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Gut microbial composition has been linked to multiple health outcomes. Yet, temporal analysis of this composition had been limited to deterministic models. In this paper, we introduce a probabilistic model for the dynamics of intestinal…

Quantitative Methods · Quantitative Biology 2018-09-03 Ruiqi Zhong , Tyler Joseph , Joao B Xavier , Itsik Pe'er

The survival of many microorganisms, like \textit{Leptospira} or \textit{Spiroplasma} bacteria, can depend on their ability to navigate towards regions of favorable viscosity. While this ability, called viscotaxis, has been observed in…

Soft Condensed Matter · Physics 2018-05-23 Benno Liebchen , Paul Monderkamp , Borge ten Hagen , Hartmut Löwen

Bacteria often develop distinct phenotypes to adapt to environmental stress. In particular, they can produce biofilms, dense communities of bacteria that live in a complex extracellular matrix. Bacterial biofilms provide a safe haven from…

Quantitative Methods · Quantitative Biology 2025-08-29 Stephen Williams , Daravuth Cheam , Michele K. Nishiguchi , Suzanne S. Sindi , Shilpa Khatri , Erica M. Rutter

The short version of new quantum quantitative Hierarchic theory, general for solids and liquids is presented. Condensed matter is considered as a system of 3D standing waves of different nature: thermal de Broglie waves (waves B), IR…

General Physics · Physics 2009-11-07 Alex Kaivarainen

Tissues and organs are composed of distinct cell types that must operate in concert to perform physiological functions. Efforts to create high-dimensional biomarker catalogs of these cells are largely based on transcriptomic single-cell…

The discovery in the early 2000's that magnetic nanoparticles (MNPs) complexed to nonviral or viral vectors can, in the presence of an external magnetic field, greatly enhance gene transfer into cells has raised much interest. This…

Quantitative Methods · Quantitative Biology 2011-11-08 José I. Schwerdt , Gerardo F. Goya , Pilar Calatayud , Claudia B. Hereñú , Paula C. Reggiani , Rodolfo G. Goya

Bacterial vaginosis (BV) increases transmission of HIV, enhances the risk of preterm labour, and its associated malodour impacts the quality of life for many women. Clinical diagnosis primarily relies on microscopy to presumptively detect a…

Experimentalists have observed phenotypic variability in isogenic bacteria populations. We explore the hypothesis that in fluctuating environments this variability is tuned to maximize a bacterium's expected log growth rate, potentially…

Populations and Evolution · Quantitative Biology 2018-07-25 Sarah E. Marzen , James P. Crutchfield

Bacteria build multicellular communities termed biofilms, which are often encased in a self-secreted extracellular matrix that gives the community mechanical strength and protection against harsh chemicals. How bacteria assemble distinct…

Biological Physics · Physics 2023-09-27 Jakub A. Kochanowski , Bobby Carroll , Merrill E. Asp , Emma Kaputa , Alison E. Patteson

Motile bacteria are known to accumulate at surfaces, eventually leading to changes in bacterial motility and bio-film formation. We use a novel two-colour, three-dimensional Lagrangian tracking technique, to follow simultaneously the body…

Advances in cellular imaging technologies, especially those based on fluorescence in situ hybridization (FISH) now allow detailed visualization of the spatial organization of human or bacterial cells. Quantifying this spatial organization…

Ocean microbes are critical to both ocean ecosystems and the global climate. Flow cytometry, which measures cell optical properties in fluid samples, is routinely used in oceanographic research. Despite decades of accumulated data,…

Methodology · Statistics 2025-04-17 Sangwon Hyun , Tim Coleman , Francois Ribalet , Jacob Bien

Quantifying fish community structure is essential for understanding biodiversity and ecosystem responses in a changing environment, yet existing survey methods provide limited high-frequency, quantitative observations. Conventional…

Computer Vision and Pattern Recognition · Computer Science 2026-05-12 Kota Ishikawa , Takuma Masui , Keita Koeda , Rickdane Gomez , Lucas Yutaka Kimura , Michio Kondoh

We developed a new endogenous approach to reveal subcellular metabolic contrast in fresh ex vivo tissues taking advantage of the time dependence of the full field optical coherence tomography interferometric signals. This method reveals…

Medical Physics · Physics 2016-01-07 Clement Apelian , Fabrice Harms , Olivier Thouvenin , A. Claude Boccara

Microrobots are considered as promising tools for biomedical applications. However, the imaging of them becomes challenges in order to be further applied on in vivo environments. Here we report the magnetic navigation of a paramagnetic…

Robotics · Computer Science 2018-09-19 Qianqian Wang , Lidong Yang , Jiangfan Yu , Chi-Ian Vong , Philip Wai Yan Chiu , Li Zhang

Biotite crystals are phyllosilicate trioctahedral micas with the general chemical formula K(Mg,Fe)3AlSi3O10(OH)2 that form a solid-solution series with iron-poor phlogopite and iron-rich annite endmembers. With a wide band gap energy and a…

Identifying local structural motifs and packing patterns of molecular solids is a challenging task for both simulation and experiment. We demonstrate two novel approaches to characterize local environments in different polymorphs of…

Materials Science · Physics 2024-04-02 Daisuke Kuroshima , Michael Kilgour , Mark E. Tuckerman , Jutta Rogal

Identification of abnormalities in red blood cells (RBC) is key to diagnosing a range of medical conditions from anaemia to liver disease. Currently this is done manually, a time-consuming and subjective process. This paper presents an…

Computer Vision and Pattern Recognition · Computer Science 2021-06-02 Annika Wong , Nantheera Anantrasirichai , Thanarat H. Chalidabhongse , Duangdao Palasuwan , Attakorn Palasuwan , David Bull

Solid state battery technology is motivated by the desire to deliver flexible power storage in a safe and efficient manner. The increasingly widespread use of batteries from mass-production facilities highlights the need for a rapid and…

Flagellar-driven locomotion plays a critical role in bacterial attachment and colonization of surfaces, contributing to the risks of contamination and infection. Tremendous attempts to uncover the underlying principles governing bacterial…

Soft Condensed Matter · Physics 2025-02-19 Xin-Xin Xu , Yangguang Tian , Yuhe Pu , Bingchen Che , Hao Luo , Yanan Liu , Yan-Jun Liu , Guangyin Jing