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  1. Abstract

    Characterization of histone proteoforms with various post‐translational modifications (PTMs) is critical for a better understanding of functions of histone proteoforms in epigenetic control of gene expression. Mass spectrometry (MS)‐based top‐down proteomics (TDP) is a valuable approach for delineating histone proteoforms because it can provide us with a bird's‐eye view of histone proteoforms carrying diverse combinations of PTMs. Here, we present the first example of coupling capillary zone electrophoresis (CZE), ion mobility spectrometry (IMS), and MS for online multi‐dimensional separations of histone proteoforms. Our CZE‐high‐field asymmetric waveform IMS (FAIMS)‐MS/MS platform identified 366 (ProSight PD) and 602 (TopPIC) histone proteoforms from a commercial calf histone sample using a low microgram amount of histone sample as the starting material. CZE‐FAIMS‐MS/MS improved the number of histone proteoform identifications by about 3 folds compared to CZE‐MS/MS alone (without FAIMS). The results indicate that CZE‐FAIMS‐MS/MS could be a useful tool for comprehensive characterization of histone proteoforms with high sensitivity.

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  2. Free, publicly-accessible full text available May 1, 2024
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  5. Correlated Equilibrium is a solution concept that is more general than Nash Equilibrium (NE) and can lead to outcomes with better social welfare. However, its natural extension to the sequential setting, the Extensive Form Correlated Equilibrium (EFCE), requires a quadratic amount of space to solve, even in restricted settings without randomness in nature. To alleviate these concerns, we apply subgame resolving, a technique extremely successful in finding NE in zero-sum games to solving general-sum EFCEs. Subgame resolving refines a correlation plan in an online manner: instead of solving for the full game upfront, it only solves for strategies in subgames that are reached in actual play, resulting in significant computational gains. In this paper, we (i) lay out the foundations to quantify the quality of a refined strategy, in terms of the social welfare and exploitability of correlation plans, (ii) show that EFCEs possess a sufficient amount of independence between subgames to perform resolving efficiently, and (iii) provide two algorithms for resolving, one using linear programming and the other based on regret minimization. Both methods guarantee safety, i.e., they will never be counterproductive. Our methods are the first time an online method has been applied to the correlated, general-sum setting. 
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  6. Food waste and insecurity are two societal challenges that coexist in many parts of the world. A prominent force to combat these issues, food rescue platforms match food donations to organizations that serve underprivileged communities, and then rely on external volunteers to transport the food. Previous work has developed machine learning models for food rescue volunteer engagement. However, having long worked with domain practitioners to deploy AI tools to help with food rescues, we understand that there are four main pain points that keep such a machine learning model from being actually useful in practice: small data, data collected only under the default intervention, unmodeled objectives due to communication gap, and unforeseen consequences of the intervention. In this paper, we introduce bandit data-driven optimization which not only helps address these pain points in food rescue, but also is applicable to other nonprofit domains that share similar challenges. Bandit data-driven optimization combines the advantages of online bandit learning and offline predictive analytics in an integrated framework. We propose PROOF, a novel algorithm for this framework and formally prove that it has no-regret. We show that PROOF performs better than existing baseline on food rescue volunteer recommendation. 
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