Thalamic volume alterations mediate glymphatic function and cognitive dysfunction in Alzheimer's disease.
The 5 matches
- [1] § RESULTS › Significant mediation of thalamic nucleus in the ALPS index and cognition ↔ 中介效应分析代码11-4更新.R, lines 269–313 · score 0.87 · ltAV, ltLP, ltMDl, rtMDl, ltMDm, ltVL
- [2] § RESULTS › ALPS‐related GM clusters ↔ 中介效应分析代码11-4更新.R, lines 269–313 · score 0.85 · ltAV, ltLP, ltMDl, rtMDl, ltMDm, ltVL
- [3] § RESULTS › Significant mediation of thalamic nucleus in the ALPS index and cognition ↔ 中介效应分析代码11-4更新.R, lines 216–267 · score 0.74 · ltMDm, ltVL, rtAV, rtMDm, rtVL, rtLP
- [4] § METHODS › Confirmatory factor analysis ↔ 1.R, lines 52–96 · score 0.69 · DSTback, N1N3, N4, N5, Stroop, BNT
- [5] § METHODS › Confirmatory factor analysis ↔ 1.R, lines 98–164 · score 0.66 · VFT, CFA, CFI, RMSEA, SRMR, TLI
Paper
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The authors' code
R · 391 lines · 15 KB · no license · 3 matches
- setwd("E:/ALPS/ALPS/mediation")
- library("mediation")
- data<-read.csv("ADNIdata需要统计的数据-mci59.csv")
- #### 6.加入协变量的线性回归中介效应分析
- # 设置随机种子
- set.seed(12345)
- # 按照lm(m ~ x + 协变量1 + 协变量2)格式加入协变量即可+ AGE + PTGENDER + PTEDUCAT +TIV(加上结果就更不显著了)
- mx = lm(rtLP ~ ALPS + AGE + PTGENDER+ PTEDUCAT, data = data)
- # 按照lm(y ~ x + m + 协变量1 + 协变量2)格式加入协变量即可
- ##左右丘脑显著
- yx = lm(ADNI_LAN ~ ALPS +rtLP+AGE + PTGENDER+ PTEDUCAT, data = data)
- mediate = mediate(mx, yx,
- treat = 'ALPS', # 处理变量(自变量),X
- mediator = 'rtLP', # 中介变量,这里为M
- sims = 1000, # 重抽样次数1000次
- boot = TRUE) # 是否使用引导法(Bootstrap)进行重抽样,这里设置为TRUE(使用引导法)
- summary(mediate)
- #ACME表示average causal mediation effects (indirect effect),即间接效应,
- #ADE为average direct effects,即直接效应。
- #total effect为总的效应。
- #Prop.mediated为中介变量解释X与Y间关联所占的百分比。
- plot(mediate)
- #右图,线都与0线交叉显示结果无统计学意义。
- lmreg1<-lm(ADNI_LAN~ ALPS+AGE+PTGENDER+PTEDUCAT+factor(APOE4), data=data)
- summary(lmreg1)
- ##批量中介
- #### 7.批量中介效应分析####
- # 定义一个名为 "TS" 的引用类,并指定字段列表
- setRefClass("TS",
- fields = list(
- m = "character", # 中介变量名
- x = "character", # 处理变量名
- xm = "formula", # 中介模型公式
- xy = "formula" # 结果模型公式
- ))
- # 创建一个 "TS" 类的新实例
- test <- new("TS")
- # 定义一个函数,用于批量中介分析
- batch_mediate <- function(ms, y, xs, df) {
- # 设置中介变量名
- test$m <- ms
- # 设置处理变量名
- test$x <- xs
- # 创建中介模型公式
- test$xm <- as.formula(paste0(ms, "~", xs, "+ AGE + PTGENDER + PTEDUCAT + APOE4"))
- # 拟合中介模型
- model_xm <- lm(test$xm, data = df)
- # 创建结果模型公式
- test$xy <- as.formula(paste0(y, "~", ms, "+", xs, "+ AGE + PTGENDER + PTEDUCAT + APOE4"))
- # 拟合结果模型
- model_xy <- lm(test$xy, data = df)
- # 进行中介分析
- model_med <- mediate(model_xm,
- model_xy,
- treat = test$x,
- mediator = test$m,
- sims = 1000, # 设置模拟次数为1000次
- boot = TRUE) # 使用引导法(Bootstrap)进行重抽样
- # 获取中介分析的摘要结果
- med_sum <- summary(model_med)
- # 提取ACME(平均因果中介效应)及其P值
- ACME <- med_sum$d0
- ACME_P <- med_sum$d0.p
- ACME_CI <- med_sum$d0.ci
- # 提取ADE(平均直接效应)及其P值
- ADE <- med_sum$z0
- ADE_P <- med_sum$z0.p
- ADE_CI <- med_sum$z0.ci
- # 计算总效应(Total Effect)
- TE <- (ACME + ADE)
- # 计算总效应的P值
- # 这里我们假设使用bootstrap p-value,通常在summary中获得
- TE_P <- med_sum$tau.p
- # 计算中介效应所占比例
- Prop_Mediated <- ACME / TE
- # 将结果存储在数据框中
- result <- data.frame(
- 'Characteristics' = ms, # 中介变量名
- 'ACME' = ACME, # 平均因果中介效应
- 'ACME_P' = ACME_P, # 平均因果中介效应的P值
- 'ACME_95CI_lower' = ACME_CI[1], # ACME的95%CI下限
- 'ACME_95CI_upper' = ACME_CI[2], # ACME的95%CI上限
- 'ADE' = ADE, # 平均直接效应
- 'ADE_P' = ADE_P, # 平均直接效应的P值
- 'ADE_95CI_lower' = ADE_CI[1], # ADE的95%CI下限
- 'ADE_95CI_upper' = ADE_CI[2], # ADE的95%CI上限
- 'Total_Effect' = TE, # 总效应
- 'Total_Effect_P' = TE_P, # 总效应的P值
- 'Prop_Mediated' = Prop_Mediated) # 中介效应所占比例
- # 返回结果
- return(result)}
- #### 8.批量中介效应分析的具体应用
- # 设置需要探索是否为中介变量M的列名
- #"ltLP", "rtLP",
- #"lSMG", "rSMG",
- #"lROL", "rROL",
- #"lSTG","rSTG",
- #"lHES","rHES",
- #"ltAV","rtAV",
- #"ltVL","rtVL",
- #"ltMDm","rtMDm",
- #"ltMDl","rtMDl",
- #"lMTG","rMTG"
- cols <-c("ltLP", "rtLP",
- "ltAV","rtAV",
- "ltVL","rtVL",
- "ltMDm","rtMDm",
- "ltMDl","rtMDl")
- # 设置随机种子
- set.seed(12345)
- #ADNI_EF2 #ADNI_LAN #ADNI_MEM #ADNI_VS
- # 使用lapply函数对列列表(cols)中的每一列应用batch_mediate函数
- res2 <- lapply(cols, # 遍历列列表(cols)
- batch_mediate, # 应用batch_mediate函数
- y = "ADNI_VS", # y参数设为因变量名"status"
- x = "ALPS", # x参数设为自变量名"age"
- df = data) # df参数设为数据框data
- # 生成结果
- library("plyr")
- res2 <- ldply(res2,data.frame)
- View(res2)
- #####9.保存数据
- write.csv(res2, file = "adni_ADNI_VS_mediation.csv", row.names = FALSE)
- ##### 10.各个中介变量的值
- #"ltLP", "rtLP", "ltAV","rtAV",
- #"ltVL","rtVL","ltMDm","rtMDm","ltMDl","rtMDl",
- #a
- lmreg1<-lm(ltLP~ ALPS+AGE+PTGENDER+PTEDUCAT+factor(APOE4), data=data)
- summary(lmreg1)
- #b
- lmreg2<-lm(ADNI_EF2~ ltLP+AGE+PTGENDER+PTEDUCAT+factor(APOE4), data=data)
- summary(lmreg2)
- #c'
- lmreg3<-lm(ADNI_EF2~ ALPS+ltLP+AGE+PTGENDER+PTEDUCAT+factor(APOE4), data=data)
- summary(lmreg3)
- #c
- lmreg4<-lm(ADNI_EF2~ ALPS+AGE+PTGENDER+PTEDUCAT+factor(APOE4), data=data)
- summary(lmreg4)
- ####8. 批量中介 中日的数据####
- library(openxlsx)
- data1<-read.xlsx("中日用来进行分析的数据-优化版本.xlsx")
- #data1<-read.xlsx("中日用来进行分析的数据.xlsx")
- # 定义一个名为 "TS" 的引用类,并指定字段列表
- setRefClass("TS",
- fields = list(
- m = "character", # 中介变量名
- x = "character", # 处理变量名
- xm = "formula", # 中介模型公式
- xy = "formula" # 结果模型公式
- ))
- # 创建一个 "TS" 类的新实例
- test <- new("TS")
- # 定义一个函数,用于批量中介分析
- batch_mediate <- function(ms, y, xs, df) {
- # 设置中介变量名
- test$m <- ms
- # 设置处理变量名
- test$x <- xs
- # 创建中介模型公式
- test$xm <- as.formula(paste0(ms, "~", xs, "+ AGE + SEX + EDU+APOE4"))
- # 拟合中介模型
- model_xm <- lm(test$xm, data = df)
- # 创建结果模型公式
- test$xy <- as.formula(paste0(y, "~", ms, "+", xs, "+ AGE + SEX + EDU+APOE4"))
- # 拟合结果模型
- model_xy <- lm(test$xy, data = df)
- # 进行中介分析
- model_med <- mediate(model_xm,
- model_xy,
- treat = test$x,
- mediator = test$m,
- sims = 1000, # 设置模拟次数为1000次
- boot = TRUE) # 使用引导法(Bootstrap)进行重抽样
- # 获取中介分析的摘要结果
- med_sum <- summary(model_med)
- # 提取ACME(平均因果中介效应)及其P值
- ACME <- med_sum$d0
- ACME_P <- med_sum$d0.p
- ACME_CI <- med_sum$d0.ci
- # 提取ADE(平均直接效应)及其P值
- ADE <- med_sum$z0
- ADE_P <- med_sum$z0.p
- ADE_CI <- med_sum$z0.ci
- # 计算总效应(Total Effect)
- TE <- (ACME + ADE)
- # 计算总效应的P值
- # 这里我们假设使用bootstrap p-value,通常在summary中获得
- TE_P <- med_sum$tau.p
- # 计算中介效应所占比例
- Prop_Mediated <- ACME / TE
- # 将结果存储在数据框中
- result <- data.frame(
- 'Characteristics' = ms, # 中介变量名
- 'ACME' = ACME, # 平均因果中介效应
- 'ACME_P' = ACME_P, # 平均因果中介效应的P值
- 'ACME_95CI_lower' = ACME_CI[1], # ACME的95%CI下限
- 'ACME_95CI_upper' = ACME_CI[2], # ACME的95%CI上限
- 'ADE' = ADE, # 平均直接效应
- 'ADE_P' = ADE_P, # 平均直接效应的P值
- 'ADE_95CI_lower' = ADE_CI[1], # ADE的95%CI下限
- 'ADE_95CI_upper' = ADE_CI[2], # ADE的95%CI上限
- 'Total_Effect' = TE, # 总效应
- 'Total_Effect_P' = TE_P, # 总效应的P值
- 'Prop_Mediated' = Prop_Mediated) # 中介效应所占比例
- # 返回结果
- return(result)}
- # 设置需要探索是否为中介变量M的列名
- cols <-c("ltLP", "rtLP",
- "ltAV","rtAV",
- "ltVL","rtVL",
- "ltMDm","rtMDm",
- "ltMDl","rtMDl")
- # 设置随机种子
- set.seed(12345)
- #execution #language #visuo #memory
- # 使用lapply函数对列列表(cols)中的每一列应用batch_mediate函数
- res4<- lapply(cols, # 遍历列列表(cols)
- batch_mediate, # 应用batch_mediate函数
- y = "memory", # y参数设为因变量
- x = "ALPS", # x参数设为自变量
- df = data1) # df参数设为数据框data
- # 生成结果
- library("plyr")
- res4 <- ldply(res4,data.frame)
- View(res4)
- #保存结果
- write.csv(res4, file = "hospital_visuo_mediation.csv", row.names = FALSE)
- res5<- lapply(cols, # 遍历列列表(cols)
- batch_mediate, # 应用batch_mediate函数
- y = "memory", # y参数设为因变量名"status"
- x = "ALPS", # x参数设为自变量名"age"
- df = data1) # df参数设为数据框data
- # 生成结果
- library("plyr")
- res5 <- ldply(res5,data.frame)
- View(res5)
- ###中日数据保存
- write.csv(res5, file = "ALPSHospitalMemory.csv", row.names = FALSE)
- data1$SEX <- factor(data1$SEX)
- mx = lm(rtMDl ~ ALPS+ AGE + SEX + EDU + APOE4, data = data1)
- # 按照lm(y ~ x + m + 协变量1 + 协变量2)格式加入协变量即可
- #左右丘脑显著 #language #execution #visuo#memory
- yx = lm(execution ~ ALPS +rtMDl+ AGE+ SEX + EDU + APOE4, data = data1)
- mediate = mediate(mx, yx,
- treat = 'ALPS', # 处理变量(自变量),X
- mediator = 'rtMDl', # 中介变量,这里为M
- sims =1000, # 重抽样次数1000次
- boot = TRUE) # 是否使用引导法(Bootstrap)进行重抽样,这里设置为TRUE(使用引导法)
- summary(mediate)
- #language #execution #visuo#memory
- model1<- lm(visuo ~ ALPS + AGE + factor(SEX) + EDU +factor(APOE4),data=data1)
- summary(model1)
- #####三、合并数据进行分析,结果显著####
- ######3.1 处理数据#####
- library(dplyr)
- df_ADNI <- data %>%
- select(PTID, AGE, PTGENDER, PTEDUCAT, TIV, APOE4,
- ADNI_MEM, ADNI_LAN, ADNI_VS, ADNI_EF2,
- ALPS, group, lROL, rROL, lSMG, rSMG,
- lHES, rHES, lSTG, rSTG, ltAV, rtAV, ltLP, rtLP,
- ltVL, rtVL, ltMDm, rtMDm, ltMDl, rtMDl, lMTG, rMTG)
- #重命名列
- df_ADNI <- df_ADNI %>%
- rename(SEX = PTGENDER,
- EDU = PTEDUCAT,
- GROUP = group,
- execution=ADNI_EF2,
- language=ADNI_LAN,
- visuo=ADNI_VS,
- memory=ADNI_MEM)
- df_hospital<- data1 %>%
- select(PTID, AGE, SEX, EDU, TIV, APOE4,GROUP,
- execution,language,visuo,memory,
- ALPS, lROL, rROL, lSMG, rSMG,
- lHES, rHES, lSTG, rSTG, ltAV, rtAV, ltLP, rtLP,
- ltVL, rtVL, ltMDm, rtMDm, ltMDl, rtMDl, lMTG, rMTG)
- df_hospital <- df_hospital %>%
- mutate(SEX = recode(SEX, "女" = "Female", "男" = "Male"))
- head(df_ADNI)
- head(df_hospital)
- combined_df <- bind_rows(df_ADNI, df_hospital) #合并数据
- ######3.2 进行批量中介分析#####
- setRefClass("TS",
- fields = list(
- m = "character", # 中介变量名
- x = "character", # 处理变量名
- xm = "formula", # 中介模型公式
- xy = "formula" # 结果模型公式
- ))
- # 创建一个 "TS" 类的新实例
- test <- new("TS")
- # 定义一个函数,用于批量中介分析
- batch_mediate <- function(ms, y, xs, df) {
- # 设置中介变量名
- test$m <- ms
- # 设置处理变量名
- test$x <- xs
- # 创建中介模型公式
- test$xm <- as.formula(paste0(ms, "~", xs, "+ AGE + SEX + EDU+APOE4"))
- # 拟合中介模型
- model_xm <- lm(test$xm, data = df)
- # 创建结果模型公式
- test$xy <- as.formula(paste0(y, "~", ms, "+", xs, "+ AGE + SEX + EDU+APOE4"))
- # 拟合结果模型
- model_xy <- lm(test$xy, data = df)
- # 进行中介分析
- model_med <- mediate(model_xm,
- model_xy,
- treat = test$x,
- mediator = test$m,
- sims = 1000, # 设置模拟次数为1000次
- boot = TRUE) # 使用引导法(Bootstrap)进行重抽样
- # 获取中介分析的摘要结果
- med_sum <- summary(model_med)
- # 提取ACME(平均因果中介效应)及其P值
- ACME <- med_sum$d0
- ACME_P <- med_sum$d0.p
- # 提取ADE(平均直接效应)及其P值
- ADE <- med_sum$z0
- ADE_P <- med_sum$z0.p
- # 计算总效应(Total Effect)
- TE <- (ACME + ADE)
- # 计算总效应的P值
- # 这里我们假设使用bootstrap p-value,通常在summary中获得
- TE_P <- med_sum$tau.p
- # 计算中介效应所占比例
- Prop_Mediated <- ACME / TE
- # 将结果存储在数据框中
- result <- data.frame(
- 'Characteristics' = ms, # 中介变量名
- 'ACME' = ACME, # 平均因果中介效应
- 'ACME_P' = ACME_P, # 平均因果中介效应的P值
- 'ADE' = ADE, # 平均直接效应
- 'ADE_P' = ADE_P, # 平均直接效应的P值
- 'Total_Effect' = TE, # 总效应
- 'Total_Effect_P' = TE_P, # 总效应的P值
- 'Prop_Mediated' = Prop_Mediated) # 中介效应所占比例
- # 返回结果
- return(result)}
- # 设置需要探索是否为中介变量M的列名
- cols <-c("ltLP", "rtLP",
- "lSMG", "rSMG",
- "lROL", "rROL",
- "lSTG","rSTG",
- "lHES","rHES",
- "ltAV","rtAV",
- "ltVL","rtVL",
- "ltMDm","rtMDm",
- "ltMDl","rtMDl",
- "lMTG","rMTG")
- # 设置随机种子
- set.seed(12345)
- #execution #language #visuo #memory
- # 使用lapply函数对列列表(cols)中的每一列应用batch_mediate函数
- res<- lapply(cols, # 遍历列列表(cols)
- batch_mediate, # 应用batch_mediate函数
- y = "memory", # y参数设为因变量名"status"
- x = "ALPS", # x参数设为自变量名"age"
- df = combined_df) # df参数设为数据框data
- # 生成结果
- library("plyr")
- res <- ldply(res,data.frame)
- View(res)
- ###结果显著
- model1 <-lm(execution~ALPS+AGE+factor(SEX)+EDU+APOE4,data=combined_df)
- summary(model1)
中介效应分析代码11-4更新.R, no license · at the source
Overview
- Epilepsy Center, Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
- Department of Neurology, Peking University First Hospital, Peking University, Beijing, China
- Peking University China‐Japan Friendship School of Clinical Medicine, Beijing, China
- Department of Neurology, China‐Japan Friendship Hospital, Beijing, China
Abstract
INTRODUCTION: Glymphatic dysfunction is implicated in Alzheimer's disease (AD), but its mechanism remains unclear. This study investigated the associations of the analysis along the perivascular space (ALPS) index, brain reserve, and cognitive outcomes across the AD continuum.
METHODS: This study enrolled two cohorts from the local hospital (n = 95) and the Alzheimer's Disease Neuroimaging Initiative (ADNI; n = 178). We calculated the diffusion tensor image ALPS to assess the whole‐brain glymphatic function and evaluated its associations with cognition and brain structure.
RESULTS: A higher ALPS index was positively associated with better executive, memory, and language abilities (p < 0.05). A lower ALPS index correlated with thalamic atrophy, involving the anterior, lateral, ventral, and midline thalamic nuclei. Thalamic atrophy mediated the link between glymphatic dysfunction and worse cognition via structural association of full or part mediation.
CONCLUSIONS: Glymphatic system deterioration correlates with cognitive decline, potentially mediated by thalamic atrophy. The thalamic nuclei may be critical in this pathway.
Reproduced under the paper's license (CC BY-NC), from the paper cited above.
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- Funding: added National Natural Science Foundation of China: 2022ZD0213300, 82201570
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Recorded: type, language, journal, volume, issue, pages, dates, 7 authors, 5 keywords, 48 references.
Cite
This paper
Chen, L., Zhou, X., Zhang, B., Hou, Y., Sun, Y., Peng, D., & for the Alzheimer's Disease Neuroimaging Initiative (ADNI). (2026). Thalamic volume alterations mediate glymphatic function and cognitive dysfunction in Alzheimer's disease. Alzheimer's & dementia (New York, N. Y.), 12(3), e70304. https://
BibTeX
@article{chen2026thalami
author = {Chen, Leian and Zhou, Xiao and Zhang, Bin and Hou, Ying and Sun, Yu and Peng, Dantao and {for the Alzheimer's Disease Neuroimaging Initiative (ADNI)}},
title = {{Thalamic volume alterations mediate glymphatic function and cognitive dysfunction in Alzheimer's disease}},
journal = {Alzheimer's \& dementia (New York, N. Y.)},
year = {2026},
month = jul,
volume = {12},
number = {3},
pages = {e70304},
publisher = {Wiley},
issn = {2352-8737},
doi = {10.1002/
url = {https://
pmid = {42564689},
pmcid = {PMC13445249}
}
RIS
TY - JOUR
AU - Chen, Leian
AU - Zhou, Xiao
AU - Zhang, Bin
AU - Hou, Ying
AU - Sun, Yu
AU - Peng, Dantao
AU - for the Alzheimer's Disease Neuroimaging Initiative (ADNI)
TI - Thalamic volume alterations mediate glymphatic function and cognitive dysfunction in Alzheimer's disease
T2 - Alzheimer's & dementia (New York, N. Y.)
J2 - Alzheimers Dement (N Y)
PY - 2026
DA - 2026/
VL - 12
IS - 3
SP - e70304
SN - 2352-8737
PB - Wiley
DO - 10.1002/
UR - https://
LA - en
ER -
CSL-JSON
{
"id": "10.1002/
"type": "article-journal",
"title": "Thalamic volume alterations mediate glymphatic function and cognitive dysfunction in Alzheimer's disease",
"container-title": "Alzheimer's & dementia (New York, N. Y.)",
"author": [
{
"family": "Chen",
"given": "Leian"
},
{
"family": "Zhou",
"given": "Xiao"
},
{
"family": "Zhang",
"given": "Bin"
},
{
"family": "Hou",
"given": "Ying"
},
{
"family": "Sun",
"given": "Yu"
},
{
"family": "Peng",
"given": "Dantao"
},
{
"literal": "for the Alzheimer's Disease Neuroimaging Initiative (ADNI)"
}
],
"container-title-short":
"volume": "12",
"issue": "3",
"page": "e70304",
"DOI": "10.1002/
"PMID": "42564689",
"PMCID": "PMC13445249",
"ISSN": "2352-8737",
"publisher": "Wiley",
"URL": "https://
"language": "en",
"issued": {
"date-parts": [
[
2026,
7,
1
]
]
}
}
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