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Biology subjects

Tu, X. M.

Publications and source records attributed to Tu, X. M..

6 recordsLinked to original sources

U-statistics-based Pairwise Discordance Regression for Joint Mean-Variability Inference in Longitudinal Studies with Missing Data

Longitudinal studies are central to scientific inquiry across disciplines; yet, statistical analyses have predominantly focused on mean trajectories while treating variability as a secondary or nuisance component. Increasing evidence suggests that temporal variability and heterogeneity themselves encode critical scientific information, particularly in studies with repeated measurements, heterogeneous populations, or rich covariate structures. The classical mixed-effects and location-scale model family represents variability through latent variable components but relies on strong parametric assumptions and often requires numerical approximation or computationally intensive estimation. Here we introduce the semiparametric pairwise discordance regression, a unified framework for longitudinal data that directly models pairwise contrasts to simultaneously characterize mean trajectories, between-subject heterogeneity, and within-subject temporal variability. By targeting pairwise discordances rather than latent variance components, the proposed approach enables robust inference without specifying full parametric distributions for latent components or error terms, provided the specified conditional moment restrictions hold. Pair-level covariate encodings further accommodate flexible covariate structures and allow variability parameters to be interpreted through pairwise contrasts or dissimilarities. Estimation and inference are carried out via (weighted) U-statistic-based generalized estimating equations (UGEE) with a valid sandwich variance estimator, and we extend the fitting procedure to accommodate missing-at-random dropout. We establish the asymptotic distributions of the resulting estimators under mild regularity conditions. Simulation studies demonstrate reliable finite-sample performance in the settings considered, including non-Gaussian errors and misspecified working correlation structures, whereas likelihood-based parametric fits can be sensitive to distributional assumptions or numerically unstable. An application to longitudinal blood pressure during pregnancy illustrates the framework on real data.

bioinformatics↗

Regression-based Modeling of Spearman's Rho for Longitudinal Metabolomics and Mental Wellness in Breast Cancer Patients

SO_SCPLOWUMMARYC_SCPLOWChemotherapy in breast cancer (BC) can substantially affect mental wellness. Advances in metabolomics enable comprehensive profiling of metabolic changes over time during and after treatment, offering insights into biological mechanisms linking chemotherapy to mental health outcomes. To study the association between metabolite profiles and mental wellness, correlation-based analyses are particularly useful. Spearmans rho is a widely used correlation measure and popular alternative to Pearsons correlation, since it also applies to non-linear association between variables. However, existing methods are not designed for longitudinal data and do not allow for covariate adjustments. In this paper, we propose a novel regression-based framework grounded in a class of semiparametric models, the functional response models, to extend this popular correlation measure to longitudinal settings with missing data under the missing at random assumption. This framework facilitates inferences about temporal changes in correlations over time and association of explanatory variables for such changes. We use simulation studies to evaluate performance of the approach with moderate sample sizes. We apply the approach to a one-year longitudinal substudy of the EPIGEN study to examine the longitudinal association between metabolite profiles and mental wellness in BC patients undergoing chemotherapy. The identified metabolites may serve as candidates for future in-depth bioinformatics analyses and translational investigations.

cancer biology↗

Testing the causal impact of amyloidosis on total Tau using a genetically informative sample of adult male twins.

INTRODUCTIONThe amyloid cascade hypothesis predicts that amyloid-beta (A{beta}) aggregation drives tau tangle accumulation. We tested competing causal and non-causal hypotheses regarding the direction of causation between A{beta}40 and A{beta}42 and total Tau (t-Tau) plasma biomarkers. METHODSPlasma A{beta}40, A{beta}42, t-Tau, and neurofilament light chain (NFL) were measured in 1,035 men (mean = 67.0 years) using Simoa immunoassays. Genetically informative twin modeling tested the direction of causation between A{beta}s and t-Tau. RESULTSNo clear evidence that A{beta}40 or A{beta}42 directly causes changes in t-Tau was observed; the alternative causal hypotheses also fit the data well. In contrast, exploratory analyses suggested a causal impact of the A{beta} biomarkers on NFL. Separately, reciprocal causation was observed between t-Tau and NFL. DISCUSSIONPlasma A{beta}40 or A{beta}42 do not appear to have a direct causal impact on t-Tau. In contrast, A{beta} aggregation may causally impact NFL in cognitively unimpaired men in their late 60s.

pathology↗

Fecal virome transplantation is sufficient to alter fecal microbiota and drive lean and obese body phenotypes in mice

BackgroundThe gastrointestinal microbiome plays a significant role in numerous host processes and has an especially large impact on modulating the host metabolism. Prior studies have shown that when mice receive fecal transplants from obese donors that were fed high-fat diets (HFD) (even when recipient mice are fed normal diets after transplantation), they develop obese phenotypes. These studies demonstrate the prominent role that the gut microbiota play in determining lean and obese phenotypes. While much of the credit has been given to gut bacteria, studies have not measured the impact of gut viruses on these phenotypes. To address this shortcoming, we gavaged mice with viromes isolated from donors fed HFD or normal chow. By characterizing the mices gut bacterial biota and weight-gain phenotypes over time, we demonstrate that viruses can shape the gut bacterial community and affect weight gain or loss. ResultsWe gavaged mice longitudinally over 4 weeks while measuring their body weights and collecting fecal samples for 16S rRNA amplicon sequencing. We evaluated mice that were fed normal chow or high-fat diets, and gavaged each group with either chow-derived fecal viromes, HFD-derived fecal viromes, or phosphate buffered saline controls. We found a significant effect of gavage type, where mice fed chow but gavaged with HFD-derived viromes gained significantly more weight than their counterparts receiving chow-derived viromes. The converse was also true: mice fed HFD but gavaged with chow-derived viromes gained significantly less weight than their counterparts receiving HFD-derived viromes. These results were replicated in two separate experiments and the phenotypic changes were accompanied by significant and identifiable differences in the fecal bacterial biota. Notably, there were differences in Lachnospirales and Clostridia in mice fed chow but gavaged with HFD-derived fecal viromes, and in Peptostreptococcales, Oscillospirales, and Lachnospirales in mice fed HFD but gavaged with chow-derived fecal viromes. Due to methodological limitations, we were unable to identify specific bacterial species or strains that were responsible for respective phenotypic changes. ConclusionsThis study confirms that virome-mediated perturbations can alter the fecal microbiome in an in vivo model and indicates that such perturbations are sufficient to drive lean and obese phenotypes in mice.

microbiology↗

The genetic and environmental etiology of blood-based biomarkers related to the risks of Alzheimer's Disease in a population-based sample of early old age men

The amyloid-tau-neurodegeneration (ATN) framework has led to an increased focus on Alzheimers disease (AD) biomarkers. The cost and invasiveness of obtaining biomarkers via cerebrospinal fluid has motivated efforts to develop sensitive blood-based biomarkers. Although AD is highly heritable, the biometric genetic and environmental etiology of blood-based biomarkers has never been explored. We therefore, analyzed plasma beta-amyloid (A{beta}40, A{beta}42, A{beta}42/40), total tautau (t-tautau), and neurofilament light (NFL) biomarkers in a sample of 1,050 men aged 60 to 73 years (m=68.2, SD=2.5) from the Vietnam Era Twin Study of Aging (VETSA). Unlike A{beta} and tautau, NFL does not define AD; however, as a biomarker of neurodegeneration it serves as the N component in the ATN framework. Univariate estimates suggest that familial aggregation in A{beta}42, A{beta}42/40, t-tau, and NFL is entirely explained by additive genetic influences accounting for 40%-58% of the total variance. All remaining variance is associated with unshared or unique environmental influences. For A{beta}40, a additive genetic (31%), shared environmental (44%), and unshared environmental (25%) influences contribute to the total variance. In the more powerful multivariate analysis of A{beta}42, A{beta}40, t-tau, and NFL, heritability estimates range from 32% to 58%. A{beta}40 and A{beta}42 are statistically genetically identical (rg = 1.00, 95%CI = 0.92,1.00) and are also moderately environmentally correlated (re = 0.66, 95%CI = 0.59, 0.73). All other genetic and environmental associations were non-significant or small. Our results suggest that plasma biomarkers are heritable and that A{beta}40 and A{beta}42 share the same genetic influences, whereas the genetic influences on plasma t-tau and NFL are mostly unique and uncorrelated with plasma A{beta} in early old-age men.

genetics↗

The genetic etiology of longitudinal measures of predicted brain ageing in a population-based sample of mid to late-age males

Magnetic resonance imaging data are being used in statistical models to predicted brain ageing (PBA) and as biomarkers for neurodegenerative diseases such as Alzheimers Disease. Despite their increasing application, the genetic and environmental etiology of global PBA indices is unknown. Likewise, the degree to which genetic influences in PBA are longitudinally stable and how PBA changes over time are also unknown. We analyzed data from 734 men from the Vietnam Era Twin Study of Aging with repeated MRI assessments between the ages 52 to 72 years. Biometrical genetic analyses twin models revealed significant and highly correlated estimates of additive genetic heritability ranging from 59% to 75%. Multivariate longitudinal modelling revealed that covariation between PBA at different timepoints could be explained by a single latent factor with 73% heritability. Our results suggest that genetic influences on PBA are detectable in midlife or earlier, are longitudinally very stable, and are largely explained by common genetic influences. HighlightsWe explored the genetic and environmental etiology of MRI-based predicted brain age (PBA) in a longitudinal sample of males starting in midlife. Genetic influences on PBA are detectable in midlife or earlier, are longitudinally very stable, and largely explained by common genetic influences.

genetics↗