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FP-Zernike:An Open-source Structural Database Construction Toolkit for Fast Structure Retrieval

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Genomics, Proteomics & Bioinformatics 2024年第1期22卷 111-119页

作者： Junhai qi Chenjie Feng Yulin shi Jianyi Yang Fa Zhang Guojun Li Renmin Han Research Center for Mathematics and Interdisciplinary Sciences Shandong UniversityQingdao 266237China BioMap Research Menlo ParkCA 94025USA College of Medical Information and Engineering Ningxia Medical UniversityYinchuan 750004China Institute of Engineering Medicine Beijing Institute of TechnologyBeijing 100081China

The release of AlphaFold2 has sparked a rapid expansion in protein model *** protein structure retrieval is crucial for the analysis of structure models,while measuring the similarity between structures is the key challenge in structural *** existing structure alignment algorithms can address this challenge,they are often ***,the state-of-the-art approach involves converting protein structures into three-dimensional(3D)Zernike descriptors and assessing similarity using Euclidean ***,the methods for computing 3D Zernike descriptors mainly rely on structural surfaces and are predominantly web-based,thus limiting their application in studying custom *** overcome this limitation,we developed FP-Zernike,a user-friendly toolkit for computing different types of Zernike descriptors based on feature *** simply need to enter a single line of command to calculate the Zernike descriptors of all structures in customized ***-Zernike outperforms the leading method in terms of retrieval accuracy and binary classification accuracy across diverse benchmark *** addition,we showed the application of FP-Zernike in the construction of the descriptor database and the protocol used for the Protein Data Bank(PDB)dataset to facilitate the local deployment of this tool for interested *** demonstration contained 590,685 structures,and at this scale,our system required only 4-9 s to complete a *** experiments confirmed that it achieved the state-of-the-art accuracy ***-Zernike is an open-source toolkit,with the source code and related data accessible at https://***/biocode/tools/BT007365/releases/0.1,as well as through a webserver at http://***/.

关键词： Zernike descriptor Structure alignment PDB dataset Open-source Retrieval system

Response of phytoplankton functional group to spring drought in a large subtropical reservoir

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Journal of Oceanology and Limnology 2024年第5期42卷 1586-1596页

作者： Yue WU qi YE Siwen CHEN Kaining CHEN Shuzhan MA Yiheng CHANG Xiaoli shi State Key Laboratory of Lake Science and Environment Nanjing Institute of Geography and LimnologyChinese Academy of SciencesNanjing 210008China University of Chinese Academy of Sciences Beijing 100049China State Environmental Protection Key Laboratory of Aquatic Ecosystem Health in the Middle and Lower Reaches of Yangtze River Jiangsu Provincial Academy of Environmental ScienceNanjing 210036China

Global warming has caused an increase in the frequency and duration of droughts *** could trigger large changes in physico-chemical conditions and phytoplankton community in waterbodies,resulting in a shift in the phytoplankton *** diatom blooms in reservoirs have been increasingly observed in the past decade in the Taihu Lake *** aim of the present study is to elucidate the impacts of droughts on aquatic environment and to determine the driving factors for the succession of the phytoplankton functional groups based on the analysis of data collected during spring from 2009 to 2020 in the Daxi *** unimodal relationship between 1-month aggregated precipitation index and phytoplankton species richness indicated the competitive exclusion occurred in extremely drought *** structural equation modeling indicated that drought-related low water level conditions intensified sediment resuspension,and increased the phosphorus-enriched nonalgal turbidity in the Daxi ***,a steady shift in the Reynolds phytoplankton functional groups from L 0,TD,J,X 2,and A(phytoplankton taxa preferring low turbidity and nutrient conditions)to TB(pennate diatoms being adapt to turbid and nutrient-rich conditions)was *** increased TP and non-algal turbidity in addition to the lowered disturbance contribute to the prevalence of Group *** the difficulties in nutrient control,timely water replenishment is often a feasible method of controlling the dominance of harmful algae for reservoir ***,alternative water sources are in high demand for ensuring ecological safety and water availability when dealing with drought.

关键词： drought reservoir sediments resuspension phytoplankton functional group diatom

Magnetism Measurements of Two-Dimensional van der Waals Antiferromagnet CrPS_(4)Using Dynamic Cantilever Magnetometry

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Chinese Physics Letters 2024年第10期41卷 123-128页

作者： qi Li Weili Zhen Ning wang Meng shi Yang Yu Senyang Pan Lin Deng Jiaqiang Cai Kang wang Lvkuan Zou Zhongming Zeng Zhaosheng wang Jinglei Zhang Anhui Province Key Laboratory of Condensed Matter Physics at Extreme Conditions High Magnetic Field LaboratoryHFIPSChinese Academy of SciencesHefei 230031China Science Island Branch of Graduate School University of Science and Technology of ChinaHefei 230026China School of Advanced Manufacturing Engineering Hefei UniversityHefei 230601China Suzhou Institute of Nano-tech and Nano-bionics Chinese Academy of SciencesSuzhou 215123China

Recent experimental and theoretical work has focused on two-dimensional van der Waals(2D vdW)magnets due to their potential applications in sensing and spintronics *** measurements of these emerging materials,conventional magnetometry often encounters challenges in characterizing the magnetic properties of small-sized vdW materials,especially for antiferromagnets with nearly compensated magnetic ***,we investigate the magnetism of 2D antiferromagnet CrPS_(4)with a thickness of 8nm by using dynamic cantilever magnetometry(DCM).

关键词： (4) magnets Magnet

Crystal structures of RNA-dependent RNA polymerases from Jingmen tick virus and Alongshan virus

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hLife 2024年第1期2卷 18-31页

作者： Zhenyang Liu qi Peng Pu Han Lu Kuai Jianxun qi Yi shi CAS Key Laboratory of Pathogen Microbiology and Immunology Institute of MicrobiologyChinese Academy of SciencesBeijingChina Beijing Life Science Academy BeijingChina International Institute of Vaccine Research and Innovation Savaid Medical SchoolUniversity of Chinese Academy of SciencesBeijingChina Center for Influenza Research and Early-warning CAS-TWAS Center of Excellence for Emerging Infectious DiseaseChinese Academy of SciencesBeijingChina Research Unit of Adaptive Evolution and Control of Emerging Viruses Chinese Academy of Medical SciencesBeijingChina

Jingmenviruses are a group of flavi-like viruses with segmented genome and have been found in various types of hosts,including humans,cattle,monkeys,bats,rodents,sheep,ticks,mosquitoes and ***,including the Jingmen tick virus(JMTV)and Alongshan virus(ALSV),have been associated with febrile illness and flu-like symptoms in *** polymerase plays critical roles in genome replication and transcription and is an ideal target for antiviral ***,we determined the crystal structures of RNA-dependent RNA polymerase(RdRp)domains of JMTV and ALSV at 2.6Åand 3.2Åresolutions,*** overall structures of JMTV and ALSV RdRp domains are similar to those from the typical unsegmented viruses in Flaviviridae family,especially the Flavivirus *** and ALSV RdRps can be divided into three subdomains and the catalytical Motif A-G are conserved like the typical flaviviruses,whereas the zinc-binding pockets are absent from the JMTV and ALSV *** 50-ends of jingmenvirus genomes are varied in length and sequence,and a highly conserved 8-nucleotide element located on the tip of stem loop A was identified and shown to be required for binding with RdRp and performing de novo replication *** findings provide important structural insights into RdRp of segmented flavivirus and reveal the key region of virus genome responsible for replication initiation,which would promote molecular understanding of segmented flavivirus replication and the structure-based design of antiviral drugs against flaviviruses.

关键词： Jingmenviruses X-rays RNA-dependent RNA polymerase replication

Deep learning-based,computer-aided classifier developed with dermoscopic images shows comparable performance to 164 dermatologists in cutaneous disease diagnosis in the Chinese population

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Chinese Medical Journal 2020年第17期133卷 2027-2036页

作者： shi-qi wang Xin-Yuan Zhang Jie Liu Cui Tao Chen-Yu Zhu Chang Shu Tao Xu Hong-Zhong Jin Department of Dermatology Peking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100730China School of Biomedical Informatics The University of Texas Health Science Center at HoustonHoustonTX 77030USA Department of Epidemiology and Statistics School of Basic MedicinePeking Union Medical CollegeInstitute of Basic Medical SciencesChinese Academy of Medical SciencesBeijing 100005China

Background:Diagnoses of Skin diseases are frequently delayed in China due to lack of dermatologists.A deep learning-based diagnosis supporting system can facilitate pre-screening patients to prioritize dermatologists’*** aimed to evaluate the classification sensitivity and specificity of deep learning models to classify skin tumors and psoriasis for Chinese population with a modest number of dermoscopic ***:We developed a convolutional neural network(CNN)based on two datasets from a consecutive series of patients who underwent the dermoscopy in the clinic of the Department of Dermatology,Peking Union Medical College Hospital,between 2016 and 2018,*** order to evaluate the feasibility of the algorithm,we used two *** I consisted of 7192 dermoscopic images for a multi-class model to differentiate three most common skin tumors and other *** II consisted of 3115 dermoscopic images for a two-class model to classify psoriasis from other inflammatory *** compared the performance of CNN with 164 dermatologists in a reader study with 130 dermoscopic *** experts’consensus was used as the reference standard except for the cases of basal cell carcinoma(BCC),which were all confirmed by ***:The accuracies of multi-class and two-class models were 81.49%±0.88%and 77.02%±1.81%,*** the reader study,for the multi-class tasks,the diagnosis sensitivity and specificity of 164 dermatologists were 0.770 and 0.962 for BCC,0.807 and 0.897 for melanocytic nevus,0.624 and 0.976 for seborrheic keratosis,0.939 and 0.875 for the"others"group,respectively;the diagnosis sensitivity and specificity of multi-class CNN were 0.800 and 1.000 for BCC,0.800 and 0.840 for melanocytic nevus,0.850 and 0.940 for seborrheic keratosis,0.750 and 0.940 for the"others"group,*** the two-class tasks,the sensitivity and specificity of dermatologists and CNN for classifying psoriasis were 0.872 and 0.838

关键词： Artificial intelligence Convolutional neural network Skin tumor Psoriasis Dermoscopy

Effects of high-pressure activated slightly acidic electrolyzed water on cleaning and sterilization of pig transfer vehicles

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International Journal of Agricultural and Biological Engineering 2024年第4期17卷 53-59页

作者： Xuedong Zhao Shengnan Tao Fei qi Hao Li Zhengxiang shi Department of Agricultural Structure and Bioenvironmental Engineering College of Water Resources&Civil EngineeringChina Agricultural UniversityBeijing 100083China Key Laboratory of Agricultural Engineering in Structure and Environment Ministry of Agriculture and Rural AffairsBeijing 100083China Beijing Engineering Research Center on Animal Healthy Environment Beijing 100083China

The establishment of biosafety system is of enormous importance to the livestock and poultry production in terms of mitigating the transmission of diseases and implementing regional prevention and control ***,the current sterilization technology presents several drawbacks,including time-consuming procedures,chemical residues,and challenges in treating the sewage after *** this study,a novel cleaning and sterilization method that combines slightly acidic electrolyzed water and high pressure water-jet was *** orthogonal test was conducted to examine the correlation between high-pressure conditions and the various non-structural parameters on the efficacy of sterilization *** a field test,the effectiveness of the technology in cleaning pig transfer vehicles was evaluated by the total plate count and variations of community *** findings revealed that the combination of process parameters,including an available chlorine concentration of 200 mg/L,rinsing pressure of 170 bar,rinsing duration of 10 s,and residence time of 15 min,resulted in a removal rate of colony concentration on the surface of pig transfer vehicles of(96.50±0.91)%.Moreover,it was demonstrated to effectively inhibit a variety of pathogenic *** innovative cleaning system has the potential to replace traditional methods and reduces pollution while saving time and *** introduces a novel approach for sterilization of transportation in livestock and poultry farms as well as the biosafety construction of the animal husbandry.

关键词： slightly acidic electrolyzed water high pressure water-jet sterilization biosafety concentrated animal production

High-frequency ultrasound features of basal cell carcinoma and its association with histological recurrence risk

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Chinese Medical Journal 2019年第17期132卷 2021-2026页

作者： shi-qi wang Jie Liu qing-Li Zhu Chen-Yang Zhao Tao Qu Feng Li Ximena Wortsman Hong-Zhong Jin Department of Dermatology Peking Union Medical College Hospital Chinese Academy of Medical Sciences and Peking Union Medical College Beijing 100730 China Department of Ultrasound Peking Union Medical College Hospital Chinese Academy of Medical Sciences and Peking Union Medical College Beijing 100730 China Department of Dermatology Faculty of Medicine University of Chile Santiago Chile Department of Imaging Institute for Diagnostic Imaging and Research of the Skin and Soft Tissues Santiago Chile

Background: Due to advances in high-frequency ultrasound technology, it is easier to detect fine structures of skin lesions. The aim of this study was to examine the ultrasonographic features and use recurrence risk stratification to assess the diagnostic performance of pre-operative ultrasound examination of basal cell carcinoma (BCC). Methods: This was a retrospective study. Forty-six BCC lesions underwent pre-operative ultrasound examination using 50- and 20- MHz probes. Ultrasonographic shape, margin, internal echoes, hyper-echoic spots, posterior echoes, and depth of the lesion were evaluated and correlated with the risk of recurrence based on histological features. Results: Forty-two patients had 46 skin lesions in total. The high-risk (n = 6) and low-risk (n = 40) groups exhibited considerable overlap in the ultrasonographic manifestations and no significant difference in margin (χ^2 = 3.231, P = 0.072), internal echo (χ^2 = 1.592, P = 0.207), or posterior echo (P = 0.169). However, high-risk BCCs tended to be irregular in shape than low-risk lesions (χ^2 = 4.313, P = 0.038). Both types presented hyper-echoic spots (χ^2 = 1.850, P = 0.174). Additionally, 78% of low-risk lesions were confined to the dermis (31/40), and 100% of high-risk lesions infiltrated into the sub-cutaneous tissue, resulting in a significant difference between the two groups (χ^2 = 10.951, P = 0.001). Ultrasound detected sub-clinical lesions in five patients. Conclusions: High-frequency ultrasound can provide important information for pre-operative evaluation of risk in BCC foci and reveal hidden lesions. The technique may play a crucial role in guiding therapeutic options for BCC.

关键词： High-frequency ultrasound Basal cell carcinoma Ultrasound Skin ultrasound Skin cancer ultrasound Skin cancer

Ultra-wide dual-band Rydberg atomic receiver based on space division multiplexing radio-frequency chip modules

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Chip 2024年第2期3卷 53-61页

作者： Li-Hua Zhang Bang Liu Zong-Kai Liu Zheng-Yuan Zhang shi-Yao Shao qi-Feng wang Yu Ma Tian-Yu Han Guang-Can Guo Dong-Sheng Ding Bao-Sen shi Key Laboratory of Quantum Information University of Science and Technology of ChinaHefei 230026China Synergetic Innovation Center of Quantum Information and Quantum Physics University of Science and Technology of ChinaHefei 230026China

Detecting microwave signals over a wide frequency range is endowed with numerous advantages as it enables simultaneous transmission of a large amount of information and access to more spectrum *** capability is crucial for applications such as microwave communication,remote sensing and ***,conventional microwave receiving systems are limited by amplifiers and band-pass filters that can only operate efficiently in a specific frequency ***,these systems can only process signals within a three-fold frequency range,which limits the data transfer bandwidth of the microwave communication *** novel atom-integrated microwave sensors,for example,radio-frequency(RF)chip–coupled Rydberg atomic receiver,provides opportunities for a large working bandwidth of microwave sensing at the atomic *** the current work,an ultrawide dual-band RF sensing scheme was demonstrated by spacedivision multiplexing two RF-chip-integrated atomic receiver *** system can simultaneously receive dual-band microwave signals that span a frequency range exceeding 6 octaves(300 MHz and 24 GHz).This work paves the way for multi-band microwave reception applications within an ultra-wide range by RF-chip-integrated Rydberg atomic sensor.

关键词： Dual-band Rydberg Radio-frequency chip Atomic receiver Space-division multiplexing

Constructing core@shell structured photothermal nanosphere with thin carbon layer confined Co-Mn bimetals for pollutant degradation and solar interfacial water evaporation

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Rare Metals 2024年第4期43卷 1686-1701页

作者： Hong-Yang Zhu Meng-Ting Liu Gang wang Rong-Rong Du Hong-Yao Zhao Hao Lu shi-qi Yang Sheng Tang Zeng-Jing Guo Jun Yang Cheng-Zhang Zhu Fu Yang School of Environmental and Chemical Engineering Jiangsu University of Science and TechnologyZhenjiang212003China School of Chemistry and Chemical Engineering Liaocheng UniversityLiaocheng252000China School of Material Science and Engineering Jiangsu University of Science and TechnologyZhenjiang212003China School of Environmental Science and Engineering Nanjing Tech UniversityNanjing210009China

Photothermal material applied in environmental governance has attracted growing *** combining the Stober method and dopamine-triggered coating strategy,Co-Mn precursor was in situ incorporated into the poly dopamine(PDA)layer over the surface of silica ***,a unique photothermal nanosphere with SiO_(2)core and thin carbon layer and dual Co-Mn oxides shell was allowed to form by sequential heat treatment in the inert atmosphere(SiO_(2)@CoMn/C).The bimetallic fraction of Co/Mn in the carbon layer and post-treatment calcination temperature was comprehensively tuned to optimize the peroxymonosulfate(PMS)activation performance of the *** state of bimetallic species was studied including their physical distribution,chemical valence,and interplay by various ***,Co oxides appear as dominant monodispersed nanoparticles(~10 nm),while Mn with cluster-like morphology is observed to uniformly distribute over thin-layer carbon and adhered to the surface of SiO_(2)nanospheres(~250 nm).The calcined temperature could tune the oxidized state of Co species,leading to the optimization of the catalytic performance of introduced dual metal *** a result,this obtained optimal catalyst integrated the advantages of exposed bimetallic CoMn species and N-doped thin carbon to deliver excellent catalytic PMS activation performance and photothermal synergetic catalytic mineralization ability for diversiform *** reactions condition controls and anion interference studies were conducted to identify the adaptability of the optimal ***,the application of solar-driven interfacial water evaporation using optimal SiO_(2)@Co_3Mn_1/C-600 catalyst was explored,showing a high water evaporation rate of 1.48 kg·m^(-2)·h^(-1)and an efficiency of 95.2%,further revealing a comprehensive governance functionality of obtained material in the complex pollution condition.

关键词： Photothermal Peroxymonosulfate(PMS)activation Bimetallic synergy Water evaporation Advanced oxidation process