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differential geometry

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https://read.qxmd.com/read/30878582/f-actin-dynamics-regulates-mammalian-organ-growth-and-cell-fate-maintenance
#1
Arianna Pocaterra, Giulia Santinon, Patrizia Romani, Irene Brian, Andrea Dimitracopoulos, Andrea Ghisleni, Alejandro Carnicer-Lombarte, Mattia Forcato, Paola Braghetta, Marco Montagner, Francesca Galuppini, Mariaceleste Aragona, Gianmaria Pennelli, Silvio Bicciato, Nils Gauthier, Kristian Franze, Sirio Dupont
BACKGROUND & AIMS: In vitro, several data indicate that cell function can be regulated by the mechanical properties of cells and of the microenvironment. Cells measure these features by developing forces via their actomyosin cytoskeleton, and respond accordingly by transducing forces into biochemical signals that instruct cell behavior. Among these, the transcriptional coactivators YAP/TAZ recently emerged as key factors mediating multiple responses to actomyosin contractility. However, whether mechanical cues regulate adult liver tissue homeostasis, and whether this occurs through YAP/TAZ, remains largely unaddressed...
March 13, 2019: Journal of Hepatology
https://read.qxmd.com/read/30876113/correlation-of-circular-differential-optical-absorption-with-geometric-chirality-in-plasmonic-meta-atoms
#2
Jon C Wilson, Philipp Gutsche, Sven Herrmann, Sven Burger, Kevin M McPeak
We report a strong correlation between the calculated broadband circular differential optical absorption (CDOA) and the geometric chirality of plasmonic meta-atoms with two-dimensional chirality. We investigate this correlation using three common gold meta-atom geometries: L-shapes, triangles, and nanorod dimers, over a broad range of geometric parameters. We show that this correlation holds for both contiguous plasmonic meta-atoms and non-contiguous structures which support plasmonic coupling effects. A potential application for this correlation is the rapid optimization of plasmonic nanostructure for maximum broadband CDOA...
February 18, 2019: Optics Express
https://read.qxmd.com/read/30869195/bone-fracture-healing-under-ilizarov-fixator-influence-of-fixator-configuration-fracture-geometry-and-loading
#3
Ganesharajah Ganadhiepan, Saeed Miramini, Minoo Patel, Priyan Mendis, Lihai Zhang
[1] This study aims to enhance the understanding of the relationship between Ilizarov fixator configuration and its effects on bone fracture healing. Using Taylor spatial frame (TSF) as an example, the roles of critical parameters (i.e. TSF ring diameter, wire pretension, fracture gap size and axial load) that govern fracture healing during the early stages were investigated by using computational modelling in conjunction with mechanical testing involving an advanced 3D optical measurement system. The computational model was first validated using the mechanical test results and then used to simulate mesenchymal stem cell (MSC) differentiations within different regions of the fracture site under various combinations of TSF ring diameter, wire pretension, fracture gap size and axial load values...
March 14, 2019: International Journal for Numerical Methods in Biomedical Engineering
https://read.qxmd.com/read/30867292/growth-and-morphogenesis-of-the-gastropod-shell
#4
Adam B Johnson, Nina S Fogel, J David Lambert
Gastropod shell morphologies are famously diverse but generally share a common geometry, the logarithmic coil. Variations on this morphology have been modeled mathematically and computationally but the developmental biology of shell morphogenesis remains poorly understood. Here we characterize the organization and growth patterns of the shell-secreting epithelium of the larval shell of the basket whelk Tritia (also known as Ilyanassa ). Despite the larval shell's relative simplicity, we find a surprisingly complex organization of the shell margin in terms of rows and zones of cells...
March 13, 2019: Proceedings of the National Academy of Sciences of the United States of America
https://read.qxmd.com/read/30865900/genetic-single-neuron-anatomy-reveals-fine-granularity-of-cortical-axo-axonic-cells
#5
Xiaojun Wang, Jason Tucciarone, Siqi Jiang, Fangfang Yin, Bor-Shuen Wang, Dingkang Wang, Yao Jia, Xueyan Jia, Yuxin Li, Tao Yang, Zhengchao Xu, Masood A Akram, Yusu Wang, Shaoqun Zeng, Giorgio A Ascoli, Partha Mitra, Hui Gong, Qingming Luo, Z Josh Huang
Parsing diverse nerve cells into biological types is necessary for understanding neural circuit organization. Morphology is an intuitive criterion for neuronal classification and a proxy of connectivity, but morphological diversity and variability often preclude resolving the granularity of neuron types. Combining genetic labeling with high-resolution, large-volume light microscopy, we established a single neuron anatomy platform that resolves, registers, and quantifies complete neuron morphologies in the mouse brain...
March 12, 2019: Cell Reports
https://read.qxmd.com/read/30850656/capturing-3d-large-strain-euler-bending-filament-dynamics-in-fibrous-media-simulations-sample-case-of-compression-collapse-in-dendritic-actin-network
#6
Jyothirmai J Simhadri, Preethi L Chandran
Cytoskeletal networks to transmission towers are comprised of slender elements. Slender filaments bend and buckle more easily than stretch. Therefore a deforming network is expected to exhaust all possible bending-based modes before engaging filament stretch. While the large-strain bending critically determines fibrous-media response, simulations use small-strain and jointed approximations. At low resolution, these approximations inflate bending resistance and delay buckling onset. The proposed string-of-continuous-beams (SOCB) approach captures 3D nonlinear Euler bending of filaments with high fidelity at low cost...
March 8, 2019: Scientific Reports
https://read.qxmd.com/read/30843826/system-independent-ultrasound-attenuation-coefficient-estimation-using-spectra-normalization
#7
Ping Gong, Pengfei Song, Chengwu Huang, Joshua Trzasko, Shigao Chen
Ultrasound attenuation coefficient estimation has diagnostic potential for clinical applications such as differentiating tumors and quantifying fat content in the liver. The two commonly used attenuation coefficient estimation methods in ultrasound array imaging system are the spectral shift method and the reference-phantom-based methods. The spectra shift method estimates the central frequency downshift along depth, whereas the reference-phantom-based methods use a well-calibrated phantom to cancel system dependent effects in attenuation estimation...
March 5, 2019: IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control
https://read.qxmd.com/read/30826909/the-morphology-of-the-human-mandible-a-computational-modelling-study
#8
Ravin Vallabh, Ju Zhang, Justin Fernandez, George Dimitroulis, David C Ackland
Cephalometric methods have been used to evaluate morphometric measurements of the mandible and quantify sex-related anatomical features; however, most studies to date employ a limited set of location-specific measurements without considering the entire three-dimensional anatomy of the mandible. The aims of this study were to develop statistical shape models (SSMs) of partially edentulous male and female mandibles to evaluate inter-subject morphological variability and secondly to assess the effectiveness of discrete clinical morphometric measurements in prediction of complete three-dimensional mandible geometry...
March 2, 2019: Biomechanics and Modeling in Mechanobiology
https://read.qxmd.com/read/30818295/random-sequential-addition-simulations-of-animal-aggregations-provide-null-models-of-group-structure
#9
Daniel Olsen, David Murphy
Apparent structure in animal aggregations such as fish and Antarctic krill schools may result from the tight packing of these elongated animals. This geometrical structure may be difficult to differentiate from behavior-induced structure resulting from individuals preferentially taking up certain positions relative to conspecifics to gain an adaptive advantage such as reduced locomotive cost. Here we use random sequential addition (RSA) simulations to quantify the effect of animal shape, aggregation organization, and aggregation density on two-dimensional school structure...
February 28, 2019: Bioinspiration & Biomimetics
https://read.qxmd.com/read/30818291/reconstruction-algorithm-for-frequency-differential-eit-using-absolute-values
#10
Tobias Menden, Jakob Orschulik, Sebastién Dambrun, Jascha Matuszczyk, Susana Aguiar Santos, Steffen Leonhardt, Marian Walter
OBJECTIVE: Tissues in the body differ by their frequency-dependent conductivity. Frequency-differential Electrical Impedance Tomography (fdEIT) is a promising technique to reconstruct the distribution of tissue inside the body by injecting current at two frequencies and measuring the resulting surface-potential. APPROACH: The Gauss-Newton method is one way to map the surface measurements to a conductivity image. Usually, the minimization function contains only weighted differential measurement data and a regularization...
February 28, 2019: Physiological Measurement
https://read.qxmd.com/read/30810546/fast-quantification-of-nanorod-geometry-by-dma-spicp-ms
#11
Jiaojie Tan, Yong Yang, Hind El Hadri, Mingdong Li, Vincent A Hackley, Michael R Zachariah
A fast, quantitative method for determining the dimensions of nanorods (i.e., length and diameter) is described, based on hyphenation of differential mobility analysis (DMA) with single particle inductively coupled plasma mass spectrometry (spICP-MS). Seven gold nanorod samples with different dimensions (diameters 11.8 nm to 38.2 nm, aspect ratios 1.8 to 6.9) were used to validate the method. We demonstrate that DMA-spICP-MS can (1) achieve quantification of both length and diameter comparable with TEM analysis, (2) make statistically meaningful measurements in minutes at low concentrations (<108 mL-1) and (3) separate nanorods from spheres and quantify the geometry of each population...
February 27, 2019: Analyst
https://read.qxmd.com/read/30803278/preparation-of-chitosan-microcapsules-containing-red-ginger-oleoresin-using-emulsion-crosslinking-method
#12
Jayanudin, Moh Fahrurrozi, Sang Kompiang Wirawan, Rochmadi
BACKGROUND: Encapsulation is one of the methods used to trap active ingredients in the wall material of microparticles. AIM: The aim of this study was to evaluate the encapsulation of red ginger oleoresin using an emulsion crosslinking method with chitosan as the wall material. METHODS: Emulsions were formed of red ginger oleoresin with chitosan in concentrations of 1%, 2%, 3%, and 4% (w/v), respectively. The emulsions were then mixed with corn oil and stirred for one hour to obtain a second set of emulsions, and glutaraldehyde saturated toluene (GST) was added dropwise in quantities of 20, 10, 6...
January 2019: Journal of Applied Biomaterials & Functional Materials
https://read.qxmd.com/read/30802044/differential-protonation-at-the-catalytic-six-iron-cofactor-of-fefe-hydrogenases-revealed-by-57-fe-nuclear-resonance-x-ray-scattering-and-quantum-mechanics-molecular-mechanics-analyses
#13
Stefan Mebs, Jifu Duan, Florian Wittkamp, Sven T Stripp, Thomas Happe, Ulf-Peter Apfel, Martin Winkler, Michael Haumann
[FeFe]-hydrogenases are efficient biological hydrogen conversion catalysts and blueprints for technological fuel production. The relations between substrate interactions and electron/proton transfer events at their unique six-iron cofactor (H-cluster) need to be elucidated. The H-cluster comprises a four-iron cluster, [4Fe4S], linked to a diiron complex, [FeFe]. We combined 57 Fe-specific X-ray nuclear resonance scattering experiments (NFS, nuclear forward scattering; NRVS, nuclear resonance vibrational spectroscopy) with quantum-mechanics/molecular-mechanics computations to study the [FeFe]-hydrogenase HYDA1 from a green alga...
February 25, 2019: Inorganic Chemistry
https://read.qxmd.com/read/30795574/the-effect-of-microfluidic-geometry-on-myoblast-migration
#14
Rahul Atmaramani, Bryan J Black, Kevin H Lam, Vinit M Sheth, Joseph J Pancrazio, David W Schmidtke, Nesreen Zoghoul Alsmadi
In vitro systems comprised of wells interconnected by microchannels have emerged as a platform for the study of cell migration or multicellular models. In the present study, we systematically evaluated the effect of microchannel width on spontaneous myoblast migration across these microchannels-from the proximal to the distal chamber. Myoblast migration was examined in microfluidic devices with varying microchannel widths of 1.5⁻20 µm, and in chips with uniform microchannel widths over time spans that are relevant for myoblast-to-myofiber differentiation in vitro...
February 21, 2019: Micromachines
https://read.qxmd.com/read/30785254/controlled-nanoscale-topographies-for-osteogenic-differentiation-of-mesenchymal-stem-cells
#15
Catarina R Pedrosa, Didier Arl, Patrick Grysan, Irfan Khan, Stéphanie Durrieu, Sivashankar Krishnamoorthy, Marie-Christine Durrieu
Nanotopography with length scales of the order of extracellular matrix elements offers the possibility of regulating cell behavior. Investigation of the impact of nanotopography on cell response has been limited by the inability to precisely control geometries, especially at high spatial resolutions and across practically large areas. In this paper, we demonstrate well-controlled and periodic nanopillar arrays of silicon and investigate their impact on osteogenic differentiation of human mesenchymal stem cells (hMSCs)...
February 20, 2019: ACS Applied Materials & Interfaces
https://read.qxmd.com/read/30783156/pressure-build-up-and-stress-variations-within-the-earth-s-crust-in-the-light-of-analogue-models
#16
Evangelos Moulas, Dimitrios Sokoutis, Ernst Willingshofer
Strength contrasts and spatial variations in rheology are likely to produce significant stress differences in the Εarth's crust. The buildup and the relaxation of stresses have important consequences for the state of stress of the brittle crust, its deformational behaviour and seismicity. We performed scaled analogue experiments of a classic wedge-type geometry wherein we introduced a weak, fluid-filled body representing a low-stress heterogeneity. The experiments were coupled to direct pressure measurements that revealed significant pressure differences from their surrounding stressed matrix...
February 19, 2019: Scientific Reports
https://read.qxmd.com/read/30778445/spatiotemporal-control-and-modeling-of-morphogen-delivery-to-induce-gradient-patterning-of-stem-cell-differentiation-using-fluidic-channels
#17
Brian O'Grady, Daniel A Balikov, Jason X Wang, Emma K Neal, Yu-Chuan Ou, Rizia Bardhan, Ethan S Lippmann, Leon M Bellan
The process of cell differentiation in a developing embryo is influenced by numerous factors, including various biological molecules whose presentation varies dramatically over space and time. These morphogens regulate cell fate based on concentration profiles, thus creating discrete populations of cells and ultimately generating large, complex tissues and organs. Recently, several in vitro platforms have attempted to recapitulate the complex presentation of extrinsic signals found in nature. However, it has been a challenge to design versatile platforms that can dynamically control morphogen gradients over extended periods of time...
February 19, 2019: Biomaterials Science
https://read.qxmd.com/read/30772345/brillouin-spectroscopy-of-normal-and-keratoconus-corneas
#18
Theo G Seiler, Peng Shao, Amira Eltony, Theo Seiler, Seok-Hyun Yun
PURPOSE: To investigate the age-dependence of Brillouin spectroscopy of the cornea and to compare normal and keratoconus corneas. DESIGN: Retrospective case-control study STUDY POPULATION: Healthy patients and patients suffering from keratoconus seen at the Institut für Refraktive und Ophthalmo-Chirurgie (IROC) between December 2016 and March 2017. METHODS: Brillouin frequency shifts of patients of 2 different groups were examined with Brillouin spectroscopy perpendicular to the corneal surface...
February 14, 2019: American Journal of Ophthalmology
https://read.qxmd.com/read/30768926/alkylphenol-inverse-agonists-of-hcn1-gating-h-bond-propensity-ring-saturation-and-adduct-geometry-differentially-determine-efficacy-and-potency
#19
Rebecca L Joyceadat, Nicole P Beyer, Georgia Vasilopoulos, Kellie Woll, Adam C Hall, Roderic G Eckenhoff, Dipti N Barman, J David Warren, Gareth R Tibbs, Peter A Goldstein
BACKGROUND AND PURPOSE: In models of neuropathic pain, inhibition of HCN1 is anti-hyperalgesic. 2,6-di-iso-propyl phenol (propofol) and its non-anesthetic congener, 2,6-di-tert-butyl phenol, inhibit HCN1 channels by stabilizing closed state(s). EXPERIMENTAL: approach Using in vitro electrophysiology and kinetic modeling, we systematically explore the contribution of ligand architecture to alkylphenol-channel coupling. KEY RESULTS: When corrected for changes in hydrophobicity (and propensity for intra-membrane partitioning), the decrease in potency upon 1-position substitution (NCO∼OH > SH > F) mirrors the ligands' H-bond acceptor (NCO > OH > SH > F) but not donor profile (OH > SH > NCO∼F)...
February 12, 2019: Biochemical Pharmacology
https://read.qxmd.com/read/30768327/holographic-r%C3%A3-nyi-entropy-at-high-energy-density
#20
Xi Dong
We show that Rényi entropies of subregions can be used to distinguish when the entire system is in a microcanonical ensemble from when it is in a canonical ensemble, at least in theories holographically dual to gravity. Simple expressions are provided for these Rényi entropies in a particular thermodynamic limit with high energy density and fixed fractional size of the subregion. Holographically, the Rényi entropies are determined by the areas of cosmic branes inserted into the bulk spacetime. They differ between a microcanonical and a canonical ensemble because the two ensembles provide different boundary conditions for the gravitational theory under which cosmic branes lead to different backreacted geometries...
February 1, 2019: Physical Review Letters
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