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Next‑Generation Sequencing‑Based Copy Number Variation Analysis in Chinese Patients with Primary Ciliary Dyskinesia Revealed Novel DNAH5 Copy Number Variations

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Phenomics

Phenomics 2024年第1期4卷 24-33页

作者： Weicheng chen Zhuoyao Guo Mengru Li Wei sheng Guoying Huang Cardiovascular Center Children’s Hospital of Fudan University399 Wanyuan RoadShanghai 201102China Respirology Department Children’s Hospital of Fudan UniversityShanghai 201102China

Primary ciliary dyskinesia(PCD)is a rare disorder characterized by extensive genetic heterogeneity.However,in the genetic pathogenesis of PCD,copy number variation(CNV)has not received sufcient attention and has rarely been reported,especially in China.Next-generation sequencing(NGS)followed by targeted CNV analysis was used in patients highly suspected to have PCD with negative results in routine whole-exome sequencing(WES)analysis.Quantitative real-time polymerase chain reaction(qPCR)and Sanger sequencing were used to confrm these CNVs.To further characterize the ciliary phenotypes,high-speed video microscopy analysis(HSVA),transmission electron microscopy(TEM),and immunofuorescence(IF)analysis were used.Patient 1(F1:II-1),a 0.6-year-old girl,came from a nonconsanguineous family-I.She presented with situs inversus totalis,neonatal respiratory distress,and sinusitis.The nasal nitric oxide level was markedly reduced.The respiratory cilia beat with reduced amplitude.TEM revealed shortened outer dynein arms(ODA)of cilia.chr5:13717907-13722661del spanning exons 71–72 was identifed by NGS-based CNV analysis.Patient 2(F2:IV-4),a 37-year-old man,and his eldest brother Patient 3(F2:IV-2)came from a consanguineous family-II.Both had sinusitis,bronchiectasis and situs inversus totalis.The respiratory cilia of Patient 2 and Patient 3 were found to be uniformly immotile,with ODA defects.Two novel homozygous deletions chr5:13720087_13733030delinsGTTTTC and chr5:13649539_13707643del,spanning exons 69–71 and exons 77–79 were identifed by NGS-based CNV analysis.Abnormalities in DNA copy number were confrmed by qPCR amplifcation.IF showed that the respiratory cilia of Patient 1 and Patient 2 were defcient in dynein axonemal heavy chain 5(DNAH5)protein expression.This report identifed three novel DNAH5 disease-associated variants by WES-based CNV analysis.Our study expands the genetic spectrum of PCD with DNAH5 in the Chinese population.

关键词： Primary ciliary dyskinesia DNAH5 gene Copy number variation Phenotypic heterogeneity

Hepatocyte growth factor promotes retinal pigment epithelium cell activity through MET/AKT signaling pathway

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International Journal of Ophthalmology(English edition) 2024年第5期17卷 806-814页

作者： Si-Rui Zhou Yu-sheng Zhu Wen-Ting Yuan Xiao-Yan Pan Tong Wang Xiao-Dong chen Faculty of Life Sciences and Medicine Northwest UniversityXi’an 710069Shaanxi ProvinceChina First Affiliated Hospital of Northwest University Northwest UniversityXi’an 710069Shaanxi ProvinceChina Department of Ophthalmology Xi’an No.1 HospitalXi’an 710002Shaanxi ProvinceChina Shaanxi Institute of Ophthalmology Shaanxi Provincial Key Lab of OphthalmologyClinical Research Center for Ophthalmology Diseases of Shaanxi ProvinceXi’an 710002Shaanxi ProvinceChina

AIM:To explore the effects of hepatocyte growth factor(HGF)on retinal pigment epithelium(RPE)cell behaviors.METHODS:The human adult retinal pigment epithelial cell line-19(ARPE-19)were treated by HGF or mesenchymalepithelial transition factor(MET)inhibitor SU11274 in vitro.Cell viability was detected by a Cell Counting Kit-8 assay.Cell proliferation and motility was detected by a bromodeoxyuridine incorporation assay and a wound healing assay,respectively.The expression levels of MET,phosphorylated MET,protein kinase B(AKT),and phosphorylated AKT proteins were determined by Western blot assay.The MET and phosphorylated MET proteins were also determined by immunofluorescence assay.RESULTS:HGF increased ARPE-19 cells’viability,proliferation and migration,and induced an increase of phosphorylated MET and phosphorylated AKT proteins.SU11274 significantly reduced cell viability,proliferation,and migration and decreased the expression of MET and AKT proteins.SU11274 suppressed HGF-induced increase of viability,proliferation,and migration in ARPE-19 cells.Additionally,SU11274 also blocked HGF-induced phosphorylation of MET and AKT proteins.CONCLUSION:HGF enhances cellular viability,proliferation,and migration in RPE cells through the MET/AKT signaling pathway,whereas this enhancement is suppressed by the MET inhibitor SU11274.HGF-induced MET/AKT signaling might be a vital contributor of RPE cells survival.

关键词： hepatocyte growth factor mesenchymal epithelial transition factor SU11274 retinal pigment epithelial cells

Prognostic significance and relationship of SMAD3 phosphoisoforms and VEGFR-1 in gastric cancer:A clinicopathological study

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World Journal of Gastrointestinal Oncology 2024年第1期16卷 118-132页

作者： Shi-Lin Lv Pei Guo Jun-Rong Zou Ren-sheng chen Ling-Yu Luo De-Qiang Huang Hospital of Gastroenterology Institute of Digestive DiseasesThe First Affiliated Hospital of Nanchang UniversityNanchang 330006Jiangxi ProvinceChina Department of Pathology Shenzhen Hospital of Southern Medical UniversityShenzhen 518000Guangdong ProvinceChina Institute of Urology The First Affiliated Hospital of Gannan Medical UniversityGanzhou 341000Jiangxi ProvinceChina Department of Pathology The First Affiliated Hospital of Nanchang UniversityNanchang 330006Jiangxi ProvinceChina

BACKGROUND The TGF-β/SMAD3 and VEGFR-1 signaling pathways play important roles in gastric cancer metastasis.SMAD3 phosphorylation is a crucial prognostic marker in gastric cancer.AIM To determine the prognostic value and relationship of SMAD3 phospho-isoforms and VEGFR-1 in gastric cancer.METHODS This was a single-center observational study which enrolled 98 gastric cancer patients and 82 adjacent normal gastric tissues from patients aged 32-84 years(median age 65)between July 2006 and April 2007.Patients were followed up until death or the study ended(median follow-up duration of 28.5 mo).The samples were used to generate tissue microarrays(TMAs)for immunohistochemical(IHC)staining.The expressions of TGF-β1,pSMAD3C(S423/425),pSMAD3L(S204),and VEGFR-1 in gastric cancer(GC)tumor tissue and normal tissue were measured by IHC staining using TMAs obtained from 98 GC patients.Prognosis and survival information of the patients was recorded by Outdo Biotech from May 2007 to July 2015.The relationship between TGF-β1,pSMAD3C(S423/425),pSMAD3L(S204),and VEGFR-1 protein expression levels was analyzed using Pearson's correlation coefficient.The relationship between protein expression levels and clinicopathological parameters was analyzed using the Chi-squared test.A survival curve was generated using the Kaplan-Meier survival analysis.RESULTS TGFβ-1 and VEGFR-1 expression was significantly upregulated in gastric cancer tissue compared to adjacent noncancerous tissue.The positive expression of phosphorylated isoforms of Smad3 varied depending on the phosphorylation site[pSMAD3C(S423/425):51.0%and pSMAD3L(S204):31.6%].High expression of pSMAD-3L(S204)was significantly correlated with larger tumors(P=0.038)and later N stages(P=0.035).Additionally,high expression of VEGFR-1 was closely correlated with tumor size(P=0.015)and pathological grading(P=0.013).High expression of both pSMAD3L(S204)and VEGFR-1 was associated with unfavorable outcomes in terms of overall survival(OS).Multivariate analysis indicated that high expression of

关键词： Gastric cancer pSMAD3L(S204) pSMAD3C(S423/425) Survival Transforming growth factor-β1 VEGFR-1

Magnetic-biased chiral molecules enabling highly oriented photovoltaic perovskites

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National Science Review 2024年第2期11卷 221-230页

作者： Jing chen Caner Deger Zhen-Huang Su Kai-Li Wang Guang-Peng Zhu Jun-Jie Wu Bing-chen He Chun-Hao chen Tao Wang Xing-Yu Gao Ilhan Yavuz Yan-Hui Lou Zhao-Kui Wang Liang-sheng Liao Institute of Functional Nano&Soft Materials(FUNSOM) Laboratory of Advanced Negative Carbon TechnologiesSoochow University Department of Physics Marmara University Shanghai Synchrotron Radiation Facility(SSRF) Shanghai Advanced Research InstituteChinese Academy of Sciences College of Energy Soochow Institute for Energy and Materials Innovations Soochow University Macao Institute of Materials Science and Engineering Macau University of Science and Technology

The interaction between sites A, B and X with passivation molecules is restricted when the conventional passivation strategy is applied in perovskite（ABX3） photovoltaics. Fortunately, the revolving A-site presents an opportunity to strengthen this interaction by utilizing an external field. Herein, we propose a novel approach to achieving an ordered magnetic dipole moment, which is regulated by a magnetic field via the coupling effect between the chiral passivation molecule and the A-site（formamidine ion） in perovskites.This strategy can increase the molecular interaction energy by approximately four times and ensure a well-ordered molecular arrangement. The quality of the deposited perovskite film is significantly optimized with inhibited nonradiative recombination. It manages to reduce the open-circuit voltage loss of photovoltaic devices to 360 mV and increase the power conversion efficiency to 25.22%. This finding provides a new insight into the exploration of A-sites in perovskites and offers a novel route to improving the device performance of perovskite photovoltaics.

关键词： perovskite photovoltaics magnetic moment A-site regulation chiral molecules

A hybrid physics-informed data-driven neural network for CO_(2) storage in depleted shale reservoirs

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Petroleum Science 2024年第1期21卷 286-301页

作者： Yan-Wei Wang Zhen-Xue Dai Gui-sheng Wang Li chen Yu-Zhou Xia Yu-Hao Zhou College of Construction Engineering Jilin UniversityChangchun130026JilinChina Institute of Intelligent Simulation and Early Warning for Subsurface Environment Jilin UniversityChangchun130026JilinChina School of Energy Resources China University of GeosciencesBeijing100083China Department of Safety Environmental Protection and Quality ManagementShengli OilfieldSinopecDongying257000ShandongChina Key Laboratory of Thermo-Fluid Science and Engineering of MOE School of Energy and Power EngineeringXi'an Jiaotong UniversityXi'an710049ShaanxiChina College of Computer Science and Technology China University of Petroleum(East China)Qingdao266580ShandongChina Department of Physics University of FribourgFribourg1700Switzerland

To reduce CO_(2) emissions in response to global climate change,shale reservoirs could be ideal candidates for long-term carbon geo-sequestration involving multi-scale transport processes.However,most current CO_(2) sequestration models do not adequately consider multiple transport mechanisms.Moreover,the evaluation of CO_(2) storage processes usually involves laborious and time-consuming numerical simulations unsuitable for practical prediction and decision-making.In this paper,an integrated model involving gas diffusion,adsorption,dissolution,slip flow,and Darcy flow is proposed to accurately characterize CO_(2) storage in depleted shale reservoirs,supporting the establishment of a training database.On this basis,a hybrid physics-informed data-driven neural network(HPDNN)is developed as a deep learning surrogate for prediction and inversion.By incorporating multiple sources of scientific knowledge,the HPDNN can be configured with limited simulation resources,significantly accelerating the forward and inversion processes.Furthermore,the HPDNN can more intelligently predict injection performance,precisely perform reservoir parameter inversion,and reasonably evaluate the CO_(2) storage capacity under complicated scenarios.The validation and test results demonstrate that the HPDNN can ensure high accuracy and strong robustness across an extensive applicability range when dealing with field data with multiple noise sources.This study has tremendous potential to replace traditional modeling tools for predicting and making decisions about CO_(2) storage projects in depleted shale reservoirs.

关键词： Deep learning Physics-informed data-driven neural network Depleted shale reservoirs CO_(2)storage Transport mechanisms

Prediction of impurity spectrum function by deep learning algorithm

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Chinese Physics B 2024年第5期33卷 52-63页

作者：刘婷韩榕生陈亮 School of Mathematics and Physics North China Electric Power UniversityBeijing 102206China Institute of Condensed Matter Physics North China Electric Power UniversityBeijing 102206China Hebei Key Laboratory of Physics and Energy Technology North China Electric Power UniversityBaoding 071003China

By using the numerical renormalization group(NRG)method,we construct a large dataset with about one million spectral functions of the Anderson quantum impurity model.The dataset contains the density of states(DOS)of the host material,the strength of Coulomb interaction between on-site electrons(U),and the hybridization between the host material and the impurity site(Γ).The continued DOS and spectral functions are stored with Chebyshev coefficients and wavelet functions,respectively.From this dataset,we build seven different machine learning networks to predict the spectral function from the input data,DOS,U,andΓ.Three different evaluation indexes,mean absolute error(MAE),relative error(RE)and root mean square error(RMSE),are used to analyze the prediction abilities of different network models.Detailed analysis shows that,for the two kinds of widely used recurrent neural networks(RNNs),gate recurrent unit(GRU)has better performance than the long short term memory(LSTM)network.A combination of bidirectional GRU(BiGRU)and GRU has the best performance among GRU,BiGRU,LSTM,and BiLSTM.The MAE peak of BiGRU+GRU reaches 0.00037.We have also tested a one-dimensional convolutional neural network(1DCNN)with 20 hidden layers and a residual neural network(ResNet),we find that the 1DCNN has almost the same performance of the BiGRU+GRU network for the original dataset,while the robustness testing seems to be a little weak than BiGRU+GRU when we test all these models on two other independent datasets.The ResNet has the worst performance among all the seven network models.The datasets presented in this paper,including the large data set of the spectral function of Anderson quantum impurity model,are openly available at https://***/10.57760/sciencedb.j00113.00192.

关键词： machine learning Anderson impurity model spectral function

Dynamic Analysis of A Deepwater Drilling Riser with A New Hang-off System

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China Ocean Engineering 2024年第1期38卷 29-41页

作者： LI Yan-wei LIU Xiu-quan WANG Jin-long chen Guo-ming CHANG Yuan-jiang sheng Lei-xiang Centre for Offshore Engineering and Safety Technology China University of PetroleumQingdao 266580China National Engineering Laboratory of Offshore Geophysical and Exploration Equipment China University of PetroleumQingdao 266580China China CNOOC Research Institute Co. Ltd.Beijing 100028China

The safety of risers in hang-off states is a vital challenge in offshore oil and gas engineering.A new hang-off system installed on top of risers is proposed for improving the security of risers.This approach leads to a challenging problem:coupling the dynamics of risers with a new hang-off system combined with multiple structures and complex constraints.To accurately analyze the dynamic responses of the coupled system,a coupled dynamic model is established based on the Euler-Bernoulli beam-column theory and penalty function method.A comprehensive analysis method is proposed for coupled dynamic analysis by combining the finite element method and the Newmarkβmethod.An analysis program is also developed in MATLAB for dynamic simulation.The simulation results show that the dynamic performances of the risers at the top part are significantly improved by the new hang-off system,especially the novel design,which includes the centralizer and articulation joint.The bending moment and lateral deformation of the risers at the top part decrease,while the hang-off joint experiences a great bending moment at the bottom of the lateral restraint area which requires particular attention in design and application.The platform navigation speed range under the safety limits of risers expands with the new hang-off system in use.

关键词： deepwater drilling riser new hang-off system dynamic analysis finite element method penalty function method

Surface engineering of Li-and Mn-rich layered oxides for superior Li-ion battery

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Tungsten 2024年第1期6卷 259-268页

作者： Lu-Xiang Ma Tian-Dong chen Chun-Xi Hai sheng-De Dong Xin He Qi Xu Hang Feng AXin Ji-Tao chen Yuan Zhou College of Materials and Chemistry and Chemical Engineering Chengdu University of TechnologyChendu 610000China Qinghai Building and Materials Research Co. LtdXining 810000China Beijing National Laboratory for Molecular Sciences College of Chemistry and Molecular EngineeringPeking UniversityBeijing 100871China

The Li-and Mn-rich layered oxides(R-LNCM)are considered as promising cathode materials for high-energy density lithium-ion batteries(LIBs).However,the interface side reaction aggravates the voltage and capacity fading between cathode material and electrolyte at high voltage,which severely hinders the practical application of LIB s.Herein,lithium polyacrylate(LiPAA)as the binder and coating agent is applied to suppress the voltage and capacity fading of R-LNCM electrode.The flexible LiPAA layers with high elasticity are capable of impeding cathode cracks on the particle surface via mechanical stress relief.Thus,superior voltage and capacity fading suppression on R-LNCM electrode is finally achieved.As a result,LiPAA-R-LNCM cathode exhibits a remarkable specific capacity of 186 mA·h·g^(-1)with~73%retention at 1℃after 200cycles.Further,the corresponding average discharge potential is maintained to~3.1 V with only~0.4 V falling.

关键词： LiPAA interphase layer Interface side reaction Cathode cracks Capacity and voltage fading suppression Liand Mn-rich cathode

Energy saving analysis for CO_(2)–O_(2)mixed injection technology in converter steelmaking

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Journal of Iron and Steel Research(International) 2024年第5期31卷 1095-1103页

作者： Bao-chen Han Chun-liang Gao Ya-qiang Li Dan Liu Guang-sheng Wei Rong Zhu Hebei Key Laboratory of Material Near-Net Forming Technology School of Material Science and EngineeringHebei University of Science and TechnologyShijiazhuang050018HebeiChina Department of Automotive Engineering Hebei Vocational University of Technology and EngineeringXingtai054000HebeiChina School of Metallurgical and Ecological Engineering University of Science and Technology BeijingBeijing100083China

Energy-saving in China's iron and steel industry still relies on the development and improvement of short-term energy saving technologies.Therefore,a special converter smelting technology incorporating energy saving was proposed.To evaluate the energy-saving potential of the CO_(2)–O_(2)mixed injection(COMI)technology,collected production data were used to develop an improved techno-economic model.Calculations reveal that the technology can save energy through auxiliary material consumption,sensible heat of solid by-product,iron loss reduction,and energy recovery.The application of COMI technology in an enterprise is cost effective,involving the energy saving potential of 0.206 GJ/t,the cost of conserved energy of−48.83 yuan/GJ,and a simple payback period of 0.35 year for a 60-million-yuan investment.Sensitivity analysis shows that the investment cost and discount rate primarily influence the cost of conserved energy of the technology.As the discount rate increased,the cost of conserved energy also gradually increased.Overall,the COMI technology is an energy-saving technology with good development prospects.

关键词： Converter steelmaking COMI technology Energy saving Techno-economic model Investment cost