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A comprehensive analysis of the Bencao(herbal)small RNA Atlas reveals novel RNA therapeutics for treating human diseases

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Science China(Life Sciences) 2023年第12期66卷 2380-2398页

作者： Yinghao Cao Yexuan Lin Na Sun Xinyi Du Yixin Dong Song Mei Xingyu Deng Xiaobei Li Shaoting Guo Kegong Tang Jiaqi Liu Xiangyu Qiao Dandan Zhao Yuhao Qin Cong Zhang Tianyi Xin Xiaohu Shi Congzhao Zhou Tao Dong De-an Guo Benedikt MKessler Dong Xu Jingyuan Song Fengming Huang Xiaoyue Wang Chengyu Jiang State Key Laboratory of Common Mechanism Research for Major Diseases Department of BiochemistryInstitute of Basic Medical Sciences Chinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijing 100005China Key Laboratory of Chinese Medicine Resources Conservation State Administration of Traditional Chinese Medicine of ChinaEngineering Research Center of Chinese Medicine Resource of Ministry of EducationInstitute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing 100193China Department of Traditional Chinese Medicine Peking Union Medical College HospitalChinese Academy of Medical SciencesBeijing 100005China Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences University of Science and Technology of ChinaHefei 230027China MRC Human Immunology Unit MRC Weatherall Institute of Molecular MedicineRadcliffe Department of MedicineUniversity of OxfordOxford OX37FZUK Chinese Academy of Medical Sciences(CAMS) CAMS Oxford Institute(COI)Nuffield Department of MedicineUniversity of OxfordOxfordOX37FZUK Shanghai Research Center for Modernization of Traditional Chinese Medicine National Engineering Laboratory for TCM Standardization TechnologyShanghai Institute of Materia MedicaChinese Academy of SciencesShanghai 201203China Target Discovery Institute Centre for Medicines DiscoveryNuffield Department of MedicineUniversity of OxfordOxfordOX37FZUK Department of Electrical Engineering and Computer Science and Christopher S.Bond Life Sciences CenterUniversity of MissouriColumbia MO 65211USA

Cross-kingdom herbal mi RNA was first reported in *** a modified herbal extraction protocol,we obtained 73,677,287sequences by RNA-seq from 245 traditional Chinese Medicine(TCM),of which 20,758,257 were unique *** constructed a Bencao(herbal)small RNA(s RNA)Atlas(http://***),annotated the sequences by sequence-based clustering,and created a nomenclature system for Bencao s *** profiles of 21,757 mi RNAs in the Atlas were highly consistent with those of plant mi RNAs in mi *** software tools,our results demonstrated that all human genes might be regulated by s RNAs from the Bencao s RNA Atlas,part of the predicted human target genes were experimentally validated,suggesting that Bencao s RNAs might be one of the main bioactive components of herbal *** established roadmaps for oligonucleotide drugs development and optimization of TCM ***,the decoctosome,a lipo-nano particle consisting of 0.5%–2.5%of the decoction,demonstrated potent medical *** propose a Bencao(herbal)Index,including small-molecule compounds(SM),protein peptides(P),nucleic acid(N),non-nucleic and non-proteinogenic large-molecule compounds(LM)and elements from Mendeleev's periodic table(E),to quantitatively measure the medical effects of botanic *** Bencao s RNA Atlas is a resource for developing gene-targeting oligonucleotide drugs and optimizing botanical medicine,and may provide potential remedies for the theory and practice of one medicine.

关键词： small RNA herbal decoction cross-kingdom regulation traditional Chinese medicine RNA oligonucleotide drug RNA therapeutics Bencao small RNA Atlas

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Technical debt and agile software development practices and processes: An industry practitioner survey

arXiv

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arXiv 2021年

作者： Holvitie, Johannes Licorish, Sherlock A. Spínola, Rodrigo O. Hyrynsalmi, Sami MacDonell, Stephen G. Mendes, Thiago S. Buchan, Jim Leppänen, Ville Turku Centre for Computer Science Software Development Laboratory Turku Finland University of Turku Department of Information Technology Turku Finland University of Otago Department of Information Science Otago Dunedin New Zealand Salvador University Graduate Program in Systems and Computer Bahia Salvador Brazil Federal University of Bahia Fraunhofer Project Center for Software and System Engineering Salvador Brazil Tampere University of Technology Pori Campus Pori Finland Federal Institute of Bahia Information Technology Department Bahia Santo Amaro Brazil Auckland University of Technology School of Engineering Computer and Mathematical Sciences Auckland New Zealand

Context: Contemporary software development is typically conducted in dynamic, resource-scarce environments that are prone to the accumulation of technical debt. While this general phenomenon is acknowledged, what remains unknown is how technical debt specifically manifests in and affects software processes, and how the software development techniques employed accommodate or mitigate the presence of this debt. Objectives: We sought to draw on practitioner insights and experiences in order to classify the effects of agile method use on technical debt management, given the popularity and perceived success of agile methods. We explore the breadth of practitioners' knowledge about technical debt;how technical debt is manifested across the software process;and the perceived effects of common agile software development practices and processes on technical debt. In doing so, we address a research gap in technical debt knowledge and provide novel and actionable managerial recommendations. Method: We designed, tested and executed a multi-national survey questionnaire to address our objectives, receiving 184 responses from practitioners in Brazil, Finland, and New Zealand. Results: Our findings indicate that: 1) Practitioners are aware of technical debt, although, there was under utilization of the concept, 2) Technical debt commonly resides in legacy systems, however, concrete instances of technical debt are hard to conceptualize which makes it problematic to manage, 3) Queried agile practices and processes help to reduce technical debt;in particular, techniques that verify and maintain the structure and clarity of implemented artifacts (e.g., Coding standards and Refactoring) positively affect technical debt management. Conclusions: The fact that technical debt instances tend to have characteristics in common means that a systematic approach to its management is feasible. However, notwithstanding the positive effects of some agile practices on technical debt management, comp

关键词： Legacy systems

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Experimental verification of group non-membership in optical circuits

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Photonics Research 2021年第9期9卷 1745-1751页

作者： KAI SUN ZI-JIAN ZHANG FEI MENG BIN CHENG ZHU CAO JIN-SHI XU MAN-HONG YUNG CHUAN-FENG LI GUANG-CAN GUO 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 Department of Physics Southern University of Science and TechnologyShenzhen 518055China Department of Computer Science The University of Hong KongPokfulamHong Kong SARChina Centre for Quantum Software and Information Faculty of Engineering and Information TechnologyUniversity of Technology SydneySydneyNSW 2007Australia Key Laboratory of Advanced Control and Optimization for Chemical Processes of Ministry of Education East China University of Science and TechnologyShanghai 200237China Shenzhen Institute for Quantum Science and Engineering Southern University of Science and TechnologyShenzhen 518055China Shenzhen Key Laboratory of Quantum Science and Engineering Southern University of Science and TechnologyShenzhen 518055China

The class quantum Merlin–Arthur(QMA),as the quantum analog of nondeterministic polynomial time,contains the decision problems whose YES instance can be verified efficiently with a quantum *** problem of deciding the group non-membership(GNM)of a group element is conjectured to be a member of *** works on the verification of GNM,which still lacks experimental demonstration,required a quantum circuit with O(n~5)group oracle ***,we provide an efficient way to verify GNM problems,in which each quantum circuit only contains O(1)group of oracle calls,and the number of qubits in each circuit is reduced by *** on this protocol,we then experimentally demonstrate the new verification process with a four-element group in an all-optical *** new protocol is validated experimentally by observing a significant completeness-soundness gap between the probabilities of accepting elements in and outside the *** work efficiently simplifies the verification of GNM and is helpful in constructing more quantum protocols based on the near-term quantum devices.

关键词： quantum element polynomial

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A systematic collection of medical image datasets for deep learning

arXiv

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arXiv 2021年

作者： Li, Johann Zhu, Guangming Hua, Cong Feng, Mingtao Bennamoun, Basheer Li, Ping Lu, Xiaoyuan Song, Juan Shen, Peiyi Xu, Xu Mei, Lin Zhang, Liang Shah, Syed Afaq Ali Bennamoun, Mohammed School of Computer Science and Technology Xidian University China School of Medicine University of Notre Dame Australia Data and Virtual Research Room Shanghai Broadband Network Center China Third Research Institute of The Ministry of Public Security China Discipline of Information Technology Media and Communications Murdoch University Australia Department of Computer Science and Software Engineering University of Western Australia Australia

The astounding success made by artificial intelligence (AI) in healthcare and other fields proves that AI can achieve human-like performance. However, success always comes with challenges. Deep learning algorithms are data-dependent and require large datasets for training. The lack of data in the medical imaging field creates a bottleneck for the application of deep learning to medical image analysis. Medical image acquisition, annotation, and analysis are costly, and their usage is constrained by ethical restrictions. They also require many resources, such as human expertise and funding. That makes it difficult for non-medical researchers to have access to useful and large medical data. Thus, as comprehensive as possible, this paper provides a collection of medical image datasets with their associated challenges for deep learning research. We have collected information of around three hundred datasets and challenges mainly reported between 2013 and 2020 and categorized them into four categories: head & neck, chest & abdomen, pathology & blood, and "others". Our paper has three purposes: 1) to provide a most up to date and complete list that can be used as a universal reference to easily find the datasets for clinical image analysis, 2) to guide researchers on the methodology to test and evaluate their methods’ performance and robustness on relevant datasets, 3) to provide a "route" to relevant algorithms for the relevant medical topics, and challenge leaderboards. © 2021, CC BY-NC-SA.

关键词： Deep learning

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Non-invasive Assessment of Hepatic Venous Pressure Gradient (HVPG) Based on MR Flow Imaging and Computational Fluid Dynamics

arXiv

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arXiv 2021年

作者： Wang, Kexin Wang, Shuo Xiong, Minghua Wang, Chengyan Wang, He Department of Physics Fudan University Shanghai China Digital Medical Research Center School of Basic Medical Sciences Fudan University Shanghai China Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention Shanghai China Shanghai Zhiyu Software Information Co. Ltd China Human Phenome Institute Fudan University Shanghai China Institute of Science and Technology for Brain-inspired Intelligence Fudan University Shanghai China Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence Fudan University Ministry of Education China

Clinically significant portal hypertension (CSPH) is a severe complication of chronic liver disease associated with cirrhosis, which is diagnosed by the measurement of hepatic venous pressure gradient (HVPG). However, HVPG measurement is invasive and therefore difficult to be widely applied in clinical routines. There is no currently available technique to measure HVPG noninvasively. Computational fluid dynamics (CFD) has been used for noninvasive measurement of vascular pressure gradient in the intracranial and coronary arteries. However, it has been scarcely employed in the hepatic vessel system due to the difficulties in reconstructing precise vascular anatomies and setting appropriate boundary conditions. Several computer tomography and ultrasound based studies have verified the effectiveness of virtual HVPG (vHVPG) by directly connecting the portal veins and hepatic veins before CFD simulations [16,12]. We apply the latest techniques of phase-contrast magnetic resonance imaging (PC-MRI) and DIXON to obtain the velocity and vessel anatomies at the same time. Besides, we improve the CFD pipeline in regards to the construction of vessel connections and reduction of calculation time. The proposed method shows high accuracy in the CSPH diagnosis in a study containing ten healthy volunteers and five patients. The MRI-based noninvasive HVPG measurement is promising in the clinical application of CSPH diagnosis. © 2021, CC BY.

关键词： Computational fluid dynamics

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Synchronous hybrid brain–computer interfaces for recognizing emergency braking intention

Brain-X

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Brain-X 2024年第1期2卷

作者： Ju, Jiawei Feleke, Aberham Genetu Li, Hongqi Li, Haiyang Institute of Neuroscience Shanghai Center for Brain Science and Brain-Inspired Technology Shanghai Shanghai China School of Mechanical Engineering Beijing Institute of Technology Beijing China School of Software Northwestern Polytechnical University Shaanxi Xi'an China The Research & Development Institute of Northwestern Polytechnical University in Shenzhen Guangdong Shenzhen China The Yangtze River Delta Research Institute of Northwestern Polytechnical University in Taicang Jiangsu Suzhou China Chemical Engineering Department Pohang University of Science and Technology Gyeongbuk Pohang South Korea

Hybrid neurophysiological signals, such as the combination of electroencephalography (EEG) and electromyography (EMG), can be used to reduce road traffic accidents by obtaining the driver's intentions in advance and accordingly applying appropriate auxiliary controls. However, whether they can be used in combination and can achieve better results in situations of detecting emergency braking from normal driving and soft braking has not been explored. This study used one feature-level (hybrid BCI-FL) and three classifier-level (hybrid BCIs-CLs) hybrid strategies, the spectral band, and spectral point features to construct recognition models. Offline and pseudo-online experiments were conducted. The recognition performance with the spectral point features showed a better result than that with spectral band features. In all experiments, the two proposed hybrid BCI strategies could achieve a detection accuracy close to or above 95%, while the detection advanced time is less than 300 ms. In particular, for the developed hybrid BCI recognition models, the hybrid BCI-FL and hybrid BCI-CL2 recognition models with spectral point features achieved 4.25% (p < 0.015) and 4.69% (p < 0.006) higher system accuracies, respectively, than that of the current better single EMG-based recognition model. This research promotes the application of hybrid EEG and EMG signals in intelligent driving assistance systems. © 2024 The Authors. Brain-X published by John Wiley & Sons Australia, Ltd on behalf of Ainuohui Medical technology.

关键词： electroencephalography electromyography emergency braking hybrid recognition

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DiffuSE: Cross-Layer Design Space Exploration of DNN Accelerator via Diffusion-Driven Optimization

arXiv

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arXiv 2025年

作者： Ren, Yi Xue, Chenhao Zhang, Jiaxing Zhang, Chen Xu, Qiang Lin, Yibo Zhang, Lining Sun, Guangyu School of Integrated Circuits China School of Software and Microelectronics Peking University Beijing China Shanghai Jiao Tong University Shanghai China Department of Computer Science and Engineering The Chinese University of Hong Kong Sha Tin Hong Kong Institute of Electronic Design Automation Peking University Wuxi China Beijing Advanced Innovation Center for Integrated Circuits Beijing China School of Electronic and Computer Engineering Peking University Shenzhen China National Center of Technology Innovation for EDA Nanjing China

The proliferation of deep learning accelerators calls for efficient and cost-effective hardware design solutions, where parameterized modular hardware generator and electronic design automation (EDA) tools play crucial roles in improving productivity and final Quality-of-Results (QoR). To strike a good balance across multiple QoR of interest (e.g., performance, power, and area), the designers need to navigate a vast design space, encompassing tunable parameters for both hardware generator and EDA synthesis tools. However, the significant time for EDA tool invocations and complex interplay among numerous design parameters make this task extremely challenging, even for experienced designers. To address these challenges, we introduce DiffuSE, a diffusion-driven design space exploration framework for cross-layer optimization of DNN accelerators. DiffuSE leverages conditional diffusion models to capture the inverse, one-to-many mapping from QoR objectives to parameter combinations, allowing for targeted exploration within promising regions of the design space. By carefully selecting the conditioning QoR values, the framework facilitates an effective trade-off among multiple QoR metrics in a sample-efficient manner. Experimental results under 7nm technology demonstrate the superiority of the proposed framework compared to previous arts. Copyright © 2025, The Authors. All rights reserved.

关键词： Space research

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Decomposition of Attributes Oriented software Trustworthiness Measure Based on Axiomatic Approaches

Decomposition of Attributes Oriented Software Trustworthines...

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IEEE International Conference on software Quality, Reliability and Security Companion (QRS-C)

作者： Hongwei Tao Yixiang Chen Hengyang Wu College of Computer and Communication Engineering Zhengzhou University of Light Industry Zhengzhou China MoE Engineering Center for Software/Hardware Co-Design Technology and Application East China Normal University Shanghai China School of Computer and Information Engineering Shanghai Polytechnic University Shanghai China

ISBN: (数字)9781728189154

ISBN: (纸本)9781728189161

In order to make the software trustworthiness measures more rigorous, we once applied axiomatic approaches to measure software trustworthiness, and established a software trustworthiness measure based on the decomposition of attributes (STMBDA for short). For the sake of validating the effectiveness of STMBDA, in this paper we use it to assess the trustworthiness of 23 spacecraft softwares whose total code is about 300,000 lines. The validation result shows that STMBDA can effectively evaluate the trustworthiness of the spacecraft softwares and identify the weak links in the development process.

关键词： Space vehicles Conferences software quality software software reliability software measurement Security

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Noncontact Doppler Radar-based Heart Rate Detection on the SVD and ANC

Noncontact Doppler Radar-based Heart Rate Detection on the S...

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IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Qiuxia Shi Bin Hu Fuze Tian Qinglin Zhao Gansu Provincial Key Laboratory of Wearable Computing School of Information Science and Engineering Lanzhou University School of Computer and Communication Lanzhou University of Technology Ministry of Education Key Laboratory of Special Functional Materials and Structural Design (Lanzhou University) Lanzhou China CAS Center for Excellence in Brain Science and Intelligence Technology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Joint Research Center for Cognitive Neurosensor Technology of Lanzhou University & Institute of Semiconductors Chinese Academy of Sciences Engineering Research Center of Open Source Software and Real-Time System(Lanzhou University) Ministry of Education Key Laboratory of Special Functional Materials and Structural Design Ministry of Education Lanzhou University Lanzhou China

ISBN: (数字)9781665468190

ISBN: (纸本)9781665468206

In the Doppler biological radar-based applications of noncontact measurement of vital signs, effectively extracting heartbeat information from weak thoracic mechanical motion is an important problem to be solved. This study is aimed at extracting heartbeat signal via the technology combined with Short Time Fourier Transform (STFT), Singular Value Decomposition (SVD) and Adaptive Noise Canceller (ANC) from radar recording. The simulated data and the data collected by Doppler radar biosensor realized in laboratory are employed to validate the proposed method. The results show that the proposed method has the ability of detection for the heart rate and heart rate variability indexes in rest state, it has certain advantages in time-consuming and detection accuracy. Therefore, the current method provides another way to process vital sign signals recorded by Doppler radar.

关键词： Biomedical measurement Noise cancellation Time measurement Doppler radar Recording Doppler effect Biosensors

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Water consumption and biodiversity:Responses to global emergency events

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Science Bulletin 2024年第16期69卷 2632-2646页

作者： Dandan Zhao Junguo Liu Laixiang Sun Klaus Hubacek Stephan Pfister Kuishuang Feng Heran Zheng Xu Peng Daoping Wang Hong Yang Lei Shen Fei Lun Xu Zhao Bin Chen Marko Keskinen Shaohui Zhang Jialiang Cai Olli Varis Water&Development Research Group Department of Built EnvironmentAalto UniversityEspoo 15200Finland School of Water Conservancy North China University of Water Resources and Electric PowerZhengzhou 450046China School of Environmental Science and Engineering Southern University of Science and TechnologyShenzhen 518055China Department of Geographical Sciences University of MarylandCollege Park 20742USA School of Finance and Management SOASUniversity of LondonLondon WC1H0XGUK Integrated Research on Energy Environment and SocietyEnergy and Sustainability Research Institute GroningenUniversity of GroningenGroningen 9747AGthe Netherlands ETH Zurich Institute of Environmental EngineeringZurich 8093Switzerland The Bartlett School of Sustainable Construction University College LondonLondon WC1E6BTUK School of Business Jiangnan UniversityWuxi 214122China Department of Computer Science and Technology University of CambridgeCambridge CB21TNUK w2e Environmental Consulting GmbH Duebendorf 8600Switzerland Key Laboratory for Resource Use and Environmental Remediation Institute of Geographic Sciences and Natural Resources ResearchChinese Academy of SciencesBeijing 100101China College of Land Science and Technology China Agricultural UniversityBeijing 100083China Institute of Blue and Green Development Shandong UniversityWeihai 264209China Fudan Tyndall Center Department of Environmental Science and EngineeringFudan UniversityShanghai 200438China School of Economics and Management Beihang UniversityBeijing 100191China International Institute for Applied Systems Analysis Laxenburg A-2361Austria

Given that it was a once-in-a-century emergency event,the confinement measures related to the coronavirus disease 2019(COVID-19)pandemic caused diverse disruptions and changes in life and work *** changes significantly affected water consumption both during and after the pandemic,with direct and indirect consequences on ***,there has been a lack of holistic evaluation of these ***,we propose a novel framework to study the impacts of this unique global emergency event by embedding an environmentally extended supply-constrained global multi-regional input-output model(MRIO)into the drivers-pressure-state-impact-response(DPSIR)*** framework allowed us to develop scenarios related to COVID-19 confinement measures to quantify country-sector-specific changes in freshwater consumption and the associated changes in biodiversity for the period of *** results suggest progressively diminishing impacts due to the implementation of COVID-19 vaccines and the socio-economic system’s self-adjustment to the new *** 2020,the confinement measures were estimated to decrease global water consumption by about 5.7% on average across all scenarios when compared with the baseline level with no confinement ***,such a decrease is estimated to lead to a reduction of around 5% in the related pressure on *** the interdependencies and interactions across global supply chains,even those countries and sectors that were not directly affected by the COVID-19 shocks experienced significant impacts:Our results indicate that the supply chain propagations contributed to 79% of the total estimated decrease in water consumption and 84%of the reduction in biodiversity loss on *** study demonstrates that the MRIO-enhanced DSPIR framework can help quantify resource pressures and the resultant environmental impacts across supply chains when facing a global emergency ***,we recommend the development o

关键词： Global emergency events Water-biodiversity causal effect COVID-19 Biodiversity MRIO-enhanced DPSIR framework Supply-chain network High-resolution water consumption dataset Supply-constrained multi-regional input-output(mixed MRIO)model

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