DSpace community: 工學院

SSRTool: A web tool for evaluating RNA secondary structure predictions based on species-specific functional interpretability

title: SSRTool: A web tool for evaluating RNA secondary structure predictions based on species-specific functional interpretability abstract: RNA secondary structures can carry out essential cellular functions alone or interact with one another to form the hierarchical tertiary structures. Experimental structure identification approa ches can show the in vitro structures of RNA molecules. However, they usually have limits in the resolution and are costly. In silico structure prediction tools are thus primarily relied on for pre-experiment analysis. Various structure prediction models have been developed over the decades. Since these tools are usually used before knowing the actual RNA structures, evaluating and ranking the pile of secondary structure predictions of a given sequence is essential in computational analysis. In this research, we implemented a web service called SSRTool (RNA Secondary Structure prediction Ranking Tool) to assist in the ranking and evaluation of the generated predicted structures of a given sequence. Based on the computed species-specific interpretability significance in four common RNA structure–function aspects, SSRTool provides three functions along with visualization interfaces: (1) Rank user-generated predictions. (2) Provide an automated streamline of structure prediction and ranking for a given sequence. (3) Infer the functional aspects of a given structure. We demonstrated the applicability of SSRTool via real case studies and reported the similar trends between computed species-specific rankings and the corresponding prediction F1 values. The SSRTool web service is available online at https://cobisHSS0.im.nuk.edu.tw/SSRTool/, http://cosbi3.ee.ncku.edu.tw/SSRTool/, or the redirecting site https://github.com/cobisLab/SSRTool/. © 2022 The Author(s)
description: 113學年度第二學期升等參考著作

An aggregation method to identify the RNA meta-stable secondary structure and its functionally interpretable structure ensemble

title: An aggregation method to identify the RNA meta-stable secondary structure and its functionally interpretable structure ensemble abstract: RNA can provide vital cellular functions through its secondary or tertiary structure. Due to the low-throughput nature of experimental approaches, studies on RNA structures mainly resort to computational methods. However, current existing tools fail to consider RNA structure ensembles and do not provide ways to decipher functional hypotheses for the new predictions. In this research, a novel method was proposed to identify the functionally interpretable structure ensemble of a given RNA sequence and provide the meta-stable structure, or the most frequently observed functional RNA cellular conformation, based on the ensemble. In the prediction of meta-stable structures, the proposed method outperformed existing tools on a yeast test set. The inferred functional aspects were then manually checked and demonstrated a micro-averaging F1 value of 0.92. Further, a biological example of the yeast ASH1-E1 element was discussed to articulate that these functional aspects can also suggest testable hypotheses. Then the proposed method was verified to be well applicable to other species through a human test set. Finally, the proposed method was demonstrated to show resistance to sequence length-dependent performance deterioration.
description: 113學年度第二學期升等參考著作

Sustainable cement and clay support in Ni-Cu/Al2O3 catalysts for enhancing hydrogen production from methanol steam reforming

title: Sustainable cement and clay support in Ni-Cu/Al2O3 catalysts for enhancing hydrogen production from methanol steam reforming abstract: Sustainable cement-clay composite is used as the support of bimetallic Ni-Cu/Al2O3 catalysts for hydrogen production from methanol steam reforming (MSR) reaction. The results indicate that higher methanol conversion and hydrogen yield can be obtained using composite supported catalysts. The cement-clay composite possesses CO2 absorption capability, which can enhance MSR performance. In the cases of a large proportion of cement, the CO2 concentration in the product is decreased by 1-2% where methanol conversion and hydrogen yield are not reduced. By varying the catalyst compositions such as Ni content, Ni-Cu/Al2O3 loading, and the weight ratio of cement and clay, 100% methanol conversion can be achieved as Ni content and Ni-Cu/Al2O3 loading increase. However, the CO concentration also increases due to the enhanced reverse water gas shift reaction. The results of the prepared 12 cement-clay-supported cases show the best performance with methanol conversion of 100%, hydrogen yield of 2.85 mol center dot(mol CH3OH)-1, and CO concentration of 5.90%. The scanning electron microscope images indicate no sintering of the spent catalyst, and the thermogravimetric analysis shows low coke formation on the catalyst surface. Overall, cement-clay replacing metal components in catalysts can efficiently reduce costs and intensify hydrogen production. (c) 2022 Hydrogen Energy Publications LLC. Published by Elsevier Ltd. All rights reserved.
description: WOS

Metal oxide-based electrochemical sensors for pesticide detection in water and food samples: a review

title: Metal oxide-based electrochemical sensors for pesticide detection in water and food samples: a review abstract: The increasing need for food and agricultural resources necessitates using pesticides to protect plants, but this approach also poses pesticide poisoning and environmental hazards. Although designing an effective pesticide detection method is challenging, various technologies collaborate to develop an effective electrochemical sensor for detection of various pesticides. This review article examines the various metal oxides, their synthesis techniques, and their applications in electrochemical sensors, particularly for environmental applications, to detect pesticides in a variety of contaminated environmental samples. Metal oxides have unique properties that make them useful for pesticide detection because of their more active sites and electrical, optical, and semiconducting properties. Samarium molybdate-based electrode materials are considered the most promising direction for the development of electrode materials for pesticide sensors due to their economy, chemical stability, multiple valences, low detection limit, high sensitivity, and high electrocatalytic activity performance. In addition, this study investigates the current research trend in the detection of pesticides using metal oxide-based sensors in environmental samples, and researchers should expect new research perspectives and ideas. Overall, the metal oxide-based pesticide detection sensors will surely aid in meeting the growing demands for food and environmental monitoring and protection. The increasing need for food and agricultural resources necessitates using pesticides to protect plants, but this approach also poses pesticide poisoning and environmental hazards.
description: WOS