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RSPSSL:A novel high-fidelity Raman spectral preprocessing scheme to enhance biomedical applications and chemical resolution visualization

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Light(Science & Applications) 2024年第2期13卷 366-386页

作者： jiaqi hu Gina Jinna Chen Chenlong Xue Pei Liang Yanqun Xiang Chuanlun Zhang Xiaokeng Chi Guoying Liu Yanfang Ye Dongyu Cui De Zhang Xiaojun yu Hong Dang Wen Zhang Junfan Chen Quan Tang Penglai Guo Ho-Pui Ho Yuchao Li Longqing Cong Perry Ping Shum State Key Laboratory of Optical Fiber and Cable Manufacture Technology Guangdong Key Laboratory of Integrated Optoelectronics IntellisenseDepartment of EEESouthern University of Science and TechnologyShenzhen 518055China College of Optical and Electronic Technology China Jiliang UniversityHangzhou 310018China Department of Nasopharyngeal Carcinoma Sun Yat-sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyGuangzhou 510060China Department of Ocean Science and Engineering Southern University of Science and TechnologyShenzhen 518055China Department of Nephrology Chaozhou People’s HospitalChaozhou 521011China Clinical Research Design Division Sun Yatsen Memorial HospitalGuangzhouGuangdong 510120China School of Automation Northwestern Polytechnical UniversityXi’anShaanxi 710072China Department of Biomedical Engineering The Chinese University of Hong KongHong KongChina Guangdong Provincial Key Laboratory of Nanophotonic Manipulation Institute of NanophotonicsJinan UniversityGuangzhou 511443China

Raman spectroscopy has tremendous potential for material analysis with its molecular fingerprinting capability in many branches of science and technology.It is also an emerging omics technique for metabolic profiling to shape precision medicine.However,precisely attributing vibration peaks coupled with specific environmental,instrumental,and specimen noise is problematic.Intelligent Raman spectral preprocessing to remove statistical bias noise and sample-related errors should provide a powerful tool for valuable information extraction.Here,we propose a novel Raman spectral preprocessing scheme based on self-supervised learning(RSPSSL)with high capacity and spectral fidelity.It can preprocess arbitrary Raman spectra without further training at a speed of~1900 spectra per second without human interference.The experimental data preprocessing trial demonstrated its excellent capacity and signal fidelity with an 88%reduction in root mean square error and a 60%reduction in infinite norm(L__(∞))compared to established techniques.With this advantage,it remarkably enhanced various biomedical applications with a 400%accuracy elevation(ΔAUC)in cancer diagnosis,an average 38%(few-shot)and 242%accuracy improvement in paraquat concentration prediction,and unsealed the chemical resolution of biomedical hyperspectral images,especially in the spectral fingerprint region.It precisely preprocessed various Raman spectra from different spectroscopy devices,laboratories,and diverse applications.This scheme will enable biomedical mechanism screening with the label-free volumetric molecular imaging tool on organism and disease metabolomics profiling with a scenario of high throughput,cross-device,various analyte complexity,and diverse applications.

关键词： spectral scheme resolution

Tetrathiafulvalene esters with high redox potentials and improved solubilities for non-aqueous redox flow battery applications

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Green Energy & Environment 2024年第5期9卷 899-908页

作者： Weikang hu jiaqi Xu Nanjie Chen Zongcai Deng Yuekun Lai Dongyang Chen College of Materials Science and Engineering Fuzhou UniversityFuzhou350116China College of Chemical Engineering Fuzhou UniversityFuzhou350116China

The exploitation of high performance redox-active substances is critically important for the development of non-aqueous redoxﬂow batteries.Herein,three tetrathiofulvalene(TTF)derivatives with different substitution groups,namely TTF diethyl ester(TTFDE),TTF tetramethyl ester(TTFTM),and TTF tetraethyl ester(TTFTE),are prepared and their energy storage properties are evaluated.It has been found that the redox potential and solubility of these TTF derivatives in conventional carbonate electrolytes increases with the number of ester groups.The battery with a catholyte of 0.2 mol L^(-1) of TTFTE delivers a speciﬁc capacity of more than 10 Ah L^(-1) at the current density of 0.5 C with two discharge voltage platforms locating at as high as 3.85 and 3.60 V vs.Li/Liþ.Its capacity retention can be improved from 2.34 Ah L^(-1) to 3.60 Ah L^(-1) after 100 cycles by the use of an anion exchange membrane to block the crossover of TTF species.The excellent cycling stability of the TIF esters is supported by their well-delocalized electrons,as revealed by the density function theory calculations.Therefore,the introduction of more and larger electron-withdrawing groups is a promising strategy to simultaneously increase the redox-potential and solubility of redox-active ma-terials for non-aqueous redoxﬂow batteries.

关键词： Non-aqueous redox flow batteries Tetrathiofulvarene Redox potential Solubility Substituent effect

Constrained re-calibration of two-equation Reynolds-averaged Navier–Stokes models

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Theoretical & Applied Mechanics Letters 2024年第2期14卷 82-89页

作者： Yuanwei Bin Xiaohan hu jiaqi Li Samuel J.Grauer Xiang I.A.Yang Department of Mechanical Engineering Pennsylvania State UniversityUniversity ParkPA 16802USA State Key Laboratory for Turbulence and Complex Systems Peking UniversityBeijing 100871China College of Engineering Peking UniversityBeijing 100871China

Machine-learned augmentations to turbulence models can be advantageous for flows within the training dataset but can often cause harm outside.This lack of generalizability arises because the constants(as well as the functions)in a Reynolds-averaged Navier–Stokes(RANS)model are coupled,and un-constrained re-calibration of these constants(and functions)can disrupt the calibrations of the baseline model,the preservation of which is critical to the model's generalizability.To safeguard the behaviors of the baseline model beyond the training dataset,machine learning must be constrained such that basic calibrations like the law of the wall are kept intact.This letter aims to identify such constraints in two-equation RANS models so that future machine learning work can be performed without violating these constraints.We demonstrate that the identified constraints are not limiting.Furthermore,they help preserve the generalizability of the baseline model.

关键词： Machine learning Turbulence modeling Reynolds-averaged Navier-Stokes

Uncertainty-Aware Physical Simulation of Neural Radiance Fields for Fluids

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Computer Modeling in Engineering & Sciences 2024年第7期140卷 1143-1163页

作者： Haojie Lian jiaqi Wang Leilei Chen Shengze Li Ruochen Cao Qingyuan hu Peiyun Zhao Key Laboratory of In-Situ Property-Improving Mining of Ministry of Education Taiyuan University of TechnologyTaiyuan030024China Henan International Joint Laboratory of Structural Mechanics and Computational Simulation College of Architectural and Civil EngineeringHuanghuai UniversityZhumadian463000China National Innovation Institute of Defense Technology Academy of Military ScienceBeijing100091China School of Software Taiyuan University of TechnologyJinzhong030600China School of Science Jiangnan UniversityWuxi214122China

This paper presents a novel framework aimed at quantifying uncertainties associated with the 3D reconstruction of smoke from2Dimages.This approach reconstructs color and density fields from 2D images using Neural Radiance Field(NeRF)and improves image quality using frequency regularization.The NeRF model is obtained via joint training ofmultiple artificial neural networks,whereby the expectation and standard deviation of density fields and RGB values can be evaluated for each pixel.In addition,customized physics-informed neural network(PINN)with residual blocks and two-layer activation functions are utilized to input the density fields of the NeRF into Navier-Stokes equations and convection-diffusion equations to reconstruct the velocity field.The velocity uncertainties are also evaluated through ensemble learning.The effectiveness of the proposed algorithm is demonstrated through numerical examples.The presentmethod is an important step towards downstream tasks such as reliability analysis and robust optimization in engineering design.

关键词： Uncertainty quantification neural radiance field physics-informed neural network frequency regularization twolayer activation function ensemble learning

The chemical characteristics of different sodium iron ethylenediaminetetraacetate sources and their relative bioavailabilities for broilers fed with a conventional corn‑soybean meal diet

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Journal of Animal Science and Biotechnology 2024年第2期15卷 826-843页

作者： Shengchen Wang Bingxin Wu Ling Zhu Weiyun Zhang Liyang Zhang We Wu jiaqi Wu Yun hu Tingting Li Xiaoyan Cui Xugang Luo College of Animal Science and Technology Yangzhou UniversityYangzhou 225000People’s Republic of China Mineral Nutrition Research Division State Key Laboratory of Animal NutritionInstitute of Animal ScienceChinese Academy of Agricultural SciencesBeijing 100193China

Background Our previous studies demonstrated that divalent organic iron(Fe)proteinate sources with higher complexation or chelation strengths as expressed by the greater quotient of formation(Qf)values displayed higher Fe bioavailabilities for broilers.Sodium iron ethylenediaminetetraacetate(NaFeEDTA)is a trivalent organic Fe source with the strongest chelating ligand EDTA.However,the bioavailability of Fe when administered as NaFeEDTA in broilers and other agricultural animals remains untested.Herein,the chemical characteristics of 12 NaFeEDTA products were determined.Of these,one feed grade NaFeEDTA(Qf=2.07×10^(8)),one food grade NaFeEDTA(Qf=3.31×10^(8)),and one Fe proteinate with an extremely strong chelation strength(Fe-Prot ES,Qf value=8,590)were selected.Their bioavailabilities relative to Fe sulfate(FeSO_(4)·7H_(2)O)for broilers fed with a conventional corn-soybean meal diet were evaluated during d 1 to 21 by investigating the effects of the above Fe sources and added Fe levels on the growth performance,hematological indices,Fe contents,activities and gene expressions of Fe-containing enzymes in various tissues of broilers.Results NaFeEDTA sources varied greatly in their chemical characteristics.Plasma Fe concentration(PI),transferrin saturation(TS),liver Fe content,succinate dehydrogenase(SDH)activities in liver,heart,and kidney,catalase(CAT)activity in liver,and SDH mRNA expressions in liver and kidney increased linearly(P<0.05)with increasing levels of Fe supplementation.However,differences among Fe sources were detected(P<0.05)only for PI,liver Fe content,CAT activity in liver,SDH activities in heart and kidney,and SDH mRNA expressions in liver and kidney.Based on slope ratios from multiple linear regressions of the above indices on daily dietary analyzed Fe intake,the average bioavailabilities of Fe-Prot ES,feed grade NaFeEDTA,and food grade NaFeEDTA relative to the inorganic FeSO_(4)·7H_(2)O(100%)for broilers were 139%,155%,and 166%,respectively.Conclusions The bioavailabilities of organic Fe sources

关键词： Broilers Chelation strengths Fe-containing enzymes NaFeEDTA Relative bioavailabilities

Neural stem cell-derived exosomes regulate cell proliferation,migration,and cell death of brain microvascular endothelial cells via the miR-9/Hes1 axis under hypoxia

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Animal Models and Experimental Medicine 2024年第1期7卷 24-35页

作者： Xiaojun Deng Xiaoyi hu Shang Wang hui Zhao Yaqin Wei jiaqi Fu Wenhui Wu Jinming Liu Caicai Zhang Lili Wang Ping Yuan Department of Critical Care Medicine Shanghai Sixth People's HospitalShanghai Jiao Tong UniversityShanghaiChina Department of Cardio-Pulmonary Circulation Shanghai Pulmonary HospitalSchool of MedicineTongji UniversityShanghaiChina Institute of Bismuth Science University of Shanghai for Science and TechnologyShanghaiChina Department of Physiology Hainan Medical University HaikouHainanChina Department of Clinical Medical Laboratory Center Hangzhou Red Cross HospitalZhejiangChina

Background:Our previous study found that mouse embryonic neural stem cell(NSC)-derived exosomes(EXOs)regulated NSC differentiation via the miR-9/Hes1 axis.However,the effects of EXOs on brain microvascular endothelial cell(BMEC)dysfunction via the miR-9/Hes1 axis remain unknown.Therefore,the current study aimed to determine the effects of EXOs on BMEC proliferation,migration,and death via the miR-9/Hes1 axis.Methods:Immunofluorescence,quantitative real-time polymerase chain reaction,cell counting kit-8 assay,wound healing assay,calcein-acetoxymethyl/propidium iodide staining,and hematoxylin and eosin staining were used to determine the role and mechanism of EXOs on BMECs.Results:EXOs promoted BMEC proliferation and migration and reduced cell death under hypoxic conditions.The overexpression of miR-9 promoted BMEC prolifera-tion and migration and reduced cell death under hypoxic conditions.Moreover,miR-9 downregulation inhibited BMEC proliferation and migration and also promoted cell death.Hes1 silencing ameliorated the effect of amtagomiR-9 on BMEC proliferation and migration and cell death.Hyperemic structures were observed in the regions of the hippocampus and cortex in hypoxia-induced mice.Meanwhile,EXO treatment improved cerebrovascular alterations.Conclusion:NSC-derived EXOs can promote BMEC proliferation and migra-tion and reduce cell death via the miR-9/Hes1 axis under hypoxic conditions.Therefore,EXO therapeutic strategies could be considered for hypoxia-induced vascular injury.

关键词： brain microvascular endothelial cells exosomes Hes1 miR-9 neural stem cells

Spatial continuous modeling of early Cenozoic carbon cycle and climate

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National Science Review 2024年第4期11卷 30-32页

作者： Yonggang Liu Jian Zhang Haoyue Zuo Zhilin He jiaqi Guo Qifan Lin Haonan Yu Jiawenjing Lan Jing Han Zhihong Song Zihan Yin Liang Zhao Yongyun hu Zhengtang Guo Laboratory for Climate and Ocean-Atmosphere Studies Department of Atmospheric and Oceanic Sciences School of Physics Peking University Key Laboratory of Cenozoic Geology and Environment Institute of Geology and GeophysicsChinese Academy of Sciences State Key Laboratory of Lithospheric Evolution Institute of Geology and Geophysics Chinese Academy of Sciences

The partial pressure of atmospheric CO2（pCO2） is determined by the carbon cycle that involves climate, biogeochemistry, and plate tectonics. In this cycle,atmospheric CO2is converted into organic carbon and carbonates by biological activities and silicate weathering, and buried as sediments. The sediments on the ocean floor are subducted into the Earth’s interior, and subsequently converted back into CO2and outgassed into the atmosphere.

关键词： ATMOSPHERIC CO2

Degeneration Directory:a multi-omics web resource for degenerative diseases

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Protein & Cell 2024年第5期15卷 385-392页

作者： Haoteng Yan Changfa Lu Chenyang Lan Si Wang Weiqi Zhang Zan He Jinghao hu jiaqi Ai Guang-hui Liu Shuai Ma Yuanchun Zhou Jing Qu State Key Laboratory of Membrane Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China State Key Laboratory of Stem Cell and Reproductive Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China Key Laboratory of Organ Regeneration and Reconstruction Institute of ZoologyChinese Academy of SciencesBeijing 100101China Advanced Innovation Center for human Brain Protection and National Clinical Research Center for Geriatric DisordersXuanwu Hospital Capital Medical UniversityBeijing 100053China Aging Translational Medicine Center International Center for Aging and CancerBeijing Municipal Geriatric Medical Research CenterXuanwu HospitalCapital Medical UniversityBeijing 100053China Computer Network Information Center Chinese Academy of SciencesBeijing 100190China The Fifth People’s Hospital of Chongqing Chongqing 400062China Aging Biomarker Consortium Beijing 100101China CAS Key Laboratory of Genomic and Precision Medicine Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Sino-Danish College University of Chinese Academy of SciencesBeijing 101408China Beijing Institute for Stem Cell and Regenerative Medicine Beijing 100101China Institute for Stem Cell and Regeneration Chinese Academy of SciencesBeijing 100101China

Background of database.Organ degeneration refers to the gradual decline in organ function and structure deterioration that occurs during aging,which represents the greatest risk factor for various degenerative diseases,including cardiovascular diseases,neurodegenerative diseases,and osteoarthritis,etc.(Aging Biomarker et al.,2023;Becker et al.,2018;Cai et al.,2022).

关键词： Directory web Becker

KLF4 facilitates chromatin accessibility remodeling in porcine early embryos

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Science China(Life Sciences) 2024年第1期67卷 96-112页

作者： Wei Zhu Guowei Bu Ruifeng hu Jixiang Zhang Lianyong Qiao Kai Zhou Tingting Wang Qiao Li Jingjing Zhang Linhui Wu Yali Xie Taotao hu Shichun Yang jiaqi Guan Xiaoyu Chu Juanjuan Shi Xia Zhang Falong Lu Xin Liu Yi-Liang Miao Institute of Stem Cell and Regenerative Biology College of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhan 430070China Key Laboratory of Agricultural Animal Genetics Breeding and Reproduction(Huazhong Agricultural University)Ministry of EducationWuhan 430070China State Key Laboratory of Molecular Developmental Biology Institute of Genetics and Developmental BiologyInnovative Academy of Seed DesignChinese Academy of SciencesBeijing 100101China Frontiers Science Center for Animal Breeding and Sustainable Production Huazhong Agricultural UniversityWuhan 430070China hubei Hongshan Laboratory Wuhan 430070China

Chromatin accessibility remodeling driven by pioneer factors is critical for the development of early embryos.Current studies have illustrated several pioneer factors as being important for agricultural animals,but what are the pioneer factors and how the pioneer factors remodel the chromatin accessibility in porcine early embryos is not clear.By employing low-input DNase-seq(liDNase-seq),we profiled the landscapes of chromatin accessibility in porcine early embryos and uncovered a unique chromatin accessibility reprogramming pattern during porcine preimplantation development.Our data revealed that KLF4 played critical roles in remodeling chromatin accessibility in porcine early embryos.Knocking down of KLF4 led to the reduction of chromatin accessibility in early embryos,whereas KLF4 overexpression promoted the chromatin openness in porcine blastocysts.Furthermore,KLF4 deficiency resulted in mitochondrial dysfunction and developmental failure of porcine embryos.In addition,we found that overexpression of KLF4 in blastocysts promoted lipid droplet accumulation,whereas knockdown of KLF4 disrupted this process.Taken together,our study revealed the chromatin accessibility dynamics and identified KLF4 as a key regulator in chromatin accessibility and cellular metabolism during porcine preimplantation embryo development.

关键词： porcine embryos liDNase-seq chromatin accessibility KLF4 mitochondrion lipid droplets