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Interpretation, Stratification and Evidence for Sequence Variants Affecting mRNA Splicing in complete Human Genome Sequences

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Genomics, Proteomics & Bioinformatics 2013年第2期11卷 77-85页

作者： ben c.shirley Eliseos J.Mucaki Tyson Whitehead Paul I.costea Pelin Akan Peter K.Rogan Department of computer Science Middlesex CollegeThe University of Western Ontario Department of Biochemistry Schulich School of Medicine and DentistryThe University of Western Ontario SHARcNET Royal Institute of Technology Science for Life Laboratory cytognomix Inc.

Information theory-based methods have been shown to be sensitive and specific for pre- dicting and quantifying the effects of non-coding mutations in Mendelian diseases. We present the Shannon pipeline software for genome-scale mutation analysis and provide evidence that the soft- ware predicts variants affecting mRNA splicing. Individual information contents （in bits） of refer- ence and variant splice sites are compared and significant differences are annotated and prioritized. The software has been implemented for cLc-Bio Genomics platform. Annotation indicates the context of novel mutations as well as common and rare SNPs with splicing effects. Potential natural and cryptic mRNA splicing variants are identified, and null mutations are distinguished from leaky mutations. Mutations and rare SNPs were predicted in genomes of three cancer cell lines （U2OS, U251 and A431）, which were supported by expression analyses. After filtering, tractable numbers of potentially deleterious variants are predicted by the software, suitable for further laboratory investigation. In these cell lines, novel functional variants comprised 6-17 inactivating mutations, 1 5 leaky mutations and 6-13 cryptic splicing mutations. Predicted effects were validated by RNA-seq analysis of the three aforementioned cancer cell lines, and expression microarray analysis of SNPs in HapMap cell lines.

关键词： Mutation mRNA splicing Information theory Next-generation sequencing Genome interpretation

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Simultaneously enhanced electrochemical performance and air stability of Ni-rich cathode with a modified washing process

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Rare Metals 2024年第1期43卷 87-97页

作者： ben-Rui Hu Ying-Yi Yuan Yu-cheng Wang Xun-Hui Xiong School of Environment and Energy Guangdong Provincial Key Laboratory of Advanced Energy Storage MaterialsSouth China University of TechnologyGuangzhou 510640China

Water washing has been regarded as one of the most effective strategies to remove surface residual lithium of nickel-rich layered oxides for lithium-ion batteries(LIBs).However,the loss of lattice lithium during the water washing process deteriorates the electrochemical performances and air ***,washing the LiNi_(0.90)co_(0.05)Al_(0.02)O_(2)(NcA) with ammonium dihydrogen phosphate(NH_(4)H_(2)PO_(4)) solution has been proposed to simultaneously enhance electrochemical performances and air stability,in which in-situ generated Li_(3)PO_(4) coating layer on surface of NcA can suppress the loss of lattice ***,as a fast ionic conductor,Li_(3)PO_(4) coating layer on NcA can prevent the direct contact with electrolyte/*** a result,the NH_(4)H_(2)PO_(4) solution washed NcA cathode can deliver a high capacity of131.9 mAh·g^(-1) at 10.0c rate as well as impressive cycle stability with a capacity retention of 83.1% after 100 cycles at 1.0c,much higher than those of water washed NcA(WS-NcA) *** exposed in air for 7 days,the NH_(4)H_(2)PO_(4) solution washed NcA electrode can more effectively maintain the structural integrity as well as the electrochemical performances than water-washed *** work provides a simple and effective approach to enhance the cycle stability and air stability of Nickel-rich cathode materials.

关键词： Layered Ni-rich cathode Residual lithium Li_(3)PO_(4)coating Rate performance Air stability

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Triple the steady-state reaction rate by decorating the In_(2)O_(3)surface with SiO_(x)for cO_(2)hydrogenation

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Journal of Energy chemistry 2024年第8期95卷 96-105,I0003页

作者： Hao Wang chun Yang Xiaoyan Yu Mingrui Wang Runze Yang Xiaowa Nie ben Hang Yin Alex c.K.Yip chunshan Song Guanghui Zhang Xinwen Guo State Key Laboratory of Fine chemicals Frontier Science Center for Smart MaterialsPSU-DUT Joint Center for Energy ResearchSchool of Chemical EngineeringDalian University of TechnologyDalian 116024LiaoningChina Department of chemistry the Chinese University of Hong KongHong Kong 999077China Paihau-Robinson Research Institute the MacDiarmid Institute for Advanced Materials and NanotechnologyVictoria University of WellingtonWellington 6012New Zealand Department of chemical and Process Engineering The University of CanterburyChristchurch 8041New Zealand

Indium oxide(In_(2)O_(3)),as a promising candidate for cO_(2)hydrogenation to c_(1) products,often suffers from sintering and activity decline,closely related to the undesirable structural evolution under reaction *** on the comprehension of the dynamic evolution,this study presents an efficient strategy to alleviate the agglomeration of In_(2)O_(3)nanoparticles by the surface decoration with highly dispersed silica species(SiO_(x)).Various structural characterizations combined with density functional theory calculations demonstrated that the sintering resulted from the over-reduction,while the enhanced stability originated from the anchoring effect of highly stable In-OSi bonds,which hinders the substantial formation of metallic In(In^(0))and the subsequent agglomeration.0.6Si/In_(2)O_(3)exhibited cO_(2)conversion rate of10.0 mmol g^(-1)h^(-1)at steady state vs.3.5 mmol g^(-1)h^(-1)on In_(2)O_(3)in cO_(2)*** steady-state activity was also achieved on Pd-modified *** to the traditional Pd/In_(2)O_(3)catalyst,the methanol production rate of Pd catalyst supported on 0.6Si/In_(2)O_(3)was enhanced by 23%,showing the potential of In_(2)O_(3)modified by SiO_(x)in serving as a platform *** work provides a promising method to design new In_(2)O_(3)-based catalysts with improved activity and stability in cO_(2)hydrogenation.

关键词： cO_(2)hydrogenation In_(2)O_(3)sintering Dynamic structural evolution Surface SiO_(x)modification DFT simulations

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The medium-temperature dependence of jet transport coefficient in high-energy nucleus-nucleus collisions

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Nuclear Science and Techniques 2024年第7期35卷 173-191页

作者： Man Xie Qing-Fei Han En-Ke Wang ben-Wei Zhang Han-Zhong Zhang Key Laboratory of Atomic and Subatomic Structure and Quantum control(MOE) Guangdong Basic Research Center of Excellence for Structure and Fundamental Interactions of MatterInstitute of Quantum Matter South China Normal UniversityGuangzhou510006China Guangdong-Hong Kong Joint Laboratory of Quantum Matter Guangdong Provincial Key Laboratory of Nuclear ScienceSouthern Nuclear Science Computing CenterSouth China Normal UniversityGuangzhou 510006China Key Laboratory of Quark and Lepton Physics(MOE)and Institute of Particle Physics Central China Normal UniversityWuhan430079China

The medium-temperature T dependence of the jet transport coefficient̂q was studied via the nuclear modification factor RAA(p_(T))and elliptical flow parameter v_(2)(p_(T))for large transverse momentum p_(T) hadrons in high-energy nucleus-nucleus *** a next-to-leading-order perturbative QcD parton model for hard scatterings with modified fragmentation functions due to jet quenching controlled by q,we check the suppression and azimuthal anisotropy for large p_(T) hadrons,and extract q by global fits to RAA(pT)and v_(2)(pT)data in A+A collisions at RHIc and LHc,*** numerical results from the best fits show that q∕T^(3) goes down with local medium-temperature T in the parton jet *** with the case of a constant q∕T^(3),the going-down T dependence of q∕T^(3) makes a hard parton jet to lose more energy near T_(c) and therefore strengthens the azimuthal anisotropy for large pT *** a result,v_(2)(p_(T))for large pT hadrons was enhanced by approximately 10%to better fit the data at RHIc/*** the first-order phase transition from QGP to the hadron phase and the additional energy loss in the hadron phase,v_(2)(p_(T))is again enhanced by 5-10%at RHIc/LHc.

关键词： Jet quenching Jet transport parameter Hadron suppression Elliptic flow coefficient Energy loss asymmetry

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Wave Attenuation and Turbulence Driven by Submerged Vegetation Under current-Wave Flow

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china Ocean Engineering 2024年第4期38卷 602-611页

作者： HUANG Yu-ming Ding Lei WANG Yi-fei cHEN ben YANG Xiao-yu DOU Xi-ping School of Water Resources and Hydropower Engineering Wuhan UniversityWuhan430072China Key Laboratory of Port Waterway and Sedimentation Engineering of MOTNanjing Hydraulic Research InstituteNanjing 210029China

A set of laboratory experiments are carried out to investigate the effect of following/opposing currents on wave *** vegetation canopies with aligned and staggered configurations were tested under the condition of various regular wave heights and current velocities,with the constant water depth being 0.60 m to create the desired submerged *** show that the vegetation-induced wave dissipation is enhanced with the increasing incident wave height.A larger velocity magnititude leads to a greater wave height attenuation for both following and opposing current ***,there is a strong positive linear correlation between the damping coefficientβand the relative wave height H_(0)/h,especially for pure wave *** the velocity profile,the distributions of U_(min)and U_(max)show different patterns under combined wave and *** time-averaged turbulent kinetic energy(TKE)vary little under pure wave and U_(c)=±0.05 m/s *** the increase of flow velocity amplitude,the time-averaged TKE shows a particularly pronounced increase trend at the top of the *** vegetation drag coefficients are obtained by a calibration *** empirical relations of drag coefficient with Reynolds and Keulegane-carpenter numbers are proposed to further understand the wave-current-vegetation interaction mechanism.

关键词： wave attenuation rigid vegetation following and opposing currents turbulent kinetic energy

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Exploring charge and spin fluctuations in infinite-layer cuprate SrcuO_(2)from a phonon perspective

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Science china(Physics,Mechanics & Astronomy) 2024年第8期67卷 159-167页

作者： Xin Du Pei-Han Sun ben-chao Gong Jian-Feng Zhang Zhong-Yi Lu Kai Liu Department of Physics and Beijing Key Laboratory of Opto-electronic Functional Materials&Micro-nano Devices Renmin University of ChinaBeijing 100872China Department of Physics School of ScienceJiangsu University of Science and TechnologyZhenjiang 212100China Institute of Physics Chinese Academy of SciencesBeijing 100190China Key Laboratory of Quantum State construction and Manipulation(Ministry of Education) Renmin University of ChinaBeijing 100872China

The infinite-layer cuprate Acu O_(2)(A=ca,Sr,Ba)possesses the simplest crystal structure among numerous cuprate superconductors and can serve as a prototypical system to explore the unconventional *** on the first-principles electronic structure calculations,we have studied the electronic and magnetic properties of the infinite-layer cuprate SrcuO_(2)from a phonon *** find that interesting fluctuations of charges,electrical dipoles,and local magnetic moments can be induced by the atomic displacements of phonon modes in SrcuO_(2)upon the hole *** all optical phonon modes of SrcuO_(2)in the antiferromagnetic Néel state,only the A_(1g)mode that involves the full-breathing O vibrations along the cu-O bonds can cause significant fluctuations of local magnetic moments on O atoms and dramatic charge redistributions between cu and O ***,due to the atomic displacements of the A_(1g)mode,both the charge fluctuations on cu and the electrical dipoles on O show a dome-like evolution with increasing hole doping,quite similar to the experimentally observed behavior of the superconducting T_(c);in comparison,the fluctuations of local magnetic moments on O display a monotonic enhancement along with the hole *** analyses indicate that around the optimal doping,there exists a large softening in the frequency of the A_(1g)phonon mode and a van Hove singularity in the electronic structure close to the Fermi level,suggesting potential electron-phonon *** work reveals the important role of the full-breathing O phonon mode playing in the infinite-layer SrcuO_(2),which may provide new insights in understanding the cuprate superconductivity.

关键词： first-principles calculations cuprate superconductors phonon charge and spin fluctuations

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Multistimuli-Responsive Luminescent Porous Organic Polymers with chiroptical Properties and Acid-Induced Degradation

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chinese Journal of chemistry 2024年第16期42卷 1886-1894页

作者： Youling He Dongyang Fan Liang Zhang Dong Wang Ting Han Rongrong Hu ben Zhong Tang center for AIE Research Shenzhen Key Laboratory of Polymer Science and TechnologyGuangdong Research Center for Interfacial Engineering of Functional MaterialsCollege of Materials Science and EngineeringShenzhen UniversityShenzhenGuangdong 518060China college of Physics and Optoelectronic Engineering Shenzhen UniversityShenzhenGuangdong 518060China Department of chemistry Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and ReconstructionThe Hong Kong University of Science and TechnologyClear Water BayKowloonHong Kong999077China State Key Laboratory of Luminescent Materials and Devices Guangdong Provincial Key Laboratory of Luminescence from Molecular AggregatesSouth China Universityof TechnologyGuangzhouGuangdong 510640China School of Science and Engineering Shenzhen Institute of Aggregate Science and TechnologyThe Chinese University of Hong KongShenzhen(CUHK-Shenzhen)Guangdong 518172China

Porous organic polymers(POPs)have attracted great attention in past *** diverse functional POPs have been developed,multistimuli-responsive POPs with excellent aggregate-state luminescence together with good chiroptical properties have rarely been ***,two pairs of Salen-type enantiomeric PoPs with multistimuli-responsive luminescence and chiral features were designed and synthesized by facile polycondensation reactions between polyfunctional aggregation-induced emission luminogen(AlEgen)-containing salicylaldehyde derivatives and chiral *** Salen units in polymer backbones as tetradentate ligands,a series of POP-metal complexes were further *** obtained POPs and metal complexes show good porosity,high thermal stability,and obvious circular dichroism ***,benefiting from the coexistence of AlEgen and Salen units in polymer structures,these POPs exhibit excellent luminescence performance in aggregate states and tunable fluorescence behaviors in response to external stimuli of Zn^(2+)ion,mechanical forces,organic solvent,and *** to the dynamic feature of Schiff base c=N bonds,the present POPs can efficiently undergo hydrolysis reactions under strong acidic conditions to reproduce the AlEgencontaining monomers,and such an acid-induced degradation process can be directly visualized and dynamically monitored via fluorescence *** properties collectively make the POPs candidate materials for applications in heterogeneous asymmetric catalysis,fluorescence sensing,biomedicine,etc.

关键词： Polymers Stimuli-responsive luminescence Porous polymers chirality Aggregation-induced emission Fluorescence Schiff bases Degradation

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Unidirectional movement behavior of underwater bubbles on the wettability gradient mesh via asymmetrical bounce

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Science china chemistry 2024年第8期67卷 2606-2613页

作者： Yuzhen Ning Zhihong Zhao Shuang ben Qiang Li cunming Yu Xudong Zhang Huawei chen Kesong Liu Lei Jiang School of Mechanical Engineering and Automation Beihang UniversityBeijing 100191China Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology School of ChemistryBeihang UniversityBeijing 100191China Research Institute of Aero-Engine Beihang UniversityBeijing 100191China School of Materials Science and Engineering Shenyang Ligong UniversityShenyang 110159China Tianmushan Laboratory Hangzhou 310023China The Analysis Testing CenterBeihang UniversityBeijing 100191China

The impact of underwater bubbles on solid surfaces with a gradient wettability is important for fundamental science and technological applications. Despite progress in the translational motion of underwater bubbles on asymmetric surface, a fundamental dynamic understanding of asymmetrical bounce behavior of the underwater bubble needs to be further ***, we investigate asymmetrical bounce of underwater bubbles after impacting the wettability gradient copper mesh *** bounce of the underwater bubble on the wettability gradient mesh(WGM) surface is composed by asymmetrical spread in the spread process and asymmetrical recoil in the recoil process, which induce the unidirectional movement ***, effective bubble-size manipulation can be easily implemented due to different volumes of bubbles remaining at different locations of WGM surface. We envision that this work will provide a new understanding of asymmetrical bounce behavior of the underwater bubble on the wettability gradient surface, and propose a novel and feasible strategy for constructing the underwater bubble manipulation system.

关键词： asymmetrical bounce unidirectional movement behavior gradient wettability

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3D Path Planning of the Solar Powered UAV in the Urban-Mountainous Environment with Multi-Objective and Multi-constraint Based on the Enhanced Sparrow Search Algorithm Incorporating the Levy Flight Strategy

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Guidance, Navigation and control 2024年第1期4卷 149-175页

作者： Pengyang Xie ben Ma Bingbing Wang Jian chen Gang Xiao college of Engineering China Agricultural UniversityBeijing 100083P.R.China State Key Laboratory of clean Energy Utilization Zhejiang UniversityHangzhou 310027P.R.China Key Laboratory of Intelligent Equipment and Robotics for Agriculture of Zhejiang Province College of Biosystems Engineering and Food ScienceZhejiang UniversityHangzhou 310058P.R.China Key Laboratory of Smart Agricultural Technology(Yangtze River Delta) Ministry of Agriculture and Rural AffairsNanjing 210044P.R.China Key Laboratory of Smart Agricultural Technology in Tropical South china Ministry of Agriculture and Rural AffairsGuangzhou 510642P.R.China State Key Laboratory of Virtual Reality Technology and Systems Beihang UniversityBeijing 100191P.R.China

In response to practical application challenges in utilizing solar-powered unmanned aerial vehicle(UAV)for remote sensing,this study presents a three-dimensional path planning method tailored for urban-mountainous *** into account constraints related to the solar-powered UAV,terrain,and mission objectives,a multi-objective trajectory optimization model is transferred into a single-objective optimization problem with weight factors and multiconstraint and is developed with a focus on three key indicators:minimizing trajectory length,maximizing energy flow e±ciency,and minimizing regional risk ***,an enhanced sparrow search algorithm incorporating the Levy flight strategy(SSA-Levy)is introduced to address trajectory planning challenges in such complex *** simulation,the proposed algorithm is compared with particle swarm optimization(PSO)and the regular sparrow search algorithm(SSA)across 17 standard test functions and a simplified simulation of urban-mountainous *** results of the simulation demonstrate the superior effectiveness of the designed improved SSA based on the Levy flight strategy for solving the established single-objective trajectory optimization model.

关键词： Solar powered UAV multi-objective optimization problem single-objective optimization problem multi-constraint sparrow search algorithm Levy flight strategy

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Genome-wide DNA methylome analysis reveals a critical role of methylation-dysregulated lncRNAs in autophagy regulation in glioblastoma

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Genes & Diseases 2024年第5期11卷 51-54页

作者： Hongying Zhao Ying Liu Meiting Fei Lin Bo Lixia Wang Yaopeng Shu Peiqi ben Li Wang college of Bioinformatics Science and Technology Harbin Medical UniversityHarbinHeilongjiang 150081China

Glioblastoma(GBM)is the most common primary malignant intracranial tumor with a very poor *** this study,we systematically analyzed the DNA methylation alterations of autophagy-related lncRNAs and their association with drug therapies in *** identified 9 DNA methylation-dysregulated lncRNA regulators of autophagy-related genes as autophagy-related lncRNAs.A dysregulated regulatory network consisting of 9 autophagy-related lncRNAs and 237 differentially expressed autophagy-related genes was *** of small molecule drug candidates that may affect DNA methylation dysregulated lncRNA activity,including 45 drug lncRNA pairs,involving 7 DNA methylation dysregulated lncRNAs and 43 ***,we identified a DNA methylation-dysregulated autophagy-related lncRNA MIR155HG as an independent prognostic indicator for GBM.

关键词： regulated alterations drugs

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