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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.
Cognitive tasks are used to probe neuronal activity during functional magnetic resonance imaging (fMRI) to detect signs of aberrant cognitive functioning in patients diagnosed with schizophrenia (SZ). However, nonlinear (inverted-U-shaped) associations between neuronal activity and task difficulty can lead to misinterpretation of group differences between patients and healthy comparison subjects (HCs). In this paper, we evaluated a novel method for correcting these misinterpretations based on conditional performance analysis.
Participants included 25 HCs and 27 SZs who performed a working memory (WM) task (N-back) with 5 load conditions while undergoing fMRI. Neuronal activity was regressed onto: 1) task load (i.e., parametric task levels), 2) marginal task performance (i.e., performance averaged over all load conditions), or 3) conditional task performance (i.e., performance within each load condition).
In most regions of interest, conditional performance analysis uniquely revealed inverted-U-shaped neuronal activity in both SZs and HCs. After accounting for conditional performance differences between groups, we observed few difference in both the pattern and level of neuronal activity between SZs and HCs within regions that are classically associated with WM functioning (e.g., posterior dorsolateral prefrontal and parietal association cortices). However, SZs did show aberrant activity within the anterior dorsolateral prefrontal cortex.
Interpretations of differences in neuronal activity between groups, and of associations between neuronal activity and performance, should be considered within the context of task performance. Whether conditional performance-based differences reflect compensation, dedifferentiation, or other processes is not a question that is easily resolved by examining activation and performance data alone.
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.
ABSTRACT IMPACT: This study will provide the essential characterization of intrinsic neural activity in human brain organoids, both at the single cell and network levels, to harness for translational purposes. OBJECTIVES/GOALS: Brain organoids are 3D, stem cell-derived neural tissues that recapitulate neurodevelopment. However, to levy their full translational potential, a deeper understanding of their intrinsic neural activity is essential. Here, we present our preliminary analysis of maturing neural activity in human forebrain organoids. METHODS/STUDY POPULATION: Forebrain organoids were generated from human iPSC lines derived from healthy volunteers. Linear microelectrode probes were employed to record spontaneous electrical activity from day 77, 100, and 130 organoids. Single unit recordings were collected during hour-long recordings, involving baseline recordings followed by glutamatergic blockade. Subsequently, tetrodotoxin, was used to abolish action potential firing. Single units were identified via spike sorting, and the spatiotemporal evolution of baseline neural properties and network dynamics was characterized. RESULTS/ANTICIPATED RESULTS: Nine organoids were recorded successfully (n=3 per timepoint). A significant difference in number of units was seen across age groups (F (2,6) = 6.4178, p = 0.0323). Post hoc comparisons by the Tukey HSD test showed significantly more units in day 130 (51.67 ±14.15) than day 77 (16.33 ±14.98) organoids. Mean firing rates were significantly different in organoids based on age, with drug condition also trending toward significance (F (6,12) = 9.97; p = 0.0028 and p = 0.08 respectively). Post hoc comparisons showed a higher baseline firing rate in day 130 (0.99Hz ±0.30) organoids than their day 77 counterparts at baseline (0.31Hz ±0.066) and glutamate blockade (0.31Hz ±0.045). Preliminary network analysis showed no modularity or small-world features; however, these features are expected to emerge as organoids mature. DISCUSSION/SIGNIFICANCE OF FINDINGS: Initial analysis of brain organoid activity demonstrates changes in single unit properties as they mature. Additional work in this area, as well as further network analyses, will confer better sense of how to rationally utilize brain organoids for translational purposes.
As industrial-organizational (I-O) psychologists, we have expertise in applying psychological and/or organizational science to the workplace. However, many of us haven’t taken the time to think about how our I-O psychology knowledge can apply to our teaching practice. We walk through some examples of how I-O psychology research can help us be better teachers, and the goal of our paper is to encourage readers to make evidence-based changes to their teaching based on I-O psychology research. We organize our discussion around four areas: training and development, diversity and inclusion, groups and teams, and leadership. Within each, we offer small, medium, and large changes that could be incorporated into classrooms. We hope that readers will be inspired to build on what they do in their classrooms to help students learn about (and be inspired by) our field.
To assess the effect on hearing of non-functioning ventilation tubes due to blockage during the first six months post-operatively, using UK national guidelines.
A prospective, observational study was conducted on 37 children who underwent bilateral ventilation tube insertion. Air and bone conduction thresholds were measured before and following surgery, and at one, three and six months post-operatively. Tube non-function was assessed by tympanometry supported by otoscopy.
Post-operatively, an average of 21 per cent of ventilation tubes were non-functioning. Ears with non-functioning tubes had significantly (p = 0.0001) poorer mean air conduction thresholds than functioning tubes, with a magnitude of 6 dB HL. Ears with otorrhoea were most affected (15 per cent). At any one visit, the air–bone gap was closed to 10 dB or less in 76 per cent of ears. Non-functioning tubes reduced this to 56 per cent. Compared with tympanometry, otoscopy underdiagnosed tube non-function due to blockage by 22 per cent.
Non-functioning of ventilation tubes occurs frequently and can be missed on otoscopy. Although it is associated with poorer air conduction thresholds, the magnitude of this difference is unlikely to warrant further intervention unless there is otorrhoea or recurrence of bilateral hearing impairment.
Few options are available for controlling bermudagrass invasion of seashore paspalum. Bermudagrass and seashore paspalum tolerance to topramezone, triclopyr, or the combination of these two herbicides were evaluated in both greenhouse and field conditions. Field treatments included two sequential applications of topramezone (15.6 g ai ha−1) alone and five rates of topramezone + triclopyr (15.6 + 43.2, 15.6 + 86.3, 15.6 + 172.6, 15.6 + 345.2, or 15.6 g ai ha−1 + 690.4 g ae ha−1). Secondary greenhouse treatments included a single application of topramezone (20.8 g ha−1) or triclopyr (258.9 g ha−1) alone, or in combination at 20.8 + 258.9 or 20.8 + 517.8 g ha−1, respectively. Greenhouse and field results showed that topramezone applications in combination with triclopyr present opposite responses between bermudagrass and seashore paspalum. Topramezone increased bermudagrass injury and decreased seashore paspalum bleaching injury compared to topramezone alone. In field evaluations, topramezone + triclopyr at 15.6 + 690.4 g ha−1 used in sequential applications resulted in >90% injury to bermudagrass, however, injury decreased over time. Furthermore, sequential applications of topramezone + triclopyr at 15.6 + 690.4 g ha−1 resulted in >50% injury to seashore paspalum. Application programs including topramezone plus triclopyr should increase bermudagrass suppression and reduce seashore paspalum injury compared to topramezone alone. However, additional studies are needed because such practices will likely require manipulation of topramezone rate, application timing, application interval, and number of applications in order to maximize bermudagrass control and minimize seashore paspalum injury.
Gravitational waves from coalescing neutron stars encode information about nuclear matter at extreme densities, inaccessible by laboratory experiments. The late inspiral is influenced by the presence of tides, which depend on the neutron star equation of state. Neutron star mergers are expected to often produce rapidly rotating remnant neutron stars that emit gravitational waves. These will provide clues to the extremely hot post-merger environment. This signature of nuclear matter in gravitational waves contains most information in the 2–4 kHz frequency band, which is outside of the most sensitive band of current detectors. We present the design concept and science case for a Neutron Star Extreme Matter Observatory (NEMO): a gravitational-wave interferometer optimised to study nuclear physics with merging neutron stars. The concept uses high-circulating laser power, quantum squeezing, and a detector topology specifically designed to achieve the high-frequency sensitivity necessary to probe nuclear matter using gravitational waves. Above 1 kHz, the proposed strain sensitivity is comparable to full third-generation detectors at a fraction of the cost. Such sensitivity changes expected event rates for detection of post-merger remnants from approximately one per few decades with two A+ detectors to a few per year and potentially allow for the first gravitational-wave observations of supernovae, isolated neutron stars, and other exotica.
The Black-capped Petrel or Diablotin Pterodroma hasitata has a fragmented and declining population estimated at c.1,000 breeding pairs. On land, the species nests underground in steep ravines with dense understorey vegetation. The only confirmed breeding sites are located in the mountain ranges of Hispaniola in the Caribbean, where habitat loss and degradation are continuing threats. Other nesting populations may still remain undiscovered but, to locate them, laborious in situ nest searches must be conducted over expansive geographical areas. To focus nest-search efforts more efficiently, we analysed the environmental characteristics of Black-capped Petrel nesting habitat and modeled suitable habitat on Hispaniola using openly available environmental datasets. We used a univariate generalized linear model to compare the habitat characteristics of active Black-capped Petrel nests sites with those of potentially available sites (i.e. random pseudo-absences). Elevation, distance to coast, and the influence of tree cover and density emerged as important environmental variables. We then applied multivariate generalized linear models to these environmental variables that showed a significant relationship with petrel nesting activity. We used the top performing model of habitat suitability model to create maps of predicted suitability for Hispaniola. In addition to areas of known petrel activity, the model identified possible nesting areas for Black-capped Petrels in habitats not previously considered suitable. Based on model results, we estimated the total area of predicted suitable nesting habitat for Black-capped Petrels on Hispaniola and found that forest loss due to hurricanes, forest fires, and encroachment from agriculture had severely decreased availability of predicted suitable habitat between 2000 and 2018.
This paper investigates hedge funds’ ability to time industry-specific returns and shows that funds’ timing ability in the manufacturing industry improves their future performance, probability of survival, and ability to attract more capital. The results indicate that the best industry-timing hedge funds in the manufacturing sector have the highest return exposure to earnings surprises. This, together with persistently sticky earnings surprises, transparent information environment in regards to earnings releases, and large post-earnings-announcement drift in the manufacturing industry, explain to a great extent why best-timing hedge funds can generate significantly larger future returns compared to worst-timing hedge funds.
The radiocarbon (14C) calibration curve so far contains annually resolved data only for a short period of time. With accelerator mass spectrometry (AMS) matching the precision of decay counting, it is now possible to efficiently produce large datasets of annual resolution for calibration purposes using small amounts of wood. The radiocarbon intercomparison on single-year tree-ring samples presented here is the first to investigate specifically possible offsets between AMS laboratories at high precision. The results show that AMS laboratories are capable of measuring samples of Holocene age with an accuracy and precision that is comparable or even goes beyond what is possible with decay counting, even though they require a thousand times less wood. It also shows that not all AMS laboratories always produce results that are consistent with their stated uncertainties. The long-term benefits of studies of this kind are more accurate radiocarbon measurements with, in the future, better quantified uncertainties.
Previous genetic association studies have failed to identify loci robustly associated with sepsis, and there have been no published genetic association studies or polygenic risk score analyses of patients with septic shock, despite evidence suggesting genetic factors may be involved. We systematically collected genotype and clinical outcome data in the context of a randomized controlled trial from patients with septic shock to enrich the presence of disease-associated genetic variants. We performed genomewide association studies of susceptibility and mortality in septic shock using 493 patients with septic shock and 2442 population controls, and polygenic risk score analysis to assess genetic overlap between septic shock risk/mortality with clinically relevant traits. One variant, rs9489328, located in AL589740.1 noncoding RNA, was significantly associated with septic shock (p = 1.05 × 10–10); however, it is likely a false-positive. We were unable to replicate variants previously reported to be associated (p < 1.00 × 10–6 in previous scans) with susceptibility to and mortality from sepsis. Polygenic risk scores for hematocrit and granulocyte count were negatively associated with 28-day mortality (p = 3.04 × 10–3; p = 2.29 × 10–3), and scores for C-reactive protein levels were positively associated with susceptibility to septic shock (p = 1.44 × 10–3). Results suggest that common variants of large effect do not influence septic shock susceptibility, mortality and resolution; however, genetic predispositions to clinically relevant traits are significantly associated with increased susceptibility and mortality in septic individuals.
Judgment and decision-making (JDM) are ubiquitous within organizations. Leaders initiate critical judgments and decisions about organizational strategy and operating procedures. Continuous judgments and decisions are generated relating to the recruitment, selection, performance management, and departure of organizational talent. Every employee makes judgments and decisions on career directions, task acceptance, resource use, and time allocations across both work and non-work tasks. Employees generate frequent high-stakes judgments and decisions in courtrooms, as well as split-second decisions in emergency rooms and cockpits. It is hard to imagine workplace decisions and judgments such as these occurring without affective processes being involved.
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.
OBJECTIVES/GOALS: Primary graft dysfunction (PGD) is acute lung injury in the first three days after lung transplant. Patients that experience PGD have increased mortality and an increased risk of chronic lung allograft dysfunction. The pathogenesis is thought to be an ischemia-reperfusion injury but is incompletely understood and there are no specific therapies. We investigated the role of the microbiome in PGD and associations with inflammation and markers of aspiration. METHODS/STUDY POPULATION: We collected airway lavage samples from lung transplant donors before procurement and recipients after reperfusion. We extracted DNA, amplified the bacterial 16S rRNA gene, and sequenced on the Illumina MiSeq platform. QIIME2 and Deblur were used for bioinformatic analysis. R packages were used for downstream analysis and visualizations. The host response was quantified using the Milipore 41-plex Luminex and an ELISA for pepsin. Clinical data was collected by the Penn Lung Transplant Outcomes Group. PGD was assessed by degree of hypoxemia and chest X-ray findings in the 72 hours after transplant. RESULTS/ANTICIPATED RESULTS: There was no significant difference in alpha diversity (Shannon index, p = 0.51), biomass (via comparison of 16S amplicon PicoGreen, p = 0.6), or beta diversity (Weighted UniFrac, p = 0.472, PERMANOVA) between subjects with PGD grade 3 (n = 36) and those that did not (n = 96). On taxonomic analysis, we found an enrichment of Prevotella in donor and recipient lungs that went on to develop PGD (p = 0.05). To follow up this finding we measured immune response and pepsin concentrations in recipient lungs. We found elevated levels in 35/41 cytokines measured in subjects that developed PGD as well as an elevation in pepsin and a correlation between pepsin concentration and Prevotella relative abundance (Figure 1). Additionally, Prevotella relative abundance had statistically significant positive correlations with multiple cytokines such as IL-6 (Pearson’s = 0.26, p = 0.009) and eotaxin (Pearson’s = 0.24, p = 0.016). DISCUSSION/SIGNIFICANCE OF IMPACT: There is an enrichment of oral anerobes in lung allografts that eventually develop PGD. This is associated with elevated levels of pepsin and markers of inflammation. These lines of evidence suggest aspiration contributes to priming the allograft for PGD.
Raw milk cheeses are commonly consumed in France and are also a common source of foodborne outbreaks (FBOs). Both an FBO surveillance system and a laboratory-based surveillance system aim to detect Salmonella outbreaks. In early August 2018, five familial FBOs due to Salmonella spp. were reported to a regional health authority. Investigation identified common exposure to a raw goats' milk cheese, from which Salmonella spp. were also isolated, leading to an international product recall. Three weeks later, on 22 August, a national increase in Salmonella Newport ST118 was detected through laboratory surveillance. Concomitantly isolates from the earlier familial clusters were confirmed as S. Newport ST118. Interviews with a selection of the laboratory-identified cases revealed exposure to the same cheese, including exposure to batches not included in the previous recall, leading to an expansion of the recall. The outbreak affected 153 cases, including six cases in Scotland. S. Newport was detected in the cheese and in the milk of one of the producer's goats. The difference in the two alerts generated by this outbreak highlight the timeliness of the FBO system and the precision of the laboratory-based surveillance system. It is also a reminder of the risks associated with raw milk cheeses.