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  1. Free, publicly-accessible full text available May 9, 2024
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  5. Ribonucleic acid (RNA) is a fundamental biological molecule that is essential to all living organisms, performing a versatile array of cellular tasks. The function of many RNA molecules is strongly related to the structure it adopts. As a result, great effort is being dedicated to the design of efficient algorithms that solve the “folding problem”—given a sequence of nucleotides, return a probable list of base pairs, referred to as the secondary structure prediction. Early algorithms largely rely on finding the structure with minimum free energy. However, the predictions rely on effective simplified free energy models that may not correctly identify the correct structure as the one with the lowest free energy. In light of this, new, data-driven approaches that not only consider free energy, but also use machine learning techniques to learn motifs are also investigated and recently been shown to outperform free energy–based algorithms on several experimental data sets. In this work, we introduce the new ExpertRNA algorithm that provides a modular framework that can easily incorporate an arbitrary number of rewards (free energy or nonparametric/data driven) and secondary structure prediction algorithms. We argue that this capability of ExpertRNA has the potential to balance out different strengths and weaknessesmore »of state-of-the-art folding tools. We test ExpertRNA on several RNA sequence-structure data sets, and we compare the performance of ExpertRNA against a state-of-the-art folding algorithm. We find that ExpertRNA produces, on average, more accurate predictions of nonpseudoknotted secondary structures than the structure prediction algorithm used, thus validating the promise of the approach. Summary of Contribution: ExpertRNA is a new algorithm inspired by a biological problem. It is applied to solve the problem of secondary structure prediction for RNA molecules given an input sequence. The computational contribution is given by the design of a multibranch, multiexpert rollout algorithm that enables the use of several state-of-the-art approaches as base heuristics and allowing several experts to evaluate partial candidate solutions generated, thus avoiding assuming the reward being optimized by an RNA molecule when folding. Our implementation allows for the effective use of parallel computational resources as well as to control the size of the rollout tree as the algorithm progresses. The problem of RNA secondary structure prediction is of primary importance within the biology field because the molecule structure is strongly related to its functionality. Whereas the contribution of the paper is in the algorithm, the importance of the application makes ExpertRNA a showcase of the relevance of computationally efficient algorithms in supporting scientific discovery.« less
  6. Abstract This paper presents the results from an international survey that investigated the impacts of the built environment on occupant well-being during the corona virus disease 2019 (COVID-19) pandemic when most professionals were forced to work from home (WFH). The survey was comprised of 81 questions focusing on the respondent's profiles, residences, home indoor environmental quality, health, and home working experiences. A total of 1460 responses were collected from 35 countries, and 1137 of them were considered complete for the analysis. The results suggest that home spatial layout has a significant impact on occupant well-being during WFH since home-life distractions and noises due to the lack of a personal workspace are likely to prevent productive work. Lack of scenic views, inadequate daylighting, and poor acoustics were also reported to be detrimental to occupant productivity and the general WFH experience. It is also revealed from this survey that temperature, relative humidity, and indoor air quality generally have higher satisfaction ratios compared with the indoor lighting and acoustic conditions, and the home layout. Hence, home design for lighting, acoustics, and layout should also receive greater attention in the future.