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Biology & Life Sciences Preprint PDF DOI

T-cell repertoire response in individuals with post-acute sequelae of COVID-19

Zachary Montague, Rhea M Grover, Andrew Baumgartner, Assya Trofimov, Jennifer Hadlock, Armita Nourmohammad · 2026

T-cells are central to SARS-CoV-2 clearance and immunological memory, yet their contribution to the persistence of post-acute sequelae of COVID-19 (PASC) remains poorly understood. The immunological f…

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AI & Data Science Preprint PDF DOI

Efficient estimation of cumulative incidence curves via data fusion with surrogates: application to integrated analysis of vaccine trial and immunobridging data

Pan Zhao, Peter B. Gilbert, Oliver Dukes, Bo Zhang · 2026

Refined vaccine regimens containing variant-matched inserts are often authorized based on historical phase 3 efficacy trials together with immunobridging studies. Phase 3 trials are essential for esta…

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AI & Data Science Preprint PDF DOI

Dealing with positivity violations in mediation analysis via weighted controlled effects, with application to assessing immune correlates of protection in antigen-experienced participants

Qijia He, Bo Zhang · 2026

Causal mediation analysis has become an important and increasingly used framework for evaluating candidate immune response biomarkers in vaccine research. A controlled effects approach has been propos…

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AI & Data Science Preprint PDF DOI

Generalized projection tests for function-valued parameters with applications to testing structural causal assumptions

Rui Wang, Albert Osom, Bo Zhang · 2026

Structural assumptions are central to the causal inference literature. In practice, it is often crucial to assess their validity or to test implications that follow from them. In many settings, such t…

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AI & Data Science Preprint PDF DOI

Data Augmentation for High-Fidelity Generation of CAR-T/NK Immunological Synapse Images

Xiang Zhang, Boxuan Zhang, Alireza Naghizadeh, Mohab Mohamed, Dongfang Liu, Ruixiang Tang, Dimitris Metaxas, Dongfang Liu · 2026

Chimeric antigen receptor (CAR)-T and NK cell immunotherapies have transformed cancer treatment, and recent studies suggest that the quality of the CAR-T/NK cell immunological synapse (IS) may serve a…

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Biology & Life Sciences Preprint PDF DOI

CEI: A Clonal Expansion Identifier for T-cell receptor clones following SARS-CoV-2 vaccination

Yunbei Pan, Christian Hofmann, Barbara Banbury, Harsh Patel, Stephanie A. Bien, Tom Chou, Otto O. Yang · 2026

Each T cell typically carries a specific T-cell receptor (TCR) that determines its specificity against an epitope presented by the HLA complex on a target cell. Antigenic challenge triggers the expans…

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Biology & Life Sciences Preprint PDF DOI

Cost-Effectiveness of Adult Hepatitis A Vaccination Strategies in Korea Under an Aging Susceptibility Profile

Yuna Lim, Gerardo Chowell, Eunok Jung · 2026

Hepatitis A severity increases sharply with age, while Korea is experiencing a cohort shift in which low seroprevalence adult cohorts are aging into older, higher fatality age groups. This demographic…

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Biology & Life Sciences Preprint PDF DOI

Immunological Density Shapes Recovery Trajectories in Long COVID

Jing Wang, Tong Zhang, Xing Niu, Jie Shen, Yiming Luo, Qiaomin Xie, Amar Sra, Zorina Galis, Jeremy Weiss · 2026

Post-acute sequelae of SARS-CoV-2 infection (Long COVID) frequently persists for months, yet drivers of clinical remission remain incompletely defined. Here we analyzed 97,564 longitudinal PASC asse…

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Biology & Life Sciences Preprint PDF DOI

Identifying expanding TCR clonotypes with a longitudinal Bayesian mixture model and their associations with cancer patient prognosis, metastasis-directed therapy, and VJ gene enrichment

David Swanson, Alexander Sherry, Cara Haymaker, Alexandre Reuben, Chad Tang · 2026

Examination of T-cell receptor (TCR) clonality has become a way of understanding immunologic response to cancer and its interventions in recent years. An aspect of these analyses is determining which …

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AI & Data Science Preprint PDF DOI

Bounds for causal mediation effects

Marie S. Breum, Vanessa Didelez, Erin E. Gabriel, Michael C. Sachs · 2025

Several frameworks have been proposed for studying causal mediation analysis. What these frameworks have in common is that they all make assumptions for point identifications that can be violated even…

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Biology & Life Sciences Preprint PDF DOI

Invariance under Structure Translation as the Origin of Host Immune Capacity Conservation from Noether's Theorem

Yexing Chen, Peng Cao · 2025

The capacity to resist pathogens is recognized as a fundamental property of the immune system, yet the capacity itself remains a phenomenological concept and lacks a defined physical basis. Its fundam…

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Biology & Life Sciences Preprint PDF DOI

A statistical framework for comparing epidemic forests

Cyril Geismar, Peter J. White, Anne Cori, Thibaut Jombar · 2025

Inferring who infected whom in an outbreak is essential for characterising transmission dynamics and guiding public health interventions. However, this task is challenging due to limited surveillance …

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Biology & Life Sciences Preprint PDF DOI

Multiomic Enriched Blood-Derived Digital Signatures Reveal Mechanistic and Confounding Disease Clusters for Differential Diagnosis

Bolin Liu, Alexander Fulton, Hector Zenil · 2025

Understanding disease relationships through blood biomarkers offers a pathway toward data driven taxonomy and precision medicine. We constructed a digital blood twin from 103 disease signatures compri…

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AI & Data Science Preprint PDF DOI

Nonparametric bounds for vaccine effects in randomized trials

Rachel Axelrod, Uri Obolski, Daniel Nevo · 2025

Vaccine randomized trials are typically designed to be blinded, ensuring that the estimated vaccine efficacy (VE) reflects the immunological effect of the vaccine. When blinding is broken, however, th…

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Biology & Life Sciences Preprint PDF DOI

Mechanical activity enables patterning and discrimination at the immune synapse

Tony Wong, Tom Chou, Suraj Shankar, Shenshen Wang · 2025

Immune cells recognize and discriminate antigens through immunological synapses - dynamic intercellular junctions exhibiting highly organized receptor-ligand patterns. While much work has focused on m…

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Computer Science Preprint PDF DOI

MetaRoundWorm: A Virtual Reality Escape Room Game for Learning the Lifecycle and Immune Response to Parasitic Infections

Xuanru Cheng, Xian Wang, Chi-lok Tai, Lik-Hang Lee · 2025

Promoting public health is challenging owing to its abstract nature, and individuals may be apprehensive about confronting it. Recently, there has been an increasing interest in using the metaverse an…

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AI & Data Science Preprint PDF DOI

Classification of autoimmune diseases from Peripheral blood TCR repertoires by multimodal multi-instance learning

Ruihao Zhang, Mao chen, Fei Ye, Dandan Meng, Yixuan Huang, Xiao Liu · 2025

T cell receptor (TCR) repertoires encode critical immunological signatures for autoimmune diseases, yet their clinical application remains limited by sequence sparsity and low witness rates. We develo…

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Biology & Life Sciences Preprint PDF DOI

Immunological mechanisms and immunoregulatory strategies in intervertebral disc degeneration

Xianyi Yan, Xi Wang, Ying Che, Peng Feng, Ting Zhang · 2025

Intervertebral discs are avascular and maintain immune privilege. However, during intervertebral disc degeneration (IDD), this barrier is disrupted, leading to extensive immune cell infiltration and l…

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Biology & Life Sciences Preprint PDF DOI

Great Short History of Microbiology Development as a Science

Daniil S. Gerassimov · 2025

The study of microorganisms, or microbiology, has demonstrated significant development since its inception and is currently a key field of biological sciences that has a huge impact on modern society …

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Biology & Life Sciences Preprint PDF DOI

Modelling Immunity in Agent-based Models

Gray Manicom, Emily Harvey, Joshua Looker, David Wu, Oliver Maclaren, Dion O' Neale · 2025

Vaccination policies play a central role in public health interventions and models are often used to assess the effectiveness of these policies. Many vaccines are leaky, in which case the observed vac…

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