simulation

Active eye modeling: a tool for estimating retinal image quality across the visual field in everyday life

This paper introduces active eye modeling to estimate retinal image quality across the visual field during everyday activities, finding that near work under dim lighting increases peripheral blur.

Estimating glioblastoma migration-to-proliferation ratio from single time-point MRI data via radial density distribution

A reaction-diffusion model fitted to shell-averaged tumor density from one pre-treatment MRI estimates glioblastoma migration/proliferation ratio (D/k); in BraTS 2017, higher D/k went with shorter overall survival.

Linking clinical border morphology to cell-scale growth mechanisms in melanoma: a segmentation-to-simulation alignment study

Across 1,581 ISIC 2018 lesions, melanoma borders differ from nevi mainly by coarse lobulation rather than fractal dimension; of six simulated mechanisms, only an imposed long-range growth-rate field reproduces this.

From Coral Color to Tissue Heating: How Host Pigments Redirect Light Within the Tissue

The paper models how coral host pigments affect light propagation and tissue heating, showing distinct roles of chromoproteins and fluorescent proteins in energy distribution and heat generation.

Mechanisms underlying the defective development of xyloglucan-deficient root hairs in Arabidopsis thaliana

This study investigates the cellular and biomechanical mechanisms behind defective root hair development in xyloglucan-deficient Arabidopsis mutants, identifying matrix-cellulose interactions as critical for anisotropic growth.

Unraveling phenotypic variation in multiscale behavioral dynamics

Comparing coarse-grained dynamics across resolutions, weighted by sampling uncertainty, yields phenotypic spaces linking E. coli run speed to CheB and showing paramecia experience narrows zebrafish variability.

Mapping the Trade-Offs That Shape Mammalian Brain Network Architecture

Across 25,000 generative-model networks scored on 29 properties, 635 human and 224 mammalian connectomes cluster in one narrow niche, trading wiring economy for computational capability and robustness.

Grow2Fold: mapping heterogeneous developmental growth to human brain folding

Grow2Fold models brain folding by integrating imaging data with mechanical simulations to show differential growth drives cortical folding patterns.

Rapid simulation of organ-scale oxygen transport for tissue ischemia prediction

The paper introduces a computational toolkit to simulate organ-scale oxygen transport and predict tissue ischemia by analyzing vessel networks and physiological conditions.

Cortical organoid diffusion MRI reveals protocol-associated spatial reproducibility and increasing apparent diffusivity with diffusion time

This study uses cortical organoids to examine diffusion MRI reproducibility and apparent diffusivity changes with diffusion time, finding increased apparent mean diffusivity in most tissue voxels.

Rapid spatial cognition in mice, with and without neocortex and hippocampus

Naive mice learn a 9-turn route in a reconfigurable 3D maze within about 20 rewards; mutants lacking neocortex and hippocampus also learn, remember and generalize, though early exploration is inefficient.

Prion Protein Deficiency Results in Synaptic, Neural Network and Behavioral Alterations

Lifelong prion protein (PrP) loss in mice lowers excitatory synaptic proteins, makes network bursts in mature cortical cultures rarer and neuronal activity more correlated, and increases adult dimming-disk escapes.

Division of labor during bacterial warfare

The paper investigates bacterial warfare by analyzing toxin production in Escherichia coli, finding that localized toxin bursts are more effective than uniform production in structured populations.

On the neural origin of hexadirectional fMRI modulations

The paper proposes experiments to distinguish mechanisms underlying hexadirectional fMRI modulations linked to grid-cell activity.

Active control of surface immobilization in the foraging behavior of Paramecium

Paramecium tetraurelia alternates fast swimming with minutes-long surface immobilization when bacteria are present; stops require calcium influx and come from halting locomotor cilia while oral cilia keep beating.

Incomplete references leave bulk deconvolution targets non-identifiable, but identification has a computable precision price

With an incomplete deconvolution reference, operator history changes estimates and associations, and the target is not point-identified; fitdrop scores remedies on shrinkage, coverage, certification and false certification, and prices measurements.

Sex differences in exploration-exploitation strategies during home-cage decision making

In 136 mice on FED3 tasks, males showed slightly higher win-stay in all three choice tasks, with higher accuracy in a deterministic bandit but not a probabilistic one.

QuantiTrack: A unified software to study protein dynamics in living cells

QuantiTrack, a MATLAB GUI, unifies single-molecule detection, tracking, quality control and mobility analyses; for glucocorticoid receptor, hormone washout cut bound fraction, dwell times and low-mobility occupancy.

Revisiting bacterial division control with likelihood inference: limited identifiability of simple models

Likelihood comparison on six E. coli mother-machine datasets finds sizer, adder, and log-foldchange division rules only weakly separable, while a neural conditional cycle-duration model fits best.

NUCGEN3D: A synthetic framework for large-scale 3D nuclear segmentation with open-source training data and models

The paper introduces NucGen3D, a synthetic framework for generating 3D nuclear segmentation datasets, and trains models that outperform existing methods on real-world data.

Structural basis for catalytic and inhibitory divergence between archaeal and bacterial ammonia monooxygenases

Archaeal ammonia monooxygenase (AMO) is a cup-shaped homotrimer using a mononuclear CuD site; inhibitors bind bacterial AMO's dicopper center directly but apparently inactivate archaeal AMO indirectly by relocating copper.

RhabdoForge: A Modular, Biophysically-Grounded Rendering Framework for Insect Vision Neuroethology

RhabdoForge provides a rendering framework for insect vision neuroethology, enabling simulation of compound eye dynamics and closed-loop visual behaviors.

Granule cells reorient cortical trajectories to separate contexts

In mice learning two tasks, cerebellar granule cells kept the low-rank geometry of premotor cortical output within each task but rotated their population trajectories apart between tasks, while cortex generalized.

Sensory experience drives glutamate spillover, presynaptic LTP and functional connectome remodeling in the barrel cortex

The paper shows that sensory experience increases glutamate release and strengthens synaptic connections in the barrel cortex, leading to changes in the functional connectome.

A Premotor Excitation-Inhibition Motif Shapes Protopodium Dynamics During Drosophila Larval Forward Crawling

In Drosophila larvae, ventral oblique (VO) muscles drive protopodium folding, and a tri-segmental A27h–A18b3–A06c premotor excitation-inhibition motif restricts their activation to a late, forward-specific window.

Anisotropic conductivity modeling for tDCS in Parkinsons disease using multidimensional diffusion MRI

tDCS fields from a multidimensional diffusion MRI conductivity model stayed within a few percent of DTI and isotropic predictions in 29 participants; whole-brain field instead tracked CSF fraction.

DNA gyrase in live bacteria forms liquid condensates through weak multivalent bonding of excess GyrB

Live E. coli gyrase clusters hold excess GyrB (B:A 2.5:1), show hexanediol-sensitive liquid-like turnover, and docking suggests GyrB bridges heterotetramers.

Thousandfold Expansion Microscopy

A four-network sodium acrylate/dimethylacrylamide hydrogel, cast ionic-within-ionic without neutral re-embedding, reaches about 1000-fold linear expansion and resolves individual peptide residues on standard confocal microscopes.

Biomarker Variability Limits Individualized Amyloid Time Estimation in Alzheimer Disease

This study evaluates how biomarker variability affects individualized amyloid time estimation in Alzheimer's disease, finding that inter-individual variability is the main source of error.

A realistic in-silico brain phantom for quantifying susceptibility anisotropy-induced error in susceptibility separation

The paper creates an in-silico brain phantom to evaluate how susceptibility anisotropy affects susceptibility separation algorithms, finding increased error in negative susceptibility estimates with anisotropy.