Learning Sequential and Structural Dependencies Between Nucleotides for RNA N6-Methyladenosine Site Identification

N6-methyladenosine(m6A)is an important RNA methylation modification involved in regulating diverse biological processes across multiple species.Hence,the identification of m6A modification sites provides valuable insight into the biological mechanisms of complex diseases at the post-transcriptional level.Although a variety of identification algorithms have been proposed recently,most of them capture the features of m6A modification sites by focusing on the sequential dependencies of nucleotides at different positions in RNA sequences,while ignoring the structural dependencies of nucleotides in their threedimensional structures.To overcome this issue,we propose a cross-species end-to-end deep learning model,namely CR-NSSD,which conduct a cross-domain representation learning process integrating nucleotide structural and sequential dependencies for RNA m6A site identification.Specifically,CR-NSSD first obtains the pre-coded representations of RNA sequences by incorporating the position information into single-nucleotide states with chaos game representation theory.It then constructs a crossdomain reconstruction encoder to learn the sequential and structural dependencies between nucleotides.By minimizing the reconstruction and binary cross-entropy losses,CR-NSSD is trained to complete the task of m6A site identification.Extensive experiments have demonstrated the promising performance of CR-NSSD by comparing it with several state-of-the-art m6A identification algorithms.Moreover,the results of cross-species prediction indicate that the integration of sequential and structural dependencies allows CR-NSSD to capture general features of m6A modification sites among different species,thus improving the accuracy of cross-species identification.

Incorporating the Built Environment Interactions into Spatial Pattern Models to Understand Urban Metabolism in Tokyo＇s Residential Area

In Tokyo, as residential areas exist in the urban areas and are composed of areas owned by individual land owners, basically spatial changes are brought by redevelopments of each sites conducted by individual circumstances and motivations. Continuous redevelopments and spatial changes can be found dispersedly in areas. Once the spatial change in a certain site occurred in an area as a building, it will be contained in the built environment of the residential area which is defined by residents, planners and designers who will take part in the following spatial changes. In Tokyo, public transportation facilities are well developed, and residents＇ daily life involves activities such as a slow walking and bicycle, etc. around the place of residence near the public transportation hubs, each living territories are formed in this kind of manner. Considering the maintenance of spatial value in residential areas while understanding transformation of visual local environment in residential areas which focuses on appearance of each spatial change in an area of street will be of significant importance. In this paper, the authors try to describe interactions of spatial changes in existing urban residential areas focusing on utility of players who might take part in the following spatial changes and the method of discrete choice model.

Modification of Cu/ZSM-5 catalyst with CeO_2 for selective catalytic reduction of NO_x with ammonia

Cu/ZSM-5 and CeO_2-modified Cu/ZSM-5 catalysts were prepared by a wetness impregnation method. The addition of CeO_2 was found to enhance the NO_x selective catalytic reduction（SCR） activity of the catalyst at low temperatures, but the high-temperature activity was weakened. The catalysts were characterized by X-ray diffraction（XRD）, nitrogen physisorption, inductively coupled plasma optical emission spectrometry（ICP-OES）, X-ray photoelectron spectroscopy（XPS）, electron paramagnetic resonance（EPR）, H_2 temperature-programmed reduction（TPR） and NH_3 temperature-programmed desorption（TPD）. The results showed that more CuO clusters instead of isolated Cu^（2＋） species were obtained on the modified catalyst. These active CuO clusters, as well as the Cu-Ce synergistic effect, improved the redox property of the catalyst and low-temperatures SCR activity via promoting the oxidation of NO to NO_2 and fast SCR reaction. The loss in high-temperatures activity was attributed to the enhanced competitive oxidation of NH_3 by O_2 and decreased surface acidity of the catalyst.

Site-specific PEGylation of Human Growth Hormone by Mutated Sortase A

Human growth hormone（hGH）, a classic therapeutic protein, which promotes growth and wound healing, is released from the pituitary gland. As a protein drug, its short half-life is its main barrier to therapeutic efficacy. Various strategies have been designed to prolong its serum half-life, the most conunon of which is the conjugation with polyethylene glycol（PEG）, as this has been shown to significantly extend protein＇s serum half-life. However, PEGylation often results in random conjugation, which can lead to impaired protein function and hinder purification, characterization and evaluation of the PEGylated protein. Therefore, site specific PEGylation is a promising direction for PEG-protein conjugation. Here we took advantages of the mutated sortase A（7M） enzyme, which can enzymati- cally ligate the universal a-amino acids to a C-terminal tagged protein. This then allows specific modification of the C-terminal of hGH with PEG. This site-specific bound PEG-hGH has similar efficacy, receptor binding and cell proliferation as wild-type hGH; however, pharmacokinetic analysis demonstrates that its serum half-life is almost 24 times that of wild-type hGH. Herein, we provided a promising advancement in the development of site specific PEGylated therapeutic proteins.