Jingshen Wang
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View article: Enhanced language models for predicting Alzheimer's disease pathology
Enhanced language models for predicting Alzheimer's disease pathology Open
Background The ability to predict individual‐level biomarker characteristics, along with cognitive decline, could represent a major advance in the care of AD patients. Advanced language models (LLMs), with their ability to interpret natura…
View article: Can language models boost the power of randomized experiments without statistical bias?
Can language models boost the power of randomized experiments without statistical bias? Open
Randomized experiments or randomized controlled trials (RCTs) are gold standards for causal inference, yet cost and sample-size constraints limit power. We introduce CALM (Causal Analysis leveraging Language Models), a statistical framewor…
View article: Variable and interactive effects of Sex, APOE ε4 and TREM2 on the deposition of tau in entorhinal and neocortical regions
Variable and interactive effects of Sex, APOE ε4 and TREM2 on the deposition of tau in entorhinal and neocortical regions Open
The canonical Alzheimer’s Disease (AD) pathological cascade posits that the accumulation of amyloid beta (Aβ) is the initiating event, accelerating the accumulation of tau in the entorhinal cortex (EC), which subsequently spreads into the …
View article: Enhanced Language Models for Predicting and Understanding HIV Care Disengagement: A Case Study in Tanzania
Enhanced Language Models for Predicting and Understanding HIV Care Disengagement: A Case Study in Tanzania Open
Summary Sustained engagement in HIV care and adherence to antiretroviral therapy (ART) are essential for achieving the UNAIDS "95-95-95" targets. Despite increased ART access, disengagement from care remains a significant issue, particular…
View article: Covariate-Adjusted Response-Adaptive Design with Delayed Outcomes
Covariate-Adjusted Response-Adaptive Design with Delayed Outcomes Open
Covariate-adjusted response-adaptive (CARA) designs have gained widespread adoption for their clear benefits in enhancing experimental efficiency and participant welfare. These designs dynamically adjust treatment allocations during interi…
View article: Genetic factors affect tau deposition in entorhinal cortex and neocortex
Genetic factors affect tau deposition in entorhinal cortex and neocortex Open
Background The amyloid cascade hypothesis posits a sequence of events proceeding from amyloid‐β (Aβ) deposition to entorhinal cortical (EC) tau to neocortical (meta‐temporal) tau. This study examined how genetics may modify relationships b…
View article: Rapid biphasic decay of intact and defective HIV DNA reservoir during acute treated HIV disease
Rapid biphasic decay of intact and defective HIV DNA reservoir during acute treated HIV disease Open
Despite antiretroviral therapy (ART), HIV persists in latently-infected cells (the HIV reservoir) which decay slowly over time. Here, leveraging >500 longitudinal samples from 67 people living with HIV (PLWH) treated during acute infection…
View article: Prevention of adverse HIV treatment outcomes: machine learning to enable proactive support of people at risk of HIV care disengagement in Tanzania
Prevention of adverse HIV treatment outcomes: machine learning to enable proactive support of people at risk of HIV care disengagement in Tanzania Open
Objectives This study aimed to develop a machine learning (ML) model to predict disengagement from HIV care, high viral load or death among people living with HIV (PLHIV) with the goal of enabling proactive support interventions in Tanzani…
View article: Variable and interactive effects of Sex, APOE ε4 and TREM2 on the deposition of tau in entorhinal and neocortical regions.
Variable and interactive effects of Sex, APOE ε4 and TREM2 on the deposition of tau in entorhinal and neocortical regions. Open
The canonical AD pathological cascade posits that the accumulation of amyloid beta (Aβ) is the initiating event, accelerating the accumulation of tau in the entorhinal cortex (EC), which subsequently spreads into the neocortex. Here in a s…
View article: Dynamic Statistical Learning in Massive Datastreams
Dynamic Statistical Learning in Massive Datastreams Open
Technological advances have necessitated statistical methodologies for analyzing large-scale datastreams comprising multiple indefinitely time series. This manuscript proposes a dynamic tracking and screening (DTS) framework for online lea…
View article: Rapid Biphasic Decay of Intact and Defective HIV DNA Reservoir During Acute Treated HIV Disease
Rapid Biphasic Decay of Intact and Defective HIV DNA Reservoir During Acute Treated HIV Disease Open
Despite antiretroviral therapy (ART), HIV persists in latently-infected cells (“the reservoir”) which decay slowly over time. Here, leveraging >500 longitudinal samples from 67 people with HIV (PWH) treated during acute infection, we devel…
View article: Rudi Kundini, Pamoja Kundini (RKPK): study protocol for a hybrid type 1 randomized effectiveness-implementation trial using data science and economic incentive strategies to strengthen the continuity of care among people living with HIV in Tanzania
Rudi Kundini, Pamoja Kundini (RKPK): study protocol for a hybrid type 1 randomized effectiveness-implementation trial using data science and economic incentive strategies to strengthen the continuity of care among people living with HIV in Tanzania Open
Background Economic incentives can improve clinical outcomes among in-care people living with HIV (PLHIV), but evidence is limited for their effectiveness among out-of-care PLHIV or those at risk of disengagement. We propose a type 1 hybri…
View article: Sensitivity analysis with iterative outlier detection for systematic reviews and meta‐analyses
Sensitivity analysis with iterative outlier detection for systematic reviews and meta‐analyses Open
Meta‐analysis is a widely used tool for synthesizing results from multiple studies. The collected studies are deemed heterogeneous when they do not share a common underlying effect size; thus, the factors attributable to the heterogeneity …
View article: Rudi Kundini, Pamoja Kundini (RKPK): study protocol for a hybrid type 1 randomized effectiveness-implementation trial using data science and economic incentive strategies to strengthen the continuity of care among people living with HIV in Tanzania
Rudi Kundini, Pamoja Kundini (RKPK): study protocol for a hybrid type 1 randomized effectiveness-implementation trial using data science and economic incentive strategies to strengthen the continuity of care among people living with HIV in Tanzania Open
Background Economic incentives can improve clinical outcomes among in-care people living with HIV (PLHIV), but evidence is limited for their effectiveness among out-of-care PLHIV or those at-risk of disengagement. We propose a type 1 hybri…
View article: Mediation Analysis with Mendelian Randomization and Efficient Multiple GWAS Integration
Mediation Analysis with Mendelian Randomization and Efficient Multiple GWAS Integration Open
Mediation analysis is a powerful tool for studying causal pathways between exposure, mediator, and outcome variables of interest. While classical mediation analysis using observational data often requires strong and sometimes unrealistic a…
View article: Adaptive Experiments Toward Learning Treatment Effect Heterogeneity
Adaptive Experiments Toward Learning Treatment Effect Heterogeneity Open
Understanding treatment effect heterogeneity has become an increasingly popular task in various fields, as it helps design personalized advertisements in e-commerce or targeted treatment in biomedical studies. However, most of the existing…
View article: Fair Adaptive Experiments
Fair Adaptive Experiments Open
Randomized experiments have been the gold standard for assessing the effectiveness of a treatment or policy. The classical complete randomization approach assigns treatments based on a prespecified probability and may lead to inefficient u…
View article: Winner's Curse Free Robust Mendelian Randomization with Summary Data
Winner's Curse Free Robust Mendelian Randomization with Summary Data Open
In the past decade, the increased availability of genome-wide association studies summary data has popularized Mendelian Randomization (MR) for conducting causal inference. MR analyses, incorporating genetic variants as instrumental variab…
View article: Debiased inference on heterogeneous quantile treatment effects with regression rank scores
Debiased inference on heterogeneous quantile treatment effects with regression rank scores Open
Understanding treatment effect heterogeneity is vital to many scientific fields because the same treatment may affect different individuals differently. Quantile regression provides a natural framework for modelling such heterogeneity. We …
View article: Statistical Inference on Multi-armed Bandits with Delayed Feedback
Statistical Inference on Multi-armed Bandits with Delayed Feedback Open
Multi armed bandit (MAB) algorithms have been increasingly used to complement or integrate with A/B tests and randomized clinical trials in e-commerce, healthcare, and policymaking. Recent developments incorporate possible delayed feedback…
View article: A robust harmonization approach for cognitive data from multiple aging and dementia cohorts
A robust harmonization approach for cognitive data from multiple aging and dementia cohorts Open
INTRODUCTION Although many cognitive measures have been developed to assess cognitive decline due to Alzheimer's disease (AD), there is little consensus on optimal measures, leading to varied assessments across research cohorts and clinica…
View article: Subgroup analysis and adaptive experiments crave for debiasing
Subgroup analysis and adaptive experiments crave for debiasing Open
Results obtained from reliably designed randomized experiments are often considered to be evidence of the highest grade for assessing the effectiveness of biomedical or behavioral interventions. Nevertheless, even with randomized experimen…
View article: Breaking the Winner's Curse in Mendelian Randomization: Rerandomized Inverse Variance Weighted Estimator
Breaking the Winner's Curse in Mendelian Randomization: Rerandomized Inverse Variance Weighted Estimator Open
Developments in genome-wide association studies and the increasing availability of summary genetic association data have made the application of two-sample Mendelian Randomization (MR) with summary data increasingly popular. Conventional t…
View article: Forward selection and post-selection inference in factorial designs
Forward selection and post-selection inference in factorial designs Open
Ever since the seminal work of R. A. Fisher and F. Yates, factorial designs have been an important experimental tool to simultaneously estimate the effects of multiple treatment factors. In factorial designs, the number of treatment combin…
View article: Additional file 3 of Single-cell transcriptomics highlights immunological dysregulations of monocytes in the pathobiology of COPD
Additional file 3 of Single-cell transcriptomics highlights immunological dysregulations of monocytes in the pathobiology of COPD Open
Additional file 3: Dataset 1. Demographics and clinical data of the 9 patients included in this study.
View article: Additional file 9 of Single-cell transcriptomics highlights immunological dysregulations of monocytes in the pathobiology of COPD
Additional file 9 of Single-cell transcriptomics highlights immunological dysregulations of monocytes in the pathobiology of COPD Open
Additional file 9: Dataset 7. Genes dynamically expressed during AT2-to-AT1 differentiation, related to Fig. S4D and S4G, in which the top 500 genes based on wald statistics were differentiation driver genes and those pro-inflammatory and/…
View article: Additional file 7 of Single-cell transcriptomics highlights immunological dysregulations of monocytes in the pathobiology of COPD
Additional file 7 of Single-cell transcriptomics highlights immunological dysregulations of monocytes in the pathobiology of COPD Open
Additional file 7: Dataset 5. Genes dynamically expressed during CD14+ classical monocyte-to-CD14+ intermediate monocyte differentiation, related to Fig. S3M and S3N, in which the top 250 genes based on wald statistics were differentiation…
View article: Additional file 8 of Single-cell transcriptomics highlights immunological dysregulations of monocytes in the pathobiology of COPD
Additional file 8 of Single-cell transcriptomics highlights immunological dysregulations of monocytes in the pathobiology of COPD Open
Additional file 8: Dataset 6. Gene lists for all co-expression gene modules of AT2s detected by WGCNA analysis shown in Fig. 4F.
View article: Additional file 4 of Single-cell transcriptomics highlights immunological dysregulations of monocytes in the pathobiology of COPD
Additional file 4 of Single-cell transcriptomics highlights immunological dysregulations of monocytes in the pathobiology of COPD Open
Additional file 4: Dataset 2. Results of differential gene expression analysis within each cell type under the conditions of aging, COPD, and smoking, respectively.
View article: Additional file 2 of Single-cell transcriptomics highlights immunological dysregulations of monocytes in the pathobiology of COPD
Additional file 2 of Single-cell transcriptomics highlights immunological dysregulations of monocytes in the pathobiology of COPD Open
Additional file 2: Figures S1–S6.