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A LiDAR Point Clouds Dataset of Ships in a Maritime Environment

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IEEE/CAA Journal of Automatica Sinica 2024年第7期11卷 1681-1694页

作者： Qiuyu zhang Lipeng Wang Hao Meng wen zhang Genghua Huang the College of Intelligent Systems Science and Engineering Harbin Engineering UniversityHarbin 150001China Key Laboratory of Space Active Opto-Electronics Technology Shanghai Institute of Technical PhysicsChinese Academy of SciencesShanghai 200083China

For the first time, this article introduces a LiDAR Point Clouds Dataset of Ships composed of both collected and simulated data to address the scarcity of LiDAR data in maritime applications. The collected data are acquired using specialized maritime LiDAR sensors in both inland waterways and wide-open ocean environments. The simulated data is generated by placing a ship in the LiDAR coordinate system and scanning it with a redeveloped Blensor that emulates the operation of a LiDAR sensor equipped with various laser beams. Furthermore,we also render point clouds for foggy and rainy weather conditions. To describe a realistic shipping environment, a dynamic tail wave is modeled by iterating the wave elevation of each point in a time series. Finally, networks serving small objects are migrated to ship applications by feeding our dataset. The positive effect of simulated data is described in object detection experiments, and the negative impact of tail waves as noise is verified in single-object tracking experiments. The Dataset is available at https://***/zqy411470859/ship_dataset.

关键词： 3D point clouds dataset dynamic tail wave fog simulation rainy simulation simulated data

Degradable magnesium alloy suture promotes fibrocartilaginous interface regeneration in a rat rotator cuff transosseous repair model

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Journal of Magnesium and Alloys 2024年第1期12卷 384-393页

作者： Baoxiang zhang wen zhang Fei zhang Chao Ning Mingyang An Ke Yang Lili Tan Qiang zhang Department of Sports Medicine Chinese PLA General HospitalBeijing 100853China Shi-changxu Innovation Center for Advanced Materials Institute of Metal ResearchChinese Academy of SciencesShenyang 110016China School of Materials Science and Engineering University of Science and Technology of ChinaShenyang 110016China Medical School of PLA Beijing 100853China Institute of Orthopedics Chinese PLA General HospitalBeijing Key Lab of Regenerative Medicine in OrthopedicsKey Lab of Musculoskeletal Trauma&War Injuries of Chinese PLABeijing 100853China

Despite transosseous rotator cuff tear repair using sutures is widely accepted for tendon-bone fixation,the fibrocartilaginous enthesis regeneration is still hardly achieved with the traditional sutures.In the present work,degradable magnesium(Mg)alloy wire was applied to suture supraspinatus tendon in a rat acute rotator cuff tear model with Vicryl Plus 4±0 absorbable suture as control.The shoulder joint humerus-supraspinatus tendon complex specimens were retrieved at 4,8,and 12 weeks after operation.The Mg alloy suture groups showed better biomechanical properties in terms of ultimate load to failure.Gross observation showed that hyperplastic response of the scar tissue at the tendon-bone interface is progressively alleviated over time in the both Mg alloy suture and Vicryl suture groups.In the histological analysis,for Mg alloy suture groups,chondrocytes appear to proliferate at 4 weeks postoperatively,and the tendon-bone interface showed an orderly structural transition zone at 8 weeks postoperatively.The collagenous fiber tended to be aligned and the tendon-bone interlocking structures apparently formed,where transitional structure from unmineralized fibrocartilage to mineralized fibrocartilage was closer to the native fibrocartilaginous enthesis.In vivo degradation of the magnesium alloy wire was completed within 12 weeks.The results indicated that Mg alloy wire was promising as degradable suture with the potential to promotes fibrocartilaginous interface regeneration in rotator cuff repair.

关键词： Rotator cuff repair Mg alloy wire Tendon-bone healing Fibrocartilaginous interface

A comprehensive review of molecular optimization in artificial intelligence-based drug discovery

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Quantitative Biology 2024年第1期12卷 15-29页

作者： Yuhang Xia Yongkang Wang Zhiwei Wang wen zhang School of Information Huazhong Agricultural UniversityWuhanChina

Drug discovery is aimed to design novel molecules with specific chemical properties for the treatment of targeting diseases. Generally, molecular optimization is one important step in drug discovery, which optimizes the physical and chemical properties of a molecule. Currently, artificial intelligence techniques have shown excellent success in drug discovery, which has emerged as a new strategy to address the challenges of drug design including molecular optimization, and drastically reduce the costs and time for drug discovery. We review the latest advances of molecular optimization in artificial intelligence-based drug discovery, including data resources, molecular properties, optimization methodologies, and assessment criteria for molecular optimization. Specifically, we classify the optimization methodologies into molecular mapping-based, molecular distribution matching-based, and guided search-based methods, respectively, and discuss the principles of these methods as well as their pros and cons. Moreover, we highlight the current challenges in molecular optimization and offer a variety of perspectives, including interpretability, multidimensional optimization, and model generalization, on potential new lines of research to pursue in future. This study provides a comprehensive review of molecular optimization in artificial intelligence-based drug discovery, which points out the challenges as well as the new prospects. This review will guide researchers who are interested in artificial intelligence molecular optimization.

关键词： artificial intelligence drug discovery molecular optimization

Deep learning for drug-drug interaction prediction:A comprehensive review

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Quantitative Biology 2024年第1期12卷 30-52页

作者： Xinyue Li Zhankun Xiong wen zhang Shichao Liu College of Informatics Huazhong Agricultural UniversityWuhanChina

The prediction of drug-drug interactions(DDIs)is a crucial task for drug safety research,and identifying potential DDIs helps us to explore the mechanism behind combinatorial therapy.Traditional wet chemical experiments for DDI are cumbersome and time-consuming,and are too small in scale,limiting the efficiency of DDI predictions.Therefore,it is particularly crucial to develop improved computational methods for detecting drug interactions.With the development of deep learning,several computational models based on deep learning have been proposed for DDI prediction.In this review,we summarized the high-quality DDI prediction methods based on deep learning in recent years,and divided them into four categories:neural network-based methods,graph neural network-based methods,knowledge graph-based methods,and multimodal-based methods.Furthermore,we discuss the challenges of existing methods and future potential perspectives.This review reveals that deep learning can significantly improve DDI prediction performance compared to traditional machine learning.Deep learning models can scale to large-scale datasets and accept multiple data types as input,thus making DDI predictions more efficient and accurate.

关键词： deep learning drug-drug interactions graph neural network knowledge graph multimodal deep learning neural network

Organoid co-culture models of the tumor microenvironment promote precision medicine

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Cancer Innovation 2024年第1期3卷 79-103页

作者： Zhaoru Gu Quanyou Wu Bingqing Shang Kaitai zhang wen zhang State Key Laboratory of Molecular Oncology Department of Etiology and CarcinogenesisNational Cancer CenterNational Clinical Research Center for CancerCancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina Department of Urology National Cancer CenterNational Clinical Research Center for CancerCancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina Department of Immunology National Cancer CenterNational Clinical Research Center for CancerCancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina

In recent years,the three-dimensional(3D)culture system has emerged as a promising preclinical model for tumor research owing to its ability to replicate the tissue structure and molecular characteristics of solid tumors in vivo.This system offers several advantages,including high throughput,efficiency,and retention of tumor heterogeneity.Traditional Matrigel-submerged organoid cultures primarily support the long-term proliferation of epithelial cells.One solution for the exploration of the tumor microenvironment is a reconstitution approach involving the introduction of exogenous cell types,either in dual,triple or even multiple combinations.Another solution is a holistic approach including patient-derived tumor fragments,air-liquid interface,suspension 3D culture,and microfluidic tumor-on-chip models.Organoid co-culture models have also gained popularity for studying the tumor microenvironment,evaluating tumor immunotherapy,identifying predictive biomarkers,screening for effective drugs,and modeling infections.By leveraging these 3D culture systems,it is hoped to advance the clinical application of therapeutic approaches and improve patient outcomes.

关键词： air-liquid interface immunotherapy organoid tumor microenvironment tumor-on-chip

Comparison of clinical features and outcomes of proliferative,fibrotic,and mixed subtypes of IgG4-related disease:A retrospective cohort study

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Chinese Medical Journal 2024年第3期137卷 303-311页

作者： Linyi Peng Xinlu zhang Jiaxin Zhou Jieqiong Li Zheng Liu Hui Lu Yu Peng Yunyun Fei Yan Zhao Xiaofeng Zeng wen zhang Department of Rheumatology and Clinical Immunology Peking Union Medical College HospitalNational Clinical Research Center for Dermatologic and Immunologic DiseasesState Key Laboratory of Complex Severe and Rare DiseasesThe Ministry of Education Key LaboratoryBeijing 100730China Institute of Clinical Medicine Peking Union Medical College Hospital(PUMCH)Chinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing 100730China

Background:Immunoglobulin G4-related disease(IgG4-RD)is a recently recognized immune-mediated disorder that can affect almost any organ in the human body.IgG4-RD can be categorized into proliferative and fibrotic subtypes based on patients’clinicopathological characteristics.This study aimed to compare the clinical manifestations,laboratory findings,and treatment outcomes of IgG4-RD among different subtypes.Methods:We prospectively enrolled 622 patients with newly diagnosed IgG4-RD at Peking Union Medical College Hospital from March 2011 to August 2021.The patients were divided into three groups according to their clinicopathological characteristics:proliferative,fibrotic,and mixed subtypes.We compared demographic features,clinical manifestations,organ involvement,laboratory tests,and treatment agents across three subtypes.We then assessed the differences in treatment outcomes among 448 patients receiving glucocorticoids alone or in combination with immunosuppressants.Moreover,risk factors of relapse were revealed by applying the univariate and multivariate Cox regression analysis.Results:We classified the 622 patients into three groups consisting of 470 proliferative patients,55 fibrotic patients,and 97 mixed patients,respectively.We found that gender distribution,age,disease duration,and frequency of allergy history were significantly different among subgroups.In terms of organ involvement,submandibular and lacrimal glands were frequently involved in the proliferative subtype,while retroperitoneum was the most commonly involved site in both fibrotic subtype and mixed subtype.The comparison of laboratory tests revealed that eosinophils(P=0.010),total IgE(P=0.006),high-sensitivity C-reactive protein(P<0.001),erythrocyte sedimentation rate(P<0.001),complement C4(P<0.001),IgG(P=0.001),IgG1(P<0.001),IgG4(P<0.001),and IgA(P<0.001),at baseline were significantly different among three subtypes.Compared with proliferative and mixed subtypes,the fibrotic subtype showed the lowest rate of relapse(log-rank P=0.014).Conclus

关键词： IgG4-related disease Proliferative subtype Fibrotic subtype Clinical features Treatment outcome

Discontinuity development patterns and the challenges for 3D discrete fracture network modeling on complicated exposed rock surfaces

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Journal of Rock Mechanics and Geotechnical Engineering 2024年第6期16卷 2154-2171页

作者： wen zhang Ming Wei Ying zhang Tengyue Li Qing Wang Chen Cao Chun Zhu Zhengwei Li Zhenbang Nie Shuonan Wang Han Yin College of Construction Engineering Jilin UniversityChangchun130026China Liaoning Nonferrous Geological Exploration and Research Institute Co. Shenyang110013China School of Earth Sciences and Engineering Hohai UniversityNanjing210098China Northeastern University Shenyang110819China

Natural slopes usually display complicated exposed rock surfaces that are characterized by complex and substantial terrain undulation and ubiquitous undesirable phenomena such as vegetation cover and rockfalls.This study presents a systematic outcrop research of fracture pattern variations in a complicated rock slope,and the qualitative and quantitative study of the complex phenomena impact on threedimensional(3D)discrete fracture network(DFN)modeling.As the studies of the outcrop fracture pattern have been so far focused on local variations,thus,we put forward a statistical analysis of global variations.The entire outcrop is partitioned into several subzones,and the subzone-scale variability of fracture geometric properties is analyzed(including the orientation,the density,and the trace length).The results reveal significant variations in fracture characteristics(such as the concentrative degree,the average orientation,the density,and the trace length)among different subzones.Moreover,the density of fracture sets,which is approximately parallel to the slope surface,exhibits a notably higher value compared to other fracture sets across all subzones.To improve the accuracy of the DFN modeling,the effects of three common phenomena resulting from vegetation and rockfalls are qualitatively analyzed and the corresponding quantitative data processing solutions are proposed.Subsequently,the 3D fracture geometric parameters are determined for different areas of the high-steep rock slope in terms of the subzone dimensions.The results show significant variations in the same set of 3D fracture parameters across different regions with density differing by up to tenfold and mean trace length exhibiting differences of 3e4 times.The study results present precise geological structural information,improve modeling accuracy,and provide practical solutions for addressing complex outcrop issues.

关键词： Complicated exposed rock surfaces Discontinuity characteristic variation Three-dimensional discrete fracture network modeling Outcrop study Vegetation cover and rockfalls

Correlation of personality with individual reproductive success in shrub-nesting birds depends on their life history style

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Avian Research 2024年第1期15卷 42-49页

作者： Jianchuan Li wen zhang Ningning Sun Yujie Wang Lifang Gao Ran Feng Liqing Fan Bo Du Tibet Museum of Natural Science Lhasa850011China School of Life Sciences Lanzhou UniversityLanzhou730000China Institute of Plateau Ecology Tibet Agricultural and Animal Husbandry UniversityLinzhi860000China

Two questions in the research of animal personality—whether there is a correlation between a personality trait and individual reproductive success,and what is the genetic basis underlying a personality trait—remain unresolved.We addressed these two questions in three shrub-nesting birds,the Azure-winged Magpie(Cyanopica cyanus,AM),White-collared Blackbird(Turdus albocinctus,WB),and Brown-cheeked Laughingthrush(Trochalopteron henrici,BL).The personality type of an individual was first identified according to its response to a territorial intruder.Then,we compared the fleeing distance,breeding parameters,and differential expressed genes(DEGs) in the brain transcriptome between bold and shy breeders.In the three species,bold breeders exhibited more aggressiveness towards an intruder of their territory than did shy breeders.The reproductive success of bold breeders was significantly higher than that of shy breeders in AM but not in WB and BL.The three species shared one DEG,crabp1,which was up-regulated in bold relative to in shy individuals.By regulating the expression of corticotropin-releasing hormone,higher crabp1 gene expression can decrease cellular response to retinoic acid.Therefore,bold individuals are insensitive to external stresses and able to exhibit more aggressiveness to intruders than their shier counterparts.Aggressiveness is beneficial to bold individuals in AM but not in WB and BL because the former could evoke neighbors to make the same response of defending against intruders but the latter could not.Although a personality trait may have the same genetic basis across species,its correlation with reproductive success depends largely on the life history style of a species.

关键词： Boldness Life history style Personality Reproductive success Transcriptome analysis

A strained π-extended[10]cycloparaphenylene carbon nanoring

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Chinese Chemical Letters 2024年第5期35卷 171-174页

作者： Kang Wei Jiayu Li wen zhang Bing Yuan Ming-De Li Pingwu Du Key Laboratory of Precision and Intelligent Chemistry Anhui Laboratory of Advanced Photon Science and TechnologyDepartment of Materials Science and EngineeringUniversity of Science and Technology of ChinaHefei 230026China Department of Chemistry and Key Laboratory for Preparation and Application of Ordered Structural Materials of Guangdong Province Shantou UniversityShantou 515063China

Herein,we report the facile synthesis of a highly strained hexabenzocoronene-containing carbon nanoring,cyclo[4]-paraphenylene[2]-2,11-hexabenzocoronenylene([4,2]CPHBC),as the segment of a[10,10]single-walled carbon nanotube([10,10]SWNT).[4,2]CPHBC was synthesized based on the platinummediated assembly of diborylbiphenyl and diborylhexabenzocoronene,forming a tetranuclear platinum complex,followed by reductive elimination.This nanoring molecule was confirmed by NMR and HRMS,and its photophysical properties were studied using steady-state and time-resolved spectroscopies.Moreover,the selective supramolecular host-guest interaction between[4,2]CPHBC and C_(60) was also investigated.

关键词： CPP Hexabenzocoronene Fullerene Supramolecular chemistry