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Aim: Metabolic interactions within a microbial community play a key role in determining the structure, function, and composition of the community. However, due to the complexity and intractability of natural microbiomes, limited knowledge is available on interspecies interactions within a community. In this work, using a binary synthetic microbiome, a methanotroph-photoautotroph (M-P) coculture, as the model system, we examined different genome-scale metabolic modeling (GEM) approaches to gain a better understanding of the metabolic interactions within the coculture, how they contribute to the enhanced growth observed in the coculture, and how they evolve over time. Methods: Using batch growth data of the model M-P coculture, we compared three GEM approaches for microbial communities. Two of the methods are existing approaches: SteadyCom, a steady state GEM, and dynamic flux balance analysis (DFBA) Lab, a dynamic GEM. We also proposed an improved dynamic GEM approach, DynamiCom, for the M-P coculture. Results: SteadyCom can predict the metabolic interactions within the coculture but not their dynamic evolutions; DFBA Lab can predict the dynamics of the coculture but cannot identify interspecies interactions. DynamiCom was able to identify the cross-fed metabolite within the coculture, as well as predict the evolution of the interspecies interactions over time. Conclusion: A new dynamic GEM approach, DynamiCom, was developed for a model M-P coculture. Constrained by the predictions from a validated kinetic model, DynamiCom consistently predicted the top metabolites being exchanged in the M-P coculture, as well as the establishment of the mutualistic N-exchange between the methanotroph and cyanobacteria. The interspecies interactions and their dynamic evolution predicted by DynamiCom are supported by ample evidence in the literature on methanotroph, cyanobacteria, and other cyanobacteria-heterotroph cocultures. 

Pressure swing adsorption (PSA) is a widely used technology to separate a gas product from impurities in a variety of fields. Due to the complexity of PSA operations, process and instrument faults can occur at different parts and/or steps of the process. Thus, effective process monitoring is critical for ensuring efficient and safe operations of PSA systems. However, multi-bed PSA processes present several major challenges to process monitoring. First, a PSA process is operated in a periodic or cyclic fashion and never reaches a steady state; Second, the duration of different operation cycles is dynamically controlled in response to various disturbances, which results in a wide range of normal operation trajectories. Third, there is limited data for process monitoring, and bed pressure is usually the only measured variable for process monitoring. These key characteristics of the PSA operation make process monitoring, especially early fault detection, significantly more challenging than that for a continuous process operated at a steady state. To address these challenges, we propose a feature-based statistical process monitoring (SPM) framework for PSA processes, namely feature space monitoring (FSM). Through feature engineering and feature selection, we show that FSM can naturally handle the key challenges in PSA process monitoring and achieve early detection of subtle faults from a wide range of normal operating conditions. The performance of FSM is compared to the conventional SPM methods using both simulated and real faults from an industrial PSA process. The results demonstrate FSM’s superior performance in fault detection and fault diagnosis compared to the traditional SPM methods. In particular, the robust monitoring performance from FSM is achieved without any data preprocessing, trajectory alignment or synchronization required by the conventional SPM methods. 

In the past few decades, we have witnessed tremendous advancements in biology, life sciences and healthcare. These advancements are due in no small part to the big data made available by various high-throughput technologies, the ever-advancing computing power, and the algorithmic advancements in machine learning. Specifically, big data analytics such as statistical and machine learning has become an essential tool in these rapidly developing fields. As a result, the subject has drawn increased attention and many review papers have been published in just the past few years on the subject. Different from all existing reviews, this work focuses on the application of systems, engineering principles and techniques in addressing some of the common challenges in big data analytics for biological, biomedical and healthcare applications. Specifically, this review focuses on the following three key areas in biological big data analytics where systems engineering principles and techniques have been playing important roles: the principle of parsimony in addressing overfitting, the dynamic analysis of biological data, and the role of domain knowledge in biological data analytics. 

Silicon/graphite (Si/Gr) nanocomposites with controlled void spaces and encapsulated by a carbon shell (Si/Gr@void@C) are synthesized by utilizing high-energy ball milling to reduce micron-sized particles to nanoscale, followed by carbonization of polydopamine (PODA) to form a carbon shell, and finally partial etching of the nanostructured Si core by NaOH solution at elevated temperatures. In particular, the effects of ball milling time and NaOH etching temperature on the electrochemical properties of Si/Gr@void@C are investigated. Increasing the ball milling time results in the improved specific capacity of Si-based anodes. Carbon coating further enhances the specific capacity and capacity retention over charge/discharge cycles. The best cycle stability is achieved after partial etching of the Si core inside Si/Gr@void@C particles at either 70 or 80 C, leading to little or no capacity decay over 130 cycles. However, it is found that both carbon coating and NaOH etching processes cause some surface oxidation of the nanostructured Si particles derived from high-energy ball milling. The surface oxidation of the nanostructured Si results in decreases in specific capacity and should be minimized in future studies. The mechanistic understanding developed in this study paves the way to further improve the electrochemical performance of Si/Gr@void@C nanocomposites in future. 

For the pulping process in a pulp & paper plant that uses wood as a raw material, it is important to have real-time knowledge about the moisture content of the woodchips so that the process can be optimized and/or controlled correspondingly to achieve satisfactory product quality while minimizing the consumption of energy and chemicals. Both destructive and non-destructive methods have been developed for estimating moisture content in woodchips, but these methods are often lab-based that cannot be implemented online, or too fragile to stand the harsh manufacturing environment. To address these limitations, we propose a non-destructive and economic approach based on 5 GHz Wi-Fi and use channel state information (CSI) to estimate the moisture content in woodchips. In addition, we propose to use statistics pattern analysis (SPA) to extract features from raw CSI data of amplitude and phase difference. The extracted features are then used for classification model building using linear discriminant analysis (LDA) and subspace discriminant (SD) classification. The woodchip moisture classification results are validated using the oven drying method. 

In the last few decades, various spectroscopic soft sensors that predict sample properties from its spectroscopic readings have been reported. To improve prediction performance, variable selection that aims to eliminate irrelevant wavelengths is often performed prior to soft sensor model building. However, due to the data-driven nature of many variable selection methods, they can be sensitive to the choice of the training data, and oftentimes the selected wavelengths show little connection to the underlying chemical bonds or function groups that determine the property of the sample. To address these limitations, we proposed a new variable selection method, namely consistency enhanced evolution for variable selection (CEEVS), which focuses on identifying the variables that are consistently selected from different training dataset. To demonstrate the effectiveness and robustness of CEEVS, we compared it with three representative variable selection methods using two published NIR datasets. We show that by identifying variables with high selection consistency, CEEVS not only achieves improved soft sensor performance, but also identifies key chemical information from spectroscopic data.