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De novo assembly of transcriptome from next-generation sequencing data

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Frontiers of Electrical and Electronic Engineering in China 2016年第2期4卷 94-105页

作者： Xuan Li yimeng Kong qiong-yi zhao Yuan-Yuan Li Pei Hao Key Laboratory of Synthetic Biology CAS Center for Excellence in Molecular Plant Sciences Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200032 China The Ugniversitvof Queensland. Queensland Brain Institute. St Lucia. QI'D 4072. Ausiralia Shanghai Center for Bioinformation Technology Shanghai Industrial Technology Institute Shanghai 201203 China Key Laboratory of Molecular Virology and Immunology institute Pasteur of Shanghai Chinese Academy of SciencesShanghai 200031 China

Reconstruction of transcriptome by de novo assembly from next generation sequencing （NGS） short-sequence reads provides an essential mean to catalog expressed genes, identify splicing isoforms, and capture the expression detail of transcripts for organisms with no reference genome available. De novo transcriptome assembly faces many unique challenges, including alternative splicing, variable expression level covering a dynamic range of several orders of magnitude, artifacts introduced by reverse transcription, etc. In the current review, we illustrate the grand strategy in applying De Bruijn Graph （DBG） approach in de novo transcriptome assembly. We further analyze many parameters proven critical in transcriptome assembly using DBG. Among them, k-met length, coverage depth of reads, genome complexity, performance of different programs are addressed in greater details. A multi-k-mer strategy balancing efficiency and sensitivity is discussed and highly recommended for de novo transcriptome assembly. Future direction points to the combination of NGS and third generation sequencing technology that would greatly enhance the power of de novo transcriptomics study.

关键词： transcriptome de novo assembly De Bruijn Graph next generation sequencing k-mer length RNA splicing performance

Liquid lens based holographic camera for real 3D scene hologram acquisition using end-to-end physical model-driven network

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Light(Science & Applications) 2024年第3期13卷 488-497页

作者： Di Wang zhao-Song Li yi Zheng You-Ran zhao Chao Liu Jin-Bo Xu yi-Wei Zheng Qian Huang Chen-Liang Chang Da-Wei Zhang Song-Lin Zhuang qiong-Hua Wang School of Instrumentation and Optoelectronic Engineering Beihang UniversityBeijing 100191China School of Optical-Electrical and Computer Engineering University of Shanghai for Science and TechnologyShanghai 200093China

With the development of artificial intelligence,neural network provides unique opportunities for holography,such as high fidelity and dynamic calculation.How to obtain real 3D scene and generate high fidelity hologram in real time is an urgent problem.Here,we propose a liquid lens based holographic camera for real 3D scene hologram acquisition using an end-to-end physical model-driven network(EEPMD-Net).As the core component of the liquid camera,the first 10 mm large aperture electrowetting-based liquid lens is proposed by using specially fabricated solution.The design of the liquid camera ensures that the multi-layers of the real 3D scene can be obtained quickly and with great imaging performance.The EEPMD-Net takes the information of real 3D scene as the input,and uses two new structures of encoder and decoder networks to realize low-noise phase generation.By comparing the intensity information between the reconstructed image after depth fusion and the target scene,the composite loss function is constructed for phase optimization,and the high-fidelity training of hologram with true depth of the 3D scene is realized for the first time.The holographic camera achieves the high-fidelity and fast generation of the hologram of the real 3D scene,and the reconstructed experiment proves that the holographic image has the advantage of low noise.The proposed holographic camera is unique and can be used in 3D display,measurement,encryption and other fields.

关键词： calculation solution holographic

Research progress on metal-organic framework compounds(MOFs)in electrocatalysis

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Journal of Environmental Sciences 2024年第7期141卷 261-276页

作者： Yutong Guo Shunzheng zhao Xiaolong Tang Honghong yi Department of Environmental Science and Engineering School of Energy and Environmental EngineeringUniversity of Science and Technology BeijingBeijing 100083China Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants Beijing 100083China

Metal-organic frameworks(MOFs)have favorable characteristics such as large specific surface area,high porosity,structural diversity,and pore surface modification,giving them great potential for development and attractive prospects in the research area of modern materials electrocatalysis.However,unsatisfactory catalytic activity and poor electronic conductivity are the main challenges facing MOFs.This review focuses on MOF-based materials used in electrocatalysis,based on the types of catalytic reactions that have used MOF-based materials in recent years along with their applications,and also looks at some new electrocatalytic materials and their future development prospects.

关键词： Metal-organic frame compounds Electrocatalysis Oxidation-reduction Nitrogen fixation to synthesize ammonia Carbon dioxide reduction

VX-509 attenuates the stemness characteristics of colorectal cancer stem-like cells by regulating the epithelial-mesenchymal transition through Nodal/Smad2/3 signaling

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World Journal of Stem Cells 2024年第2期16卷 207-227页

作者： Yun Yuan Xu-Fan Zhang Yu-Chen Li Hong-Qing Chen Tian Wen Jia-Lian Zheng Zi-yi zhao qiong-ying Hu Department of Laboratory Medicine Hospital of Chengdu University of Traditional Chinese MedicineChengdu 610072Sichuan ProvinceChina Department of Nuclear Medicine Hospital of Chengdu University of Traditional Chinese MedicineChengdu 610072Sichuan ProvinceChina College of Medical Technology Chengdu University of Traditional Chinese MedicineChengdu 611137Sichuan ProvinceChina Department of Hepatology Affiliated Hospital of Liaoning University of Traditional Chinese MedicineShenyang 110032Liaoning ProvinceChina Hospital of Chengdu University of Traditional Chinese Medicine Chengdu 610072Sichuan ProvinceChina Traditional Chinese Medicine Regulating Metabolic Diseases Key Laboratory of Sichuan Province Chengdu 610072Sichuan ProvinceChina

BACKGROUND Colorectal cancer stem cells(CCSCs)are heterogeneous cells that can self-renew and undergo multidirectional differentiation in colorectal cancer(CRC)patients.CCSCs are generally accepted to be important sources of CRC and are responsible for the progression,metastasis,and therapeutic resistance of CRC.Therefore,targeting this specific subpopulation has been recognized as a promising strategy for overcoming CRC.AIM To investigate the effect of VX-509 on CCSCs and elucidate the underlying mechanism.METHODS CCSCs were enriched from CRC cell lines by in conditioned serum-free medium.Western blot,Aldefluor,transwell and tumorigenesis assays were performed to verify the phenotypic characteristics of the CCSCs.The anticancer efficacy of VX-509 was assessed in HCT116 CCSCs and HT29 CCSCs by performing cell viability analysis,colony formation,sphere formation,flow cytometry,and western blotting assessments in vitro and tumor growth,immunohistochemistry and immunofluorescence assessments in vivo.RESULTS Compared with parental cells,sphere cells derived from HCT116 and HT29 cells presented increased expression of stem cell transcription factors and stem cell markers and were more potent at promoting migration and tumori-genesis,demonstrating that the CRC sphere cells displayed CSC features.VX-509 inhibited the tumor malignant biological behavior of CRC-stem-like cells,as indicated by their proliferation,migration and clonality in vitro,and suppressed the tumor of CCSC-derived xenograft tumors in vivo.Besides,VX-509 suppressed the CSC character-istics of CRC-stem-like cells and inhibited the progression of epithelial-mesenchymal transition(EMT)signaling in vitro.Nodal was identified as the regulatory factor of VX-509 on CRC stem-like cells through analyses of differen-tially expressed genes and CSC-related database information.VX-509 markedly downregulated the expression of Nodal and its downstream phosphorylated Smad2/3 to inhibit EMT progression.Moreover,VX-509 reversed the dedifferentiation of CCSCs and inhibit

关键词： Colorectal cancer stem cells Stemness VX-509 Epithelial-mesenchymal transition Nodal

Deep tectonics and seismogenic mechanisms of the seismic source zone of the Jishishan M_(s)6.2 earthquake on December 18,2023,at the northeast margin of the Tibetan Plateau

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Earth and Planetary Physics 2024年第3期8卷 514-521页

作者： qiong Wang ShuYu Li Xinyi Li Yue Wu PanPan zhao Yuan Gao Key Laboratory of Earthquake Prediction Institute of Earthquake ForecastingChina Earthquake AdministrationBeijing 100036China Institute of Geophysics China Earthquake AdministrationBeijing 100081China

On December 18,2023,an M_(s)6.2 earthquake occurred in Jishishan,Gansu Province,China.This earthquake happened in the eastern region of the Qilian Orogenic Belt,which is situated at the forefront of the NE margin of the Tibetan Plateau(i.e.,Qinghai-Tibet Plateau),encompassing a rhombic-shaped area that intersects the Qilian-Qaidam Basin,Alxa Block,Ordos Block,and South China Block.In this study,we analyzed the deep tectonic pattern of the Jishishan earthquake by incorporating data on the crustal thickness,velocity structure,global navigation satellite system(GNSS)strain field,and anisotropy.We discovered that the location of the earthquake was related to changes in the crustal structure.The results showed that the Jishishan M_(s)6.2 earthquake occurred in a unique position,with rapid changes in the crustal thickness,Vp/Vs,phase velocity,and S-wave velocity.The epicenter of the earthquake was situated at the transition zone between high and low velocities and was in proximity to a low-velocity region.Additionally,the source area is flanked by two high-velocity anomalies from the east and west.The principal compressive strain orientation near the Lajishan Fault is primarily in the NNE and NE directions,which align with the principal compressive stress direction in this region.In some areas of the Lajishan Fault,the principal compressive strain orientations show the NNW direction,consistent with the direction of the upper crustal fast-wave polarization from local earthquakes and the phase velocity azimuthal anisotropy.These features underscore the relationship between the occurrence of the Jishishan M_(s)6.2 earthquake and the deep inhomogeneous structure and deep tectonic characteristics.The NE margin of the Tibetan Plateau was thickened by crustal extension in the process of northeastward expansion,and the middle and lower crustal materials underwent structural deformation and may have been filled with salt-containing fluids during the extension process.The presence of this weak layer makes it easier for strong ea

关键词： Jishishan M_(s)6.2 earthquake crustal structure anisotropy stress and strain seismogenic mechanism northeast margin of the Tibetan Plateau

Protein neddylation and its role in health and diseases

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Signal Transduction and Targeted Therapy 2024年第5期9卷 1869-1904页

作者： Shizhen Zhang Qing Yu Zhijian Li Yongchao zhao yi Sun Department of Breast Surgery the Second Affiliated HospitalZhejiang University School of MedicineHangzhou 310029China Cancer Institute(Key Laboratory of Cancer Prevention and Intervention China National Ministry of Education)the Second Affiliated HospitalZhejiang University School of MedicineHangzhou 310029China Institute of Translational Medicine Zhejiang University School of MedicineHangzhou 310029China Department of Thyroid Surgery Zhejiang Cancer HospitalInstitute of Basic Medicine and Cancer(IBMC)Chinese Academy of SciencesHangzhou 310022China Key Laboratory of Head&Neck Cancer Translational Research of Zhejiang Province Hangzhou 310022China Department of Hepatobiliary and Pancreatic Surgery Zhejiang University School of MedicineHangzhou 310029China Zhejiang Provincial Key Laboratory of Pancreatic Disease The First Affiliated HospitalZhejiang University School of MedicineHangzhou 310029China Zhejiang University Cancer Center Hangzhou 310029China Leading Innovative and Entrepreneur Team Introduction Program of Zhejiang Hangzhou 310024China Research Center for Life Science and Human Health Binjiang Institute of Zhejiang UniversityHangzhou 310053China

NEDD8(Neural precursor cell expressed developmentally downregulated protein 8)is an ubiquitin-like protein that is covalently attached to a lysine residue of a protein substrate through a process known as neddylation,catalyzed by the enzyme cascade,namely NEDD8 activating enzyme(E1),NEDD8 conjugating enzyme(E2),and NEDD8 ligase(E3).The substrates of neddylation are categorized into cullins and non-cullin proteins.Neddylation of cullins activates CRLs(cullin RING ligases),the largest family of E3 ligases,whereas neddylation of non-cullin substrates alters their stability and activity,as well as subcellular localization.Significantly,the neddylation pathway and/or many neddylation substrates are abnormally activated or over-expressed in various human diseases,such as metabolic disorders,liver dysfunction,neurodegenerative disorders,and cancers,among others.Thus,targeting neddylation becomes an attractive strategy for the treatment of these diseases.In this review,we first provide a general introduction on the neddylation cascade,its biochemical process and regulation,and the crystal structures of neddylation enzymes in complex with cullin substrates;then discuss how neddylation governs various key biological processes via the modification of cullins and non-cullin substrates.We further review the literature data on dysregulated neddylation in several human diseases,particularly cancer,followed by an outline of current efforts in the discovery of small molecule inhibitors of neddylation as a promising therapeutic approach.Finally,few perspectives were proposed for extensive future investigations.

关键词： NEDD8 attached attractive

Endoscopic band ligation or endoscopic tissue adhesive injection in the treatment of gastric varices:Which is better?

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World Journal of Gastroenterology 2024年第21期30卷 2827-2828页

作者： Li-Zhi yi Sheng-Bing zhao Department of Gastroenterology The People’s Hospital of LeshanLeshan 614000Sichuan ProvinceChina Department of Gastroenterology Changhai HospitalThe Second Military Medical University/Naval Medical UniversityShanghai 200433China

The combination of endoscopic ultrasound with endoscopic treatment of type 1 gastric variceal hemorrhage may improve the robustness and generalizability of the findings in future studies.Moreover,the esophageal varices should also be included in the evaluation of treatment efficacy in subsequent studies to reach a more convincing conclusion.

关键词： Gastric varices Esophageal varices Endoscopic band ligation Endoscopic tissue adhesive injection Endoscopic ultrasound

Self assembled electron blocking and lithiophilic interface towards dendrite-free solid-state lithium battery

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Chinese Chemical Letters 2024年第4期35卷 220-225页

作者： Caixia Li yi Qiu Yufeng zhao Wuliang Feng Institute for Sustainable Energy&College of Sciences Shanghai UniversityShanghai 200444China Key Laboratory of Advanced Energy Materials Chemistry(Ministry of Education) Nankai UniversityTianjin 300071China

The poor interfacial contact is one of the biggest challenges that solid-state lithium batteries suffer from.Reducing the solid-state electrolyte surface energy by transforming the interface from lithiophobic to lithiophilic is effective to promote the interfacial contact, but electronic conductive interphases usually increase the risk of electron attack, thus leading to uncontrollable Li dendrite growth. Herein, we propose a self-assembled thermodynamic stable Li I interphase to simultaneously improve the interfacial contact between the garnet electrolyte Li_7La_(3)Zr_(2)O_(12)(LLZO) and Li anode, and prohibit the electron attack. The direct contact between LLZO and Li and the high temperature Li melting process was ascribed to Zr4+reduction, which facilitated Li dendrite formation and propagation. With the modification of the high lithiophilic I_(2) thin film, the area specific interfacial resistance of LLZO/Li was reduced from 1525 Ω/cm^(2) to 57 Ω/cm^(2). More importantly, LLZO was protected from being reduced due to the outstanding electronic insulativity of the Li I interphase, which leaded to a high critical current density of 1.2/7.0 m A/cm^(2) in the time/capacity-constant modes, respectively.

关键词： Li_7La_(3)Zr_(2)O_(12) LiI interphase Interfacial contact Li dendrite Thermodynamic stable

Predictive value of neutrophil-to-lymphocyte ratio in coronary chronic total occlusion patients

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Journal of Geriatric Cardiology 2024年第5期21卷 542-549页

作者： Qian LI Yue YU Ya-qiong ZHOU yi zhao Jin WU Yuan-Jing WU Bin DU Pei-Jian WANG Tao ZHENG Department of Cardiovascular Medicine the First Affiliated Hospital of Xi’an Jiaotong UniversityXi’anChina Department of Cardiology First Affiliated Hospital of Chengdu Medical CollegeChengduChina Department of Neurology the First Affiliated Hospital of Xi’an Jiaotong UniversityXi’anChina

BACKGROUND The neutrophil to lymphocyte ratio(NLR)has been reported as a novel predictor for atherosclerosis and car-diovascular outcomes.This study aimed to determine the effects of NLR on long-term clinical outcomes of chronic total occlusion(CTO)patients.METHODS A total of 670 patients with CTO who met the inclusion criteria were included at the end of the follow-up period.Patients were divided into tertiles according to their baseline NLR levels at admission:low(n=223),intermediate(n=223),and high(n=224).The incidence of major adverse cardiac events(MACEs)during the follow-up period,including all-cause death,nonfatal myocardial infarction(MI),or ischemia-driven revascularization,were compared among the three groups.RESULTS Major adverse cardiac events were observed in 27 patients(12.1%)in the low tertile,40(17.9%)in the intermediate tertile,and 61(27.2%)in the high NLR tertile(P<0.001).Kaplan-Meier analysis demonstrated a significantly higher incidence of MACE,ischemia-driven coronary revascularization,non-fatal MI,and mortality in patients within the high tertile than those in the low and intermediate groups(all P<0.001).Multivariable COX regression analysis showed that the high tertile of baseline NLR level showed a strong association with the risk of MACE(hazard ratio[HR]=2.21;95%confidence interval[CI]:1.21-4.03;P=0.009),ischemia-driven coronary revascularization(HR=3.19;95%CI:1.56-6.52;P=0.001),MI(HR=2.61;95%CI:1.35-5.03;P=0.043)and mortality(HR=3.78;95%CI:1.65-8.77;P=0.001).CONCLUSION Our findings suggest that NLR is an inexpensive and readily available biomarker that can independently pre-dict cardiovascular risk in patients with CTO.

关键词： patients coronary occlusion