickness, composition, defects and aberrations. Simulations are commonly used to validate or interpret real experimental images, but they come at a cost of either long computation times or specialist hardware such as graphics processing units. Recent works in compressive sensing for experimental STEM images have shown that it is possible to significantly reduce the amount of acquired signal and still recover the full image without significant loss of image quality, and therefore it is proposed here that similar methods can be applied to STEM simulations. In this paper, we demonstrate a method that can significantly increase the efficiency of STEM simulations through a targeted sampling strategy, along with a new approach to independently subsample each frozen phonon layer. We show the effectiveness of this method by simulating a SrTiO3 grain boundary and monolayer 2H-MoS2 containing a sulphur vacancy using the abTEM software. We also show how this method is not limited to only traditional multislice methods, but also increases the speed of the PRISM simulation method. Furthermore, we discuss the possibility for STEM simulations to seed the acquisition of real data, to potentially lead the way to self-driving (correcting) STEM.

Computational mechanisms underpinning greater exploratory behaviour in excess weight relative to healthy weight adolescents.

Obesity in adolescence is associated with cognitive changes that lead to difficulties in shifting unhealthy habits in favour of alternative healthy behaviours, similar to addictive behaviours. An outstanding question is whether this shift in goal-directed behaviour is driven by over-exploitation or over-exploration of rewarding outcomes. Here, we addressed this question by comparing explore/exploit behaviour on the Iowa Gambling Task in 43 adolescents with excess weight against 38 adolescents with healthy weight. We computationally modelled both exploitation behaviour (e.g., reinforcement sensitivity and inverse decay parameters), and explorative behaviour (e.g., maximum directed exploration value). We found that overall, adolescents with excess weight displayed more behavioural exploration than their healthy-weight counterparts - specifically, demonstrating greater overall switching behaviour. Computational models revealed that this behaviour was driven by a higher maximum directed exploration value in the excess-weight group (U = 520.00, p = .005, BF10 = 5.11). Importantly, however, we found substantial evidence that groups did not differ in reinforcement sensitivity (U = 867.00, p = .641, BF10 = 0.30). Overall, our study demonstrates a preference for exploratory behaviour in adolescents with excess weight, independent of sensitivity to reward. This pattern could potentially underpin an intrinsic desire to explore energy-dense unhealthy foods - an as-yet untapped mechanism that could be targeted in future treatments of obesity in adolescents.

A Novel Lepidoptera bioassay analysed using a reduced GUTS model.

Lepidopteran species can be both pests and also beneficial pollinators for agricultural crops. However, despite these important roles, the effects of pesticides on this diverse taxa are relatively understudied. To facilitate the assessment of pesticides and other chemical hazards on this taxa, we present a novel bioassay capable of testing chemical sensitivity to lepidopteran larvae through dietary exposure. We used Mamestra brassicae caterpillars as a model lepidopteran and tested their sensitivity for the organophosphate insecticide chlorpyrifos. We exposed larvae to an artificial diet spiked with chlorpyrifos and monitored survival over time, as well as weight change over a 96-hour exposure period. To test the repeatability and reliability of the developed bioassay, the experiment was repeated three times. The survival in time data collected enabled analysis with the General Unified Threshold of Survival (GUTS) model, recently recognized by EFSA as a ready-to-use tool for regulatory purposes. The GUTS modelling was used to derive a set of relevant toxicokinetic and toxicodynamic parameters relating to the larval response to exposure over time. We found that across the three repeats studies there was no more than a threefold difference in LC50 values (13.1, 18.7 and 8.1 mg/Kg) at 48 h and fourfold difference at 96 h, highlighting the repeatability of the bioassay. We also highlighted the potential of the method to observe sub-lethal effects such as changes in weight. Finally, we discuss the applications of this new bioassay method to chemical risk assessments and its potential for use in other scenarios, such as mixture or pulsed exposure testing.

Modelling the effects of the pyrethroid insecticide cypermethrin on the life cycle of the soil dwelling annelid Enchytraeus crypticus, an original experimental design to calibrate a DEB-TKTD model.

The Dynamic Energy Budget theory (DEB) enables ecotoxicologists to model the effects of chemical stressors on organism life cycles through the coupling of toxicokinetic-toxicodynamic (TK-TD) models. While good progress has been made in the application of DEB-TKTD models for aquatic organisms, applications for soil fauna are scarce, due to the lack of dedicated experimental designs suitable for collecting the required time series effect data. Enchytraeids (Annelida: Clitellata) are model organisms in soil ecology and ecotoxicology. They are recognised as indicators of biological activity in soil, and chemical stress in terrestrial ecosystems. Despite this, the application of DEB-TKTD models to investigate the impact of chemicals has not yet been tested on this family. Here we assessed the impact of the pyrethroid insecticide cypermethrin on the life cycle of Enchytraeus crypticus. We developed an original experimental design to collect the data required for the calibration of a DEB-TKTD model for this species. E. crypticus presented a slow initial growth phase that has been successfully simulated with the addition of a size-dependent food limitation for juveniles in the DEB model. The DEB-TKTD model simulations successfully agreed with the data for all endpoints and treatments over time. The highlighted physiological mode of action (pMoA) for cypermethrin was an increase of the growth energy cost. The threshold for effects on survival was estimated at 73.14 mg kg- 1, and the threshold for effects on energy budget (i.e., sublethal effects) at 19.21 mg kg- 1. This study demonstrates that DEB-TKTD models can be successfully applied to E. crypticus as a representative soil species, and may improve the ecological risk assessment for terrestrial ecosystems, and our mechanistic understanding of chemical effects on non-target species.

Computational models of exploration and exploitation characterise onset and efficacy of treatment in methamphetamine use disorder.

People with Methamphetamine Use Disorder (PwMUD) spend substantial time and resources on substance use, which hinders their ability to explore alternate reinforcers. Gold-standard behavioural treatments attempt to remedy this by encouraging action towards non-drug reinforcers, but substance use often persists. We aimed to unravel the mechanistic drivers of this behaviour by applying a computational model of explore/exploit behaviour to decision-making data (Iowa Gambling Task) from 106 PwMUD and 48 controls. We then examined the longitudinal link between explore/exploit mechanisms and changes in methamphetamine use 6 weeks later. Exploitation parameters included reinforcement sensitivity and inverse decay (i.e., number of past outcomes used to guide choices). Exploration parameters included maximum directed exploration value (i.e., value of trying novel actions). The Timeline Follow Back measured changes in methamphetamine use. Compared to controls, PwMUD showed deficits in exploitative decision-making, characterised by reduced reinforcement sensitivity, U = 3065, p = 0.009, and less use of previous choice outcomes, U = 3062, p = 0.010. This was accompanied by a behavioural pattern of frequent shifting between choices, which appeared consistent with random exploration. Furthermore, PwMUD with greater reductions of methamphetamine use at 6 weeks had increased directed exploration (ß = 0.22, p = 0.045); greater use of past choice outcomes (ß = -0.39, p = 0.002) and greater choice consistency (ß = -0.39, p = 0.002). Therefore, limited computational exploitation and increased behavioural exploration characterise PwMUD's presentation to treatment, while increased directed exploration, use of past choice outcomes and choice consistency predict greater reductions of methamphetamine use.

High-efficiency diffraction gratings for EUV and soft x-rays using spin-on-carbon underlayers.

We report on the fabrication and characterization of high-resolution gratings with high efficiency in the extreme ultraviolet (EUV) and soft x-ray ranges using spin-on-carbon (SOC) underlayers. We demonstrate the fabrication of diffraction gratings down to 20 nm half-pitch (HP) on Si3N4membranes with a bilayer of hydrogen silsesquioxane (HSQ) and spin-on-carbon and show their performance as a grating mask for extreme ultraviolet interference lithography (EUV-IL). High-resolution patterning of HSQ is possible only for thin films due to pattern collapse. The combination of this high-resolution resist with SOC circumvents this problem and enables the fabrication of high aspect ratio nanostructures. Rigorous coupled-wave analysis shows that the bilayer gratings exhibit higher diffraction efficiency than what is feasible with a grating made of HSQ. We also demonstrate a simple and accurate method to experimentally measure the diffraction efficiency of high-resolution gratings by measuring the relative ratio of the dose-to-clear curves of the photoresist. The measured diffraction efficiencies are in good agreement with the theoretically predicted values. Furthermore, we verify our calculations and measurements by printing line/space patterns in chemically amplified resists down to 10 nm HP with both HSQ and bilayer grating masks using EUV-IL. The improved diffraction efficiency of the bilayers is expected to have applications not only in gratings for interference lithography, but also in Fresnel zone plates and gratings for spectroscopy in the EUV and soft x-ray ranges.

Predicting Mixture Effects over Time with Toxicokinetic-Toxicodynamic Models (GUTS): Assumptions, Experimental Testing, and Predictive Power.

Current methods to assess the impact of chemical mixtures on organisms ignore the temporal dimension. The General Unified Threshold model for Survival (GUTS) provides a framework for deriving toxicokinetic-toxicodynamic (TKTD) models, which account for effects of toxicant exposure on survival in time. Starting from the classic assumptions of independent action and concentration addition, we derive equations for the GUTS reduced (GUTS-RED) model corresponding to these mixture toxicity concepts and go on to demonstrate their application. Using experimental binary mixture studies with Enchytraeus crypticus and previously published data for Daphnia magna and Apis mellifera, we assessed the predictive power of the extended GUTS-RED framework for mixture assessment. The extended models accurately predicted the mixture effect. The GUTS parameters on single exposure data, mixture model calibration, and predictive power analyses on mixture exposure data offer novel diagnostic tools to inform on the chemical mode of action, specifically whether a similar or dissimilar form of damage is caused by mixture components. Finally, observed deviations from model predictions can identify interactions, e.g., synergism or antagonism, between chemicals in the mixture, which are not accounted for by the models. TKTD models, such as GUTS-RED, thus offer a framework to implement new mechanistic knowledge in mixture hazard assessments.

Off-Target Stoichiometric Binding Identified from Toxicogenomics Explains Why Some Species Are More Sensitive than Others to a Widely Used Neonicotinoid.

Neonicotinoids are currently licensed for use in 120 countries, making accurate nontarget species sensitivity predictions critical. Unfortunately, such predictions are fraught with uncertainty, as sensitivity is extrapolated from only a few test species and neonicotinoid sensitivities can differ greatly between closely related taxa. Combining classical toxicology with de novo toxicogenomics could greatly improve sensitivity predictions and identify unexpectedly susceptible species. We show that there is a >30-fold differential species sensitivity (DSS) for the neonicotinoid imidacloprid between five earthworm species, a critical nontarget taxon. This variation could not be explained by differential toxicokinetics. Furthermore, comparing key motif expression in subunit genes of the classical nicotinic acetylcholine receptor (nAChR) target predicts only minor differences in the ligand binding domains (LBDs). In contrast, predicted dissimilarities in LBDs do occur in the highly expressed but nonclassical targets, acetylcholine binding proteins (AChBPs). Critically, the predicted AChBP divergence is capable of explaining DSS. We propose that high expression levels of putative nonsynaptic AChBPs with high imidacloprid affinities reduce imidacloprid binding to critical nAChRs involved in vital synaptic neurotransmission. This study provides a clear example of how pragmatic interrogation of key motif expression in complex multisubunit receptors can predict observed DSS, thereby informing sensitivity predictions for essential nontarget species.

Are methamphetamine users compulsive? Faulty reinforcement learning, not inflexibility, underlies decision making in people with methamphetamine use disorder.

Methamphetamine use disorder involves continued use of the drug despite negative consequences. Such 'compulsivity' can be measured by reversal learning tasks, which involve participants learning action-outcome task contingencies (acquisition-contingency) and then updating their behaviour when the contingencies change (reversal). Using these paradigms, animal models suggest that people with methamphetamine use disorder (PwMUD) may struggle to avoid repeating actions that were previously rewarded but are now punished (inflexibility). However, difficulties in learning task contingencies (reinforcement learning) may offer an alternative explanation, with meaningful treatment implications. We aimed to disentangle inflexibility and reinforcement learning deficits in 35 PwMUD and 32 controls with similar sociodemographic characteristics, using novel trial-by-trial analyses on a probabilistic reversal learning task. Inflexibility was defined as (a) weaker reversal phase performance, compared with the acquisition-contingency phases, and (b) persistence with the same choice despite repeated punishments. Conversely, reinforcement learning deficits were defined as (a) poor performance across both acquisition-contingency and reversal phases and (b) inconsistent postfeedback behaviour (i.e., switching after reward). Compared with controls, PwMUD exhibited weaker learning (odds ratio [OR] = 0.69, 95% confidence interval [CI] [0.63-0.77], p < .001), though no greater accuracy reduction during reversal. Furthermore, PwMUD were more likely to switch responses after one reward/punishment (OR = 0.83, 95% CI [0.77-0.89], p < .001; OR = 0.82, 95% CI [0.72-0.93], p = .002) but just as likely to switch after repeated punishments (OR = 1.03, 95% CI [0.73-1.45], p = .853). These results indicate that PwMUD's reversal learning deficits are driven by weaker reinforcement learning, not inflexibility.

Lack of longitudinal changes in cognition in individuals with methamphetamine use disorder during the first 6 weeks after commencing treatment.

Background: Methamphetamine use disorder (MUD) associates with cognitive impulsivity deficits. However, few studies have examined longitudinal changes in cognition, and it remains unclear if deficits resolve during early recovery.Objectives: To compare: (1) cognitive function of individuals with MUD at treatment onset and six-weeks later with controls tested over the same period; (2) cognitive changes in MUD-individuals who remained abstinent versus relapsed.Method: We recruited 108 participants meeting DSM-IV-TR criteria for methamphetamine dependence (81 males) and 50 demographically matched controls (38 males); 77 methamphetamine- dependent participants (59 males) and 48 controls (36 males) were retained at follow-up. We administered response inhibition, delay discounting and uncertainty-based decision-making tests at both endpoints. Relapse was defined as methamphetamine concentrations >0.4 ng/mg at follow-up in hair toxicology.Results: We found a significant time-by-group interaction on uncertainty-based decision-making (effect size: η2 = .05), although post-hoc tests to disentangle this interaction yielded inconclusive results (p-range = .14-.40; BF10-range = 0.43-1.67). There were no significant time-by-group interactions on response inhibition or delay discounting, with the former likely a null effect (η2-interaction = .003 and .02; BFincl = 0.23 and 0.71). There were no significant differences in cognitive recovery between individuals who maintained abstinence (n = 12) versus relapsed (n = 65) (η2-range = .003-.04), although evidence was inconclusive toward whether findings reflected true null effects (BFincl-range = 0.33-0.75).Conclusion: We did not find evidence that MUD-related cognitive impulsivity deficits improve beyond practice effects over 6 weeks. Findings do not support previous, albeit conflicting, evidence of early recovery of cognitive deficits in MUD.

Disability-Related Costs of Children with Disabilities in the Philippines.

The assessment of disability-related costs among children remains a largely under-researched subject with related questions rarely included in surveys. This paper addresses this issue through a unique mixed methods study conducted in the Philippines combining a nationally representative survey and in-depth interviews with families and health professionals. To quantify the extra costs associated with disabilities, the research used the standard of living approach, whereby expenditure levels of families with children with and without disabilities were compared in relation to different measures of living standards. The results find consistent evidence of high extra costs among households that have children with disabilities and point to health expenses as the leading source. Using an asset index as the indicator of living standards, a child with a disability is estimated to require between 40% and 80% extra expenditure to reach the same living standard of other children. However, the size of extra costs is substantially higher when the measure of the standard of living relies on a broader set of deprivations. In such cases, higher estimates of extra costs are likely to be the result of the lack of an inclusive environment. Critically, this points to the need to provide not only financial support but also inclusive services, especially in health and education.

The genome sequence of the red compost earthworm, Lumbricus rubellus (Hoffmeister, 1843).

We present a genome assembly from an individual Lumbricus rubellus (the red compost earthworm; Annelida; Clitellata; Haplotaxida; Lumbricidae). The genome sequence is 787.5 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 15.81 kilobases in length. Gene annotation of this assembly on Ensembl identified 33,426 protein coding genes.

Proof-of-concept trial of Goal Management Training+ to improve executive functions and treatment outcomes in methamphetamine use disorder.

BACKGROUND: Deficits in executive function are common in methamphetamine use disorder (MUD), likely contributing to difficulties in sustained treatment success. Cognitive remediation interventions are designed to treat such deficits but have not been adapted to the needs of people with MUD. This study presents a proof-of-concept trial to evaluate a new cognitive remediation program for MUD, Goal Management Training+ (GMT+). METHODS: This was a cluster-randomised crossover trial comparing GMT+ with a psychoeducation-based control (Brain Health Workshop; BHW). GMT+ is a therapist-administered group-based cognitive remediation for executive dysfunction comprising four 90-minute weekly sessions and daily journal activities. BHW is a lifestyle psychoeducation program matched to GMT+ for therapist involvement, format, and duration. Participants (n = 36; GMT n = 17; BHW n = 19) were recruited from therapeutic communities in Victoria, Australia. Primary outcomes included intervention acceptability, feasibility, and improvements in self-reported executive function. Secondary outcomes included cognitive tests of executive function, severity of methamphetamine dependence, craving, and quality of life. We performed mixed linear modelling and calculated Hedges' g effect sizes. RESULTS: GMT+ participant ratings and program retention indicated high acceptability. There was no difference between GMT+ and BHW on self-reported executive function (g = 0.06). Cognitive tasks suggested benefits of GMT+ on information gathering (g = 0.88) and delay-discounting (g = 0.80). Severity of methamphetamine dependence decreased more in GMT+ (g = 1.47). CONCLUSIONS: GMT+ was well-accepted but did not improve self-reported executive functioning. Secondary outcomes suggested GMT+ was beneficial for objective cognitive performance and severity of dependence.

Ultrasensitive humidity detection using metal-organic framework-coated microsensors.

The use of metal-organic framework (MOF) thin films to detect water vapor across a wide concentration range is demonstrated using MOF-functionalized quartz surface acoustic wave (SAW) sensors. A range of 3-14,800 ppmv was obtained with thin films of the MOF Cu(3)(benzenetricarboxylate)(2) (Cu-BTC) deposited by an automated layer-by-layer method. Devices coated by a manual technique demonstrated sensitivity from 0.28 to 14,800 ppmv, the limit of our test system. This exceeds the sensitivity of many commercially available sensors. Cu-BTC layers were covalently bonded directly to the silicon oxide surface, allowing devices to be heated beyond 100 °C to desorb water adsorbed in the pores without decomposition, thereby regenerating the sensors. Sensor response as a function of coating thickness was evaluated, showing that the SAW sensor response is bounded by maximum and minimum layer thicknesses. Computer simulation of H(2)O uptake shows a multistep adsorption isotherm defined by initial adsorption at open Cu-sites, followed by pore-filling and finally full saturation. Modeling and experimental results are consistent. Calculated uptake values suggest an efficient adsorption of H(2)O by Cu-BTC. These results provide the first convincing evidence that MOF functionalization of compact sensing technologies such as SAW devices and microcantilevers can compete with state-of-the art devices.