ARTICLE | doi:10.20944/preprints202307.0848.v1
Subject: Computer Science And Mathematics, Mathematical And Computational Biology Keywords: Root-related proteins; Deep learning; Graph convolutional network; Multi-head attention; Network embedding
Online: 12 July 2023 (12:41:34 CEST)
The root system plays an irreplaceable role in plant growth. Its improvement can increase crop productivity. However, such system is still mysterious for us. The underlying mechanism has not been fully uncovered. The investigation on proteins related to the root system is an important means to complete this task. In the previous time, lack of root-related proteins makes it impossible to adopt machine learning methods for designing efficient models for the discovery of novel root-related proteins. Recently, a public database on root-related proteins was set up and machine learning methods can be applied in this field. In this study, we proposed a machine learning based model, named Graph-Root, for identification of root-related proteins. The features derived from protein sequences and one network were extracted, where the former features were processed by graph convolutional neural network and multi-head attention, and the later features abstracted the linkage between proteins. These features were fed into the fully connected layer to make prediction. The 5-fold cross-validation and independent tests suggested its good performance. It also outperformed the only one previous model, SVM-Root. Furthermore, the importance of each feature type and component in the proposed model was investigated.
ARTICLE | doi:10.20944/preprints202303.0345.v2
Subject: Computer Science And Mathematics, Artificial Intelligence And Machine Learning Keywords: neural architecture search; machine learning; computer vision
Online: 29 March 2023 (02:14:14 CEST)
Existing one-shot neural architecture search (NAS) methods have to conduct a search over a giant super-net, which leads to the huge computational cost. To reduce such cost, in this paper, we propose a method, called FTSO, to divide the whole architecture search into two sub-steps. Specifically, in the first step, we only search for the topology, and in the second step, we search for the operators. FTSO not only reduces NAS’s search time from days to 0.68 seconds, but also significantly improves the found architecture's accuracy. Our extensive experiments on ImageNet show that within 18 seconds, FTSO can achieve a 76.4% testing accuracy, 1.5% higher than the SOTA, PC-DARTS. In addition, FTSO can reach a 97.77% testing accuracy, 0.27% higher than the SOTA, with nearly 100% (99.8%) search time saved, when searching on CIFAR10.
ARTICLE | doi:10.20944/preprints202311.1196.v1
Subject: Chemistry And Materials Science, Nanotechnology Keywords: Ag@Cu2O core-shell; rGO; 4-NP; chemical catalytic
Online: 20 November 2023 (03:24:11 CET)
We successfully fabricated Ag@Cu2O core-shell decorated on reduced graphene oxide (rGO) nanocomposites (ACRN) by a simple and convenient in situ substitution method. The properties of these ACRN with heterostructure layers were characterized by scanning and transmission electron microscopies and absorption spectroscopy. We used p-nitrophenol (4-NP) as a probe molecule to determine the chemical catalytic activity of the ACRN. Upon introduction of rGO, a high electron transfer efficiency was achieved; thus, the catalytic activity was improved significantly. Therefore, the ACRN exhibited significantly improved catalytic activity for the reduction of 4-NP and showed the high application value in the removal of toxic and harmful substances from water. In addition, the fabricated ACRN was used for the reduction of organic dyes and explosive pollutants to generate nontoxic products. Furthermore, the high charge redistribution and transfer among Ag, Cu2O and rGO in the ACRN induced the high catalytic reduction of organic pollutants, indicating the excellent potential of these materials for applications in water pollution treatment.
ARTICLE | doi:10.20944/preprints202311.0635.v1
Subject: Physical Sciences, Optics And Photonics Keywords: Embedded spatial-temporal convolutional neural network (EST-CNN); aerosols classification; fire smokes; interferential aerosol
Online: 9 November 2023 (11:46:42 CET)
Photoelectric smoke detectors are the most cost-effective devices for very early fire alarms. However, due to different light intensity response values for different fire smoke and interference from interferential aerosols, they have a high false alarm rate, which limits their popularity in Chinese homes. To address these issues, an embedded spatial-temporal convolutional neural network (EST-CNN) model is proposed for real fire smokes identification and aerosols (fire smokes and interferential aerosol) classification. EST-CNN consists of three modules including information fusion, scattering feature extraction, and aerosol classification. Moreover, a two dimensional spatial-temporal scattering (2D-TS) matrix is designed to fuse the scattered light intensities in different channels and adjacent time slices, which is the output of the information fusion module and the input of the scattering feature extraction module. EST-CNN is trained and tested with experimental data measured on the established fire test platform using the developed dual-wavelength dual-angle photoelectric smoke detector. The optimal network parameters are selected through extensive experiments resulting in an average classification accuracy of 95.6% for different aerosols with only 66 kB network parameters. The experimental results demonstrate the feasibility of the designed EST-CNN model to be directly installed in existing commercial photoelectric smoke detectors to realize aerosol classification.
ARTICLE | doi:10.20944/preprints202305.0381.v1
Subject: Environmental And Earth Sciences, Remote Sensing Keywords: improved continuum removal; abundance normalization; continuum removal band depth (CRBD); linear correlation; carbonate mineral inversion
Online: 6 May 2023 (05:22:50 CEST)
Mapping or quantitative inversion through remote sensing technology is an active way for mineral monitoring in large or uncultivated forest areas. Different spectral features of minerals, induced by ionic composition, can be identified which are related to mineral type or abundance. Based on the distinctive spectral absorption around 2.33µm induced by the carbonate ion, we use it as an analytic target to propose an improved continuum removal (ICR) algorithm to couple with normalized abundance to evaluate the relationship between continuum removal band depth (CRBD) and carbonate ion abundance. Through experimentally testing with synthetic and real image data, ICR with ratio abundance normalization can enhance the linear relation of CRBD and abundance. We find this technique performs best for abundance retrieval. The lowest root mean square error is 0.0400 for synthetic data and the mean relative error is as low as 6.80% for real image data. Compared with five other algorithms, coupling normalized carbonate mineral abundance with ICR can improve the quantitative retrieval accuracy of carbonate ion. By using a hyperspectral library, we also present a way to retrieve abundance without ground samples. These results make the quantitative inversion of mineral abundance more reasonable by distinct or enhanced features and provide great potential for use to extend mineral information extraction in the absence of sample data, even for surveys of the Moon and Mars for mineral quantitative analysis.
ARTICLE | doi:10.20944/preprints202306.2039.v1
Subject: Environmental And Earth Sciences, Sustainable Science And Technology Keywords: sponge city; grey and green infrastructure; stormwater management model; integrated environmental benefits; monetary value; stormwater use
Online: 28 June 2023 (13:09:00 CEST)
The implementation of grey and green infrastructure is an effective mean to address urban flooding and nonpoint source pollution, but due to the complexity of the process and the diver-sity of benefits, there is a lack of measurement for their comprehensive benefits. Adopting a typ-ical university in Beijing as an example, this paper simulated the multidimensional benefits of the water quantity, water quality, and ecology of grey and green facility renovation by coupling the storm water management model (SWMM) and InfoWorks Integrated Catchment Manage-ment (ICM). Monetization methods and economical means were employed to characterize the comprehensive benefits. The results showed that grey and green infrastructure retrofitting re-duces the number of severe overflow nodes in the study area by 54.35%, the total overflow vol-ume by 22.17%, and the nonpoint source pollution level by approximately 80% under the heavy rain scenario and 60% under the rainstorm scenario. The annual benefits of grey and green infra-structure renovation reached ¥765,600/year, of this amount, ¥83,100/year is from hydrological regulation, ¥454,100/year is from nonpoint source pollution reduction, and ¥228,300/year is from ecological improvement. The benefits of green facilities were higher than those of grey facilities, and the combined benefits were negatively correlated with the rainfall level, with a total bene-fit–cost ratio of 1.19. The results provide methodological and data support for grey and green in-frastructure retrofitting within the context of sponge cities.
Subject: Engineering, Automotive Engineering Keywords: solid sensible heat storage; thermal calculation; fluid-solid coupling; heat transfer characteristics; experimental investigation
Online: 5 October 2020 (10:53:24 CEST)
Electric heating and solid thermal storage system (EHSTSS) is widely used in district clean heating and the flexibility adjustment of combined heat and power (CHP) unit. It has been an effective way to absorb renewable energy. Aiming at the thermal design calculation and experimental verification of EHSTSS, the thermal calculation and the heat transfer characteristics of the EHSTSS are investigated in this paper. Firstly, a thermal calculation method for the EHSTSS is proposed in the paper. The calculation flow and calculation method for key parameters of heating system, heat storage system, heat exchange system and fan-circulating system in the EHSTSS are studied. Then, the instantaneous heat transfer characteristics of the thermal storage system (TSS) in the EHSTSS are analyzed, and the heat transfer process of ESS is simulated by FLUENT software. The uniform temperature distribution in the heat storage and release process of the TSS verifies the good heat transfer characteristics of the EHSTSS. Finally, EHSTSS test verification platform is built, and the historical operation data of the EHSTSS is analyzed. During the heating and release thermal process, the maximum temperature standard deviation of each temperature measurement point is 28.3℃ and 59℃respectively. The correctness of the thermal calculation of the EHSTSS is verified.
ARTICLE | doi:10.20944/preprints202208.0540.v1
Subject: Environmental And Earth Sciences, Atmospheric Science And Meteorology Keywords: urban waterlogging risk; extreme rain; drainage capacity; Shanghai
Online: 31 August 2022 (08:55:36 CEST)
Waterlogging induced by rain in urban areas has a potential risk impact on property and safety. This paper focuses on the impact of rain on waterlogging and evaluates the waterlogging risk in the central city of Shanghai. A simplified waterlogging depth model is developed in different areas with different drainage capacity and rainfall in consumption of simplifying the effect of complex terrain characteristics and hydrological situation. Based on urban waterlogging depth and its classification collection, a Rain-induced Urban Waterlogging Risk Model(RUWRM) is further established to evaluate waterlogging risk in the central city. The results show that waterlogging depth is closely linked with rainfall and drainage, with a linear relationship between them. More rainfall leads to higher waterlogging risk, especially in the central city with imperfect drainage facilities. Rain-induced urban waterlogging risk model can rapidly gives the waterlogging rank caused by rainfall with a clear classification collection. The results of waterlogging risk prediction indicate that it is confident to get the urban waterlogging risk rank well and truly in advance with more accurate rainfall prediction. This general study is a contribution that allows the public, policy makers and relevant departments of urban operation to assess the appropriate management to reduce traffic intensity and personal safety or strategy to lead to less waterlogging risk.
ARTICLE | doi:10.20944/preprints202304.0600.v1
Subject: Biology And Life Sciences, Food Science And Technology Keywords: IDA mice; Antarctic krill peptide-iron; iron-regulated genes; iron bioavailability; in vivo antioxidant capacity
Online: 20 April 2023 (03:15:22 CEST)
Antarctic krill protein-iron complex and peptide-iron complex were obtained to investigate their iron bioavailability, expression of iron-regulated genes, and in vivo antioxidant capacity. Results indicated that Antarctic krill peptide-iron complex increased significantly the hemoglobin (Hb), serum iron (SI) and iron content in the liver and spleen in iron-deficiency anemia (IDA) mice (P < 0.05) compared with those of Antarctic krill protein-iron complex. Despite the gene expressions of divalent metal transporter 1(DMT1), transferrin (Tf) and transferrin receptor (TfR) could be better regulated by both Antarctic krill peptide-iron complex and protein-iron complex, the relative iron bioavailability of the Antarctic krill peptide-iron complex group (152.53±21.05%) was significantly higher than that of the protein-iron complex group (112.75±9.60%) (P<0.05). Moreover, Antarctic krill peptide-iron complex could enhance the antioxidant enzyme activities of superoxidase dismutase (SOD) and glutathione peroxidase (GSH-Px), reduce the malondialdehyde (MDA) level in IDA mice compared with the protein-iron complex, reducing the cell damage caused by IDA. Therefore, these results demonstrated that Antarctic krill peptide-iron complex could be used as a highly efficient and multifunctional iron supplement.
REVIEW | doi:10.20944/preprints202205.0158.v1
Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: Parkinson’s disease; Epigenetic targets; Histone deacetylases; Inhibitors; PROTACs
Online: 12 May 2022 (05:41:21 CEST)
Parkinson’s disease (PD) is a chronic progressive neurodegenerative disease that increasingly become a global threat for the elder people's health and life. Although there are some drugs in clinic for treating PD, these treatments only can alleviate the symptoms of PD patients but fail in curative therapies. Therefore, seeking other potential mechanisms to develop more effective treatments that can modify the course of PD is still highly desirable. In the last two decades, histone deacetylases as an important group of epigenetic targets in drug discovery have attracted much attention. This review is focused on the current knowledge about histone deacetylases involved in PD pathophysiology and their inhibitors used in PD study. Further perspectives related to small molecules that can inhibit or degrade histone deacetylases to treat PD are also discussed.
ARTICLE | doi:10.20944/preprints202111.0093.v1
Subject: Chemistry And Materials Science, Food Chemistry Keywords: waxy rice starch; α-amylase; protein; amylopectin structure
Online: 4 November 2021 (08:00:31 CET)
Waxy rice is one of the most popular traditional crops served as a staple food in China. In this study, the effect of different factors including α-amylase activity, protein, and amylopectin structure on the pasting properties of four waxy rice varieties were investigated. Rice flours treated with AgNO3 solution, DL-dithiothreitol (DTT) or protease, suggested that both α-amylase activity and protein significantly decrease the pasting viscosity of waxy rice flours. Chain length distribution of amylopectin as measured by high performance ion exchange chromatography (HPAEC-PAD) showed that starch with higher ratio of short chain leading to a higher pasting viscosity. X-Ray diffractograms showed that the crystal type of all the four varieties of rice starches were characteristic A-type. Relative crystallinity of each rice starch was further calculated, and a higher crystallization resulted in a higher viscosity. Our study would provide a fundamental knowledge of the relationship between different factors and waxy starch pasting properties, as well as be a reference for controlling the quality of waxy rice starch-based food.
ARTICLE | doi:10.20944/preprints202205.0184.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: amyloid precursor protein; photothrombotic stroke; ischemia; alpha-secretase; beta-secretase; gamma-secretase
Online: 13 May 2022 (08:39:09 CEST)
Photothrombotic stroke (PTS) stimulates the level of N- and C-terminal fragments of Amyloid precursor protein (APP) growth in the cytoplasm of ischemic penumbra cells not earlier but at 24 hours. Here we have shown that APP fragments are visualized in thin unmyelinated fibers of neurons, in containing mitochondria large fibers and in synapses but absent in the nuclei. At 24 hours after PTS, some elements of the destroyed tissue accumulated a significant amount of APP protein. The level of ADAM10 α-secretase decreased on the first day after PTS in the rat brain cortex and ADAM-10 co-localized with the lipid raft marker caveolin-1. PTS caused no changes in the level of β-secretase BACE1 either on the first day after PTS or in the early recovery period. The expression of proteins of the γ-secretase complex: presenilin-1 and nicastrin increased in astrocytes, but not in penumbra neurons after PTS. The β-secretase inhibitor LY2886721 did not affect the infarct size of the mouse cerebral cortex and the level of apoptosis of cells in the perifocal region after PTS. Whereas the inhibitor of γ-secretase DAPT reduced the expression of glial fibrillary acidic protein (GFAP) in astrocytes, prevented the growth of apoptosis of mouse cerebral cortex cells reducing the infarct volume on the 7th and 14th days after PTS. DAPT may be considered as a drug for stroke therapy.