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Cone-beam computed tomography noise reduction method based on U-Net with convolutional block attention module in proton therapy

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Nuclear Science and Techniques 2024年第7期35卷 89-100页

作者： xing-yue ruan Xiu-Fang Li Meng-Ya Guo Mei Chen Ming Lv Rui Li Zhi-Ling Chen Shanghai Institute of Applied Physics Chinese Academy of SciencesShanghai201800China University of Chinese Academy of Sciences Beijing100049China Shanghai Advanced Research Institute Chinese Academy of SciencesShanghai201210China Department of Radiation Oncology Ruijin HospitalShanghai Jiao Tong University School of MedicineShanghai200025China Shanghai Key Laboratory of Proton therapy Shanghai201801China

Cone-beam computed tomography(CBCT) is mostly used for position verification during the treatment process. However,severe image artifacts in CBCT hinder its direct use in dose calculation and adaptive radiation therapy re-planning for proton therapy. In this study, an improved U-Net neural network named CBAM-U-Net was proposed for CBCT noise reduction in proton therapy, which is a CBCT denoised U-Net network with convolutional block attention modules. The datasets contained 20 groups of head and neck images. The CT images were registered to CBCT images as ground truth. The original CBCT denoised U-Net network, sCTU-Net, was trained for model performance comparison. The synthetic CT(SCT) images generated by CBAM-U-Net and the original sCTU-Net are called CBAM-SCT and U-Net-SCT images, respectively. The HU accuracies of the CT, CBCT, and SCT images were compared using four metrics: mean absolute error(MAE), root mean square error(RMSE), peak signal-to-noise ratio(PSNR), and structure similarity index measure(SSIM). The mean values of the MAE, RMSE, PSNR, and SSIM of CBAM-SCT images were 23.80 HU, 64.63 HU, 52.27 dB, and 0.9919, respectively,which were superior to those of the U-Net-SCT images. To evaluate dosimetric accuracy, the range accuracy was compared for a single-energy proton beam. The γ-index pass rates of a 4 cm × 4 cm scanned field and simple plan were calculated to compare the effects of the noise reduction capabilities of the original U-Net and CBAM-U-Net on the dose calculation results. CBAM-U-Net reduced noise more effectively than sCTU-Net, particularly in high-density tissues. We proposed a CBAM-U-Net model for CBCT noise reduction in proton therapy. Owing to the excellent noise reduction capabilities of CBAM-U-Net, the proposed model provided relatively explicit information regarding patient tissues. Moreover, it maybe be used in dose calculation and adaptive treatment planning in the future.

关键词： Proton therapy Cone-beam CT CBAM-U-Net γ-index

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Learning Top-K Subtask Planning Tree Based on Discriminative Representation Pretraining for Decision-making

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Machine Intelligence Research 2024年第4期21卷 782-800页

作者： Jingqing ruan Kaishen Wang Qingyang Zhang Dengpeng xing Bo Xu Institute of Automation Chinese Academy of SciencesBeijing 100190China School of Future Technology University of Chinese Academy of SciencesBeijing 100049China School of Artificial Intelligence University of Chinese Academy of SciencesBeijing 100049China

Decomposing complex real-world tasks into simpler subtasks and devising a subtask execution plan is critical for humans to achieve effective ***,replicating this process remains challenging for AI agents and naturally raises two questions:(1)How to extract discriminative knowledge representation from priors?(2)How to develop a rational plan to decompose complex problems?To address these issues,we introduce a groundbreaking framework that incorporates two main ***,our multiple-encoder and individual-predictor regime goes beyond traditional architectures to extract nuanced task-specific dynamics from datasets,enriching the feature space for ***,we innovate in planning by introducing a top-K subtask planning tree generated through an attention mechanism,which allows for dynamic adaptability and forward-looking *** framework is empirically validated against challenging benchmarks BabyAI including multiple combinatorially rich synthetic tasks(e.g.,GoToSeq,SynthSeq,BossLevel),where it not only outperforms competitive baselines but also demonstrates superior adaptability and effectiveness incomplex task decomposition.

关键词： Reinforcement learning representation learning subtask planning task decomposition pretraining.

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Enhancing Multi-agent Coordination via Dual-channel Consensus

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Machine Intelligence Research 2024年第2期21卷 349-368页

作者： Qingyang Zhang Kaishen Wang Jingqing ruan Yiming Yang Dengpeng xing Bo Xu Institute of Automation Chinese Academy of SciencesBeijing 100190China School of Future Technology University of Chinese Academy of SciencesBeijing 100049China School of Artificial Intelligence University of Chinese Academy of SciencesBeijing 100049China

Successful coordination in multi-agent systems requires agents to achieve *** works propose methods through information sharing,such as explicit information sharing via communication protocols or exchanging information implicitly via behavior ***,these methods may fail in the absence of communication channels or due to biased *** this work,we propose to develop dual-channel consensus(DuCC)via contrastive representation learning for fully cooperative multi-agent systems,which does not need explicit communication and avoids biased *** comprises two types of consensus:temporally extended consensus within each agent(inner-agent consensus)and mutual consensus across agents(inter-agent consensus).To achieve DuCC,we design two objectives to learn representations of slow environmental features for inner-agent consensus and to realize cognitive consistency as inter-agent *** DuCC is highly general and can be flexibly combined with various MARL *** extensive experiments on StarCraft multi-agent challenge and Google research football demonstrate that our method efficiently reaches consensus and performs superiorly to state-of-the-art MARL algorithms.

关键词： Multi-agent reinforcement learning contrastive representation learning consensus multi-agent cooperation cognitive consistency

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Insight into Lithium–sulfur batteries performance enhancement: from metal nanoparticles to metal nanoclusters to single metal atoms

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Tungsten 2024年第3期6卷 504-521页

作者： Shuang Ma Qing-Ling ruan Xue-Cheng Liu Gui-Jun Zhu Die Yuan Ling-Qiao Hu Yu-Mei Huang xing-xing Gu Chongqing Key Laboratory of Catalysis and New Environmental Materials College of Environment and Resources Chongqing Technology and Business University National Research Base of Intelligent Manufacturing Service Chongqing Technology and Business University

Lithium-sulfur(Li-S) batteries have attracted much attention and developed rapidly in recent years due to their high energy density,low cost,and ***,its commercialization process still encounters various *** them,the sulfur cathode is easy to dissolve and shuttle,resulting in the loss of active substances and the severe growth of lithium anode dendrites,which is one of the biggest *** the redox conversion kinetics of sulfur cathode is expected to fundamentally alleviate the shuttle phenomenon of poly ***,this paper reviews the effects of metal nanoparticles to metal nanoclusters to metal single-atom catalysts on improving the redox of Li-S batteries,to let researchers better understand the size effect on the kinetics of sulfur cathodes in Li-S batteries,which will provide important guidance for the future large-scale commercialization of Li-S batteries.

关键词： Lithium–sulfur batteries Metal nanoparticles Metal nanoclusters Metal single atoms Size effects

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Stable watt-level mode-locked noise-like pulse from an all-PM fiber oscillator at 2 μm

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Chinese Optics Letters 2024年第6期22卷 154-157页

作者： Meng Wang Junjia Ding Deqin Ouyang Yewang Chen Junqing Zhao xing Liu Shuangchen ruan Key Laboratory of Advanced Optical Precision Manufacturing Technology of Guangdong Higher Education Institutes Sino-German College of Intelligent ManufacturingShenzhen Technology UniversityShenzhen 518118China

We have experimentally presented a watt-level noise-like (NL) pulse mode-locked all-polarization-maintaining(PM) fiber laser centered at ~1995 nm, which can directly generate stable NL pulses with a maximum output power of ~1.017 W and pulse energy of ~0.61 μJ, representing the highest output power of mode-locked NL pulse at 2 μm from any fiber oscillators,to the best of our knowledge. The mode-locked NL pulse laser exhibits an excellent stability with a power fluctuation of~0.1% in 8 h of monitoring, and a signal-to-noise ratio of ~83 dB at a fundamental frequency of ~1.662 MHz. Moreover, the pulse envelope and coherence spike width of the NL pulse can be widely tuned from ~4.5 ns to ~16 ns, and ~364 fs to~323 fs, respectively, with the enhancement of the pump power. Such an all-PM fiber oscillator is the ideal seed source for the implementation of a high-power NL pulse laser and has potential valuable applications in mid-infrared spectroscopy and industrial processing.

关键词： Tm-doped fiber laser mode locking noise-like pulse

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Suppressor tRNA in gene therapy

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Science China(Life Sciences) 2024年第10期67卷 2120-2131页

作者： Jingjing ruan Xiaoxiao Yu Huixia Xu Wenrui Cui Kaiye Zhang Chenyang Liu Wenlong Sun Xiaodan Huang Lei An yue Zhang The Children's Hospital National Clinical Research Center for Child HealthZhejiang University School of MedicineLiangzhu LaboratoryHangzhou 310000China Liangzhu Laboratory Zhejiang University School of MedicineHangzhou 311121China Department of Thoracic and Cardiovascular Surgery Huaihe Hospital of Henan UniversityHenan UniversityKaifeng 475000China Translational Medicine Center Huaihe Hospital of Henan UniversityHenan UniversityKaifeng 475000China Eye Center The Second Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhou 310009China

Suppressor tRNAs are engineered or naturally occurring transfer RNA molecules that have shown promise in gene therapy for diseases caused by nonsense mutations,which result in premature termination codons(PTCs)in coding sequence,leading to truncated,often nonfunctional *** t RNAs can recognize and pair with these PTCs,allowing the ribosome to continue translation and produce a full-length *** review introduces the mechanism and development of suppressor t RNAs,compares suppressor tRNAs with other readthrough therapies,discusses their potential for clinical therapy,limitations,and *** also summarize the applications of suppressor tRNAs in both in vitro and in vivo,offering new insights into the research and treatment of nonsense mutation diseases.

关键词： suppressor tRNA PTC nonsense mutation readthrough gene therapy

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BSAlign:A Library for Nucleotide Sequence Alignment

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Genomics, Proteomics & Bioinformatics 2024年第2期22卷 135-142页

作者： Haojing Shao Jue ruan Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120China

Increasing the accuracy of the nucleotide sequence alignment is an essential issue in genomics *** classic dynamic programming(DP)algorithms(e.g.,Smith–Waterman and Needleman–Wunsch)guarantee to produce the optimal result,their time complexity hinders the application of large-scale sequence *** optimization efforts that aim to accelerate the alignment process generally come from three perspectives:redesigning data structures[e.g.,diagonal or striped Single Instruction Multiple Data(SIMD)implementations],increasing the number of parallelisms in SIMD operations(e.g.,difference recurrence relation),or reducing search space(e.g.,banded DP).However,no methods combine all these three aspects to build an ultra-fast *** this study,we developed a Banded Striped Aligner(BSAlign)library that delivers accurate alignment results at an ultra-fast speed by knitting a series of novel methods together to take advantage of all of the aforementioned three perspectives with highlights such as active F-loop in striped vectorization and striped move in banded *** applied our new acceleration design on both regular and edit distance pairwise *** achieved 2-fold speed-up than other SIMD-based implementations for regular pairwise alignment,and 1.5-fold to 4-fold speed-up in edit distance-based implementations for long *** is implemented in C programing language and is available at https://***/ruanjue/bsalign.

关键词： Pairwise alignment Edit distance Striped vectorization Banded dynamic programming F evaluation

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Dynamic Response of Foundations during Startup of High-Frequency Tunnel Equipment

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Computer Modeling in Engineering & Sciences 2024年第7期140卷 821-844页

作者： Dawei ruan Mingwei Hu College of Civil and Transportation Engineering Shenzhen UniversityShenzhen518060China State Key Laboratory of Intelligent Geotechnics and Tunnelling Shenzhen UniversityShenzhen518060China Key Laboratory of Coastal Urban Resilient Infrastructures of Ministry of Education Shenzhen UniversityShenzhen518060China Underground Polis Academy Shenzhen UniversityShenzhen518060China Shenzhen Key Laboratory of Green Efficient and Intelligent Construction of Underground Metro StationShenzhen UniversityShenzhen518060China

The specialized equipment utilized in long-line tunnel engineering is evolving towards large-scale,multifunctional,and complex *** vibration caused by the high-frequency units during regular operation is supported by the foundation of the units,and the magnitude of vibration and the operating frequency fluctuate in different engineering contexts,leading to variations in the dynamic response of the *** high-frequency units yield significantly diverse outcomes under different startup conditions and times,resulting in failure to meet operational requirements,influencing the normal function of the tunnel,and causing harm to the foundation structure,personnel,and property in severe *** article formulates a finite element numerical computation model for solid elements using three-dimensional elastic body theory and integrates field measurements to substantiate and ascertain the crucial parameter configurations of the finite element *** proposing a comprehensive startup timing function for high-frequency dynamic machines under different startup conditions,simulating the frequency andmagnitude variations during the startup process,and suggesting functions for changes in frequency and magnitude,a simulated startup schedule function for high-frequency machines is created through *** into account the selection of the transient dynamic analysis step length,the dynamic response results for the lower dynamic foundation during its fundamental frequency crossing process are *** validation checks if the structural magnitude surpasses the safety threshold during the critical phase of unit startup traversing the structural resonance *** design recommendations for high-frequency units’dynamic foundations are provided,taking into account the startup process of the machine and ensuring the safe operation of the tunnel.

关键词： Tunnel equipment high-frequency units startup conditions transient dynamics dynamic response foundation design

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A microphysical investigation of different convective cells during the precipitation event with sustained high-resolution observations

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Frontiers of Earth Science 2024年第2期18卷 279-295页

作者： Ziheng HUANG Zheng ruan Debin SU State Key Laboratory of Severe Weather Chinese Academy of Meteorological SciencesBeijing 100081China College of Electronic Engineering Chengdu University of Information TechnologyChengdu 610225China Key Laboratory of Atmospheric Sounding China Meteorological AdministrationChengdu 610225China

The growth and breakup processes of raindrops within a cloud influence the rain intensity and the sizes of raindrops on the *** Doppler velocity spectrum acquired by a vertically pointing radar(VPR)contains information on atmospheric turbulence and the size classification of falling *** this study,the four types of Convective Cells(CC)during precipitation events with more than 700 mm of precipitation in southern China are *** characteristics of four types of CCs correspond to the isolated convection,the early stage,the mature stage,and the decline stage of organizational convection,in that *** analysis using retrieval of vertical air motion(Vair)and raindrop evolution in clouds from Doppler velocity spectra collected by C-band VPR revealed the growth and breakup of falling raindrops with dynamic *** raindrops appear in the early stages and are accompanied by ice particles,which are impacted by the falling path᾽s *** aggregation,which is primarily related to the alternation of updraft and downdraft,accounts for the mature stage᾽s high efficiency of surface *** CCs in the decline stage originate from the shallow uplift in the weak and broad downdraft under conditions of enough water *** updraft dominates the stage of isolated *** of convective cells could be more accurately represented in model evaluations.

关键词： cloud microphysics convective systems convective cell vertically pointing radar observations Doppler velocity spectrum

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CircPTEN-MT from PTEN regulates mitochondrial energy metabolism

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Journal of Genetics and Genomics 2024年第5期51卷 531-542页

作者： Danhui ruan Jiancheng Xu Yang Liu Juan Luo Xuyang Zhao Yuhua Li Guangxi Wang Jiawen Feng Hui Liang yue Yin Jianyuan Luo Yuxin Yin Institute of Systems Biomedicine Department of PathologySchool of Basic Medical SciencesBeijing Key Laboratory of Tumor Systems BiologyPeking University International Cancer InstitutePeking-Tsinghua Center of Life SciencesPeking University Health Science CenterBeijing 100191China Institute of Precision Medicine Peking University Shenzhen HospitalShenzhenGuangdong 518036China Department of Pharmacology School of Basic Medical SciencesPeking University Health Science CenterBeijing 100191China Department of Medical Genetics Center for Medical GeneticsSchool of Basic Medical SciencesPeking University Health Science CenterBeijing 100191China Soochow University Cancer Institute SuzhouJiangsu 215127China

Phosphatase and tensin homolog(PTEN)is a multifunctional gene involved in a variety of physiological and pathological *** RNAs(circRNAs)are generated from back-splicing events during mRNA processing and participate in cell biological processes through binding to RNAs or ***,PTEN-related circRNAs are largely ***,we report that circPTEN-mitochondria(MT)(hsa_circ_0002934)is a circular RNA encoded by exons 3,4,and 5 of PTEN and is a critical regulator of mitochondrial energy ***-MT is localized to mitochondria and physically associated with leucine-rich pentatricopeptide repeat-containing protein(LRPPRC),which regulates posttranscriptional gene expression in *** down circPTEN-MT reduces the interaction of LRPPRC and steroid receptor RNA activator(SRA)stem-loop interacting RNA binding protein(SLIRP)and inhibits the polyadenylation of mitochondrial mRNA,which decreases the mRNA level of the mitochondrial complex I subunit and reduces mitochondrial membrane potential and adenosine triphosphate *** data demonstrate that circPTEN-MT is an important regulator of cellular energy *** study expands our understanding of the role of PTEN,which produces both linear and circular RNAs with different and independent functions.

关键词： Circular RNA LRPPRC Mitochondrial energy metabolism mtDNA post-transcriptional regulation

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