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Reduced non-cpG methylation is a potential epigenetic target after spinal cord injury

Neural Regeneration Research 2023年第11期18卷 2489-2496页

作者： Zhourui Wu chen Li Ran Zhu Yiqiu cao thomas c.chen Liming cheng Key Laboratory of Spine and Spinal cord Injury Repair and Regeneration(Tongji University) Ministry of EducationShanghaiChina Division of Spine Department of OrthopedicsTongji HospitalTongji University School of MedicineShanghaiChina Institute of Spinal and Spinal cord Injury Tongji University School of MedicineShanghaiChina Department of Neurosurgery Keck School of MedicalUniversity of Southern CaliforniaLos AngelesCAUSA

DNA methylation is a critical epigenetic regulator in the occurrence and development of diseases and is closely related to various functional responses in relation to spinal cord injury.To investigate the role of DNA methylation in spinal cord injury,we constructed a library with reduced-representation bisulfite sequencing data obtained at various time points(day 0-42)after spinal cord injury in mice.Global DNA methylation levels,specifically non-cpG(cHG and cHH)methylation levels,decreased modestly following spinal cord injury.Stages post-spinal cord injury were classified as early(day 0-3),intermediate(day7-14),and late(day 28-42)based on similarity and hie rarchical cluste ring of global DNA methylation patterns.The non-cpG methylation level,which included cHG and cHH methylation levels,was markedly reduced despite accounting for a minor proportion of total methylation abundance.At multiple genomic sites,including the 5’untranslated regions,promoter,exon,intron,and 3’untranslated regions,the non-cpG methylation level was markedly decreased following spinal cord injury,whereas the cpG methylation level remained unchanged at these locations.Approximately one-half of the differentially methylated regions were located in intergenic areas;the other differentially methylated regions in both cpG and non-cpG regions were cluste red in intron regions,where the DNA methylation level was highest.The function of genes associated with differentially methylated regions in promoter regions was also investigated.From Gene Ontology analysis results,DNA methylation was implicated in a number of essential functional responses to spinal cord injury,including neuronal synaptic connection creation and axon regeneration.Notably,neither cpG methylation nor non-cpG methylation was implicated in the functional response of glial or inflammatory cells.In summary,our work elucidated the dynamic pattern of DNA methylation in the spinal co rd following injury and identified reduced noncpG methylation as an epigenetic target after spinal cor

关键词： cpG methylation cytosine fraction differentially methylated regions DNA methylation DNA methyltransferases dynamic signatures Gene Ontology non-cpG methylation single-cell RNA-Seq spinal cord injury

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Insights into carbon dioxide sequestration into coal seams through coupled gas flow-adsorption-deformation modelling

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Journal of Rock Mechanics and Geotechnical Engineering 2024年第1期16卷 26-40页

作者： Hywel thomas Min chen Geoenvironmental Research centre Cardiff School of EngineeringCardiff UniversityQueen’s BuildingsThe ParadeNewport RoadCardiffCF243AAUK Key Laboratory of Marine Geology Tongji UniversityShanghai200092China

Injecting carbon dioxide(cO_(2))into coal seams may unlock substantial carbon sequestration potential.Since the coal acts like a carbon filter,it can preferentially absorb significant amounts of cO_(2).To explore this further,desorption of the adsorbed gas due to pressure drop is investigated in this paper,to achieve an improved understanding of the long-term fate of injected cO_(2) during post-injection period.This paper presents a dual porosity model coupling gas flow,adsorption and geomechanics for studying coupled processes and effectiveness of cO_(2) sequestration in coals.A new adsorption?desorption model derived based on thermodynamics is incorporated,particularly,the desorption hysteresis is considered.The reliability of the proposed adsorption-desorption isotherm is examined via validation tests.It is indicated that occurrence of desorption hysteresis is attributed to the adsorption-induced pore deformation.After injection ceases,the injected gas continues to propagate further from the injection well,while the pressure in the vicinity of the injection well experiences a significant drop.Although the adsorbed gas near the well also decreases,this decrease is less compared to that in pressure because of desorption hysteresis.The unceasing spread of cO_(2) and drops of pressure and adsorbed gas depend on the degree of desorption hysteresis and heterogeneity of coals,which should be considered when designing cO_(2) sequestration into coal seams.

关键词： cO_(2)geological storage coal seam Adsorption Desorption hysteresis

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Applying Machine Learning Approach to Explore childhood circumstances and Self-Rated Health in Old Age-china and the US,2020-2021

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china cDc weekly 2024年第11期6卷 213-218,I0008-I0013页

作者： Shutong Huo Derek Feng thomas M.Gill Xi chen Department of Health Society&BehaviorPublic HealthUniversity of CaliforniaIrvineCAUSA Department of Statistics and Data Science Yale UniversityNew HavenCTUS Department of Internal Medicine Yale School of MedicineNew HavenCTUS Department of Health Policy and Management Yale School of Public HealthNew HavenCTUS Department of Economics Yale UniversityNew HavenCTUS.

Introduction:childhood circumstances impact senior health,prompting the introduction of machine learning methods to assess their individual and collective contributions to senior health.Methods:Using health and retirement study(HRS)and china Health and Retirement Longitudinal Study(cHARLS),we analyzed 2,434 American and 5,612 chinese participants aged 60 and above.conditional inference trees and forests were employed to estimate the influence of childhood circumstances on self-rated health(SRH).Results:The conventional method estimated higher inequality of opportunity(IOP)values in both china(0.039,accounting for 22.67%of the total Gini coefficient 0.172)and the US(0.067,accounting for 35.08%of the total Gini coefficient 0.191).In contrast,the conditional inference tree yielded lower estimates(china:0.022,accounting for 12.79%of 0.172;US:0.044,accounting for 23.04%of 0.191),as did the forest(china:0.035,accounting for 20.35%of 0.172;US:0.054,accounting for 28.27%of 0.191).childhood health,financial status,and regional differences were key determinants of senior health.The conditional inference forest consistently outperformed others in predictive accuracy,as demonstrated by lower out-of-sample mean squared error(MSE).Discussion:The findings emphasize the need for early-life interventions to promote health equity in aging populations.Machine learning showcases the potential in identifying contributing factors.

关键词： collective inequality estimates

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Development of gradient boosting-assisted machine learning data-driven model for free chlorine residual prediction

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Frontiers of Environmental Science & Engineering 2024年第2期18卷 35-46页

作者： Wiley Helm Shifa Zhong Elliot Reid thomas Igou Yongsheng chen School of civil and Environmental Engineering Georgia Institute of TechnologyAtlantaGA 30332USA School of Ecological and Environmental Sciences East China Normal UniversityShanghai 200241China

chlorine-based disinfection is ubiquitous in conventional drinking water treatment (DWT) and serves to mitigate threats of acute microbial disease caused by pathogens that may be present in source water. An important index of disinfection efficiency is the free chlorine residual (FcR), a regulated disinfection parameter in the US that indirectly measures disinfectant power for prevention of microbial recontamination during DWT and distribution. This work demonstrates how machine learning (ML) can be implemented to improve FcR forecasting when supplied with water quality data from a real, full-scale chlorine disinfection system in Georgia, USA. More precisely, a gradient-boosting ML method (catBoost) was developed from a full year of DWT plant-generated chlorine disinfection data, including water quality parameters (e.g., temperature, turbidity, pH) and operational process data (e.g., flowrates), to predict FcR. Four gradient-boosting models were implemented, with the highest performance achieving a coefficient of determination, R2, of 0.937. Values that provide explanations using Shapley’s additive method were used to interpret the model’s results, uncovering that standard DWT operating parameters, although non-intuitive and theoretically non-causal, vastly improved prediction performance. These results provide a base case for data-driven DWT disinfection supervision and suggest process monitoring methods to provide better information to plant operators for implementation of safe chlorine dosing to maintain optimum FcR.

关键词： Machine learning Data-driven modeling Drinking water treatment Disinfection chlorination

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The impact of demographic dynamics on food consumption and its environmental outcomes:Evidence from china

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Journal of Integrative Agriculture 2024年第2期23卷 414-429页

作者： Shaoting Li Xuan chen Yanjun Ren thomas Glauben college of Economics and Management Northwest A&F UniversityYangling 712100China Leibniz Institute of Agricultural Development in Transition Economies(IAMO) Halle(Saale)06120Germany Sino-German center for Agricultural and Food Economics Northwest A&F UniversityYangling 712100China

With increasing population and changing demographics,food consumption has experienced a significant transition in quantity and quality.However,a dearth of knowledge remains regarding its environmental impacts and how it responds to demographic dynamics,particularly in emerging economies like china.Using the two-stage Quadratic Almost Demand System(QUAIDS)model,this study empirically examines the impact of demographic dynamics on food consumption and its environmental outcomes based on the provincial data from 2000 to 2020 in china.Under various scenarios,according to changes in demographics,we extend our analysis to project the long-term trend of food consumption and its environmental impacts,including greenhouse gas(GHG)emissions,water footprint(WF),and land appropriation(LA).The results reveal that an increase in the proportion of senior people significantly decreases the consumption of grain and livestock meat and increases the consumption of poultry,egg,and aquatic products,particularly for urban residents.Moreover,an increase in the proportion of males in the population leads to higher consumption of poultry and aquatic products.correspondingly,in the current scenario of an increased aging population and sex ratio,it is anticipated that GHG emissions,WF,and LA are likely to decrease by 1.37,2.52,and 3.56%,respectively.More importantly,in the scenario adhering to the standards of nutritional intake according to the Dietary Guidelines for chinese Residents in 2022,GHG emissions,WF,and LA in urban areas would increase by 12.78,20.94,and 18.32%,respectively.Our findings suggest that changing demographics should be considered when designing policies to mitigate the diet-environment-health trilemma and achieve sustainable food consumption.

关键词： demographic dynamics food consumption environmental impacts nutrition intakes

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Effects of layer interactions on instantaneous stability of finite Stokes flows

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Applied Mathematics and Mechanics(English Edition) 2024年第1期45卷 69-84页

作者： chen ZHAO Zhenli chen c.T.MUTASA Dong LI School of Aeronautics Northwestern Polytechnical UniversityXi'an 710072China

The stability analysis of a finite Stokes layer is of practical importance in flow control. In the present work, the instantaneous stability of a finite Stokes layer with layer interactions is studied via a linear stability analysis of the frozen phases of the base flow. The oscillations of two plates can have different velocity amplitudes, initial phases, and frequencies. The effects of the Stokes-layer interactions on the stability when two plates oscillate synchronously are analyzed. The growth rates of two most unstable modes when δ ckness and the half height of the channel, respectively. However, their vorticities are different. The vorticity of the most unstable mode is symmetric, while the other is asymmetric. The Stokes-layer interactions have a destabilizing effect on the most unstable mode when δ ct when δ > 0.68. However, the interactions always have a stabilizing effect on the other unstable mode. It is explained that one of the two unstable modes has much higher dissipation than the other one when the Stokes-layer interactions are strong. We also find that the stability of the Stokes layer is closely related to the inflectional points of the base-flow velocity profile. The effects of inconsistent velocity-amplitude, initial phase, and frequency of the oscillations on the stability are analyzed. The energy of the most unstable eigenvector is mainly distributed near the plate of higher velocity amplitude or higher oscillation frequency. The effects of the initial phase difference are complicated because the base-flow velocity is extremely sensitive to the initial phase.

关键词： finite Stokes layer instantaneous stability Stokes-layer interaction asynchronous oscillation

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Spatiotemporal dynamics of the social structure of Indo-Pacific humpback dolphins(Sousa chinensis)in Xiamen waters from 2007 to 2019

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Zoological Research 2024年第2期45卷 439-450页

作者： Yi Lu Xin-Rong Xu Bing-Yao chen thomas A Jefferson Holly Fearnbach Guang Yang Jiangsu Key Laboratory for Biodiversity and Biotechnology College of Life SciencesNanjing Normal UniversityNanjingJiangsu 210023China clymene Enterprises LakesideCalifornia 92040USA Marine Mammal Research SR3SeaLife ResponseRehabilitation and ResearchWA 98275USA Southern Marine Science and Engineering Guangdong Laboratory(Guangzhou) No.1119Haibin RoadNansha DistrictGuangzhouGuangdong 511458China

As highly social animals,Indo-Pacific humpback dolphins(Sousa chinensis)exhibit community differentiation.Nevertheless,our understanding of the external and internal factors influencing these dynamics,as well as their spatiotemporal variations,is still limited.In the present study,variations in the social structure of an endangered Indo-Pacific humpback dolphin population in Xiamen Bay,china,were monitored over two distinct periods(2007–2010 and 2017–2019)to analyze the effects of habitat utilization and the composition of individuals within the population.In both periods,the population demonstrated a strikingly similar pattern of social differentiation,characterized by the division of individuals into two main clusters and one small cluster.Spatially,the two primary clusters occupied the eastern and western waters,respectively,although the core distribution area of the eastern cluster shifted further eastward between the two periods.Despite this distribution shift,the temporal stability of the social structure and inter-associations within the eastern cluster remained unaffected.A subset of 16individuals observed in both periods,comprising 51.6%and 43.2%of the population in each respective period,emerged as a foundational element of the social structure and may be responsible for sustaining social structure stability,especially during the 2007–2010 period.These observations suggest that the composition of dominant individuals,an internal factor,had a more substantial influence on the formation of the social network than changes in habitat use,an external factor.consequently,the study proposes distinct conservation measures tailored to each of the two main clusters.

关键词： Social differentiation Social structure Sousa chinensis Dynamics conservation

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comparison of trigeminal lateralization with differing stimulants

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World Journal of Otorhinolaryngology-Head and Neck Surgery 2024年第1期10卷 66-69页

作者： Tiffany chen Nicolas S.Poupore Michael c.Shih thomas S.Edwards Shaun A.Nguyen Zachary M.Soler Rodney J.Schlosser Department of Otolaryngology‐Head and Neck Surgery Medical University of South CarolinaCharlestonSouth CarolinaUSA

Trigeminal-specific stimulants have been shown to activate different receptors preferentially and this likely accounts for variation in sensory perception.It is unclear whether trigeminal sensitivity is similar across different transient receptor potential(TRP)receptors or if dysfunction of different receptors results in differing patient symptoms.Therefore,a prospective cohort study was conducted,consisting of trigeminal lateralization testing with three different stimulants(eucalyptol,isothiocyanate,acetic acid),olfaction testing with Sniffin'Sticks,and measurement of various patient‐reported outcome measures(PROMs).A total of 50 participants were enrolled across the olfactory spectrum.Mean TDI score was 27.1±8.3(range 7.0–39.5)with 38%normosmic and 62%dysosmic.Mean trigeminal lateralization scores out of 20 in the overall cohort were 16.18(2.78)for eucalyptol,14.94(3.49)for mustard oil,and 15.28(3.68)for vinegar.Eucalyptol showed a significant correlation with threshold scores of Sniffin'Sticks.A significant correlation was found between acetic acid and various PROMs.None of the lateralization scores of the trigeminal stimulants correlated to each other significantly and there was no correlation to age.The lack of correlation suggests that the measured sensitivity of one type of TRP receptor may not translate to similar sensitivity of the other receptors.Additional investigations with TRPV1 and TRPA1 agonists are needed to corroborate our findings.

关键词： chemosensory olfaction trigeminal TRP receptor

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The anti-inflammatory effects of exercise on autoimmune diseases:A 20-year systematic review

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Journal of Sport and Health Science 2024年第3期13卷 353-367,I0001页

作者： Beibei Luo Dao Xiang Xiaorong Ji Xuan chen Rui Li Shuxin Zhang Yujun Meng David c.Nieman Peijie chen School of Exercise and Health Shanghai University of SportShanghai 200438China Shanghai Key Laboratory of Human Performance Shanghai University of SportShanghai 200438China Department of Diving and Hyperbaric Medicine Naval Medical CenterShanghai 200433China National Key Laboratory of Immunity and Inflammation Naval Medical UniversityShanghai 200433China Human Performance Laboratory Appalachian State UniversityNorth Carolina Research CampusKannapolisNC 28081USA Research Institute for Doping control Shanghai University of SportShanghai 200438China

Background:The anti-inflammatory effect of exercise may be an underlying factor in improving several autoimmune diseases.The aim of this systematic review was to examine the evidence on the role of exercise training in mitigating inflammation in adolescents and adults with autoimmune disease.Methods:PubMed,Web of Science,and Embase databases were systematically reviewed for related studies published between January 1,2003,and August 31,2023.All randomized and non-randomized controlled trials of exercise interventions with autoimmune disease study participants that evaluated inflammation-related biomarkers were included.The quality of evidence was assessed using the Tool for the assEssment of Study qualiTy and reporting in EXercise scale and cochrane bias risk tool.Results:A total of 14,565 records were identified.After screening the titles,abstracts,and full texts,87 were eligible for the systematic review.These studies were conducted in 25 different countries and included a total of 2779 participants(patients with autoimmune disease,in exercise or control groups).Overall,the evidence suggests that inflammation-related markers such as c-reactive protein,interleukin 6,and tumor necrosis factor a were reduced by regular exercise interventions.Regular exercise interventions combined with multiple exercise modes were associated with greater benefits.conclusion:Regular exercise training by patients with autoimmune disease exerts an anti-inflammatory influence.This systematic review provides support for the promotion and development of clinical exercise intervention programs for patients with autoimmune disease.Most patients with autoimmune disease can safely adopt moderate exercise training protocols,but changes in inflammation biomarkers will be modest at best.Acute exercise interventions are ineffective or even modestly but transiently pro-inflammatory.

关键词： Autoimmune diseases cytokines Inflammation Physical activity Training

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Mechanistic insight into cr(Ⅵ)retention by Si-containing ferrihydrite

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Journal of Environmental Sciences 2024年第5期139卷 217-225页

作者： Ying Hu Qiang Xue Honghan chen Huaming Guo Kenneth c.carroll Song Wang MOE Key Laboratory of Groundwater circulation and Environmental Evolution School of Water Resources and EnvironmentChina University of Geosciences(Beijing)Beijing 100083China Beijing Key Laboratory of Water Resources and Environmental Engineering School of Water Resources and EnvironmentChina University of GeosciencesBeijing 100083China State Key Laboratory of Biogeology and Environmental Geology China University of GeosciencesBeijing 100083China Plant&Environmental Science New Mexico State UniversityNM 88003USA Institute of Theoretical chemistry College of ChemistryJilin UniversityChangchun 130023China

Hexavalent chromium[cr(Ⅵ)]causes serious harm to the environment due to its high toxicity,solubility,and mobility.Ferrihydrites(Fh)are the main adsorbent and trapping agent of cr(Ⅵ)in soils and aquifers,and they usually coexist with silicate(Si),forming Si-containing ferrihydrite(Si-Fh)mixtures.However,the mechanism of cr(Ⅵ)retention by Si-Fh mixtures is poorly understood.In this study,the behaviors and mechanisms of cr(Ⅵ)adsorption onto Si-Fh with different Si/Fe molar ratios was investigated.Transmission electron microscope,Fourier transform infrared spectroscopy,X-ray diffraction,X-ray photoelectron spectroscopy,and other techniques were used to characterize Si-Fh and cr(Ⅵ)-loading of Si-Fh.The results show that specific surface area of Si-Fh increases gradually with increasing Si/Fe ratios,but cr(Ⅵ)adsorption on Si-Fh decreases with increasing Si/Fe ratios.This is because with an increase in Si/Fe molar ratio,the point of zero charge of Si-Fh gradually decreases and electrostatic repulsion between Si-Fh and cr(Ⅵ)increases.However,the complexation of cr(Ⅵ)is enhanced due to the increase in adsorbed hydroxyl(A-OH-)on Si-Fh with increasing Si/Fe molar ratio,which partly counteracts the effect of the electrostatic repulsion.Overall,the increase in the electrostatic repulsion has a greater impact on adsorption than the additional complexation with Si-Fh.Density functional theory calculation further supports this observation,showing the increases in electron variation of bonding atoms and reaction energies of inner spherical complexes with the increase in Si/Fe ratio.

关键词： Hexavalent chromium Ferrihydrite Si/Fe ratio cr(Ⅵ)Adsorption

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