arXiv preprints from January 1, 2026 through September 5, 2026 — 00:31:58 EST
Here, we report high-order functional network connectivity as a promising way for studying the brain connectome. Traditional functional connectivity approaches capture only pairwise relationships between brain regions, overlooking complex multivariate dependencies that underlie cognition and behavior. First, we demonstrated that...
Cortical neurons fire sparsely -- often fewer than one spike per sensory window -- making rate coding insufficient and temporal coding a necessity. That conduction delays convert firing order into synchrony is long established. What governs which class of temporal feature a neuron detects -- one volley of coincident input, or two in a...
The vertex model is widely used to describe the mechanics of epithelial tissues, but its conventional formulation assumes that all cells remain tightly packed and always share edges with their neighbors, making it difficult to represent local detachment or gap formation. Here, we propose a minimal extension of the vertex model that...
Forensic body fluid identification is crucial for reconstructing crime scene events. While DNA analysis provides individualization, it lacks information about the fluid's origin. We developed and evaluated three complementary proteomic approaches using LC-HRMS/MS to identify blood, saliva, semen, urine, and vaginal fluid, including...
Isotopic fractionation factors for oxygen and silicon in selected silicates (quartz, enstatite, forsterite, lizardite, kaolinite) have been calculated using first-principles methods. Good agreement between theory and experiment is obtained in the case of oxygen. In the case of silicon, agreement and differences with existing estimates...
Agent-based models (ABMs) provide a natural framework for representing cell-level rules and spatial heterogeneity in bacterial infections, but their computational cost limits their use for macroscopic tissue-scale simulations and broad parameter exploration. We derive a deterministic coarse-grained description for a class of...
T-cell immunity acts as a major defense system against controlling viral infections in vertebrates. During viral entry, innate immune cells degrade the viral proteins (antigens) and present them on their surface via Major Histocompatibility (MHC) proteins. T-cell receptors (TCRs) recognize these antigens/peptides presented by MHC...
How 3D genome architecture contributes to transcriptional specificity across neuronal cell types remains unclear. Here, we used multiplexed chromatin tracing to map chromatin architecture and cell identity at single-cell resolution in the adult Drosophila brain. We found that enhancer-promoter (E-P) proximity was increased in...
The last five-plus years have seen many protein engineering disciplines transformed by advances in machine learning (ML), but the same cannot be said for directed evolution. Reflecting on a previously co-authored perspective, I discuss why I believe this to be the case, arguing that a disconnect between the goals of...
Histology images contain rich morphological information and can provide insights into pathological processes. However, deriving hypotheses relating morphological phenotypes to clinical attributes is bottlenecked by a manual image interpretation step. Here, we demonstrate that this process can be automated through interpretable deep...
The brain is highly proficient at making sense of noisy and ambiguous sensory inputs. Predictive processing hypothesises that this ability relies on prediction. However, it is unclear why the brain would have evolved to predict the sensory world, a computationally expensive process, in order to aid perception. Here we use simulations...
Bayesian phylogenetic and phylodynamic analyses can be very time-consuming, owing to the combination of complex models that are used to estimate key parameters from increasingly large genomic data sets and their associated metadata. The use of high-performance computer hardware can -- to a certain extent -- alleviate the computational...
The extracellular matrix (ECM) is a fibrous and dynamic network that plays a critical role in development, homeostasis, and disease. Cells both respond to and remodel the ECM, engaging in a mechanical reciprocity that shapes tissues. To study these interactions, computational models have been developed that simulate either ECM...
Species area curves, which describe the number of species present as a function of area, have long been used to understand biodiversity and inform conservation efforts. While understanding the number of species is important, it leaves out information about the population sizes of each species. In this work, we examine the relationship...
This paper argues that fungal mycelial networks exhibit minimal cognition through memory-integrated adaptive regulation. Drawing on cybernetic and enactivist frameworks, I develop a non-representational account of memory as the organism's capacity to modulate behavior based on temporally extended environmental coupling. I propose four...
Existing cell embedding methods predominantly rely on transcriptomic or proteomic measurements and represent each cell as a holistic entity, thereby overlooking the subcellular localization of individual molecules. Moreover, they rarely incorporate protein structural information, despite its fundamental role in determining molecular...
Digital twin technologies could transform neuroscience and biomedicine by creating predictive computational representations of living organisms. However, most animal digital twins model neural circuits, anatomy, or biomechanics separately rather than integrating the processes that generate behavior. We argue that animal digital twins...
This chapter reconstructs the McCulloch-Pitts program as a physics of neural computation rather than the familiar cartoon of a binary neuron. The 1943 logical calculus is developed in both directions: given a net, characterize the propositions realized by its activity; given an admissible logical expression, construct a net that...
We study a trait-structured population model incorporating mutation, selection and density-dependent regulation on a countably infinite trait space. The underlying stochastic process is a continuous-time Markov chain in which individuals reproduce at a trait-independent rate, offspring traits are determined by a mutation kernel on...
A central challenge in movement ecology is to describe ecologically meaningful residence sites from raw tracking data due to heterogeneous sampling frequency and uncertain site boundaries. Here, we develop a greedy nearest-neighbor clustering approach with local reassignment and polygon-based site construction that generates...
Artificial intelligence (AI) is transforming brain-computer interfaces (BCIs) from task-specific neural decoders into adaptive systems that complete language, smooth movement, regulate rehabilitation support and adjust stimulation. These capabilities can increase speed, fluency, usability and clinical reach, yet conventional...
The hypothalamic pituitary adrenal (HPA) axis is a key regulatory system coordinating endocrine responses to physiological and psychological stress. While the ACTH stimulation test remains a cornerstone of adrenal function assessment, its interpretation is complicated by the dynamic and adaptive nature of the HPA axis under chronic...
When the rates of ligand binding are measured by methods such as surface plasmon resonance, it is common practice to use the observed rate constants for the onset and offset of binding to estimate an equilibrium constant for ligand binding. If this agrees with the equilibrium constant found as the EC50 for binding at equilibrium, this...
Predicting transcriptional responses to specific perturbations is critical for understanding cellular regulatory mechanisms and accelerating drug discovery. Single-cell RNA sequencing destroys each measured cell, yielding only unpaired populations of control and perturbed cells. However, existing methods typically model perturbation...
When the rates of ligand binding are measured by methods such as surface plasmon resonance, it is common practice to use the observed rate constants for the onset and offset of binding to estimate an equilibrium constant for ligand binding. If this agrees with the equilibrium constant found as the EC50 for binding at equilibrium, this...