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Background: Schools are high-risk settings for SARS-CoV-2 transmission, but necessary for children's educational and social-emotional wellbeing. Previous research suggests that wastewater monitoring can detect SARS-CoV-2 infections in controlled residential settings with high levels of accuracy. However, its effective accuracy, cost, and feasibility in non-residential community settings is unknown., Methods: The objective of this study was to determine the effectiveness and accuracy of community-based passive wastewater and surface (environmental) surveillance to detect SARS-CoV-2 infection in neighborhood schools compared to weekly diagnostic (PCR) testing. We implemented an environmental surveillance system in nine elementary schools with 1700 regularly present staff and students in southern California. The system was validated from November 2020 to March 2021., Findings: In 447 data collection days across the nine sites 89 individuals tested positive for COVID-19, and SARS-CoV-2 was detected in 374 surface samples and 133 wastewater samples. Ninety-three percent of identified cases were associated with an environmental sample (95% CI: 88%-98%); 67% were associated with a positive wastewater sample (95% CI: 57%-77%), and 40% were associated with a positive surface sample (95% CI: 29%-52%). The techniques we utilized allowed for near-complete genomic sequencing of wastewater and surface samples., Interpretation: Passive environmental surveillance can detect the presence of COVID-19 cases in non-residential community school settings with a high degree of accuracy., Funding: County of San Diego, Health and Human Services Agency, National Institutes of Health, National Science Foundation, Centers for Disease Control., Competing Interests: Authors declare they have no competing interests., (© 2023 The Author(s).)

Recent years have seen growing interest in leveraging deep learning models for monitoring epilepsy patients based on electroencephalographic (EEG) signals. However, these approaches often exhibit poor generalization when applied outside of the setting in which training data was collected. Furthermore, manual labeling of EEG signals is a time-consuming process requiring expert analysis, making fine-tuning patient-specific models to new settings a costly proposition. In this work, we propose the Maximum-Mean-Discrepancy Decoder (M2D2) for automatic temporal localization and labeling of seizures in long EEG recordings to assist medical experts. We show that M2D2 achieves 76.0% and 70.4% of F1-score for temporal localization when evaluated on EEG data gathered in a different clinical setting than the training data. The results demonstrate that M2D2 yields substantially higher generalization performance than other state-of-the-art deep learning-based approaches.

Atomistic Molecular Dynamics (MD) simulations provide researchers the ability to model biomolecular structures such as proteins and their interactions with drug-like small molecules with greater spatiotemporal resolution than is otherwise possible using experimental methods. MD simulations are notoriously expensive computational endeavors that have traditionally required massive investment in specialized hardware to access biologically relevant spatiotemporal scales. Our goal is to summarize the fundamental algorithms that are employed in the literature to then highlight the challenges that have affected accelerator implementations in practice. We consider three broad categories of accelerators: Graphics Processing Units (GPUs), Field-Programmable Gate Arrays (FPGAs), and Application Specific Integrated Circuits (ASICs). These categories are comparatively studied to facilitate discussion of their relative trade-offs and to gain context for the current state of the art. We conclude by providing insights into the potential of emerging hardware platforms and algorithms for MD.

Brain-inspired Hyper-dimensional(HD) computing is a novel and efficient computing paradigm. However, highly parallel architectures such as Processing-in-Memory(PIM) are bottle-necked by reduction operations required such as accumulation. To reduce this bottle-neck of HD computing in PIM, we present Stochastic-HD that combines the simplicity of operations in Stochastic Computing (SC) with the complex task solving capabilities of the latest HD computing algorithms. Stochastic-HD leverages deterministic SC, which enables all of HD operations to be done as highly parallel bitwise operations and removes all reduction operations, thus improving the throughput of PIM. To this end, we propose an in-memory hardware design for Stochastic-HD that exploits its high level of parallelism and robustness to approximation. Our hardware uses in-memory bitwise operations along with associative memory-like operations to enable a fast and energy-efficient implementation. With Stochastic-HD, we were able to reach a comparable accuracy with the Baseline-HD. Furthermore, by proposing an integrated Stochastic-HD retraining approach Stochastic-HD is able to reduce the accuracy loss to just 0.3%. We additionally accelerate the retraining process in our hardware design to create an end-to-end accelerator for Stochastic-HD. Finally, we also add support for HD Clustering to Stochastic-HD, which is the first to map the HD Clustering operations to the stochastic domain. As compared to the best PIM design for HD, Stochastic-HD is also 4.4% more accurate and 43.1× more energy-efficient., Competing Interests: SG was employed by the company IBM research. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Morris, Hao, Gupta, Khaleghi, Aksanli and Rosing.)

Increasing data volumes on high-throughput sequencing instruments such as the NovaSeq 6000 leads to long computational bottlenecks for common metagenomics data preprocessing tasks such as adaptor and primer trimming and host removal. Here, we test whether faster recently developed computational tools (Fastp and Minimap2) can replace widely used choices (Atropos and Bowtie2), obtaining dramatic accelerations with additional sensitivity and minimal loss of specificity for these tasks. Furthermore, the taxonomic tables resulting from downstream processing provide biologically comparable results. However, we demonstrate that for taxonomic assignment, Bowtie2's specificity is still required. We suggest that periodic reevaluation of pipeline components, together with improvements to standardized APIs to chain them together, will greatly enhance the efficiency of common bioinformatics tasks while also facilitating incorporation of further optimized steps running on GPUs, FPGAs, or other architectures. We also note that a detailed exploration of available algorithms and pipeline components is an important step that should be taken before optimization of less efficient algorithms on advanced or nonstandard hardware. IMPORTANCE In shotgun metagenomics studies that seek to relate changes in microbial DNA across samples, processing the data on a computer often takes longer than obtaining the data from the sequencing instrument. Recently developed software packages that perform individual steps in the pipeline of data processing in principle offer speed advantages, but in practice they may contain pitfalls that prevent their use, for example, they may make approximations that introduce unacceptable errors in the data. Here, we show that differences in choices of these components can speed up overall data processing by 5-fold or more on the same hardware while maintaining a high degree of correctness, greatly reducing the time taken to interpret results. This is an important step for using the data in clinical settings, where the time taken to obtain the results may be critical for guiding treatment.

Recent years have seen a growing interest in the development of non-invasive devices capable of detecting seizures which can be worn in everyday life. Such devices must be lightweight and unobtrusive which severely limit their on-board computing power and battery life. In this paper, we propose a novel technique based on hyperdimensional (HD) computing to detect epileptic seizures from 2-channel surface EEG recordings. The proposed technique eliminates the need for complicated feature extraction techniques required in conventional ML algorithms. The HD algorithm is also simple to implement and does not require expert knowledge for architectural optimizations needed for approaches based on neural networks. In addition, our proposed technique is light-weight and meets the computation and memory constraints of ultra-small devices. Experimental results on a publicly available dataset indicates our approach improves the accuracy compared to state-of-the-art techniques while consuming smaller or comparable power.