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BioTreasury:a community-based repository enabling indexing and rating of bioinformatics tools

Science China(Life Sciences) 2024年第2期67卷 221-229页

作者： Qi Zhao Xin Zhou Jingxing Wu Jieyi Cai Xiaoqiong Bao Lin Tang Chaoye wang Chunlei Liu Yukai wang Yuyan Teng Mohan Zheng weiping Mu Zhixiang zuo Yubin Xie Xiaotong Luo Jian Ren School of Life Sciences State Key Laboratory of Oncology in South ChinaCancer CenterGuangdong Provincial Clinical Research Center for CancerSun Yat-sen UniversityGuangzhou 510060China Institute of Precision Medicine The First Affiliated HospitalSun Yat-sen UniversityGuangzhou 510080China Guangdong Institute of Gastroenterology Department of General SurgeryGuangdong Provincial Key Laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated HospitalSun Yat-sen UniversityGuangzhou 510275China

The exponential growth of bioinformatics tools in recent years has posed challenges for scientists in selecting the most suitable one for their data analysis ***,to aid scientists in making informed choices,a community-based platform that indexes and rates bioinformatics tools is urgently *** this study,we introduce Bio Treasury(http://***),an integrated communitybased repository that provides an interactive platform for users and developers to share their experiences in various bioinformatics *** Treasury offers a comprehensive collection of well-indexed bioinformatics software,tools,and databases,totaling over 10,000 *** the past two years,we have continuously improved and maintained Bio Treasury,adding several exciting features,including creating structured homepages for every tool and user,a hierarchical category of bioinformatics tools and classifying tools using large language model(LLM).Bio Treasury streamlines the tool submission process with intelligent ***,Bio Treasury provides a wide range of social features,for example,enabling users to participate in interactive discussions,rate tools,build and share tool collections for the *** believe Bio Treasury can be a valuable resource and knowledge-sharing platform for the biomedical *** empowers researchers to effectively discover and evaluate bioinformatics tools,fostering collaboration and advancing bioinformatics research.

关键词： bioinformatics tools index tool database rating system large language model tool collections shari

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Investigation on the Novel High-performance Copper/Graphene Composite Conductor for High Power Density Motor

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CES Transactions on Electrical Machines and Systems 2024年第1期8卷 80-85页

作者： Jiaxiao wang Tingting zuo Jiangli Xue Yadong Ru Yue Wu Zhuang Xu Yongsheng Liu Zhaoshun Gao Puqi Ning Tao Fan Xuhui wen Li Han Liye Xiao Shanghai University of Electric Power Shanghai 200090Chinaand the Institute of Electrical EngineeringChinese Academy of SciencesShanghai 200090China the Institute of Electrical Engineering Chinese Academy of SciencesBeijing 100190China with Shanghai University of Electric Power Shanghai 200090China

High-performance Cu/Graphene composite wire synergistically strengthened by nano Cr_(3)C_(2) phase was directly synthesized via hot press sintering followed by severe cold plastic deformation, using liquid paraffin and CuCr alloy powder as the raw materials. Since graphene is in situ formed under the catalysis of copper powder during the sintering process, the problem that graphene is easy to agglomerate and difficult to disperse uniformly in the copper matrix has been solved. The nano Cr_(3)C_(2)-particles nailed at the interface favor to improve the interface bonding. The Cu/Graphene composite possesses high electrical conductivity, hardness, and plasticity. The composite wire exhibits high electrical conductivity of 96.93% IACS, great tensile strength of 488MPa, and excellent resistance to softening. Even after annealing at 400℃ for 1 h, the tensile strength can still reach 268 MPa with a conductivity of about 99.14% *** wire's temperature coefficient of resistance(TCR) is largely reduced to 0.0035/℃ due to the complex structure,which leads the wire to present low resistivity at higher temperatures. Such Cu/Graphene composite wire with excellent comprehensive performance has a good application prospect in high-power density motors.

关键词： Cu/Graphene composite Mechanical properties Electrical property Microstructure Temperature coefficient of resistance

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Neuroprotective potential for mitigating ischemia-reperfusion-induced damage

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Neural Regeneration Research 2025年第8期20卷 2199-2217页

作者： Zi Ye Runqing Liu Hangxing wang Aizhen zuo Cen Jin Nan wang Huiqi Sun Luqian Feng Hua Yang The Clinical Medical College Guizhou Medical UniversityGuiyangGuizhou ProvinceChina Division of Infectious Diseases Department of Internal MedicinePeking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina School of Medical Imaging Guizhou Medical UniversityGuiyangGuizhou ProvinceChina Division of Gastroenterology First Affiliated Hospital of Zhengzhou UniversityZhengzhouHenan ProvinceChina The Second Clinical Medical College Lanzhou UniversityLanzhouGansu ProvinceChina Department of Neurosurgery Affiliated Hospital of Guizhou Medical UniversityGuiyangGuizhou ProvinceChina

Reperfusion following cerebral ischemia causes both structural and functional damage to brain tissue and could aggravate a patient's condition;this phenomenon is known as cerebral ischemia-reperfusion *** studies have elucidated the neuroprotective role of the sirtuin protein family(Sirtuins)in modulating cerebral ischemia-reperfusion ***,the potential of utilizing it as a novel intervention target to influence the prognosis of cerebral ischemia-reperfusion injury requires additional *** this review,the origin and research progress of Sirtuins are summarized,suggesting the involvement of Sirtuins in diverse mechanisms that affect cerebral ischemia-reperfusion injury,including inflammation,oxidative stress,blood-brain barrier damage,apoptosis,pyroptosis,and *** therapeutic avenues related to Sirtuins that may improve the prognosis of cerebral ischemia-reperfusion injury were also investigated by modulating Sirtuins expression and affecting representative pathways,such as nuclear factor-kappa B signaling,oxidative stress mediated by adenosine monophosphate-activated protein kinase,and the forkhead box *** review also summarizes the potential of endogenous substances,such as RNA and hormones,drugs,dietary supplements,and emerging therapies that regulate Sirtuins *** review also reveals that regulating Sirtuins mitigates cerebral ischemia-reperfusion injury when combined with other risk *** Sirtuins show promise as a potential target for the treatment of cerebral ischemiareperfusion injury,most recent studies are based on rodent models with circadian rhythms that are distinct from those of humans,potentially influencing the efficacy of Sirtuinstargeting drug ***,this review provides new insights into the role of Sirtuins in the pathology and treatment of cerebral ischemia-reperfusion injury.

关键词： apoptosis autophagy blood-brain barrier dietary supplements drug hormones inflammation neuroprotection oxidative stress prognosis pyroptosis reperfusion injury risk factors RNA therapeutics

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Endoscopic ultrasound-guided biliary drainage vs percutaneous transhepatic bile duct drainage in the management of malignant obstructive jaundice

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World Journal of Gastrointestinal Surgery 2024年第6期16卷 1592-1600页

作者： Qin-Qin Zhu Bing-Fang Chen Yue Yang Xue-Yong zuo wen-Hui Liu Ting-Ting wang Yin Zhang Department of Gastroenterology The Third Affiliated Hospital of Soochow University(The First People’s Hospital of Changzhou)Changzhou 213000Jiangsu ProvinceChina Department of Hepatobiliary and Pancreatic Surgery The Third Affiliated Hospital of Soochow University(The First People’s Hospital of Changzhou)Changzhou 213000Jiangsu ProvinceChina

BACKGROUND Malignant obstructive jaundice(MOJ)is a condition characterized by varying degrees of bile duct stenosis and obstruction,accompanied by the progressive development of malignant tumors,leading to high morbidity and mortality ***,the two most commonly employed methods for its management are percutaneous transhepatic bile duct drainage(PTBD)and endoscopic ultrasound-guided biliary drainage(EUS-BD).While both methods have demonstrated favorable outcomes,additional research needs to be performed to determine their relative *** compare the therapeutic effectiveness of EUS-BD and PTBD in treating *** This retrospective analysis,conducted between September 2015 and April 2023 at The Third Affiliated Hospital of Soochow University(The First People’s Hospital of Changzhou),involved 68 patients with *** patients were divided into two groups on the basis of surgical procedure received:EUS-BD subgroup(n=33)and PTBD subgroup(n=35).Variables such as general data,preoperative and postoperative indices,blood routine,liver function indices,myocardial function indices,operative success rate,clinical effectiveness,and complication rate were analyzed and compared between the *** In the EUS-BD subgroup,hospital stay duration,bile drainage volume,effective catheter time,and clinical effect-iveness rate were superior to those in the PTBD subgroup,although the differences were not statistically significant(P>0.05).The puncture time for the EUS-BD subgroup was shorter than that for the PTBD subgroup(Pwere significantly lower than those in the PTBD subgroup(Pwer than in the PTBD subgroup(P<0.05).CONCLUSION EUS-BD may reduce the number of punctures,improve liver and myocardial functions,alleviate traumatic stress,and decrease complication rates in MOJ treatment

关键词： Percutaneous hepatic biliary drainage Endoscopic ultrasound-guided biliary drainage Malignant obstructive jaundice Clinical effect Liver function Postoperative complications

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Unexpected Diversity in Ecosystem Nutrient Responses to Experimental Drought in Temperate Grasslands

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Phyton-International Journal of Experimental Botany 2024年第4期93卷 831-841页

作者： Biying Qiu Niwu Te Lin Song Yuan Shi Chuan Qiu Xiaoan zuo Qiang Yu Jianqiang Qian Zhengwen wang Honghui Wu wentao Luo School of Life Sciences Hebei UniversityBaoding071002China Liaoning Northwest Grassland Ecosystem National Observation and Research Station Erguna Forest-Steppe Ecotone Research StationInstitute of Applied EcologyChinese Academy of SciencesShenyang110164China Northwest Institute of Eco-Environment and Resources Chinese Academy of SciencesLanzhou730030China School of Grassland Science Beijing Forestry UniversityBeijing100083China College of Forestry Henan Agricultural UniversityZhengzhou450002China State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China Institute of Agricultural Resources and Regional PlanningChinese Academy of Agricultural SciencesBeijing100081China Key Laboratory of Arable Land Quality Monitoring and Evaluation Ministry of Agriculture and Rural AffairsInstitute of Agricultural Resources and Regional PlanningChinese Academy of Agricultural SciencesBeijing100081China

The responses of ecosystem nitrogen (N) and phosphorus (P) to drought are an important component of globalchange studies. However, previous studies were more often based on site-specific experiments, introducing a significantuncertainty to synthesis and site comparisons. we investigated the responses of vegetation and soil nutrientsto drought using a network experiment of temperate grasslands in Northern China. Drought treatment (66%reduction in growing season precipitation) was imposed by erecting rainout shelters, respectively, at the driest,intermediate, and wettest sites. we found that vegetation nutrient concentrations increased but soil nutrient concentrationsdecreased along the aridity gradient. Differential responses were observed under experimentaldrought among the three grassland sites. Specifically, the experimental drought did not change vegetation andsoil nutrient status at the driest site, while strongly reduced vegetation but increased soil nutrient concentrationsat the site with intermediate precipitation. On the contrary, experimental drought increased vegetation N concentrationsbut did not change vegetation P and soil nutrient concentrations at the wettest site. In general, the differentialeffects of drought on ecosystem nutrients were observed between manipulative and observationalexperiments as well as between sites. Our research findings suggest that conducting large-scale, consistent, andcontrolled network experiments is essential to accurately evaluate the effects of global climate change on terrestrialecosystem bio-geochemistry.

关键词： Climate change drought experiment precipitation nutrient cycles

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Photobiomodulation inhibits the expression of chondroitin sulfate proteoglycans after spinal cord injury via the Sox9 pathway

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Neural Regeneration Research 2024年第1期19卷 180-189页

作者： Zhihao Zhang Zhiwen Song Liang Luo Zhijie Zhu Xiaoshuang zuo Cheng Ju Xuankang wang Yangguang Ma Tingyu Wu Zhou Yao Jie Zhou Beiyu Chen Tan Ding Zhe wang Xueyu Hu Department of Orthopedics Xijing HospitalFourth Military Medical UniversityXi’anShaanxi ProvinceChina

Both glial cells and glia scar greatly affect the development of spinal cord injury and have become hot spots in research on spinal cord injury *** cellular deposition of dense extracellular matrix proteins such as chondroitin sulfate proteoglycans inside and around the glial scar is known to affect axonal growth and be a major obstacle to autogenous *** proteins are thus candidate targets for spinal cord injury *** previous studies demonstrated that 810 nm photo biomodulation inhibited the formation of chondroitin sulfate proteoglycans after spinal cord injury and greatly improved motor function in model ***,the specific mechanism and potential targets involved remain to be *** this study,to investigate the therapeutic effect of photo biomodulation,we established a mouse model of spinal cord injury by T9 clamping and irradiated the injury site at a power density of 50 mW/cm~2 for 50 minutes once a day for 7 consecutive *** found that photobiomodulation greatly restored motor function in mice and down regulated chondroitin sulfate proteoglycan expression in the injured spinal *** analysis revealed that photobiomodulation inhibited the expression of proteoglycan-related genes induced by spinal cord injury,and versican,a type of proteoglycan,was one of the most markedly changed *** staining showed that after spinal cord injury,versican was present in astrocytes in spinal cord *** expression of versican in primary astrocytes cultured in vitro increased after inflammation induction,whereas photobiomodulation inhibited the expression of ve ***,we found that the increased levels of p-Smad3,p-P38 and p-Erk in inflammatory astrocytes were reduced after photobiomodulation treatment and after delivery of inhibitors including FR 180204,(E)-SIS3,and SB *** suggests that Sma d 3/Sox9 and MAP K/Sox9 pathways may be involved in the effects of photobiomodulatio

关键词： chondroitin sulfate proteoglycans Erk MAPK P38 photobiomodulation principal component analysis Smad3 Sox9 spinal cord injury versican

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Development of Machine Learning Methods for Accurate Prediction of Plant Disease Resistance

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Engineering 2024年第9期40卷 100-110页

作者： Qi Liu Shi-min zuo Shasha Peng Hao Zhang Ye Peng wei Li Yehui Xiong Runmao Lin Zhiming Feng Huihui Li Jun Yang Guo-Liang wang Houxiang Kang State Key Laboratory for Biology of Plant Diseases and Insect Pests Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing 100193China Zhongshan Biological Breeding Laboratory&Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding Agricultural College of Yangzhou UniversityYangzhou 225009China Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization and College of Agronomy Hunan Agricultural UniversityChangsha 410128China State Key Laboratory of Crop Gene Resources and Breeding Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China College of Plant Protection Hunan Agricultural UniversityChangsha 410128China Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests Ministry of Education College of Plant ProtectionHainan UniversityHaikou 570228China MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests Department of Plant BiosecurityCollege of Plant ProtectionChina Agricultural UniversityBeijing 100193China Department of Plant Pathology Ohio State UniversityColumbusOH 43210USA

The traditional method of screening plants for disease resistance phenotype is both time-consuming and *** selection offers a potential solution to improve efficiency,but accurately predicting plant disease resistance remains a *** this study,we evaluated eight different machine learning(ML)methods,including random forest classification(RFC),support vector classifier(SVC),light gradient boosting machine(lightGBM),random forest classification plus kinship(RFC_K),support vector classification plus kinship(SVC_K),light gradient boosting machine plus kinship(lightGBM_K),deep neural network genomic prediction(DNNGP),and densely connected convolutional networks(DenseNet),for predicting plant disease *** results demonstrate that the three plus kinship(K)methods developed in this study achieved high prediction ***,these methods achieved accuracies of up to 95%for rice blast(RB),85%for rice black-streaked dwarf virus(RBSDV),and 85%for rice sheath blight(RSB)when trained and applied to the rice diversity panel I(RDPI).Furthermore,the plus K models performed well in predicting wheat blast(WB)and wheat stripe rust(WSR)diseases,with mean accuracies of up to 90%and 93%,*** assess the generalizability of our models,we applied the trained plus K methods to predict RB disease resistance in an independent population,rice diversity panel II(RDPII).Concurrently,we evaluated the RB resistance of RDPII cultivars using spray *** the predictions with the spray inoculation results,we found that the accuracy of the plus K methods reached 91%.These findings highlight the effectiveness of the plus K methods(RFC_K,SVC_K,and lightGBM_K)in accurately predicting plant disease resistance for RB,RBSDV,RSB,WB,and *** methods developed in this study not only provide valuable strategies for predicting disease resistance,but also pave the way for using machine learning to streamline genome-based crop breeding.

关键词： Predicting plant disease resistance Genomic selection Machine learning Genome-wide association study

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Aging hallmarks of the primate ovary revealed by spatiotemporal transcriptomics

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Protein & Cell 2024年第5期15卷 364-384页

作者： Huifen Lu Ying Jing Chen Zhang Shuai Ma weiqi Zhang Daoyuan Huang Bin Zhang Yuesheng zuo Yingying Qin Guang-Hui Liu Yang Yu Jing Qu Si wang Advanced Innovation Center for Human Brain Protection National Clinical Research Center for Geriatric DisordersXuanwu Hospital Capital Medical UniversityBeijing 100053China State Key Laboratory of Stem Cell and Reproductive Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China Aging Translational Medicine Center International Center for Aging and CancerBeijing Municipal Geriatric Medical Research CenterXuanwu HospitalCapital Medical UniversityBeijing 100053China State Key Laboratory of Membrane Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Beijing Institute for Stem Cell and Regenerative Medicine Beijing 100101China CAS Key Laboratory of Genomic and Precision Medicine Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China Institute for Stem cell and Regeneration CASBeijing 100101China China National Center for Bioinformation Beijing 100101China The Fifth People’s Hospital of Chongqing Chongqing 400062China Sino-Danish College University of Chinese Academy of SciencesBeijing 101408China Sino-Danish Center for Education and Research Beijing 101408China Department of Obstetrics and Gynecology Center for Reproductive MedicinePeking UniversityThird HospitalBeijing 100191China Clinical Stem Cell Research Center Peking UniversityThird HospitalBeijing 100191China Center for Reproductive Medicine Cheeloo College of MedicineShandong UniversityJinan 250012China Key Laboratory of Reproductive Endocrinology of Ministry of Education National Research Center for Assisted Reproductive Technology and Reproductive GeneticsShandong Key Laboratory of Reproductive MedicineShandong Provincial Clinical Research Center for Reproductive HealthJinan 250012China Key Laboratory of Organ Regeneration and Reconstruction Institute of ZoologyChinese Academy of SciencesBeijing 100101China Aging Biomarker Consortium Beijing 100101China

The ovary is indispensable for female reproduction,and its age-dependent functional decline is the primary cause of ***,the molecular basis of ovarian aging in higher vertebrates remains poorly ***,we apply spatiotemporal transcriptomics to benchmark architecture organization as well as cellular and molecular determinants in young primate ovaries and compare these to aged primate *** a global view,somatic cells within the non-follicle region undergo more pronounced transcriptional fluctuation relative to those in the follicle region,likely constituting a hostile microenvironment that facilitates ovarian ***,we uncovered that inflammation,the senescent-associated secretory phenotype,senescence,and fibrosis are the likely primary contributors to ovarian aging(PCOA).Of note,we identified spatial co-localization between a PCOA-featured spot and an unappreciated MT2(Metallothionein 2)highly expressing spot(MT2^(high))characterized by high levels of inflammation,potentially serving as an aging hotspot in the primate ***,with advanced age,a subpopulation of MT2^(high)accumulates,likely disseminating and amplifying the senescent signal *** study establishes the first primate spatiotemporal transcriptomic atlas,advancing our understanding of mechanistic determinants underpinning primate ovarian aging and unraveling potential biomarkers and therapeutic targets for aging and age-associated human ovarian disorders.

关键词： spatial transcriptome primate ovary aging senescence inflammation

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Two different autorefractors for vision screening in children and adolescents

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International Journal of Ophthalmology(English edition) 2024年第2期17卷 331-338页

作者： Xiao-Jun Chen Lin-Jie Liu Bing Sun Dan-Dan Jiang Shu-Shu zuo Yan-Hui wang Chun-Hua Zhang Yan-Yan Chen School of Optometry and Ophthalmology Wenzhou Medical UniversityWenzhou 325027Zhejiang ProvinceChina National Clinical Research Center for Ocular Diseases Eye HospitalWenzhou Medical UniversityWenzhou 325027Zhejiang ProvinceChina

AIM:To compare the consistency of two autorefractors(Tianle RM-9000 and Topcon KR-800)for school-age myopia children,and to provide a basis for largescale data analysis and ***:The refractive error in 909 subjects(age 4–18y)were measured using both autorefractors without *** data were analyzed using Fourier decomposition and the correlation coefficients,intraclass correlation coefficients(ICC),and Bland-Altman limits of agreement(LoA)for each parameter were ***:There was a strong correlation between the spherical equivalent(SE),sphere diopter(DS),and cylinder diopter(DC)readings of the Tianle RM-9000 and those of the Topcon KR-800,with correlation coefficient values of 0.98,0.98 and 0.83 and ICC values of 0.99,0.99 and 0.93,***,the correlation coefficients and ICC values of J0 and J45 were unreliable(R=-0.004,-0.034;both ICCwere significantly biased toward myopia compared with the Topcon KR-800,and the mean differences were-0.072,-0.026,-0.091 D,respectively(all Pwere in the clinically acceptable *** J0 and J45,the mean differences were close to zero(P=0.43,0.84);however,the 95%LoA were relatively wide(J0 SD:0.53;95%CI:-1.00,1.10;J45 SD:0.52;95%CI:-1.00,1.00).CONCLUSION:The two autorefractors are consistent with each other,as the differences in SE,DS,and DC were within the clinically acceptable *** can compare the data measured by either device in different studies and use the two devices in the same study to generate a dataset that can be analyzed ***,the J0 and J45 vectors are unreliable and should not be used to assess astigmatism.

关键词： refractive error autorefractors school-age myopia children

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Application of Regularization Methods in the Sky Map Reconstruction of the Tianlai Cylinder Pathfinder Array

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Research in Astronomy and Astrophysics 2024年第2期24卷 24-35页

作者： Kaifeng Yu Shifan zuo Fengquan Wu Yougang wang Xuelei Chen National Astronomical Observatories Chinese Academy of SciencesBeijing 100101China Key Laboratory of Radio Astronomy and Technology Chinese Academy of SciencesBeijing 100101China School of Astronomy and Space Science University of Chinese Academy of SciencesBeijing 100049China Key Laboratory of Cosmology and Astrophysics(Liaoning)&College of Sciences Northeastern UniversityShenyang 110819China Center of High Energy Physics Peking UniversityBeijing 100871China

The Tianlai cylinder pathfinder is a radio interferometer array to test 21 cm intensity mapping techniques in the post-reionization *** works in passive drift scan mode to survey the sky visible in the northern *** deal with the large instantaneous field of view and the spherical sky,we decompose the drift scan data into m-modes,which are linearly related to the sky *** sky map is reconstructed by solving the linear interferometer *** to incomplete uv coverage of the interferometer baselines,this inverse problem is usually ill-posed,and regularization method is needed for its *** this paper,we use simulation to investigate two frequently used regularization methods,the Truncated Singular Value Decomposition(TSVD),and the Tikhonov regularization *** the regularization parameter is very important for its *** employ the generalized cross validation method and the L-curve method to determine the optimal *** compare the resulting maps obtained with the different regularization methods,and for the different parameters derived using the different *** both methods can yield good maps for a range of regularization parameters,in the Tikhonov method the suppression of noisy modes are more gradually applied,produce more smooth maps which avoids some visual artefacts in the maps generated with the TSVD method.

关键词： techniques interferometric-methods numerical-cosmology observations-radio continuum general

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