Tootfinder

A contact process with stronger mutations on trees
F\'abio Lopes, Alejandro Rold\'an-Correa
https://arxiv.org/abs/2509.08112 https://arxiv.org/pdf/…

A contact process with stronger mutations on trees
We consider a spatial stochastic model for a pathogen population growing inside a host that attempts to eliminate the pathogens through its immune system. The pathogen population is divided into different types. A pathogen can either reproduce by generating a pathogen of its own type or produce a pathogen of a new type that does not yet exist in the population. Pathogens with living ancestral types are protected against the host's immune system as long as their progenitors are still alive. Each…

Self-organized hyperuniformity in a minimal model of population dynamics
Tal Agranov, Natan Wiegenfeld, Omer Karin, Benjamin D. Simons
https://arxiv.org/abs/2509.08077 https://

Self-organized hyperuniformity in a minimal model of population dynamics
We identify a novel scenario for hyperuniformity in a generic model of population dynamics that has been recently introduced to account for biological memory in the immune system and epigenetic inheritance. In this model, individuals' competition over a shared resource guides the population towards a critical steady state with prolonged individual life time. Here we uncover that the spatially extended model is characterized by hyperuniform density fluctuations. A hydrodynamic theory is derived …

"We can conclude that the brain has the capacity to distinguish virtual infectious patterns,
become activated,
and link this activation to a downstream response,
⭐️ resulting in systemic immunity,"
wrote Camilla Jandus, co-author of the study paper
https://www.

Human immune system reacts to the mere sight of infection
Researchers monitored brain activity when people were shown images of sick-looking avatars via VR. The brain appeared to spark an immune response.

Limitation
Who recognizes his limitations is healthy;
Who ignores his limitations is sick.
The sage recognizes this sickness as a limitation.
And so becomes immune.
-- Lao Tse, "Tao Te Ching"

🎃 How modified RNA tricks the innate immune system
#rna

How modified RNA tricks the innate immune system
The innate immune system is the body's first line of defense against pathogens and foreign substances. An essential component of this system are pattern recognition receptors, which recognize non-self RNA—such as that from viruses and bacteria—and trigger an immune response.

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
https://arxiv.org/abs/2509.01367

MetaRoundWorm: A Virtual Reality Escape Room Game for Learning the Lifecycle and Immune Response to Parasitic Infections
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 and gamification as novel educational techniques to improve learning experiences related to the immune system. Thus, we present MetaRoundWorm, an immersive virtual reality (VR) escape room game designed to enhance the understanding of parasitic infections and host immune responses through interactive…

Phase Transitions in a Particle Model for the Self-Adaptive Response to Cancer Dynamics
Christian Kuehn, Quirin Vogel
https://arxiv.org/abs/2508.03577 https://

Phase Transitions in a Particle Model for the Self-Adaptive Response to Cancer Dynamics
In this paper, we present a probabilistic analysis of a dynamical particle model for the self-adaptive immune response to cancer, as proposed by the first author in a previous work. The model is motivated by the interplay between immune surveillance and cancer evolution. We rigorously confirm the sharp phase transition in immune system learning predicted in the original work. Additionally, we compute the expected amount of information acquired by the immune system about cancer cells over time. …

An Immune Infiltration-Based Risk Scoring System for Prognostic Stratification in Colorectal Adenocarcinoma
Oluwafemi Ogundare
https://arxiv.org/abs/2507.18832 https://

An Immune Infiltration-Based Risk Scoring System for Prognostic Stratification in Colorectal Adenocarcinoma
Background: Colorectal adenocarcinoma (CRC) remains a leading cause of cancer-related mortality worldwide, with variable patient outcomes despite treatment advances. Traditional prognostic methods based on clinicopathological variables alone do not fully capture the biological complexity of the disease. This study aims to develop a risk scoring system based on genes associated with tumor-infiltrating immune cells (TIIC-associated genes) to improve prognostic assessment in CRC. Methods: RNA-se…

Beyond the Algorithm: A Field Guide to Deploying AI Agents in Clinical Practice
Jack Gallifant, Katherine C. Kellogg, Matt Butler, Amanda Centi, Patrick F. Doyle, Sayon Dutta, Joyce Guo, Matthew J. Hadfield, Esther H. Kim, David E. Kozono, Hugo JWL Aerts, Adam B. Landman, Raymond H. Mak, Rebecca G. Mishuris, Tanna L. Nelson, Guergana K. Savova, Elad Sharon, Benjamin C. Silverman, Umit Topaloglu, Jeremy L. Warner, Danielle S. Bitterman

Beyond the Algorithm: A Field Guide to Deploying AI Agents in Clinical Practice
Large language models (LLMs) integrated into agent-driven workflows hold immense promise for healthcare, yet a significant gap exists between their potential and practical implementation within clinical settings. To address this, we present a practitioner-oriented field manual for deploying generative agents that use electronic health record (EHR) data. This guide is informed by our experience deploying the "irAE-Agent", an automated system to detect immune-related adverse events from clinical …

The RFKJr. situation is generally terrible and all, but apparently CDC managed to keep enough conditions in the "high risk" qualifications to cover just about everyone.
#Covid #Vaccines

Dynamics of memory B cells and plasmablasts in healthy individuals
Andrea Mazzolini, Aleksandra M. Walczak, Thierry Mora
https://arxiv.org/abs/2510.02812 https://

Dynamics of memory B cells and plasmablasts in healthy individuals
Our adaptive immune system relies on the persistence over long times of a diverse set of antigen-experienced B cells to encode our memories of past infections and to protect us against future ones. While longitudinal repertoire sequencing promises to track the long-term dynamics of many B cell clones simultaneously, sampling and experimental noise make it hard to draw reliable quantitative conclusions. Leveraging statistical inference, we infer the dynamics of memory B cell clonal dynamics and …

A time-adaptive optimization approach for reconstructing immune response in a mathematical model of acute HIV infection using clinical data
L. Beilina, I. Gainova, G. Bocharov
https://arxiv.org/abs/2508.13123

A time-adaptive optimization approach for reconstructing immune response in a mathematical model of acute HIV infection using clinical data
The paper proposes a time-adaptive optimization approach for determining the time-dependent immune response function in a mathematical model of acute HIV infection, using clinical data from four untreated patients. We formulate the problem as a parameter identification problem for an immune response system of ODE which includes novel component integrated into the third equation of the classical three-equation HIV model. Tikhonov's regularization method, Lagrangian approach, from which we deri…

trAIce3D: A Prompt-Driven Transformer Based U-Net for Semantic Segmentation of Microglial Cells from Large-Scale 3D Microscopy Images
MohammadAmin Alamalhoda, Arsalan Firoozi, Alessandro Venturino, Sandra Siegert
https://arxiv.org/abs/2507.22635

trAIce3D: A Prompt-Driven Transformer Based U-Net for Semantic Segmentation of Microglial Cells from Large-Scale 3D Microscopy Images
The shape of a cell contains essential information about its function within the biological system. Segmenting these structures from large-scale 3D microscopy images is challenging, limiting clinical insights especially for microglia, immune-associated cells involved in neurodegenerative diseases. Existing segmentation methods mainly focus on cell bodies, struggle with overlapping structures, perform poorly on noisy images, require hyperparameter tuning for each new dataset, or rely on tedious …

Since taking office, Donald Trump and his government have placed restrictions on some lawyers and law firms, including their ability to freely represent clients, mostly because they have done legal work that the president has opposed or they have been associated with prosecutors who investigated him.
https://www.theguardian.com/law/2025/oct/03/trumps-crackdown-on-lawyers-shows-no-place-is-immune-says-us-bar-chief?CMP=Share_iOSApp_Other

First passage times to T cell activation
Tony Wong, Ikchang Cho, Maria R. D'Orsogna, Tom Chou
https://arxiv.org/abs/2510.01694 https://arxiv.org/pdf/25…

First passage times to T cell activation
Effective recognition of foreign antigens by the adaptive immune system relies on T cells being activated by antigen-presenting cells (APCs) in lymph nodes. Here, diffusing T cells may encounter cognate APCs that present matching antigen fragments or non-cognate ones that do not; they are also subject to degradation. We develop a stochastic model in which T cell-APCs interact via a sequence of recognition steps, represented as a multistage Markov chain. T cells are successfully activated only i…

Reaction enhancement by flux-limited chemotaxis
Jing An, Alexander Kiselev, Yao Yao
https://arxiv.org/abs/2508.13704 https://arxiv.org/pdf/2508.13704

Reaction enhancement by flux-limited chemotaxis
Chemotaxis plays a crucial role in a variety of processes in biology and ecology. Quite often it acts to improve efficiency of biological reactions; one example is the immune system signalling, where infected tissues release chemokines attracting monocytes to fight invading bacteria. Another example is reproduction, where eggs release pheromones that attract sperm. In this paper, we analyze a system of two reacting densities, one of which is chemotactic on another. Since the speed of any biolog…

Modeling the Effects of Over and Under Doses Antibiotic Treatment to Bacterial Resistance in Presence of Immune System
Uzzwal Kumar Mallick, Jobayer Ahmed, Khan Anik Islam, Pulak Kundu
https://arxiv.org/abs/2509.16687

Modeling the Effects of Over and Under Doses Antibiotic Treatment to Bacterial Resistance in Presence of Immune System
Antibiotic resistance presents a growing global health threat by diminishing the effectiveness of treatments and allowing once-manageable bacterial infections to persist. This study develops and analyzes an optimization-based mathematical model to investigate the impact of varying antibiotic dosages on bacterial resistance, incorporating the role of the immune system. Additionally, to capture the effects of over and underdosing, a floor function is newly introduced into the model as a switch fu…

Biocompatibility of Nanomaterials in Medical Applications
Marvellous Eyube, Courage Enuesueke, Marvellous Alimikhena
https://arxiv.org/abs/2507.22966 https://

Biocompatibility of Nanomaterials in Medical Applications
Biocompatibility is a critical factor in the application of nanomaterials in medical fields, as these materials must interact safely and effectively with biological systems to be viable for therapeutic and diagnostic use. This article investigates the biocompatibility of nanomaterials, focusing on their interactions with biological cells, tissues, and the immune system. Key properties such as surface chemistry, size, shape, and material composition are examined, as they significantly influence …

Adaptive mechanical proofreading toward faithful clonal selection
Qing Xu, Shenshen Wang
https://arxiv.org/abs/2509.17422 https://arxiv.org/pdf/2509.17422

Adaptive mechanical proofreading toward faithful clonal selection
To ensure faithful information transmission, cells utilize nonequilibrium drives to reduce errors. Kinetic proofreading is a classic mechanism known to sharpen ligand discrimination by T lymphocytes. It remains an open question whether the adaptive immune system relies solely on kinetic proofreading to boost fidelity. Here, we suggest an alternative: an enhanced form of mechanical proofreading (MPR) in which adaptive force exertion via dynamic cell-cell contact allows faithful selection of high…

Cells mark other cells for destruction by the immune system through opsonization. Sigils to destroy objects are the most closely guarded secrets in Chaos Magic (don’t dare ask my fox for one that works on a certain car brand)
Here is the sigil to mark an object for removal in my organization.
https://

Bayesian inference of antibody evolutionary dynamics using multitype branching processes
Athanasios G. Bakis, Ashni A. Vora, Tatsuya Araki, Tongqiu Jia, Jared G. Galloway, Chris Jennings-Shaffer, Gabriel D. Victora, Yun S. Song, William S. DeWitt, Frederick A. Matsen IV, Volodymyr M. Minin
https://arxiv.org/abs/2508.09519

Bayesian inference of antibody evolutionary dynamics using multitype branching processes
When our immune system encounters foreign antigens (i.e., from pathogens), the B cells that produce our antibodies undergo a cyclic process of proliferation, mutation, and selection, improving their ability to bind to the specific antigen. Immunologists have recently developed powerful experimental techniques to investigate this process in mouse models. In one such experiment, mice are engineered with a monoclonal B-cell precursor and immunized with a model antigen. B cells are sampled from sac…

Enhancing Coherence with a Clock Transition and Dynamical Decoupling in the Cr$_7$Mn Molecular Nanomagnet
Guanchu Chen (Department of Physics and Astronomy, Amherst College, Amherst, USA, Department of Physics, University of Massachusetts Amherst, Amherst, USA), Brendan C. Sheehan (Department of Physics and Astronomy, Amherst College, Amherst, USA, Department of Physics, University of Massachusetts Amherst, Amherst, USA), Ilija Nikolov (Department of Physics and Astronomy, Amherst Coll…

Enhancing Coherence with a Clock Transition and Dynamical Decoupling in the Cr$_7$Mn Molecular Nanomagnet
Molecular magnets are attractive as spin qubits due to their chemical tunability, addressability through electron-spin resonance techniques, and long coherence times. Clock transitions (CTs), for which the system is immune to the effect of magnetic-field fluctuations to first order, provide a method to enhance the coherence time $T_2$, and to reveal mechanisms of decoherence that are not due to such fluctuations. Here we investigate two variants of Cr$_7$Mn, a spin-1 molecular nanomagnet, at fi…

Mathematical Validation of a Cancer Model
Marcela V. Reale, Gustavo Paccosi, David H. Margarit, Lilia Romanelli
https://arxiv.org/abs/2508.10910 https://ar…

Mathematical Validation of a Cancer Model
Understanding cancer cell differentiation is essential for advancing its detection, diagnosis, and treatment. Mathematical models significantly contribute to this by providing a theoretical framework to understand the complex interactions between cancer stem cells, differentiated cancer cells, and immune system components. Such models depend on experimental data and computational simulations to predict tumor dynamics, offering insights into how different cell populations evolve over time. Howev…