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  1. Free, publicly-accessible full text available January 1, 2024
  2. Free, publicly-accessible full text available October 1, 2023
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  4. Free, publicly-accessible full text available September 1, 2023
  5. High throughput CRISPR screens are revolutionizing the way scientists unravel the genetic underpinnings of novel and evolved phenotypes. One of the critical challenges in accurately assessing screening outcomes is accounting for the variability in sgRNA cutting efficiency. Poorly active guides targeting genes essential to screening conditions obscure the growth defects that are expected from disrupting them. Here, we develop acCRISPR, an end-to-end pipeline that identifies essential genes in pooled CRISPR screens using sgRNA read counts obtained from next-generation sequencing. acCRISPR uses experimentally determined cutting efficiencies for each guide in the library to provide an activity correction to the screening outcomes, thus determining the fitness effect of disrupted genes. This is accomplished by calculating an optimization metric that quantifies the tradeoff between guide activity and library coverage, which is maximized to accurately classify genes essential to screening conditions. CRISPR-Cas9 and -Cas12a screens were carried out in the non-conventional oleaginous yeast Yarrowia lipolytica to determine a high-confidence set of essential genes for growth under glucose, a common carbon source used for the industrial production of oleochemicals. acCRISPR was also used in gain-and loss-of-function screens under high salt and low pH conditions to identify known and novel genes that were related to stressmore »tolerance. Collectively, this work presents an experimental-computational framework for CRISPR-based functional genomics studies that may be expanded to other non-conventional organisms of interest.« less
    Free, publicly-accessible full text available August 13, 2023
  6. Topological photonics offers enhanced control over electromagnetic fields by providing a platform for robust trapping and guiding of topological states of light. By combining the strong coupling between topological photons with phonons in hexagonal boron nitride (hBN), we demonstrate a platform to control and guide hybrid states of light and lattice vibrations. The observed topological edge states of phonon-polaritons are found to carry nonzero angular momentum locked to their propagation direction, which enables their robust transport. Thus, these topological quasiparticles enable the funneling of infrared phonons mediated by helical infrared photons along arbitrary pathways and across sharp bends, thereby offering opportunities for applications ranging from Raman and vibrational spectroscopy with structured phonon-polaritons to directional heat dissipation.
  7. The root system is critical for the survival of nearly all land plants and a key target for improving abiotic stress tolerance, nutrient accumulation, and yield in crop species. Although many methods of root phenotyping exist, within field studies, one of the most popular methods is the extraction and measurement of the upper portion of the root system, known as the root crown, followed by trait quantification based on manual measurements or 2D imaging. However, 2D techniques are inherently limited by the information available from single points of view. Here, we used X-ray computed tomography to generate highly accurate 3D models of maize root crowns and created computational pipelines capable of measuring 71 features from each sample. This approach improves estimates of the genetic contribution to root system architecture and is refined enough to detect various changes in global root system architecture over developmental time as well as more subtle changes in root distributions as a result of environmental differences. We demonstrate that root pulling force, a high-throughput method of root extraction that provides an estimate of root mass, is associated with multiple 3D traits from our pipeline. Our combined methodology can therefore be used to calibrate and interpret rootmore »pulling force measurements across a range of experimental contexts or scaled up as a stand-alone approach in large genetic studies of root system architecture.« less
  8. Singh R.P., Chalivendra V. (Ed.)
    Thin-walled structures have been widely used in automotive and aerospace industries to improve the system crashworthiness and impact protection. However, during manufacturing, transporting and handling processes, initial geometric imperfections are inevitably introduced to the thin-walled structures, which imposes negative impacts to the mechanical performance and service life of the thin-walled structures. In this study, we have introduced structural imperfection with controlled geometry and dimension to thin-walled steel tubes and characterized the mechanical response of these empty tubes and LN-filled tubes by quasi-static compression tests. Results show, the structural imperfection reduces the energy absorption capacity of empty tubes by about 20%. As the tube is filled with LN, the structural imperfection does not affect the energy absorption capacity of LN filled tube. The enhanced imperfection resistance is attributed to the suppression of imperfection growth caused by the strong liquid-solid interaction between the LN and tube wall. These findings suggest that the LN filling material can effectively reduce the adverse impact of structural imperfection and shed light on future design of thin-walled energy absorption devices.
  9. Ghate, A ; Krishnaiyer, K. ; Paynabar, K. (Ed.)
    Maintaining an appropriate staffing level is essential to providing a healthy workplace environment at nursing homes and ensuring quality care among residents. With the widespread Covid-19 pandemic, staff absenteeism frequently occurs due to mandatory quarantine and providing care to their inflicted family members. Even though some of the staff show up for work, they may have to perform additional pandemic-related protection duties. In combination, these changes lead to an uncertain reduction in the quantity of care each staff member able to provide in a future shift. To alleviate the staff shortage concern and maintain the necessary care quantity, we study the optimal shift scheduling problem for a skilled nursing facility under probabilistic staff shortage in the presence of pandemic-related service provision disruptions. We apply a two-stage stochastic programming approach to our study. Our objective is to assign staff (i.e., certified nursing aids) to shifts to minimize the total staffing cost associated with contract staff workload, the adjusted workload for the changing resident demand, and extra workload due to required sanitization. Thus, the uncertainties considered arise from probabilistic staff shortage in addition to resident service need fluctuation. We model the former source of uncertainty with a geometric random variable for eachmore »staffer. In a proof-of-the-concept study, we consider realistic COVID-19 pandemic response measures recommended by the Indiana state government. We extract payment parameter estimates from the COVID-19 Nursing Home Dataset publicly available by the Centers for Medicare and Medicaid Services (CMS). We conclude with our numerical experiments that when a skilled nursing facility is at low risk of the pandemic, the absenteeism rate and staff workload increase slightly, thus maintaining the current staffing level can still handle the service disruptions. On the other hand, under high-risk circumstances, with the sharp increase of the absence rate and workload, a care facility likely needs to hire additional full-time staff as soon as possible. Our research offers insights into staff shift scheduling in the face of uncertain staff shortages and service disruption due to pandemics and prolonged disasters.« less