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PICOTEES:a privacy-preserving online service of phenotype exploration for genetic-diagnostic variants from Chinese children cohorts

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Journal of Genetics and Genomics 2024年第2期51卷 243-251页

作者： Xinran dong Yulan Lu Lanting Guo Chuan Li Qi Ni Bingbing Wu Huijun Wang Lin Yang Songyang Wu Qi Sun hao Zheng Wenhao Zhou Shuang Wang Center for Molecular Medicine Children's Hospital of Fudan UniversityShanghai 201102China Key Laboratory of Birth Defects Children's Hospital of Fudan UniversityShanghai 201102China Department of Bioinformatics Hangzhou Nuowei Information Technology Co.LtdHangzhouZhejiang 310000China The Third Research Institute of the Ministry of Public Security Shanghai 200031China Xiamen Campus of Children's Hospital of Fudan University XiamenFujian 361006China Institutes for Systems Genetics West China HospitalChengduSichuan 610041China Shanghai Putuo People's Hospital Tongji UniversityShanghai 200060China

The growth in biomedical data resources has raised potential privacy concerns and risks of genetic information leakage. For instance, exome sequencing aids clinical decisions by comparing data through web services, but it requires significant trust between users and providers. To alleviate privacy concerns, the most commonly used strategy is to anonymize sensitive data. Unfortunately, studies have shown that anonymization is insufficient to protect against reidentification attacks. Recently, privacy-preserving technologies have been applied to preserve application utility while protecting the privacy of biomedical data. We present the PICOTEES framework, a privacy-preserving online service of phenotype exploration for genetic-diagnostic variants (https://***:3000/). PICOTEES enables privacy-preserving queries of the phenotype spectrum for a single variant by utilizing trusted execution environment technology, which can protect the privacy of the user's query information, backend models, and data, as well as the final results. We demonstrate the utility and performance of PICOTEES by exploring a bioinformatics dataset. The dataset is from a cohort containing 20,909 genetic testing patients with 3,152,508 variants from the Children's Hospital of Fudan University in China, dominated by the Chinese Han population (>99.9%). Our query results yield a large number of unreported diagnostic variants and previously reported pathogenicity.

关键词： Privacy protecti on Rare diseases in children Genetic testing Web system Trusted executi on envir onment

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MIR1868 negatively regulates rice cold tolerance at both the seedling and booting stages

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The Crop Journal 2024年第2期12卷 375-383页

作者： Yang Shen Xiaoxi Cai Yan Wang Wanhong Li dongpeng Li hao Wu Weifeng dong Bowei Jia Mingzhe Sun Xiaoli Sun Crop Stress Molecular Biology Laboratory Heilongjiang Bayi Agricultural UniversityDaqing 163319HeilongjiangChina

Low temperature causes rice yield losses of up to 30%–40%,therefore increasing its cold tolerance is a breeding target.Few genes in rice are reported to confer cold tolerance at both the vegetative and reproductive stages.This study revealed a rice-specific 24-nt miRNA,miR1868,whose accumulation was suppressed by cold stress.Knockdown of MIR1868 increased seedling survival,pollen fertility,seed setting,and grain yield under cold stress,whereas its overexpression conferred the opposite phenotype.Knockdown of MIR1868 increased reactive oxygen species(ROS)scavenging and soluble sugar content under cold stress by increasing the expression of peroxidase genes and sugar metabolism genes,and its overexpression produced the opposite effect.Thus,MIR1868 negatively regulated rice cold tolerance via ROS scavenging and sugar accumulation.

关键词： Rice Cold tolerance miRNA ROS scavenging Soluble sugar accumulation

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Covariance matrix estimation with pipeline structure in array signal processing

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The Journal of China Universities of Posts and Telecommunications 2024年

作者： Chen Ligang Cai Weijie Liu Zhihui dong Tao Zeng hao School of Microelectronics and Communication Engineering Chongqing University Space Star Technology Company Limited

Estimating the covariance matrix of the received signal is a vital step in array signal processing. The traditional estimation method is completed generally by offline way after receiving the continuous sampling snapshots， which can not meet requirements of real-time performance. In this paper， the calculation of covariance matrix is divided into four pipeline operations， which are multiplication， accumulation， subtraction and division， respectively.The new method leverages the parallel computing function of field programmable gate array(FPGA) to calculate the covariance matrix adopting a pipeline estimation method at each time when the array receives a new sampling snapshot. Compared with the traditional method， the new method not only improves the real-time performance， but also reduces the error in calculation caused by the rapid direction of arrival(DOA) change of the interested signal when the target is highly maneuverable.

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Appendicitis combined with Meckel’s diverticulum obstruction, perforation, and inflammation in children: Three case reports

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World Journal of Clinical Cases 2024年第4期12卷 865-871页

作者： Yi-Meng Sun Wang Xin Yu-Fang Liu Zhe-Ming Guan hao-Wen Du Ning-Ning Sun Yong-dong Liu School of Clinical Medicine Weifang Medical UniversityWeifang 261000Shandong ProvinceChina Department of Pediatric Surgery Weifang People’s HospitalWeifang 261000Shandong ProvinceChina Department of Burn Surgery Weifang People’s HospitalWeifang 261000Shandong ProvinceChina

BACKGROUND Meckel’s diverticulum is a common congenital malformation of the small intestine,with the three most common complications being obstruction,per-foration,and inflammation.To date,only a few cases have been reported world-wide.In children,the clinical symptoms are similar to appendicitis.As most of the imaging features are nonspecific,the preoperative diagnosis is not precise.In addition,the clinical characteristics are highly similar to pediatric acute appendicitis,thus special attention is necessary to distinguish Meckel’s diver-ticulum from pediatric appendicitis.Patients with poor disease control should undergo laparoscopic exploration to avoid serious complications,including intestinal necrosis,intestinal perforation and gastrointestinal bleeding.CASE SUMMARY This report presents three cases of appendicitis in children combined with intestinal obstruction,which was caused by fibrous bands(ligaments)arising from the top part of Meckel's diverticulum,diverticular perforation,and diver-ticular inflammation.All three patients,aged 11-12 years,had acute appendicitis as their initial clinical presentation.All were treated by laparoscopic surgery with a favorable outcome.A complete dataset including clinical presentation,dia-gnostic imaging,surgical information,and histopathologic findings was also provided.CONCLUSION Preoperative diagnosis of Meckel’s diverticulum and its complications is challenging because its clinical signs and complications are similar to those of appendicitis in children.Laparoscopy combined with laparotomy is useful for diagnosis and treatment.

关键词： Meckel’s diverticulum Complications Intestinal obstruction Perforation Appendicitis in children Mesodiverticular band Ligament Diverticular disease Case report

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Learning the imaging mechanism directly from optical microscopy observations

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Photonics Research 2024年第1期12卷 7-26页

作者： ZE-hao WANG LONG-KUN SHAN TONG-TIAN WENG TIAN-LONG CHEN XIANG-dong CHEN ZHANG-YANG WANG GUANG-CAN GUO FANG-WEN SUN CAS Key Laboratory of Quantum Information University of Science and Technology of ChinaHefei 230026China CAS Center for Excellence in Quantum Information and Quantum Physics University of Science and Technology of ChinaHefei 230026China University of Texas at Austin AustinTexas 78705USA Hefei National Laboratory University of Science and Technology of ChinaHefei 230088China

The optical microscopy image plays an important role in scientific research through the direct visualization of the nanoworld,where the imaging mechanism is described as the convolution of the point spread function(PSF)and emitters.Based on a priori knowledge of the PSF or equivalent PSF,it is possible to achieve more precise exploration of the nanoworld.However,it is an outstanding challenge to directly extract the PSF from microscopy images.Here,with the help of self-supervised learning,we propose a physics-informed masked autoencoder(PiMAE)that enables a learnable estimation of the PSF and emitters directly from the raw microscopy images.We demonstrate our method in synthetic data and real-world experiments with significant accuracy and noise robustness.PiMAE outperforms DeepSTORM and the Richardson–Lucy algorithm in synthetic data tasks with an average improvement of 19.6%and 50.7%(35 tasks),respectively,as measured by the normalized root mean square error(NRMSE)metric.This is achieved without prior knowledge of the PSF,in contrast to the supervised approach used by DeepSTORM and the known PSF assumption in the Richardson–Lucy algorithm.Our method,PiMAE,provides a feasible scheme for achieving the hidden imaging mechanism in optical microscopy and has the potential to learn hidden mechanisms in many more systems.

关键词： optical emitter mechanism

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Single-atom Rh catalysts for efficiently degrading Rhodamine B with high concentration

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Rare Metals 2024年第5期43卷 2331-2338页

作者： Shou-Yao Hu Jian-Ping Guan Run-Ze Ma Yu Tao dong-hao Liu Jia-Xin Gong Yu Xiong Department of Chemistry and Chemical Engineering Central South University

Highly concentrated dye wastewater has a serious effect on the quality of natural waters; thus, developing novel catalysts to degrade dyes rapidly and efficiently is of great significance. For the first time, this study reports an Rh single atom loaded on a nitrogen-doped carbon(SA-Rh/CN) catalyst. This catalyst exhibits an excellent processing capacity for high concentrations of Rhodamine B(Rh B),high catalytic activity(95.7% degradation of Rh B in60 min) and excellent stability(93.5% degradation efficiency after 10 stable runs),

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Rational design multi-color-emissive chemiluminescent carbon nanodots in a single solvothermal reaction

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Nano Research 2024年第6期17卷 4651-4660页

作者： Guang-Song Zheng Cheng-Long Shen Yuan Deng Kai-Kai Liu Jin-hao Zang Lin dong Qing Lou Chong-Xin Shan Henan Key Laboratory of Diamond Optoelectronic Materials and Devices Key Laboratory of Materials PhysicsMinistry of Educationand School of Physics and MicroelectronicsZhengzhou UniversityZhengzhou 450052China

Recently,the chemiluminescence(CL)induced by carbon nanodots(CDs)has intrigued researchers’extensive interests in various applications due to its special light emission principle.However,the difficulty of synthesizing chemiluminescent CDs with full-spectrum emission severely hinders the further regulation of the CL emission mechanism.Herein,the multi-color-emissive chemiluminescent CDs are rational designed and further synthesized by regulating the sp2-hybrid core and sp3-hybrid surface from the citrate-ammonia molecular in a single solvothermal reaction.More experimental characterizations and density functional theory calculations reveal that the higher temperature can promote the crosslinking polymerization/carbonization of carbon core and the higher protonation of solvent can determine the core size of final CDs,resulting in the variant CL emission from molecular-,crosslinking-and core-states.Thus,the CL emission of the CDs can be further synthesized by tuning the luminescence chromophores in the formation process via regulating the temperature and solvent,enabling the applications of the CL CDs in illumination and information encryption.This study paves a new technology to understand the luminescence of CDs and affords an industry translational potential over traditional chemiluminescent molecular.

关键词： carbon nanodots chemiluminescence regulation energy level alignment mechanism

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Individual dynamics and local heterogeneity provide a microscopic view of the epidemic spreading

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Chinese Physics B 2024年第5期33卷 656-663页

作者：朱友源沈瑞哲董昊王炜 Kuang Yaming Honors School Nanjing UniversityNanjing 210023China Collaborative Innovation Center of Advanced Microstructures National Laboratory of Solid State MicrostructureSchool of PhysicsNanjing UniversityNanjing 210093China Institute for Brain Sciences Nanjing UniversityNanjing 210023China State Key Laboratory of Analytical Chemistry for Life Science Nanjing UniversityNanjing 210023China

The COVID-19 pandemic has caused severe global disasters,highlighting the importance of understanding the details and trends of epidemic transmission in order to introduce efficient intervention measures.While the widely used deterministic compartmental models have qualitatively presented continuous “analytical” insight and captured some transmission features,their treatment usually lacks spatiotemporal variation.Here,we propose a stochastic individual dynamical(SID)model to mimic the random and heterogeneous nature of epidemic propagation.The SID model provides a unifying framework for representing the spatiotemporal variations of epidemic development by tracking the movements of each individual.Using this model,we reproduce the infection curves for COVID-19 cases in different areas globally and find the local dynamics and heterogeneity at the individual level that affect the disease outbreak.The macroscopic trend of virus spreading is clearly illustrated from the microscopic perspective,enabling a quantitative assessment of different interventions.Seemingly,this model is also applicable to studying stochastic processes at the “meter scale”,e.g.,human society’s collective dynamics.

关键词： Brownian motion epidemic spreading heterogeneity

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Measurement of the high energyγ-rays from heavy ion reactions usingČerenkov detector

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Nuclear Science and Techniques 2024年第2期35卷 123-130页

作者： Da-Wei Si Yan Zhou Sheng Xiao Zhi Qin dong Guo Yu-hao Qin Yi-Jie Wang Bo-Yuan Zhang Bai-Ting Tian Zhi-Gang Xiao Department of Physics Tsinghua UniversityBeijing 100084China

The energetic bremsstrahlung photons up to 100 MeV produced in heavy ion collisions can be used as a sensitive probe for short-range correlation in atomic nuclei. The energy of the γ-rays can be measured by collecting the Čerenkov light in the medium induced by the fast electrons generated in the Compton scattering or electromagnetic shower of the incident γray. Two types of detectors based on pure water and lead glass as sensitive materials were designed for this purpose. The γresponse and optical photon propagation in the detectors were simulated based on electromagnetic and optical processes in Geant4. The inherent energy resolutions of 0.022(4) + 0.51(2)∕E^(1/2)_(γ) for water and 0.0026(3) + 0.446(3)∕E^(1/2)_(γ) for lead glass were obtained. The geometry sizes of the lead glass and water were optimized to 30 cm × 30 cm × 30 cm and 60 cm × 60 cm ×120 cm, respectively, to detect high-energy γ-rays at 160 MeV. The Hough transform method was applied to reconstruct the direction of the incident γ-rays, providing the ability to experimentally distinguish the high-energy γ-rays produced in the reactions on the target from random background cosmic-ray muons.

关键词： Bremsstrahlungγ-rays Čerenkov Geant4 Energy resolution Direction reconstruction Hough transform

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Refinement ofα′Martensite by Oxygen in Selective Laser Melted Ti-6Al-4V

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Acta Metallurgica Sinica(English Letters) 2024年第5期37卷 777-792页

作者： Hasfi FNurly Jinhu Zhang Dechun Ren Yusheng Cai Haibin Ji dongsheng Xu Zhicheng dong hao Wang Qingmiao Hu Jiafeng Lei Rui Yang School of Materials Science and Engineering University of Science and Technology of ChinaShenyang 110016China Shi-Changxu Innovation Center for Advanced Materials Institute of Metal ResearchChinese Academy of SciencesShenyang 110016China School of Materials and Chemistry/Interdisciplinary Centre for Additive Manufacturing University of Shanghai for Science and TechnologyShanghai 200093China Centre for Adaptive System Engineering ShanghaiTech UniversityShanghai 201210China

Oxygen is crucial in influencing the microstructure evolution of selective laser melted(SLMed)Ti–6Al–4V,significantly impacting its applicability in various sectors.Therefore,this study investigates the influnce of oxygen on microstructure evolution,particularlyα′martensite transformation and refinement mechanisms.Four alloys,Ti–6Al–4V–xO(x=0.11,0.16,0.21,and 0.25 wt%),were fabricated by the SLM process.The martensite start temperature(M_(s))of Ti–6Al–4V,as evaluated by computation,is 656.8°C,and oxygen was found to increase the M_(s) by about 10°C per 0.1 wt%.The SLMed alloy samples exhibit[001]_(β)growth texture along the build direction.Crystallographic analysis of martensite morphology suggests internal twinning on{1011}planes as the lattice invariant strain,which becomes more predominant with increasing oxygen content.Refinement of α′martensite plates by oxygen is due to increased lattice distortion,reduced prior β grain size,and oxygen segregation toβgrain boundaries.Our findings contribute to improving the understanding of the effect of oxygen on the transformation mechanism ofα′martensite during SLM of Ti–6Al–4V.

关键词： Selective laser melting α′Martensite Martensite start temperature Oxygen Ti-6Al-4V

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