Deterministic compartment models(CMs)and stochastic models,including stochastic CMs and agent-based models,are widely utilized in epidemic modeling.However,the relationship between CMs and their corresponding stochast...Deterministic compartment models(CMs)and stochastic models,including stochastic CMs and agent-based models,are widely utilized in epidemic modeling.However,the relationship between CMs and their corresponding stochastic models is not well understood.The present study aimed to address this gap by conducting a comparative study using the susceptible,exposed,infectious,and recovered(SEIR)model and its extended CMs from the coronavirus disease 2019 modeling literature.We demonstrated the equivalence of the numerical solution of CMs using the Euler scheme and their stochastic counterparts through theoretical analysis and simulations.Based on this equivalence,we proposed an efficient model calibration method that could replicate the exact solution of CMs in the corresponding stochastic models through parameter adjustment.The advancement in calibration techniques enhanced the accuracy of stochastic modeling in capturing the dynamics of epidemics.However,it should be noted that discrete-time stochastic models cannot perfectly reproduce the exact solution of continuous-time CMs.Additionally,we proposed a new stochastic compartment and agent mixed model as an alternative to agent-based models for large-scale population simulations with a limited number of agents.This model offered a balance between computational efficiency and accuracy.The results of this research contributed to the comparison and unification of deterministic CMs and stochastic models in epidemic modeling.Furthermore,the results had implications for the development of hybrid models that integrated the strengths of both frameworks.Overall,the present study has provided valuable epidemic modeling techniques and their practical applications for understanding and controlling the spread of infectious diseases.展开更多
Diet/sugar-free soft drinks are considered to be healthier than regular soft drinks.However,few studies have examined the relationship between the types of soft drinks(regular and diet/sugar-free)and lung cancer(LC)/a...Diet/sugar-free soft drinks are considered to be healthier than regular soft drinks.However,few studies have examined the relationship between the types of soft drinks(regular and diet/sugar-free)and lung cancer(LC)/all-cancer(AC)risk.In this study,we comprehensively assessed the influence of the type of soft drink consumption on LC/AC risk based on the Prostate,Lung,Colorectal,and Ovarian(PLCO)Cancer Screening Trial.Multivariable Cox proportional hazards and competing risks Fine-Gray regression models adjusted for relevant confounders were used to estimate hazard ratios(HRs)and subdistribution HRs for different types of soft drink consumption.In the PLCO population,female subgroup,and the ever/current smoker subgroup,consumption of both regular and diet soft drinks was associated with a significantly reduced risk of LC compared with no soft drinks at all.For the non-lung cancer(NLC)risk,consumption of only diet soft drinks had a significant positive association for the total population and female subgroup.Based on our findings,it was suggested that partial replacement of regular soft drinks with diet soft drinks might be beneficial to LC prevention,especially for females and ever/current smokers.Additionally,completely replacing regular soft drinks with diet soft drinks might be detrimental to NLC prevention,especially for females.展开更多
To investigate whether genetic variants may provide additional prognostic value to improve the existing clinical staging system for gastric cancer(GC),we performed two genome-wide association studies(GWASs)of GC survi...To investigate whether genetic variants may provide additional prognostic value to improve the existing clinical staging system for gastric cancer(GC),we performed two genome-wide association studies(GWASs)of GC survival in the Jiangsu(N=1049)and Shanghai(N=1405)cohorts.By using a TCGA dataset,we validated genetic markers identified from a meta-analysis of these two Chinese cohorts to determine GC survival-associated loci.Then,we constructed a weighted polygenic hazard score(PHS)and developed a nomogram in combination with clinical variables.We also evaluated prognostic accuracy with the time-dependent receiver operating characteristic(ROC)curve,net reclassification improvement(NRI)and integrated discrimination improvement(IDI).We identified a single nucleotide polymorphism(SNP)of rs1618332 at 15q15.1 that was associated with the survival of GC patients with a P value of 4.12×10^(-8),and we also found additional 25 SNPs having consistent associations among these two Chinese cohort and TCGA cohort.The PHS derived from these 26 SNPs(PHS-26)was an independent prognostic factor for GC survival(all P<0.001).The 5-year AUC of PHS-26 was 0.68,0.66 and 0.67 for Jiangsu,Shanghai and their pooled cohorts,respectively,which increased to 0.80,0.82 and 0.81,correspondingly,after being integrated into a nomogram together with variables of the clinical model.The PHS-26 could improve the NRIs by 16.20%,4.90%and 8.70%,respectively,and the IDIs by 11.90%,8.00%and 9.70%,respectively.The 26-SNP based PHS could substantially improve the accuracy of prognostic assessment and might facilitate precision medicine for GC patients.展开更多
Background:A polygenic risk score(PRS)derived from 112 single-nucleotide polymorphisms(SNPs)for gastric cancer has been reported in Chinese populations(PRS-112).However,its performance in other populations is unknown....Background:A polygenic risk score(PRS)derived from 112 single-nucleotide polymorphisms(SNPs)for gastric cancer has been reported in Chinese populations(PRS-112).However,its performance in other populations is unknown.A functional PRS(fPRS)using functional SNPs(fSNPs)may improve the generalizability of the PRS across populations with distinct ethnicities.Methods:We performed functional annotations on SNPs in strong linkage disequilibrium(LD)with the 112 previously reported SNPs to identify fSNPs that affect protein-coding or transcriptional regulation.Subsequently,we constructed an fPRS based on the fSNPs by using the LDpred2-infinitesimal model and then analyzed the performance of the PRS-112 and fPRS in the risk prediction of gastric cancer in 457,521 European participants of the UK Biobank cohort.Finally,the performance of the fPRS in combination with lifestyle factors were evaluated in predicting the risk of gastric cancer.Results:During 4,582,045 person-years of follow-up with a total of 623 incident gastric cancer cases,we found no significant association between the PRS-112 and gastric cancer risk in the European population(hazard ratio[HR]=1.00[95%confidence interval(CI)0.93–1.09],P=0.846).We identified 125 fSNPs,including seven deleterious protein-coding SNPs and 118 regulatory non-coding SNPs,and used them to construct the fPRS-125.Our result showed that the fPRS-125 was significantly associated with gastric cancer risk(HR=1.11[95%CI,1.03–1.20],P=0.009).Compared to participants with a low fPRS-125(bottom quintile),those with a high fPRS-125(top quintile)had a higher risk of incident gastric cancer(HR=1.43[95%CI,1.12–1.84],P=0.005).Moreover,we observed that participants with both an unfavorable lifestyle and a high genetic risk had the highest risk of incident gastric cancer(HR=4.99[95%CI,1.55–16.10],P=0.007)compared to those with both a favorable lifestyle and a low genetic risk.Conclusion:These results indicate that the fPRS-125 derived from fSNPs may act as an indicator to measure the genetic risk of gastric cancer in the European population.展开更多
Introduction:The cost-effectiveness of vaccination strategies plays a crucial role in managing infectious diseases such as influenza within public health systems.This study evaluated the cost-effectiveness of vaccinat...Introduction:The cost-effectiveness of vaccination strategies plays a crucial role in managing infectious diseases such as influenza within public health systems.This study evaluated the cost-effectiveness of vaccination compliance strategies by comparing an“adherence”strategy,which promoted continuous vaccination uptake,with a“volunteer”strategy through model-based simulations.Methods:We developed a novel hybrid model that integrates continuous-time agent-based models(ABMs)with a Markov model to simulate vaccination behaviors and disease dynamics at the individual level.The model incorporated socioeconomic factors,vaccine efficacy,and population interactions to evaluate the long-term health outcomes and associated costs of different vaccination compliance strategies.Results:Simulation results demonstrated that the“adherence”strategy significantly enhanced vaccination coverage and reduced influenza cases,yielding an incremental cost-effectiveness ratio(ICER)of 33,847 CNY per quality-adjusted life year(QALY)gained,indicating superior cost-effectiveness compared to the“volunteer”strategy.Discussion:Our findings support implementing targeted influenza vaccination compliance strategies,presenting an innovative approach to strengthening public health interventions and enhancing vaccination program effectiveness.The hybrid model shows promise in informing public health policy and practice,warranting further investigation of its applications across diverse public health contexts.展开更多
What is already known about this topic?China is rapidly encountering population aging,yet studies on aging are limited by the traditional aging measure:chronological age,particularly in the field of genomics.Several p...What is already known about this topic?China is rapidly encountering population aging,yet studies on aging are limited by the traditional aging measure:chronological age,particularly in the field of genomics.Several promising aging measures have been proposed,but they lack comparative evaluation.展开更多
Although genome-wide association studies have identified more than eighty genetic variants associated with non-small cell lung cancer(NSCLC)risk,biological mechanisms of these variants remain largely unknown.By integr...Although genome-wide association studies have identified more than eighty genetic variants associated with non-small cell lung cancer(NSCLC)risk,biological mechanisms of these variants remain largely unknown.By integrating a large-scale genotype data of 15581 lung adenocarcinoma(AD)cases,8350 squamous cell carcinoma(SqCC)cases,and 27355 controls,as well as multiple transcriptome and epigenomic databases,we conducted histology-specific meta-analyses and functional annotations of both reported and novel susceptibility variants.We identified 3064 credible risk variants for NSCLC,which were overrepresented in enhancer-like and promoter-like histone modification peaks as well as DNase I hypersensitive sites.Transcription factor enrichment analysis revealed that USF1 was AD-specific while CREB1 was SqCC-specific.Functional annotation and genebased analysis implicated 894 target genes,including 274 specifics for AD and 123 for SqCC,which were overrepresented in somatic driver genes(ER=1.95,P=0.005).Pathway enrichment analysis and Gene-Set Enrichment Analysis revealed that AD genes were primarily involved in immune-related pathways,while SqCC genes were homologous recombination deficiency related.Our results illustrate the molecular basis of both wellstudied and new susceptibility loci of NSCLC,providing not only novel insights into the genetic heterogeneity between AD and SqCC but also a set of plausible gene targets for post-GWAS functional experiments.展开更多
Since late 2019,the beginning of coronavirus disease 2019(COVID-19)pandemic,transmission dynamics models have achieved great development and were widely used in predicting and policymaking.Here,we provided an introduc...Since late 2019,the beginning of coronavirus disease 2019(COVID-19)pandemic,transmission dynamics models have achieved great development and were widely used in predicting and policymaking.Here,we provided an introduction to the history of disease transmission,summarized transmission dynamics models into three main types:compartment extension,parameter extension and population-stratified extension models,highlight the key contribution of transmission dynamics models in COVID-19 pandemic:estimating epidemiological parameters,predicting the future trend,evaluating the effectiveness of control measures and exploring different possibilities/scenarios.Finally,we pointed out the limitations and challenges lie ahead of transmission dynamics models.展开更多
To the Editor:Preterm birth(PTB),defined as livebirth before 37 completed weeks of gestation,is associated with a high degree of immaturity of various organs,and thus are at greater risk.of a range of short-term and l...To the Editor:Preterm birth(PTB),defined as livebirth before 37 completed weeks of gestation,is associated with a high degree of immaturity of various organs,and thus are at greater risk.of a range of short-term and long-term comorbidities.[1]The estimated PTB prevalence in Bangladesh,already among the highest at 19.1%,[2] is even higher in rural areas in Bangladesh,[3]posing a significant economic and emotional burden to these families and the country.展开更多
基金supported by the National Natural Science Foundation of China(Grant Nos.82173620 to Yang Zhao and 82041024 to Feng Chen)partially supported by the Bill&Melinda Gates Foundation(Grant No.INV-006371 to Feng Chen)Priority Academic Program Development of Jiangsu Higher Education Institutions.
文摘Deterministic compartment models(CMs)and stochastic models,including stochastic CMs and agent-based models,are widely utilized in epidemic modeling.However,the relationship between CMs and their corresponding stochastic models is not well understood.The present study aimed to address this gap by conducting a comparative study using the susceptible,exposed,infectious,and recovered(SEIR)model and its extended CMs from the coronavirus disease 2019 modeling literature.We demonstrated the equivalence of the numerical solution of CMs using the Euler scheme and their stochastic counterparts through theoretical analysis and simulations.Based on this equivalence,we proposed an efficient model calibration method that could replicate the exact solution of CMs in the corresponding stochastic models through parameter adjustment.The advancement in calibration techniques enhanced the accuracy of stochastic modeling in capturing the dynamics of epidemics.However,it should be noted that discrete-time stochastic models cannot perfectly reproduce the exact solution of continuous-time CMs.Additionally,we proposed a new stochastic compartment and agent mixed model as an alternative to agent-based models for large-scale population simulations with a limited number of agents.This model offered a balance between computational efficiency and accuracy.The results of this research contributed to the comparison and unification of deterministic CMs and stochastic models in epidemic modeling.Furthermore,the results had implications for the development of hybrid models that integrated the strengths of both frameworks.Overall,the present study has provided valuable epidemic modeling techniques and their practical applications for understanding and controlling the spread of infectious diseases.
基金supported by the National Natural Science Foundation of China (Projects No. 82173620to Y.Z. and 82204156 to D.Y.)Priority Academic Program Development of Jiangsu Higher Education Institution
文摘Diet/sugar-free soft drinks are considered to be healthier than regular soft drinks.However,few studies have examined the relationship between the types of soft drinks(regular and diet/sugar-free)and lung cancer(LC)/all-cancer(AC)risk.In this study,we comprehensively assessed the influence of the type of soft drink consumption on LC/AC risk based on the Prostate,Lung,Colorectal,and Ovarian(PLCO)Cancer Screening Trial.Multivariable Cox proportional hazards and competing risks Fine-Gray regression models adjusted for relevant confounders were used to estimate hazard ratios(HRs)and subdistribution HRs for different types of soft drink consumption.In the PLCO population,female subgroup,and the ever/current smoker subgroup,consumption of both regular and diet soft drinks was associated with a significantly reduced risk of LC compared with no soft drinks at all.For the non-lung cancer(NLC)risk,consumption of only diet soft drinks had a significant positive association for the total population and female subgroup.Based on our findings,it was suggested that partial replacement of regular soft drinks with diet soft drinks might be beneficial to LC prevention,especially for females and ever/current smokers.Additionally,completely replacing regular soft drinks with diet soft drinks might be detrimental to NLC prevention,especially for females.
基金supported by National Natural Science Foundation of China(82125033,81872702,82103932,82003534)Natural Science Foundation of Jiangsu Province(BK20200674).
文摘To investigate whether genetic variants may provide additional prognostic value to improve the existing clinical staging system for gastric cancer(GC),we performed two genome-wide association studies(GWASs)of GC survival in the Jiangsu(N=1049)and Shanghai(N=1405)cohorts.By using a TCGA dataset,we validated genetic markers identified from a meta-analysis of these two Chinese cohorts to determine GC survival-associated loci.Then,we constructed a weighted polygenic hazard score(PHS)and developed a nomogram in combination with clinical variables.We also evaluated prognostic accuracy with the time-dependent receiver operating characteristic(ROC)curve,net reclassification improvement(NRI)and integrated discrimination improvement(IDI).We identified a single nucleotide polymorphism(SNP)of rs1618332 at 15q15.1 that was associated with the survival of GC patients with a P value of 4.12×10^(-8),and we also found additional 25 SNPs having consistent associations among these two Chinese cohort and TCGA cohort.The PHS derived from these 26 SNPs(PHS-26)was an independent prognostic factor for GC survival(all P<0.001).The 5-year AUC of PHS-26 was 0.68,0.66 and 0.67 for Jiangsu,Shanghai and their pooled cohorts,respectively,which increased to 0.80,0.82 and 0.81,correspondingly,after being integrated into a nomogram together with variables of the clinical model.The PHS-26 could improve the NRIs by 16.20%,4.90%and 8.70%,respectively,and the IDIs by 11.90%,8.00%and 9.70%,respectively.The 26-SNP based PHS could substantially improve the accuracy of prognostic assessment and might facilitate precision medicine for GC patients.
基金supported by grants from the National Natural Science Foundation of China(Nos.82125033,82230110,81872702,82003534,and 82273714)the Natural Science Foundation of Jiangsu Province(No.BK20200674)CAMS Innovation Fund for Medical Sciences(No.2019RU038).
文摘Background:A polygenic risk score(PRS)derived from 112 single-nucleotide polymorphisms(SNPs)for gastric cancer has been reported in Chinese populations(PRS-112).However,its performance in other populations is unknown.A functional PRS(fPRS)using functional SNPs(fSNPs)may improve the generalizability of the PRS across populations with distinct ethnicities.Methods:We performed functional annotations on SNPs in strong linkage disequilibrium(LD)with the 112 previously reported SNPs to identify fSNPs that affect protein-coding or transcriptional regulation.Subsequently,we constructed an fPRS based on the fSNPs by using the LDpred2-infinitesimal model and then analyzed the performance of the PRS-112 and fPRS in the risk prediction of gastric cancer in 457,521 European participants of the UK Biobank cohort.Finally,the performance of the fPRS in combination with lifestyle factors were evaluated in predicting the risk of gastric cancer.Results:During 4,582,045 person-years of follow-up with a total of 623 incident gastric cancer cases,we found no significant association between the PRS-112 and gastric cancer risk in the European population(hazard ratio[HR]=1.00[95%confidence interval(CI)0.93–1.09],P=0.846).We identified 125 fSNPs,including seven deleterious protein-coding SNPs and 118 regulatory non-coding SNPs,and used them to construct the fPRS-125.Our result showed that the fPRS-125 was significantly associated with gastric cancer risk(HR=1.11[95%CI,1.03–1.20],P=0.009).Compared to participants with a low fPRS-125(bottom quintile),those with a high fPRS-125(top quintile)had a higher risk of incident gastric cancer(HR=1.43[95%CI,1.12–1.84],P=0.005).Moreover,we observed that participants with both an unfavorable lifestyle and a high genetic risk had the highest risk of incident gastric cancer(HR=4.99[95%CI,1.55–16.10],P=0.007)compared to those with both a favorable lifestyle and a low genetic risk.Conclusion:These results indicate that the fPRS-125 derived from fSNPs may act as an indicator to measure the genetic risk of gastric cancer in the European population.
基金Supported by the National Natural Science Foundation of China(Project Nos.82473732 to Fang Shao,82404383 to Mengyi Lu,82173620 and 82373690 to Yang Zhao,and 82204156 to Dongfang You)Additional funding was provided through the Priority Academic Program Development of Jiangsu Higher Education Institutions(PAPD)The study also received partial support from the Bill&Melinda Gates Foundation(Project No.INV-006371 to Feng Chen).
文摘Introduction:The cost-effectiveness of vaccination strategies plays a crucial role in managing infectious diseases such as influenza within public health systems.This study evaluated the cost-effectiveness of vaccination compliance strategies by comparing an“adherence”strategy,which promoted continuous vaccination uptake,with a“volunteer”strategy through model-based simulations.Methods:We developed a novel hybrid model that integrates continuous-time agent-based models(ABMs)with a Markov model to simulate vaccination behaviors and disease dynamics at the individual level.The model incorporated socioeconomic factors,vaccine efficacy,and population interactions to evaluate the long-term health outcomes and associated costs of different vaccination compliance strategies.Results:Simulation results demonstrated that the“adherence”strategy significantly enhanced vaccination coverage and reduced influenza cases,yielding an incremental cost-effectiveness ratio(ICER)of 33,847 CNY per quality-adjusted life year(QALY)gained,indicating superior cost-effectiveness compared to the“volunteer”strategy.Discussion:Our findings support implementing targeted influenza vaccination compliance strategies,presenting an innovative approach to strengthening public health interventions and enhancing vaccination program effectiveness.The hybrid model shows promise in informing public health policy and practice,warranting further investigation of its applications across diverse public health contexts.
基金Supported by the National Natural Science Foundation of China(Grant ID:81941020,82192903,82192904)the Science Fund for Distinguished Young Scholars of Jiangsu Province(BK20211533)+1 种基金the Natural Science Foundation of Jiangsu Province(BK20221183)the Nanjing Medical Science and Technique Development Foundation(JQX18009).
文摘What is already known about this topic?China is rapidly encountering population aging,yet studies on aging are limited by the traditional aging measure:chronological age,particularly in the field of genomics.Several promising aging measures have been proposed,but they lack comparative evaluation.
基金the Key International(Regional)Cooperative Research Project(No.81820108028)the National Natural Science Foundation of China(Nos.81521004,81922061,81973123,and 81803306)+2 种基金the Science Foundation for Distinguished Young Scholars of Jiangsu(No.BK20160046)the Priority Academic Program for the Development of Jiangsu Higher Education Institutions(Public Health and Preventive Medicine).the National Cancer Institute,National Institutes of Health of USA through grants U01-CA063673,UM1-CA167462,and U01-CA167462.
文摘Although genome-wide association studies have identified more than eighty genetic variants associated with non-small cell lung cancer(NSCLC)risk,biological mechanisms of these variants remain largely unknown.By integrating a large-scale genotype data of 15581 lung adenocarcinoma(AD)cases,8350 squamous cell carcinoma(SqCC)cases,and 27355 controls,as well as multiple transcriptome and epigenomic databases,we conducted histology-specific meta-analyses and functional annotations of both reported and novel susceptibility variants.We identified 3064 credible risk variants for NSCLC,which were overrepresented in enhancer-like and promoter-like histone modification peaks as well as DNase I hypersensitive sites.Transcription factor enrichment analysis revealed that USF1 was AD-specific while CREB1 was SqCC-specific.Functional annotation and genebased analysis implicated 894 target genes,including 274 specifics for AD and 123 for SqCC,which were overrepresented in somatic driver genes(ER=1.95,P=0.005).Pathway enrichment analysis and Gene-Set Enrichment Analysis revealed that AD genes were primarily involved in immune-related pathways,while SqCC genes were homologous recombination deficiency related.Our results illustrate the molecular basis of both wellstudied and new susceptibility loci of NSCLC,providing not only novel insights into the genetic heterogeneity between AD and SqCC but also a set of plausible gene targets for post-GWAS functional experiments.
基金the National Natural Science Foundation of China(No.82041024 to F.C.,81973142 to Y.W.)the Bill&Melinda Gates Foundation(Investment ID:INV-006371).
文摘Since late 2019,the beginning of coronavirus disease 2019(COVID-19)pandemic,transmission dynamics models have achieved great development and were widely used in predicting and policymaking.Here,we provided an introduction to the history of disease transmission,summarized transmission dynamics models into three main types:compartment extension,parameter extension and population-stratified extension models,highlight the key contribution of transmission dynamics models in COVID-19 pandemic:estimating epidemiological parameters,predicting the future trend,evaluating the effectiveness of control measures and exploring different possibilities/scenarios.Finally,we pointed out the limitations and challenges lie ahead of transmission dynamics models.
基金This study was supported by grants from the State's Key Project of Research and Development Program(No.2016YFE0204900)the U.S.National Institute of Envi-ronmental Health Sciences(NIEHS)of the National Institutes of Health(NIH)grant(No.R01 ES015533)+3 种基金National Natural Science Foundation of China(No.81530088)the Key International(Regional)Cooperative Research Project(No.81820108028)National Key Research and Development Program of China(No.2018YFC0910500)the Priority Academic Program Development of Jjiangsu Higher Education Institutions.Sponsors had no role in the design of the study,the collection and analysis of data,or the preparation of the manuscript.
文摘To the Editor:Preterm birth(PTB),defined as livebirth before 37 completed weeks of gestation,is associated with a high degree of immaturity of various organs,and thus are at greater risk.of a range of short-term and long-term comorbidities.[1]The estimated PTB prevalence in Bangladesh,already among the highest at 19.1%,[2] is even higher in rural areas in Bangladesh,[3]posing a significant economic and emotional burden to these families and the country.
