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An inferred functional impact map of genetic variants in rice

Molecular Plant 2021年第9期14卷 1584-1599页

作者： Hu Zhao Jiacheng Li ling Yang Gang Qin Chunjiao Xia Xingbing Xu Yangmeng Su Yinmeng Liu Luchang Ming ling-ung chen Lizhong Xiong Weibo Xie National Key Laboratory of Crop Genetic Improvement Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina Hubei Key Laboratory of Agricultural Bioinformatics College of InformaticsHuazhong Agricultural UniversityWuhanChina State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources College of Life Science and TechnologyGuangxi UniversityNanningChina

Interpreting the functional impacts of genetic variants(GVs)is an important challenge for functional genomic studies in crops and next-generation breeding.Previous studies in rice(Oryza sativa)have focused mainly on the identification of GVs,whereas systematic functional annotation of GVs has not yet been performed.Here,we present a functional impact map of GVs in rice.We curated haplotype information for 17397026 GVs from sequencing data of 4726 rice accessions.We quantitatively evaluated the effects of missense mutations in coding regions in each haplotype based on the conservation of amino acid residues and obtained the effects of 918848 non-redundant missense GVs.Furthermore,we generated high-quality chromatin accessibility(CA)data from six representative rice tissues and used these data to train deep convolutional neural network models to predict the impacts of 5067405 GVs for CA in regulatory regions.We characterized the functional properties and tissue specificity of the GV effects and found that large-effect GVs in coding and regulatory regions may be subject to selection in different directions.Finally,we demonstrated how the functional impact map could be used to prioritize causal variants in mapping populations.This impact map will be a useful resource for accelerating gene cloning and functional studies in rice,and can be freely queried in RiceVarMap V2.0(http://***).

关键词： ricegenetic variantschromatin accessibilityfunctional impact mapdeep learning

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Evaluation of 3D crustal seismic velocity models in southwest China:Model performance,limitation,and prospects

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Science China Earth Sciences 2024年第2期67卷 604-619页

作者： Xin WANG ling chen Qi-Fu chen Key Laboratory of Earth and Planetary Physics Institute of Geology and GeophysicsChinese Academy of SciencesBeijing100029China College of Earth and Planetary Sciences University of Chinese Academy of SciencesBeijing100049China State Key Laboratory of Lithospheric Evolution Institute of Geology and GeophysicsChinese Academy of SciencesBeijing100029China

Southwest China is a tectonically and seismically active region,witnessing strong deformation due to the collision between the Indian and Eurasian plates.Constraining the subsurface velocity structure of this region is thus important in understanding the tectonics and geodynamic processes of continental collision and in mitigating seismic hazards.Numerous studies have provided various 3D seismic velocity models in southwest China.However,discrepancies exist among these models,and less effort has been made to quantify the reliability and accuracy of these existing velocity models.In this study,we use regional 3D waveform simulation to evaluate the performance of various regional crustal 3D velocity models in reproducing observed seismograms.We particularly focus on two recent earthquake sequence in the region,the 2021 Yunnan Yangbi MS_(6.4) earthquake sequence and the 2022 Sichuan Luding MS_(6.8) earthquake sequence.The tested 3D velocity models include the Southwest China Community Velocity model V1.0,the Unified Seismic Tomography Models for Continental China Lithosphere V2.0,the adjoint full waveform tomography model of the crustal and upper mantle beneath Eastern Tibetan Plateau,and the shallow seismic structure model beneath continental China.Our results show that the tested 3D velocity models generally capture well long-period(ling.The full-waveform tomography model shows a slighter better performance than the other models,especially for the body-waves,highlighting the advantages of full-waveform method in achieving sub-wavele

关键词： Southwest China Seismic tomography models Shallow Structures Waveform simulation Model evaluation

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An overview and perspective of identifying lunar craters

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Science China Earth Sciences 2024年第5期67卷 1395-1416页

作者： Yan JIANG Changyi Xu ling chen State Key Laboratory of Lithospheric Evolution Institute of Geology and GeophysicsChinese Academy of SciencesBeijing 100029China College of Earth and Planetary Sciences University of Chinese Academy of SciencesBeijing 100029China Key Laboratory of Earth and Planetary Physics Institute of Geology and GeophysicsChinese Academy of SciencesBeijing 100049China

The spatiotemporal evolution of lunar impact craters is crucial for investigating lunar interior structure,internal and external dynamic processes,and interplanetary impact history.Advances in lunar crater identification are reviewed based on topography and gravity data,and the features and mechanisms of topographic or buried craters are analyzed regarding morphology,gravity anomalies,gravity gradients,and the underlying crust-mantle interface relief.Based on the compiled crater catalog,the early lunar impact flux and thermal evolution are further discussed according to the basin ages and their interior structures.For some ancient impact basins,the crater size-frequency distribution measurements revealed age discrepancies from previous studies,suggesting that the lunar late heavy bombardment event started at~3.95 Ga.The degraded bulge structures of the crust-mantle interface beneath mare basins reveal that these basins formed on the lunar crust surface under high-temperature conditions and underwent prolonged relaxation compared to highland basins.Finally,we reveal that the up-to-date identification of lunar buried craters remains inaccurate and incomplete,preventing us from accurately reconstructing lunar and interplanetary impact histories.Therefore,we propose that a gravity model constructed using localized orthogonal basis functions can be useful for identifying lunar craters.

关键词： Moon Gravity field Craters Impact flux Early evolution

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Diagnostic values of questionnaires of Convergence Insufficiency Symptom Survey and College of Optometrists Vision Development Quality of Life in the screening of convergence insufficiency

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International Journal of Ophthalmology(English edition) 2024年第5期17卷 904-908页

作者： ling Xiong Qian chen Ye Wu Department of Ophthalmology West China HospitalSichuan University/Laboratory of Optometry and Vision ScienceWest China School of MedicineChengdu 610041Sichuan ProvinceChina Department of Clinical Research Management Center of BiostatisticsDesignMeasurement and EvaluationWest China HospitalSichuan UniversityChengdu 610041Sichuan ProvinceChina

AIM:To compare and analyse the diagnostic efficacy of the College of Optometrists Vision Development Quality of Life Questionnaire(COVD-QOL)and the Convergence Insufficiency Symptom Survey(CISS)in detecting convergence insufficiency and to compare their diagnostic value in clinical applications.METHODS:Using the diagnostic test method,62 adult patients with convergence insufficiency(age:24.74±3.75y)and 62 normal participants(age:23.61±3.13y)who visited the Optometry Clinic of West China Hospital of Sichuan University from April 2021 to January 2023 were included.All subjects completed the CISS and COVD-QOL.Statistical analysis of the sensitivity and specificity of the CISS and COVD-QOL and comparison and joint experimental analysis of their diagnostic efficacy were performed.RESULTS:The sensitivity of the CISS and COVD-QOL for convergence insufficiency was 64.5%and 71.0%,respectively,while the specificity was 96.8%and 67.7%,respectively.Compared to the CISS alone,the combination of the CISS and COVD-QOL demonstrated lower sensitivity and specificity.The areas under the receiver operating characteristic curve of CISS,COVD-QOL and CISS combined with COVD-QOL were 0.806,0.694 and 0.782,respectively.CONCLUSION:Considering the low sensitivity of the CISS and the low specificity of the COVD-QOL,it is recommended to supplement these questionnaires with other screening tests for the detection of convergence insufficiency.

关键词： convergence insufficiency symptom survey College of Optometrists Vision Development Quality of Life Questionnaire convergence insufficiency asthenopia

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A two-step multi-frequency receiver function inversion method for shallow crustal S-wave velocity structure and its application across the basin-mountain range belts in Northeast China

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Science China Earth Sciences 2024年第3期67卷 687-703页

作者： Ruihao YANG Xu WANG ling chen Mingye FENG Qifu chen State Key Laboratory of Lithospheric Evolution Institute of Geology and GeophysicsChinese Academy of SciencesBeijing 100029China College of Earth and Planetary Sciences University of Chinese Academy of SciencesBeijing 100049China Key Laboratory of Earth and Planetary Physics Institute of Geology and GeophysicsChinese Academy of SciencesBeijing 100029China

A shallow crustal velocity structure(above 10 km depth) is essential for understanding the crustal structures and deformation and assessing the exploration prospect of natural resources, and also provides priori information for imaging deeper crustal and mantle structure. Passive-source seismic methods are cost-effective and advantageous for regional-scale imaging of shallow crustal structures compared to active-source methods. Among these passive methods, techniques utilizing receiver function waveforms and/or body-wave amplitude ratios have recently gained prominence due to their relatively high spatial resolution. However, in basin regions, reverberations caused by near-surface unconsolidated sedimentary layers often introduce strong non-uniqueness and uncertainty, limiting the applicability of such methods. To address these challenges, we propose a two-step inversion method that uses multi-frequency P-RF waveforms and P-RF horizontal-to-vertical amplitude ratios. Synthetic tests indicate that our two-step inversion method can mitigate the non-uniqueness of the inversion and enhance the stability of the results. Applying this method to teleseismic data from a linear seismic array across the sedimentary basins in Northeast China, we obtain a high-resolution image of the shallow crustal S-wave velocity structure along the array. Our results reveal significant differences between the basins and mountains. The identification of low-velocity anomalies(<2.8 km s^(-1)) at depths less than 1.0 km beneath the Erlian Basin and less than 2.5 km beneath the Songliao Basin suggests the existence of sedimentary layers. Moreover, the high-velocity anomalies(~3.4–3.8 km s^(-1)) occurring at depths greater than 7 km in the Songliao Basin may reflect mafic intrusions emplaced during the Early Cretaceous. Velocity anomaly distribution in our imaging result is consistent with the location of the major faults, uplifts, and sedimentary depressions, as well as active-source seismic results. This application further validates the eff

关键词： Receiver function Frequency dependence Two-step inversion Shallow crustal velocity structures Unconsolidated sedimentary basins

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Acute Bacillus cereus endophthalmitis caused by ocular perforation injury and occult intravitreal cilium implantation:a case report

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International Journal of Ophthalmology(English edition) 2024年第5期17卷 976-978页

作者： ling Zhang Bin chen Wei-Min He Department of Ophthalmology West China HospitalSichuan UniversityChengdu 610041Sichuan ProvinceChina Department of Ophthalmology the People’s Hospital of LeshanLeshan 614000Sichuan ProvinceChina

Dear Editor,We present a case of acute Bacillus cereus(B.cereus)endophthalmitis in a patient with an intraocular perforation injury combined with occult intravitreal cilium implantation.B.cereus endophthalmitis is a severe intraocular infection commonly caused by post-traumatic injuries.It often leads to significant vision loss or even eye loss within 12-48h[1].The presence of an intraocular foreign body(IOFB)increases the risk of infection,while early surgical removal of IOFBs can prevent endophthalmitis,some IOFBs are difficult to detect preoperatively.The Medical Ethics Review Board of West China Hospital of Sichuan University waived application for a clinical study because this was a retrospective report of a single patient based on imaging and because no human experimentation was involved.The patient provided written informed consent to use the imaging data for publication.

关键词： endophthalmitis ilium injuries

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Cross-species transmission and host range genes in poxviruses

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Virologica Sinica 2024年第2期39卷 177-193页

作者： chen-Hui Yang A-ling Song Ye Qiu Xing-Yi Ge College of Biology Hunan Provincial Key Laboratory of Medical VirologyHunan UniversityChangsha410012China

The persistent epidemic of human mpox, caused by mpox virus (MPXV), raises concerns about the future spread ofMPXV and other poxviruses. MPXV is a typical zoonotic virus which can infect human and cause smallpox-likesymptoms. MPXV belongs to the Poxviridae family, which has a relatively broad host range from arthropods tovertebrates. Cross-species transmission of poxviruses among different hosts has been frequently reported andresulted in numerous epidemics. Poxviruses have a complex linear double-strand DNA genome that encodeshundreds of proteins. Genes related to the host range of poxvirus are called host range genes (HRGs). This reviewbriefly introduces the taxonomy, phylogeny and hosts of poxviruses, and then comprehensively summarizes thecurrent knowledge about the cross-species transmission of poxviruses. In particular, the HRGs of poxvirus aredescribed and their impacts on viral host range are discussed in depth. We hope that this review will provide acomprehensive perspective about the current progress of researches on cross-species transmission and HRGvariation of poxviruses, serving as a valuable reference for academic studies and disease control in the future.

关键词： Poxvirus Host range gene(HRG) Host spectrum Cross-species transmission

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Exogenous insulin autoimmune syndrome:A case report and review of literature

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World Journal of Clinical Cases 2024年第9期12卷 1691-1697页

作者： ling-ling Xu Jia-Xin chen Jing-Ping cheng Ni Luo Medical College School of MedicineWuhan University of Science and TechnologyWuhan 430065Hubei ProvinceChina Department of Gerontology CR&WISCO General Hospital Affiliated to Wuhan University of Science and TechnologyWuhan 430080Hubei ProvinceChina

BACKGROUND Insulin autoimmune syndrome(IAS)is a severe manifestation of spontaneous hypoglycemia.It is characterized by elevated levels of immune-reactive insulin and highly potent insulin autoantibodies(IAAs),which are induced by endogenous insulin circulating in the bloodstream.It is distinguished by recurring instances of spontaneous hypoglycemia,the presence of IAA within the body,a substantial elevation in serum insulin levels,and an absence of prior exogenous insulin administration.Nevertheless,recent studies show that both conventional insulin and its analogs can induce IAS episodes,giving rise to the notion of nonclassical IAS.Therefore,more attention should be paid to these diseases.CASE SUMMARY In this case report,we present a rare case of non-classical IAS in an 83-year-old male patient who present with symptoms of a psychiatric disorder.Upon symptom onset,the patient exhibited Whipple's triad(including hypoglycemia,blood glucose level less than 2.8 mmol/L during onset,and rapid relief of hypoglycemic symptoms after glucose administration).Concurrently,his serum insulin level was significantly elevated,which contradicted his C-peptide levels.After a comprehensive examination,the patient was diagnosed with exogenous insulin autoimmune syndrome.Considering that the patient had type 2 diabetes mellitus and a history of exogenous insulin use before disease onset,it was presumed that non classical IAS was induced by this condition.The PubMed database was used to search for previous cases of IAS and non-classical IAS to analyze their characteristics and treatment approaches.CONCLUSION The occurrence of non-classical IAS is associated with exogenous insulin or its analogs,as well as with sulfhydryl drugs.Symptoms can be effectively alleviated through the discontinuation of relevant medications,administration of hormones or immunosuppressants,plasma exchange,and lifestyle adjustments.

关键词： Insulin autoimmune syndrome Type 2 diabetes Exogenous insulin Insulin autoantibodies Hypoglycemia Case report

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LaMnO_(3)/Co_(3)O_(4) nanocomposite for enhanced triethylamine sensing properties

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Journal of Rare Earths 2024年第4期42卷 733-742页

作者： Jian Zhang Yanping chen ling Li Xue chen Wenya An Xiujuan Qian Yuye Tao School of Science Shandong Jianzhu UniversityJinan250100China

LaMnO_(3) modified Co_(3)O_(4) nanocomposites were prepared by simple hydrothermal method co mbined with sol-gel method.The gas sensitivity properties of pure Co_(3)O_(4) and LaMnO_(3)/Co_(3)O_(4) with different composite proportions are compared.It is found that 0.6-LMO/Co_(3)O_(4) sensor has higher sensitivity to triethylamine(TEA)than pure Co_(3)O_(4) sensor,which is improved by 9.27 times.And the working temperature is reduced from 150 to 130℃.Besides,it has excellent gas selectivity and repeatability.The improvement of the gas sensitivity of LaMnO_(3)/Co_(3)O_(4) sensor may be due to the fact that LaMnO_(3) is an effective catalyst,and the catalytic performance perhaps is beneficial to improving the sensing performance.In addition,the formation of p-p heterojunctions may be the key factor to improve the gas sensing performance.This work provides a new Co_(3)O_(4)-based gas sensing material for the detection of TEA.

关键词： Gas sensing Co_(3)O_(4) LaMnO_(3) Triethylamine Rareearths

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Challenging anticoagulation therapy for multiple primary malignant tumors combined with thrombosis:A case report and review of literature

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World Journal of Clinical Cases 2024年第9期12卷 1704-1711页

作者： Jia-Xin chen ling-ling Xu Jing-Ping cheng Xun-Hua Xu Department of Gerontology China Resources and Wisco General HospitalWuhan University of Science and TechnologyWuhan 430080Hubei ProvinceChina Medical College Wuhan University of Science and TechnologyWuhan 430065Hubei ProvinceChina Department of Gerontology China Resources and Wisco General HospitalWuhan 430080Hubei ProvinceChina Department of Radiology China Resources and Wisco General HospitalWuhan 430080Hubei ProvinceChina

BACKGROUND Venous thromboembolism significantly contributes to patient deterioration and mortality.Management of its etiology and anticoagulation treatment is intricate,necessitating a comprehensive consideration of various factors,including the bleeding risk,dosage,specific anticoagulant medications,and duration of therapy.Herein,a case of lower extremity thrombosis with multiple primary malignant tumors and high risk of bleeding was reviewed to summarize the shortcomings of treatment and prudent anticoagulation experience.CASE SUMMARY An 83-year-old female patient was admitted to the hospital due to a 2-wk history of left lower extremity edema that had worsened over 2 d.Considering her medical history and relevant post-admission investigations,it was determined that the development of left lower extremity venous thrombosis and pulmonary embolism in this case could be attributed to a combination of factors,including multiple primary malignant tumors,iliac venous compression syndrome,previous novel coronavirus infection,and inadequate treatment for prior thrombotic events.However,the selection of appropriate anticoagulant medications,determination of optimal drug dosages,and establishment of an appropriate duration of anticoagulation therapy were important because of concurrent thrombocytopenia,decreased quantitative fibrinogen levels,and renal insufficiency.CONCLUSION Anticoagulant prophylaxis should be promptly initiated in cases of high-risk thrombosis.Individualized anticoagulation therapy is required for complex thrombosis.

关键词： Venous thromboembolism Cancer-associated thrombosis Anticoagulation therapy iliac vein compression syndrome COVID-19 Thrombocytopenia Case report

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