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Prescreening of large-effect markers with multiple strategies improves the accuracy of genomic prediction

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Journal of Integrative Agriculture 2024年第5期23卷 1634-1643页

作者： Keanning Li Bingxing An Mang Liang Tianpeng Chang Tianyu Deng Lili Du Sheng Cao Yueying Du Hongyan Li Lingyang Xu Lupei Zhang xue gao Junya LI Huijiang gao Laboratory of Molecular Biology and Bovine Breeding Institute of Animal SciencesChinese Academy of Agricultural SciencesBeijing 100193China Shaanxi Key Laboratory of Molecular Biology for Agriculture College of Animal Science and TechnologyNorthwest A&F UniversityYangling712100China College of Computer and Information Engineering Tianjin Agricultural UniversityTianjin 300384China College of Animal Science and Technology Qingdao Agricultural UniversityQingdao 266109China Tongliao Animal Agriculture Development Service Center Tongliao 028000China

Presently,integrating multi-omics information into a prediction model has become a ameliorate strategy for genomic selection to improve genomic prediction accuracy.Here,we set the genomic and transcriptomic data as the training population data,using BSLMM,TWAS,and eQTL mapping to prescreen features according to |β_(b)|>0,top 1%of phenotypic variation explained(PVE),expression-associated single nucleotide polymorphisms(eSNPs),and egenes(false discovery rate(FDR)<0.01),where these loci were set as extra fixed effects(named GBLUP-Fix)and random effects(GFBLUP)to improve the prediction accuracy in the validation population,respectively.The results suggested that both GBLUP-Fix and GFBLUP models could improve the accuracy of longissimus dorsi muscle(LDM),water holding capacity(WHC),shear force(SF),and pH in Huaxi cattle on average from 2.14 to 8.69%,especially the improvement of GFBLUP-TWAS over GBLUP was 13.66%for SF.These methods also captured more genetic variance than GBLUP.Our study confirmed that multi-omics-assisted large-effects loci prescreening could improve the accuracyofgenomic prediction.

关键词： multi-omics data features prescreening eQTL mapping Huaxi cattle genomic selection

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Application of alginate in inflammatory bowel disease

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Biomedical Engineering Communications 2024年第2期3卷 10-16页

作者： Rui-xue Kang Ying Zhuang Ming-Jie Liu Qi Han Wei-Li Zhang Wei-Yu Fan xue gao Jia-Zheng Zhou Jian-Bin Zhang Collage of Pharmacy Dalian Medical UniversityDalian 116044China Laboratory Animal Center Dalian Medical UniversityDalian 116044China

Inflammatory bowel disease(IBD)represents a chronic inflammatory condition profoundly impacting the gastrointestinal tract.Its prevalence has markedly risen in both developed and developing nations over recent decades.Despite the absence of definitive etiological elucidation,therapeutic strategies predominantly revolve around pharmacological interventions aimed at symptom mitigation.Alginate(AG)is a polysaccharide of marine origin that has garnered significant attention due to its inherent biocompatibility,pH sensitivity,and cross-linking.Its exploration within drug delivery systems for IBD treatment stems from its natural sourcing,non-cytotoxic nature,and economic viability.Notably,AG demonstrates facile interpolymeric cross-linking,facilitating the formation of a cohesive network conducive to sustained drug release kinetics.AG-based carrier systems for sustained drug release,and targeted drug delivery have been widely studied.This article reviews the pathogenesis of IBD and the current drugs,AG-based drug delivery systems and their properties in alleviating IBD.The prospect of further development of AG in the field of biopharmaceutical and drug delivery is prospected.

关键词： alginate inflammatory bowel disease drug delivery

High success rate of fiberscope-monitored intubation via a supraglottic airway device BlockBusterTMin good device positioning: A prospective observational study

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中华医学杂志(英文版) 2024年第7期137卷 871-873页

作者： Hu Zhenfa Su Kai Miao Huihui gao xue xue Fushan Tian Ming Department of Anesthesiology Beijing Friendship Hospital Capital Medical University Beijing 100050 China Beijing Shijitan Hospital Beijing 100038

Characterization of SH3GLB1 in the Checkfor auditory system and its potential role in updates mitophagy

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Genes & Diseases 2024年第4期11卷 61-64页

作者： xue gao Weiqian Wang Jincao Xu Shasha Huang Kun Yang Jinyuan Yang Yijin Chen Guojian Wang Mingyu Han Zhendong Wang Dongyang Kang Yongyi Yuan Pu Dai College of Otolaryngology Head and Neck Surgery Chinese PLA General HospitalChinese PLA Medical SchoolBeijing 100853China National Clinical Research Center for Otolaryngologic Diseases State Key Lab of Hearing ScienceMinistry of EducationBeijing 100853China Beijing Key Lab of Hearing Impairment Prevention and Treatment Chinese PLA Medical SchoolBeijing 100853China Department of Otolaryngology PLA Rocket Force Characteristic Medical CenterBeijing 100088China

Mitochondria energize the inner ear to maintain the cochlear potential createdbythe striavascularis,assist the motility of outer hair cells,perform synaptic processes,and maintain the spontaneous and sound-driven discharges of the spiral ganglion neurons(SGNs).Mitophagy deficiencies induce the accumulation of damaged organelles and mitochondria in cells and are a primary cause of drug-induced hearing loss.

关键词： auditory maintain potential

From germline genome to highly fragmented somatic genome:genome-wide DNA rearrangement during the sexual process in ciliated protists

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Marine Life Science & Technology 2024年第1期6卷 31-49页

作者： Liping Lyu xue Zhang Yunyi gao Tengteng Zhang Jinyu Fu Naomi A.Stover Feng gao Key Laboratory of Evolution&Marine Biodiversity(Ministry of Education) and Institute of Evolution&Marine BiodiversityOcean University of ChinaQingdao 266003China Department of Biology Bradley UniversityPeoriaIL 61625USA Laoshan Laboratory Qingdao 266237China

Genomes are incredibly dynamic within diverse eukaryotes and programmed genome rearrangements(PGR)play important roles in generating genomic diversity.However,genomes and chromosomes in metazoans are usually large in size which prevents our understanding of the origin and evolution of PGR.To expand our knowledge of genomic diversity and the evolutionary origin of complex genome rearrangements,we focus on ciliated protists(ciliates).Ciliates are single-celled eukaryotes with highly fragmented somatic chromosomes and massively scrambled germline genomes.PGR in ciliates occurs extensively by removing massive amounts of repetitive and selfish DNA elements found in the silent germline genome dur-ing development of the somatic genome.We report the partial germline genomes of two spirotrich ciliate species,namely Strombidium cf.sulcatum and Halteria grandinella,along with the most compact and highly fragmented somatic genome for S.cf.sulcatum.We provide the first insights into the genome rearrangements of these two species and compare these features with those of other ciliates.Our analyses reveal:(1)DNA sequence loss through evolution and during PGR in S.cf.sulcatum has combined to produce the most compact and efficient nanochromosomes observed to date;(2)the compact,transcriptome-like somatic genome in both species results from extensive removal of a relatively large number of shorter germline-specific DNA sequences;(3)long chromosome breakage site motifs are duplicated and retained in the somatic genome,revealing a complex model of chromosome fragmentation in spirotrichs;(4)gene scrambling and alternative pro-cessing are found throughout the core spirotrichs,offering unique opportunities to increase genetic diversity and regulation in this group.

关键词： Alternative processing Ciliates Gene scrambling Genome rearrangement Germline genome Somatic genome

Research on ozone formation sensitivity based on observational methods:Development history,methodology,and application and prospects in China

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Journal of Environmental Sciences 2024年第4期138卷 543-560页

作者： Wanghui Chu Hong Li Yuanyuan Ji Xin Zhang Likun xue Jian gao Cong An State Key Laboratory of Environmental Criteria and Risk Assessment Chinese Research Academy of Environmental SciencesBeijing 100012China Environment Research Institute Shandong UniversityQingdao 266237China

Observation-based method for O_(3)formation sensitivity research is an important tool to analyze the causes of ground-level O_(3)pollution,which has broad application potentials in determining the O_(3)pollution formation mechanism and developing prevention and control strategies.This paper outlined the development history of research on O_(3)formation sensitivity based on observational methods,described the principle and applicability of the methodology,summarized the relative application results in China and provided recommendations on the prevention and control of O_(3)pollution in China based on relevant study results,and finally pointed out the shortcomings and future development prospects in this field in China.The overview study showed that the O_(3)formation sensitivity in some urban areas in China in recent years presented a gradual shifting tendency from the VOC-limited regime to the transition regime or the NO_(x)-limited regime due to the implementation of the O_(3)precursors emission reduction policies;O_(3)pollution control strategies and precursor control countermeasures should be formulated based on local conditions and the dynamic control capability of O_(3)pollution control measures should be improved.There are still some current deficiencies in the study field in China.Therefore,it is recommended that a stereoscopic monitoring network for atmospheric photochemical components should be further constructed and improved;the atmospheric chemical mechanisms should be vigorously developed,and standardized methods for determining the O_(3)formation sensitivity should be established in China in the near future.

关键词： Observation-based method Ozone formation sensitivity Ozone pollution prevention and control VOCs NO_(x) OBM

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Toward a fundamental understanding of the heterogeneous multiphysics behaviors of silicon monoxide/graphite composite anodes

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Carbon Energy 2024年第1期6卷 142-158页

作者： Xiang gao Suli Li Jiachen xue Dianyang Hu Jun Xu Department of Mechanical Engineering and Engineering Science University of North Carolina at CharlotteCharlotteNorth CarolinaUSA Vehicle Energy and Safety Laboratory(VESL) Battery ComplexityAutonomous Vehicleand Electrification(BATT CAVE)Research CenterUniversity of North Carolina at CharlotteCharlotteNorth CarolinaUSA Zhuhai CosMX Battery Co.Ltd. ZhuhaiGuangdongChina School of Data Science University of North Carolina at CharlotteCharlotteNorth CarolinaUSA

Silicon monoxide(SiO)(silicon[Si]mixed with silicon dioxide[SiO_(2)])/graphite(Gr)composite material is one of the most commercially promising anode materials for the next generation of high-energy-density lithium-ion batteries.The major bottleneck for SiO/Gr composite anode is the poor cyclability arising from the stress/strain behaviors due to the mismatch between two heterogenous materials during the lithiation/delithiation process.To date,a meticulous and quantitative understanding of the highly nonlinear coupling behaviors of such materials is still lacking.Herein,an electro–chemo–mechanics-coupled detailed model containing particle geometries is established.The underlying mechanism of the regulation between SiO and Gr components during electrochemical cycling is quantitatively revealed.We discover that increasing the SiO weight percentage(wt%)reduces the utilization efficiency of the active materials at the same 1C rate charging and enhances the hindering effects of stress-driven flux on diffusion.In addition,the mechanical constraint demonstrates a balanced effect on the overall performance of cells and the local behaviors of particles.This study provides new insights into the fundamental interactions between SiO and Gr materials and advances the investigation methodology for the design and evaluation of next-generation high-energydensity batteries.

关键词： interactions lithium-ion batteries mechanical constraint multiphysics modeling Si-based anode

Geochemical fractionation and potential release behaviour of heavy metals in lead–zinc smelting soils

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Journal of Environmental Sciences 2024年第5期139卷 1-11页

作者： Xinghua Luo Chao Xiang Chuan Wu Wenyan gao Wenshun Ke Jiaqing Zeng Waichin Li Shengguo xue School of Metallurgy and Environment Central South UniversityChangsha 410083China Chinese National Engineering Research Center for Control and Treatment of Heavy Metal Pollution Central South UniversityChangsha 410083China Department of Science and Environmental Studies The Education University of Hong KongHong Kong 999077China

The lack of understanding of heavy metal speciation and solubility control mechanisms in smelting soils limits the effective pollution control.In this study smelting soils were investigated by an advanced mineralogical analysis(AMICS),leaching tests and thermodynamic modelling.The aims were to identify the partitioning and release behaviour of Pb,Zn,Cd and As.The integration of multiple techniques was necessary and displayed coherent results.In addition to the residual fraction,Pb and Zn were predominantly associated with reducible fractions,and As primarily existed as the crystalline iron oxide-bound fractions.AMICS quantitative analysis further confirmed that Fe oxyhydroxides were the common dominant phase for As,Cd,Pb and Zn.In addition,a metal arsenate(paulmooreite)was an important mineral host for Pb and As.The pH-stat leaching indicted that the release of Pb,Zn and Cd increased towards low pH values while release of As increased towards high p H values.The separate leaching schemes were associated with the geochemical behaviour under the control of minerals and were confirmed by thermodynamic modelling.PHREEQC calculations suggested that the formation of arsenate minerals(schultenite,mimetite and koritnigite)and the binding to Fe oxyhydroxides synchronously controlled the release of Pb,Zn,Cd and As.Our results emphasized the governing role of Fe oxyhydroxides and secondary insoluble minerals in natural attenuation of heavy metals,which provides a novelty strategy for the stabilization of multi-metals in smelting sites.

关键词： Smelting soils Heavy metal Fractionation AMICS Geochemical modelling

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Projected changes in Köppen-Trewartha climate zones under 1.5-4℃global warming targets over mid-high latitudes of Northern Asia using an ensemble of RegCM4 simulations

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Advances in Climate Change Research 2024年第2期15卷 185-196页

作者： Jie WU xue-Jie gao Xian-Bing TANG Filippo GIORGI School of Geography and Environmental Engineering Gannan Normal UniversityGanzhou 341000China Climate Change Research Center Institute of Atmospheric PhysicsChinese Academy of SciencesBeijing 100029China Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters Nanjing University of Information Science&TechnologyNanjing 210044China University of Chinese Academy of Sciences Beijing 100049China The Abdus Salam International Centre for Theoretical Physics Trieste 34100Italy

Mid-high latitude Northern Asia is one of the most vulnerable and sensitive areas to global warming,but relatively less studied previously.We used an ensemble of a regional climate model(RegCM4)projections to assess future changes in surface air temperature,precipitation and Köppen-Trewartha(K-T)climate types in Northern Asia under the 1.5-4℃global warming targets.RegCM4 is driven by five CMIP5 global models over an East Asia domain at a grid spacing of 25 km.Validation of the present day(1986-2005)simulations shows that the ensembles of RegCM4(ensR)and driving GCMs(ensG)reproduce the major characters of the observed temperature,precipitation and K-T climate zones reasonably well.Greater and more realistic spatial detail is found in RegCM4 compared to the driving GCMs.A general warming and overall increases in precipitation are projected over the region,with these changes being more pronounced at higher warming levels.The projected warming by ensR shows different spatial patterns,and is in general lower,compared to ensG in most months of the year,while the percentage increases of precipitation are maximum during the cold months.The future changes in K-T climate zones are characterized by a substantial expansion of Dc(temperature oceanic)and retreat of Ec(sub-arctic continental)over the region,reaching∼20%under the 4℃warming level.The most notable change in climate types in ensR is found over Japan(∼60%),followed by Southern Siberia,Mongolia,and the Korean Peninsula(∼40%).The largest change in the K-T climate types is found when increasing from 2 to 3℃.The results will help to better assess the impacts of climate change and in implementation of appropriate adaptation measures over the region.

关键词： Mid-high latitudes of Northern Asia Köppen climate zones Global warming targets Regional climate model