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Uncovering Turbulent Dynamics in Stenotic Flows from 4D-flow MRI Measurements via Resolvent Analysis and Data Assimilation

arXiv:2606.03838v1 Announce Type: new Abstract: This study presents a hybrid experimental and computational framework that couples in vitro 4D phase-contrast magnetic resonance imaging (4D-flow MRI) measurements with data assimilation and linear modeling to characterize the flow linear amplification mechanisms. We manufacture an idealized stenosis phantom with a cosine-shaped contraction and acquire three-dimensional (3D) mean velocity measurements at Reynolds number 3960 using 4D-flow MRI....

arXiv Physics 7d ago

Time-Resolved Stress Analysis of Tissue Simulants During Needle-Free Jet Injection

arXiv:2606.07691v1 Announce Type: new Abstract: Needle-free jet injection generates transient internal stress fields that can influence tissue deformation, pain-related stimulation, and cellular-level mechanical responses. However, the penetration mechanics have often been inferred from cavity deformation and interpreted mainly as shear-dominated behavior. In this study, high-speed photoelastic measurements were used to visualize and quantify optically integrated stress responses in a 5 wt%...

arXiv Physics 1d ago

Disentangling spanwise asymmetries in unsteady wing wakes: global mode sensitivity and spatio-temporal harmonic resolvent analyses

arXiv:2606.00859v1 Announce Type: new Abstract: We investigate the emergence of long-time spanwise asymmetries in an unsteady wake downstream of a finite-span wing by disentangling flow asymmetries into symmetric and anti-symmetric components using global mode (structural) sensitivity and spatio-temporal harmonic resolvent analysis. The global mode sensitivity analysis shows that asymmetric modes emerge when symmetric and anti-symmetric eigenmodes appear as pairs and exhibit high levels of...

arXiv Physics 8d ago

Personalized reference genome-based pipeline reveals comprehensive haplotype-resolved views of cancer genomes

Cancer genome analysis relies on standard human reference genomes but detecting somatic alterations in highly repetitive or individual-specific regions remains challenging. We developed the Personalized Reference genome-based Cancer Genome Analysis Pipeline (PRCGAP), to our knowledge, the first comprehensive pipeline integrating haplotype-resolved analyses of somatic point mutations, structural variants, copy number, and DNA methylation on personalized diploid reference genomes. We applied...

bioRxiv 11d ago

Ultra-low biomass sequencing workflow (LBV-Seq) enables de novo metagenomic reconstruction of DNA and RNA viral genomes

Genome-resolved virome analysis remains inaccessible for many samples, including those with clinical relevance, because viral nucleic acid recovered after enrichment is often too scarce to support de novo genome assembly. As a result, many analyses are limited to sparse read-level detection, which cannot recover divergent viruses, resolve strains, or interpret gene-level variation. Here, we developed Low Biomass Viral Sequencing (LBV-Seq), a workflow that couples low-input viral sample...

bioRxiv 11d ago

Ontology-constrained multi-LLM scoring of hypothesis support in the predictive processing literature

arXiv:2606.05206v1 Announce Type: cross Abstract: Fragmentation is common in interdisciplinary fields with diverse methods and theoretical commitments. Predictive coding neuroscience is a clear example: its literature spans computational theory, electrophysiology, imaging, behavior, and modeling, creating a synthesis problem that conventional meta-analysis cannot easily resolve. Here, we describe a local multi-LLM pipeline for ontology-constrained literature synthesis.

arXiv CS 5d ago

Slice-Profile-Enabled Phase Distribution Graphs for MRI Simulation

arXiv:2606.09233v1 Announce Type: new Abstract: MRI simulation often separates two descriptions that are both essential for realistic sequence analysis: Bloch dynamics for waveform-resolved radiofrequency (RF) excitation, and phase-graph methods for coherence-pathway evolution. Extended Phase Graph (EPG) models provide pathway tracking, and Phase--Distribution Graphs (PDG) extend this idea to spatially resolved $k$-space simulation, but existing PDG formulations rely on hard-pulse RF mixing...

arXiv Physics 1d ago

Chromap Suite: an open-source single-binary platform for agentic multiomic RNA + ATAC profiling

Single-cell multiomic profiling of RNA expression and chromatin accessibility is now a standard tool for resolving regulatory state in single cells, but existing analysis toolchains have lagged. Cell Ranger ARC, the proprietary multiomic pipeline, uses a custom broad peak caller rather than the MACS3 narrow peaks that the ATAC field has consolidated on, and its restrictive end-user licence forbids redistribution of analysis pipelines that include it. A fully open-source,...

bioRxiv 4d ago

FitED: A User-Centric, Extensible Software Environment for Robust Peak-Profile and General Functional Data Fitting

Announce Type: replace Abstract: Reliable parameter extraction from experimental data is essential for quantitative analysis across spectroscopy, diffraction, photoluminescence, chromatography, microscopy, and time-resolved measurements. However, nonlinear fitting often remains difficult to reproduce, especially when complex models, correlated parameters, uncertain derived quantities, and user-dependent fitting choices are involved. We present FitED, a Python-based desktop application for...

arXiv Physics 9d ago

FitED: A User-Centric, Extensible Software Environment for Robust Peak-Profile and General Functional Data Fitting

Announce Type: replace-cross Abstract: Reliable parameter extraction from experimental data is essential for quantitative analysis across spectroscopy, diffraction, photoluminescence, chromatography, microscopy, and time-resolved measurements. However, nonlinear fitting often remains difficult to reproduce, especially when complex models, correlated parameters, uncertain derived quantities, and user-dependent fitting choices are involved. We present FitED, a Python-based desktop application...

arXiv CS 9d ago