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  • Yan, J., Cai, J., Zhang, B., Wang, Y., Wong, D. F., & Siu, S. W. I. (2022). Recent Progress in the Discovery and Design of Antimicrobial Peptides Using Traditional Machine Learning and Deep Learning. Antibiotics, 11(10), 1451. https://doi.org/10.3390/antibiotics11101451

    Antimicrobial resistance has become a critical global health problem due to the abuse of conventional antibiotics and the rise of multi-drug-resistant microbes. Antimicrobial peptides (AMPs) are a group of natural peptides that show promise as next-generation antibiotics due to their low toxicity to the host, broad spectrum of biological activity, including antibacterial, antifungal, antiviral, and anti-parasitic activities, and great therapeutic potential, such as anticancer, anti-inflammatory, etc. Most importantly, AMPs kill bacteria by damaging cell membranes using multiple mechanisms of action rather than targeting a single molecule or pathway, making it difficult for bacterial drug resistance to develop. However, experimental approaches used to discover and design new AMPs are very expensive and time-consuming. In recent years, there has been considerable interest in using in silico methods, including traditional machine learning (ML) and deep learning (DL) approaches, to drug discovery. While there are a few papers summarizing computational AMP prediction methods, none of them focused on DL methods. In this review, we aim to survey the latest AMP prediction methods achieved by DL approaches. First, the biology background of AMP is introduced, then various feature encoding methods used to represent the features of peptide sequences are presented. We explain the most popular DL techniques and highlight the recent works based on them to classify AMPs and design novel peptide sequences. Finally, we discuss the limitations and challenges of AMP prediction.

  • He, Q.-Q., Siu, S. W. I., & Si, Y.-W. (2022). Attentive recurrent adversarial domain adaptation with Top-k pseudo-labeling for time series classification. Applied Intelligence. https://doi.org/10.1007/s10489-022-04176-x

    The key challenge of Unsupervised Domain Adaptation (UDA) for analyzing time series data is to learn domain-invariant representations by capturing complex temporal dependencies. In addition, existing unsupervised domain adaptation methods for time series data are designed to align marginal distribution between source and target domains. However, existing UDA methods (e.g. R-DANN Purushotham et al. (2017), VRADA Purushotham et al. (2017), CoDATS Wilson et al. (2020)) neglect the conditional distribution discrepancy between two domains, leading to misclassification of the target domain. Therefore, to learn domain-invariant representations by capturing the temporal dependencies and to reduce the conditional distribution discrepancy between two domains, a novel Attentive Recurrent Adversarial Domain Adaptation with Top-k time series pseudo-labeling method called ARADA-TK is proposed in this paper. In the experiments, our proposed method was compared with the state-of-the-art UDA methods (R-DANN, VRADA and CoDATS). Experimental results on four benchmark datasets revealed that ARADA-TK achieves superior classification accuracy when it is compared to the competing methods.

  • Alex, D., Cardoso, S. D., Ramos, A., & Gonçalves, D. (2022). Behavioural and endocrine responses to non-interactive live and video conspecifics in males of the Siamese fighting fish. Current Zoology, zoac078. https://doi.org/10.1093/cz/zoac078

    The physiological mechanisms underlying variation in aggression in fish remain poorly understood. One possibly confounding variable is the lack of standardization in the type of stimuli used to elicit aggression. The presentation of controlled stimuli in videos, a.k.a. video playback, can provide better control of the fight components. However, this technique has produced conflicting results in animal behaviour studies and needs to be carefully validated. For this, a similar response to the video and an equivalent live stimulus needs to be demonstrated. Further, different physiological responses may be triggered by live and video stimuli and it is important to demonstrate that video images elicit appropriate physiological reactions. Here, the behavioural and endocrine response of male Siamese fighting fish Betta splendens to a matched for size conspecific fighting behind a one-way mirror, presented live or through video playback, was compared. The video playback and live stimulus elicited a strong and similar aggressive response by the focal fish, with a fight structure that started with stereotypical threat displays and progressed to overt attacks. Post-fight plasma levels of the androgen 11-ketotestosterone were elevated as compared to controls, regardless of the type of stimuli. Cortisol also increased in response to the video images, as previously described for live fights in this species. These results show that the interactive component of a fight, and its resolution, are not needed to trigger an endocrine response to aggression in this species. The study also demonstrates for the first time in a fish a robust endocrine response to video stimuli and supports the use of this technique for researching aggressive behaviour in B. splendens.

  • Liao, S., Tao, C., Wen, H., Yang, W., Liu, J., Jamieson, J. W., Dias, Á. A., Zhu, C., Liang, J., Li, W., Ding, T., Li, X., & Zhang, H. (2022). Hydrothermal remobilization of subseafloor sulfide mineralization along mid-ocean ridges contributes to the global oceanic zinc isotopic mass balance. Geochimica et Cosmochimica Acta, 335, 56–67. https://doi.org/10.1016/j.gca.2022.08.022

    Hydrothermal activity on mid-ocean ridges is an important mechanism for the delivery of Zn from the mantle to the surface environment. Zinc isotopic fractionation during hydrothermal activity is mainly controlled by the precipitation of Zn-bearing sulfide minerals, in which isotopically light Zn is preferentially retained in solid phases rather than in solution during mineral precipitation. Thus, seafloor hydrothermal activity is expected to supply isotopically heavy Zn to the ocean. Here, we studied sulfide-rich samples from the Duanqiao-1 hydrothermal field, located on the Southwest Indian Ridge. We report that, at the hand-specimen scale, late-stage conduit sulfide material has lower δ66Zn values (−0.05 ± 0.15 ‰; n = 19) than early-stage material (+0.13 ± 0.15 ‰; n = 10). These lower values correlate with enrichments in Pb, As, Cd, and Ag, and elevated δ34S values. We attribute the low δ66Zn values to the remobilization of earlier sub-seafloor Zn-rich mineralization. Based on endmember mass balance calculations, and an assumption of a fractionation factor (αZnS-Sol.) of about 0.9997 between sphalerite and its parent solution, the remobilized Zn was found consist of about 1/3 to 2/3 of the total Zn in the fluid that formed the conduit samples. Our study suggests that late-stage subsurface hydrothermal remobilization may release isotopically-light Zn to the ocean, and that this process may be common along mid-ocean ridges, thus increasing the size of the previously identified isotopically light Zn sink in the ocean.

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Last update from database: 5/21/24, 11:02 PM (UTC)

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