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OcBSA:An NGS-based bulk segregant analysis tool for outcross populations

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Molecular Plant 2024年第4期17卷 648-657页

作者： Lingkui zhang Yanfeng duan Zewei zhang Lei zhang Shumin Chen Chengcheng Cai Shaoguang duan Kang zhang Guangcun Li Feng Cheng State Key Laboratory of Vegetable Biobreeding Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural AffairsKey Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural AffairsSino-Dutch Joint Laboratory of Horticultural GenomicsInstitute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing 100081China

Constructing inbred lines for self-incompatible species and species with long generation times is challenging,making the use of F1 outcross/segregating populations the main strategy for genetic studies of such ***,there is a lack of dedicated algorithms/tools for rapid quantitative trait locus(QTL)mapping using the F1 *** this end,we have designed and developed an algorithm/tool called OcBSA specifically for QTL mapping of F1 *** transforms the four-haplotype inheritance problem from the two heterozygous diploid parents of the F1 population into the two-haplotype inheritance problem common in current genetic studies by removing the two haplotypes from the heterozygous parent that do not contribute to phenotype segregation in the F1 *** of OcBSA on 1800 simulated F1 populations demonstrated its advantages over other currently available tools in terms of sensitivity and *** addition,the broad applicability of OcBSA was validated by QTL mapping using seven reported F1 populations of apple,pear,peach,citrus,grape,tea,and *** also used OcBSA to map the QTL for flower color in a newly constructed F1 population of potato generated in this *** OcBSA mapping result was verified by the insertion or deletion markers to be consistent with a previously reported locus harboring the ANTHOCYANIN 2 gene,which regulates potato flower *** together,these results highlight the power and broad utility of OcBSA for QTL mapping using F1 populations and thus a great potential for functional gene mining in outcrossing *** ease of use,we have developed both Windows and Linux versions of OcBSA,which are freely available at:https://***/Bioinformaticslab/OcBSA.

关键词： outcross BSA self-incompatible F1 population QTL mapping potato

Gene therapy for monogenic disorders: challenges, strategies, and perspectives

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Journal of Genetics and Genomics 2024年第2期51卷 133-143页

作者： Yi zhang zhi-Ying Wu Department of Medical Genetics and Center for Rare Diseases Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang 310009China Department of Neurology Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang 310009China Key Laboratory of Medical Neurobiology of Zhejiang Province HangzhouZhejiang 310009China

Monogenic disorders refer to a group of human diseases caused by mutations in single genes. While disease-modifying therapies have offered some relief from symptoms and delayed progression for some monogenic diseases, most of these diseases still lack effective treatments. In recent decades, gene therapy has emerged as a promising therapeutic strategy for genetic disorders. Researchers have developed various gene manipulation tools and gene delivery systems to treat monogenic diseases. Despite this progress, concerns about inefficient delivery, persistent expression, immunogenicity, toxicity, capacity limitation, genomic integration, and limited tissue specificity still need to be addressed. This review gives an overview of commonly used gene therapy and delivery tools, along with the challenges they face and potential strategies to counter them.

关键词： Gene therapy Monogenic diseases Geneediting Genedelivery Challenges

Study on the tribological properties of metal rolling bearing under lubrication with diketone lubricants

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Science China(Technological Sciences) 2024年第7期67卷 2003-2017页

作者： DU ShaoNan zhang ChenHui LUO zhi State Key Laboratory of Tribology in Advanced Equipment Tsinghua UniversityBeijing 100084China Beijing National Laboratory of Molecular Sciences CAS Key Laboratory of Engineering PlasticsInstitute of ChemistryChinese Academy of SciencesBeijing 100190China

In this article, 1-(4-ethylphenyl)-nonane-1,3-dione(0206) was prepared by Claisen condensation. By mixing 0206, chelate, and base oil in a ratio of 3.2:4.8:2, a diketone lubricant(PAO=14(20%)) that can achieve superlubricity was prepared and applied to bearing lubrication experiments. The experimental results show that when the bearing was lubricated by base oil, the friction coefficient(COF) and temperature rise decreased with the decrease of the viscosity of PAO. When PAO=14(20%) was used as the lubricant, the COF of the bearing was the lowest(0.001), and the wear morphology was comparable to that of the bearing lubricated with commercial lubricant. Compared with the base oil with the same viscosity, it is found that the COF and temperature rise of the bearing lubricated by PAO=14(20%) were lower under any experimental conditions. And when the amount of lubricant added was 10 μL, the COF of the bearing lubricated by PAO=14(20%) reached a very low value(0.0004).Bearing ball surface analysis identified the formation of diketone adsorption films. Combined with the previous PAO=14(20%)superlubricity mechanism, it was considered that the occurrence of tribochemical reaction and the bearing effect of chelates were the main reasons for the existence of ultra-low friction coefficient and low wear. In addition, when there were polar molecules in the lubricant, they were adsorbed on the metal surface through tribochemical reactions, resulting in many irregular pits on the surface.

关键词： superlubricity diketone chelate tribochemical recations bearing lubrication

Deciphering and integrating invariants for neural operator learning with various physical mechanisms

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National Science Review 2024年第4期11卷 111-122页

作者： Rui zhang Qi Meng zhi-Ming Ma Academy of Mathematics and Systems Science Chinese Academy of Sciences(CAS) Microsoft Research

Neural operators have been explored as surrogate models for simulating physical systems to overcome the limitations of traditional partial differential equation(PDE) solvers. However, most existing operator learning methods assume that the data originate from a single physical mechanism, limiting their applicability and performance in more realistic scenarios. To this end, we propose the physical invariant attention neural operator(PIANO) to decipher and integrate the physical invariants for operator learning from the PDE series with various physical mechanisms. PIANO employs self-supervised learning to extract physical knowledge and attention mechanisms to integrate them into dynamic convolutional *** to existing techniques, PIANO can reduce the relative error by 13.6%–82.2% on PDE forecasting tasks across varying coefficients, forces or boundary conditions. Additionally, varied downstream tasks reveal that the PI embeddings deciphered by PIANO align well with the underlying invariants in the PDE systems, verifying the physical significance of PIANO.

关键词： neural operator PDE solver contrastive learning physical invariants

CO_(2) capture by modified clinoptilolite and its regeneration performance

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International Journal of Coal Science & Technology 2024年第2期11卷 81-90页

作者： Bo Jiang Bo zhang Xuqin duan Yi Xing School of Energy and Environmental Engineering University of Science and Technology BeijingBeijing 100083China Beijing Key Laboratory of Resource-Oriented Treatment of Industrial Pollutants University of Science and Technology BeijingBeijing 100083China YangQuan Coal Industry(Group)Co.Ltd. Yangquan 045000China School of Civil and Resource Engineering University of Science and Technology BeijingBeijing 100083China

This study focuses on CO_(2) capture by pressure swing adsorption(PSA),with modified clinoptilolite as the *** clinoptilolite is modified by roasting,by acid pickling,by a combination of acid pickling and roasting,and by ion *** by acid pickling-roasting and by ion exchange are found to give the highest CO_(2) adsorption capacities,of 730 mL/g and 876.7 mL/g,*** is found that regeneration of clinoptilolite by a combination of vacuum desorption and heating enables recovery of as much as 89%of its previous CO_(2) adsorption *** examine the CO_(2) adsorption capacity of clinoptilolite when applied to mixed gas,a simulated coking exhaust containing 12%CO_(2) and 4%O_(2) is used,and it is found that ion exchange modified clinoptilolite achieves a CO_(2) removal efficiency of 92.5%.A BET test reveals that acid pickling-roasting and Na^(+) modification enhance the porosity of clinoptilolite,thereby improving its adsorption *** work demonstrates the feasibility of applying modified clinoptilolite as an effective adsorbent for COO_(2)capture,providing a promising tool for dealing with greenhouse gases.

关键词： Clinoptilolite Carbon dioxide capture Pressure swing adsorption(PSA)

The Negative Thermal Expansion Property of NdMnO_(3) Based on Pores Effect and Phase Transition

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Journal of Wuhan University of Technology(Materials Science) 2024年第1期39卷 39-43页

作者：李玉成张扬 zhang Muqun duan Rong LIU Xiteng Department of Avionics Engineering Aviation Maintenance NCO Academy of Air Force Engineering UniversityXinyang 464000China

A novel negative thermal expansion(NTE) material NdMnO_(3) was synthesized by solid-state method at 1 523 K. The crystal structure, phase transition, pores effect and negative expansion properties of NdMnO_(3) were investigated by variable temperature X-ray diffraction(XRD), scanning electron microscope(SEM) and variable temperature Raman spectra. The compound exhibits NTE properties in the orderly O' phase crystal structure. When the temperature is from 293 to 759 K, the ceramic NdMnO_(3) shows negative thermal expansion of-4.7×10^(-6)/K. As temperature increases, the ceramic NdMnO_(3) presents NTE property range from 759 to 1 007 K. The average linear expansion coefficient is-18.88×10^(-6)/K. The physical mechanism of NTE is discussed and clarified through experiments.

关键词： negative thermal expansion NdMnO_(3) pores effect phase transition

A Novel On-Site-Real-Time Method for Identifying Characteristic Parameters Using Ultrasonic Echo Groups and Neural Network

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Chinese Journal of Mechanical Engineering 2024年第1期37卷 215-228页

作者： Shuyong duan Jialin zhang Heng Ouyang Xu Han Guirong Liu State Key Laboratory of Reliability and Intelligence of Electrical Equipment Hebei University of TechnologyTianjin 300401China Department of Aerospace Engineering and Engineering Mechanics University of CincinnatiCincinnati 45221USA

On-site and real-time non-destructive measurement of elastic constants for materials of a component in a in-service structure is a challenge due to structural complexities,such as ambiguous boundary,variable thickness,nonuniform material *** work develops for the first time a method that uses ultrasound echo groups and artificial neural network(ANN)for reliable on-site real-time identification of material *** use of echo groups allows the use of lower frequencies,and hence more accommodative to structural *** train the ANNs,a numerical model is established that is capable of computing the waveform of ultrasonic echo groups for any given set of material properties of a given *** waveform of an ultrasonic echo groups at an interest location on the surface the structure with material parameters varying in a predefined range are then computed using the numerical *** results in a set of dataset for training the ANN *** the ANN is trained,the material parameters can be identified simultaneously using the actual measured echo waveform as input to the *** tests have been conducted both numerically and experimentally to evaluate the effectiveness and accuracy of the currently proposed *** results show that the maximum identification error of numerical example is less than 2%,and the maximum identification error of experimental test is less than 7%.Compared with currently prevailing methods and equipment,the proposefy the density and thickness,in addition to the elastic ***,the reliability and accuracy of inverse prediction is significantly ***,it has broad applications and enables real-time field measurements,which has not been fulfilled by any other available methods or equipment.

关键词： Parameter identification Ultrasonic echo group High-precision modeling Artificial neural network NDT

SNR-adaptive deep joint source-channel coding scheme for image semantic transmission with convolutional block attention module

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The Journal of China Universities of Posts and Telecommunications 2024年第1期31卷 1-11页

作者： Yang Yujia Liu Yiming zhang Wenjia zhang zhi State Key Laboratory of Networking and Switch Technology Beijing University of Posts and TelecommunicationsBeijing 100876China

With the development of deep learning(DL),joint source-channel coding(JSCC)solutions for end-to-end transmission have gained a lot of *** deep JSCC schemes support dynamically adjusting the rate according to different channel conditions during transmission,enhancing robustness in dynamic wireless ***,most of the existing adaptive JSCC schemes only consider different channel conditions,ignoring the different feature importance in the image processing and *** uniform compression of different features in the image may result in the compromise of critical image details,particularly in low signal-to-noise ratio(SNR)*** address the above issues,in this paper,a dual attention mechanism is introduced and an SNR-adaptive deep JSCC mechanism with a convolutional block attention module(CBAM)is proposed,in which matrix operations are applied to features in spatial and channel dimensions *** proposed solution concatenates the pooling feature with the SNR level and passes it sequentially through the channel attention network and spatial attention network to obtain the importance evaluation *** show that the proposed solution outperforms other baseline schemes in terms of peak SNR(PSNR)and structural similarity(SSIM),particularly in low SNR scenarios or when dealing with complex image content.

关键词： semantic communication joint source-channel coding image transmission

Indefinite metacavities coupled to a mirror:bound states in the continuum with anomalous resonance scaling

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Photonics Research 2024年第3期12卷 598-607页

作者： QIANG zhang PEIXIANG LI zhiYUAN GU SHAODING LIU ZEJUN duan College of Electronic Information and Optical Engineering Taiyuan University of TechnologyTaiyuan 030024China Key Laboratory of Advanced Transducers and Intelligent Control System Ministry of EducationTaiyuan University of TechnologyTaiyuan 030024China

Indefinite metacavities(IMCs)made of hyperbolic metamaterials show great advantages in terms of extremely small mode volume due to large wave vectors endowed by the unique hyperbolic ***,quality(Q)factors of IMCs are limited by Ohmic loss of metals and radiative loss of leaked *** the fact that Ohmic loss of metals is inevitable in IMCs,the radiative loss can be further suppressed by leakage *** we propose a mirror coupled IMC structure which is able to operate at Fabry–Pérot bound states in the continuum(BICs)while the hyperbolic nature of IMCs is *** the BIC point,the radiative loss of magnetic dipolar cavity modes in IMCs is completely absent,resulting in a considerably increased Q factor(>90).Deviating from the BIC point,perfect absorption bands(>0.99)along with a strong near-field intensity enhancement(>1.8×10^(4))appear when the condition of critical coupling is almost *** proposed BICs are robust to the geometry and material composition of IMCs and anomalous scaling law of resonance is verified during the tuning of optical *** also demonstrate that the Purcell effect of the structure can be significantly improved under BIC and quasi-BIC regimes due to the further enhanced Q factor to mode volume *** results provide a new train of thought to design ultra-small optical nanocavities that may find many applications benefitting from strong light–matter interactions.

关键词： hyperbolic mirror definite