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Summary: Background: While many patients seem to recover from SARS-CoV-2 infections, many patients report experiencing SARS-CoV-2 symptoms for weeks or months after their acute COVID-19 ends, even developing new symptoms weeks after infection. These long-term effects are called post-acute sequelae of SARS-CoV-2 (PASC) or, more commonly, Long COVID. The overall prevalence of Long COVID is currently unknown, and tools are needed to help identify patients at risk for developing long COVID. Methods: A working group of the Rapid Acceleration of Diagnostics-radical (RADx-rad) program, comprised of individuals from various NIH institutes and centers, in collaboration with REsearching COVID to Enhance Recovery (RECOVER) developed and organized the Long COVID Computational Challenge (L3C), a community challenge aimed at incentivizing the broader scientific community to develop interpretable and accurate methods for identifying patients at risk of developing Long COVID. From August 2022 to December 2022, participants developed Long COVID risk prediction algorithms using the National COVID Cohort Collaborative (N3C) data enclave, a harmonized data repository from over 75 healthcare institutions from across the United States (U.S.). Findings: Over the course of the challenge, 74 teams designed and built 35 Long COVID prediction models using the N3C data enclave. The top 10 teams all scored above a 0.80 Area Under the Receiver Operator Curve (AUROC) with the highest scoring model achieving a mean AUROC of 0.895. Included in the top submission was a visualization dashboard that built timelines for each patient, updating the risk of a patient developing Long COVID in response to clinical events. Interpretation: As a result of L3C, federal reviewers identified multiple machine learning models that can be used to identify patients at risk for developing Long COVID. Many of the teams used approaches in their submissions which can be applied to future clinical prediction questions. Funding: Research reported in this RADx® Rad publication was supported by the National Institutes of Health. Timothy Bergquist, Johanna Loomba, and Emily Pfaff were supported by Axle Subcontract: NCATS-STSS-P00438.

Abstract Background During the COVID-19 pandemic, United Kingdom (UK) stop smoking services had to shift to remote delivery models due to social distancing regulations, later reintroducing face-to-face provision. The “Living Well Smokefree” service in North Yorkshire County Council adopted a hybrid model offering face-to-face, remote, or a mix of both. This evaluation aimed to assess the hybrid approach’s strengths and weaknesses and explore potential improvements. Methods Conducted from September 2022 to February 2023, the evaluation consisted of three components. First, qualitative interviews involved 11 staff and 16 service users, analysed thematically. Second, quantitative data from the QuitManager system that monitored the numbers and proportions of individuals selecting and successfully completing a 4-week quit via each service option. Third, face-to-face service expenses data was used to estimate the value for money of additional face-to-face provision. The qualitative findings were used to give context to the quantitative data via an “expansion” approach and complementary analysis. Results Overall, a hybrid model was seen to provide convenience and flexible options for support. In the evaluation, 733 individuals accessed the service, with 91.3% selecting remote support, 6.1% face-to-face, and 2.6% mixed provision. Remote support was valued by service users and staff for promoting openness, privacy, and reducing stigma, and was noted as removing access barriers and improving service availability. However, the absence of carbon monoxide monitoring in remote support raised accountability concerns. The trade-off in “quantity vs. quality” of quits was debated, as remote support reached more users but produced fewer carbon monoxide-validated quits. Primarily offering remote support could lead to substantial workloads, as staff often extend their roles to include social/mental health support, which was sometimes emotionally challenging. Offering service users a choice of support options was considered more important than the “cost-per-quit”. Improved dissemination of information to support service users in understanding their options for support was suggested. Conclusions The hybrid approach allows smoking cessation services to evaluate which groups benefit from remote, face-to-face, or mixed options and allocate resources accordingly. Providing choice, flexible provision, non-judgmental support, and clear information about available options could improve engagement and match support to individual needs, enhancing outcomes.

Objective: The effects of Coronavirus disease 2019 (COVID-19) infection and altered processes of care on nonelective coronary artery bypass grafting (CABG) outcomes remain unknown. We hypothesized that patients with COVID-19 infection would have longer hospital lengths of stay and greater mortality compared with COVID-negative patients, but that these outcomes would not differ between COVID-negative and pre-COVID controls. Methods: The National COVID Cohort Collaborative 2020-2022 was queried for adult patients undergoing CABG. Patients were divided into COVID-negative, COVID-active, and COVID-convalescent groups. Pre-COVID control patients were drawn from the National Surgical Quality Improvement Program database. Adjusted analysis of the 3 COVID groups was performed via generalized linear models. Results: A total of 17,293 patients underwent nonelective CABG, including 16,252 COVID-negative, 127 COVID-active, 367 COVID-convalescent, and 2254 pre-COVID patients. Compared to pre-COVID patients, COVID-negative patients had no difference in mortality, whereas COVID-active patients experienced increased mortality. Mortality and pneumonia were higher in COVID-active patients compared to COVID-negative and COVID-convalescent patients. Adjusted analysis demonstrated that COVID-active patients had higher in-hospital mortality, 30- and 90-day mortality, and pneumonia compared to COVID-negative patients. COVID-convalescent patients had a shorter length of stay but a higher rate of renal impairment. Conclusions: Traditional care processes were altered during the COVID-19 pandemic. Our data show that nonelective CABG in patients with active COVID-19 is associated with significantly increased rates of mortality and pneumonia. The equivalent mortality in COVID-negative and pre-COVID patients suggests that pandemic-associated changes in processes of care did not impact CABG outcomes. Additional research into optimal timing of CABG after COVID infection is warranted.

Objectives To evaluate the effectiveness of COVID-19 vaccinations (initial and booster) during pre-Delta, Delta and Omicron dominant periods among pregnant people via (1) COVID-19 incident and severe infections among pregnant people who were vaccinated versus unvaccinated and (2) post-COVID-19 vaccination breakthrough infections and severe infections among vaccinated females who were pregnant versus non-pregnant.Design Retrospective cohort study using nationally sampled electronic health records data from the National COVID Cohort Collaborative, 10 December 2020 –7 June 2022.Participants Cohort 1 included pregnant people (15–55 years) and cohort 2 included vaccinated females of reproductive age (15–55 years).Exposures (1) COVID-19 vaccination and (2) pregnancy.Main outcome measures Adjusted HRs (aHRs) for COVID-19 incident or breakthrough infections and severe infections (ie, COVID-19 infections with related hospitalisations).Results In cohort 1, 301 107 pregnant people were included. Compared with unvaccinated pregnant people, the aHRs for pregnant people with initial vaccinations during pregnancy of incident COVID-19 were 0.77 (95% CI 0.62 to 0.96) and 0.88 (95% CI 0.73 to 1.07) and aHRs of severe COVID-19 infections were 0.65 (95% CI 0.47 to 0.90) and 0.79 (95% CI 0.51 to 1.21) during the Delta and Omicron periods, respectively. Compared with pregnant people with full initial vaccinations, the aHR of incident COVID-19 for pregnant people with booster vaccinations was 0.64 (95% CI 0.58 to 0.71) during the Omicron period. In cohort 2, 934 337 vaccinated people were included. Compared with vaccinated non-pregnant females, the aHRs of severe COVID-19 infections for people with initial vaccinations during pregnancy was 2.71 (95% CI 1.31 to 5.60) during the Omicron periods.Conclusions Pregnant people with initial and booster vaccinations during pregnancy had a lower risk of incident and severe COVID-19 infections compared with unvaccinated pregnant people across the pandemic stages. However, vaccinated pregnant people still had a higher risk of severe infections compared with non-pregnant females.

We present JWST and Atacama Large Millimeter/submillimeter Array (ALMA) imaging for the lensing system SPT0418−47, which includes a strongly lensed, dusty, star-forming galaxy at redshift z = 4.225 and an associated multiply imaged companion. The JWST NIRCam and MIRI imaging observations presented in this paper were acquired as part of the Early Release Science program Targeting Extremely Magnified Panchromatic Lensed Arcs and Their Extended Star formation (TEMPLATES). This data set provides robust mutiwavelength detections of stellar light in both the main (SPT0418A) and companion (SPT0418B) galaxies, while the ALMA detection of [C ii ] emission confirms that SPT0418B lies at the same redshift as SPT0418A. We infer that the projected physical separation of the two galaxies is 4.42 ± 0.05 kpc. We derive total magnifications of μ = 29 ± 1 and μ = 4.1 ± 0.7 for SPT0418A and SPT0418B, respectively. We use both prospector and cigale to derive stellar masses. We find that SPT0418A has a stellar mass of ${M}_{* }={3.4}_{-0.6}^{+1.1}\times {10}^{10}{M}_{\odot }$ from prospector or M _* = 1.5 ± 0.3 × 10 ^10 M _⊙ from cigale . The stellar mass ratio of SPT0418A and SPT0418B is roughly between 4 and 7 ( ${4.2}_{-1.6}^{+1.9}$ for prospector and 7.5 ± 3.7 for cigale ). We see evidence of extended structure associated with SPT0418A that is suggestive of a tidal feature. These features, along with the close projected proximity, imply that the system is interacting. Interestingly, the star formation rates and stellar masses of both galaxies are consistent with the main sequence of star-forming galaxies at this epoch, indicating that this ongoing interaction has not noticeably elevated the star formation levels.

This paper explores the application and advantages of remote sensing, machine learning, and mid-infrared spectroscopy (MIR) as a popular proximal sensing spectroscopy tool in the estimation of soil organic carbon (SOC). It underscores the practical implications and benefits of the integrated approach combining machine learning, remote sensing, and proximal sensing for SOC estimation and prediction across a range of applications, including comprehensive soil health mapping and carbon credit assessment. These advanced technologies offer a promising pathway, reducing costs and resource utilization while improving the precision of SOC estimation. We conducted a comparative analysis between MIR-predicted SOC values and laboratory-measured SOC values using 36 soil samples. The results demonstrate a strong fit (R² = 0.83), underscoring the potential of this integrated approach. While acknowledging that our analysis is based on a limited sample size, these initial findings offer promise and serve as a foundation for future research. We will be providing updates when we obtain more data. Furthermore, this paper explores the potential for commercialising these technologies in Australia, with the aim of helping farmers harness the advantages of carbon markets. Based on our study’s findings, coupled with insights from the existing literature, we suggest that adopting this integrated SOC measurement approach could significantly benefit local economies, enhance farmers’ ability to monitor changes in soil health, and promote sustainable agricultural practices. These outcomes align with global climate change mitigation efforts. Furthermore, our study’s approach, supported by other research, offers a potential template for regions worldwide seeking similar solutions.

Data competitions have become a popular approach to crowdsource new data analysis methods for general and specialized data science problems. Data competitions have a rich history in plant phenotyping, and new outdoor field datasets have the potential to embrace solutions across research and commercial applications. We developed the Global Wheat Challenge as a generalization competition in 2020 and 2021 to find more robust solutions for wheat head detection using field images from different regions. We analyze the winning challenge solutions in terms of their robustness when applied to new datasets. We found that the design of the competition had an influence on the selection of winning solutions and provide recommendations for future competitions to encourage the selection of more robust solutions.

Head (panicle) density is a major component in understanding crop yield, especially in crops that produce variable numbers of tillers such as sorghum and wheat. Use of panicle density both in plant breeding and in the agronomy scouting of commercial crops typically relies on manual counts observation, which is an inefficient and tedious process. Because of the easy availability of red–green–blue images, machine learning approaches have been applied to replacing manual counting. However, much of this research focuses on detection per se in limited testing conditions and does not provide a general protocol to utilize deep-learning-based counting. In this paper, we provide a comprehensive pipeline from data collection to model deployment in deep-learning-assisted panicle yield estimation for sorghum. This pipeline provides a basis from data collection and model training, to model validation and model deployment in commercial fields. Accurate model training is the foundation of the pipeline. However, in natural environments, the deployment dataset is frequently different from the training data (domain shift) causing the model to fail, so a robust model is essential to build a reliable solution. Although we demonstrate our pipeline in a sorghum field, the pipeline can be generalized to other grain species. Our pipeline provides a high-resolution head density map that can be utilized for diagnosis of agronomic variability within a field, in a pipeline built without commercial software.

The number of leaves at a given time is important to characterize plant growth and development. In this work, we developed a high-throughput method to count the number of leaves by detecting leaf tips in RGB images. The digital plant phenotyping platform was used to simulate a large and diverse dataset of RGB images and corresponding leaf tip labels of wheat plants at seedling stages (150,000 images with over 2 million labels). The realism of the images was then improved using domain adaptation methods before training deep learning models. The results demonstrate the efficiency of the proposed method evaluated on a diverse test dataset, collecting measurements from 5 countries obtained under different environments, growth stages, and lighting conditions with different cameras (450 images with over 2,162 labels). Among the 6 combinations of deep learning models and domain adaptation techniques, the Faster-RCNN model with cycle-consistent generative adversarial network adaptation technique provided the best performance (R2 = 0.94, root mean square error = 8.7). Complementary studies show that it is essential to simulate images with sufficient realism (background, leaf texture, and lighting conditions) before applying domain adaptation techniques. Furthermore, the spatial resolution should be better than 0.6 mm per pixel to identify leaf tips. The method is claimed to be self-supervised since no manual labeling is required for model training. The self-supervised phenotyping approach developed here offers great potential for addressing a wide range of plant phenotyping problems. The trained networks are available at https://github.com/YinglunLi/Wheat-leaf-tip-detection.

Sorghum, a genetically diverse C4 cereal, is an ideal model to study natural variation in photosynthetic capacity. Specific leaf nitrogen (SLN) and leaf mass per leaf area (LMA), as well as, maximal rates of Rubisco carboxylation (Vcmax), phosphoenolpyruvate (PEP) carboxylation (Vpmax), and electron transport (Jmax), quantified using a C4 photosynthesis model, were evaluated in two field-grown training sets (n=169 plots including 124 genotypes) in 2019 and 2020. Partial least square regression (PLSR) was used to predict Vcmax (R2=0.83), Vpmax (R2=0.93), Jmax (R2=0.76), SLN (R2=0.82), and LMA (R2=0.68) from tractor-based hyperspectral sensing. Further assessments of the capability of the PLSR models for Vcmax, Vpmax, Jmax, SLN, and LMA were conducted by extrapolating these models to two trials of genome-wide association studies adjacent to the training sets in 2019 (n=875 plots including 650 genotypes) and 2020 (n=912 plots with 634 genotypes). The predicted traits showed medium to high heritability and genome-wide association studies using the predicted values identified four QTL for Vcmax and two QTL for Jmax. Candidate genes within 200 kb of the Vcmax QTL were involved in nitrogen storage, which is closely associated with Rubisco, while not directly associated with Rubisco activity per se. Jmax QTL was enriched for candidate genes involved in electron transport. These outcomes suggest the methods here are of great promise to effectively screen large germplasm collections for enhanced photosynthetic capacity.