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https://www.readbyqxmd.com/read/29223037/a-microfabricated-platform-for-the-study-of-chondrogenesis-under-different-compressive-loads
#1
Reza Kowsari-Esfahan, Azadeh Jahanbakhsh, Mohammad Said Saidi, Shahin Bonakdar
Microfluidic devices are beneficial in miniaturizing and multiplexing various cellular assays in a single platform. Chondrogenesis is known to pertain to chemical, topographical, and mechanical cues in the microenvironment. Mechanical cues themselves have numerous parameters such as strain magnitude, frequency, and stimulation time. Effects of different strain magnitudes on the chondrogenic differentiation of adult stem cells have not been explored thoroughly. Here, a new multilayer microdevice is presented for the unidirectional compressive stimulation of cells in a three-dimensional cell culture...
December 5, 2017: Journal of the Mechanical Behavior of Biomedical Materials
https://www.readbyqxmd.com/read/29222815/evaluation-and-comparison-of-2-on-farm-tests-for-estimating-somatic-cell-count-in-quarter-milk-samples-from-lactating-dairy-cattle
#2
S A Kandeel, A A Megahed, F K Arnaout, P D Constable
BACKGROUND: The somatic cell count (SCC) is commonly used to monitor udder health and diagnose subclinical intramammary infection (IMI) in dairy cattle. HYPOTHESIS: The Somaticell test (ST) and California mastitis test (CMT) are clinically useful cow-side tests for diagnosing subclinical IMI. ANIMALS: One hundred and eleven dairy cows at dry-off and 92 cows within 4-7 days postcalving. METHODS: Quarter foremilk samples were obtained and analyzed with a DeLaval cell counter (DCC, reference method), ST, and CMT...
December 9, 2017: Journal of Veterinary Internal Medicine
https://www.readbyqxmd.com/read/29222748/analyzing-and-designing-cell-factories-with-optflux
#3
Paulo Vilaça, Paulo Maia, Hugo Giesteira, Isabel Rocha, Miguel Rocha
OptFlux was launched in 2010 as the first open-source and user-friendly platform containing all the major methods for performing metabolic engineering tasks in silico. Main features included the possibility of performing microbial strain simulations with widely used methods such as Flux Balance Analysis and strain design using Evolutionary Algorithms. Since then, OptFlux suffered a major re-factoring to improve its efficiency and reliability, while many features were added in the form of novel plug-ins, such as the BioVisualizer and the over/under expression plug-ins...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29222674/effect-of-rehabilitation-exercise-durations-on-the-dynamic-bone-repair-process-by-coupling-polymer-scaffold-degradation-and-bone-formation
#4
Quan Shi, Qiang Chen, Nicola Pugno, Zhi-Yong Li
Implantation of biodegradable scaffold is considered as a promising method to treat bone disorders, but knowledge of the dynamic bone repair process is extremely limited. In this study, based on the representative volume cell of a periodic scaffold, the influence of rehabilitation exercise duration per day on the bone repair was investigated by a computational framework. The framework coupled scaffold degradation and bone remodeling. The scaffold degradation was described by a function of stochastic hydrolysis independent of mechanical stimulation, and the bone formation was remodeled by a function of the mechanical stimulation, i...
December 8, 2017: Biomechanics and Modeling in Mechanobiology
https://www.readbyqxmd.com/read/29222519/virtual-screening-for-inhibitors-of-the-human-tslp-tslpr-interaction
#5
Dries Van Rompaey, Kenneth Verstraete, Frank Peelman, Savvas N Savvides, Koen Augustyns, Pieter Van Der Veken, Hans De Winter
The pro-inflammatory cytokine thymic stromal lymphopoietin (TSLP) plays a pivotal role in the pathophysiology of various allergy disorders that are mediated by type 2 helper T cell (Th2) responses, such as asthma and atopic dermatitis. TSLP forms a ternary complex with the TSLP receptor (TSLPR) and the interleukin-7-receptor subunit alpha (IL-7Rα), thereby activating a signaling cascade that culminates in the release of pro-inflammatory mediators. In this study, we conducted an in silico characterization of the TSLP:TSLPR complex to investigate the drugability of this complex...
December 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29222455/binding-modes-of-teixobactin-to-lipid-ii-molecular-dynamics-study
#6
Yang Liu, Yaxin Liu, Mary B Chan-Park, Yuguang Mu
Teixobactin (TXB) is a newly discovered antibiotic targeting the bacterial cell wall precursor Lipid II (LII). In the present work, four binding modes of TXB on LII were identified by a contact-map based clustering method. The highly flexible binary complex ensemble was generated by parallel tempering metadynamics simulation in a well-tempered ensemble (PTMetaD-WTE). In agreement with experimental findings, the pyrophosphate group and the attached first sugar subunit of LII are found to be the minimal motif for stable TXB binding...
December 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29222424/structural-insight-into-a-ce15-esterase-from-the-marine-bacterial-metagenome
#7
Concetta De Santi, Osman Absm Gani, Ronny Helland, Adele Williamson
The family 15 carbohydrate esterase (CE15) MZ0003, which derives from a marine Arctic metagenome, has a broader substrate scope than other members of this family. Here we report the crystal structure of MZ0003, which reveals that residues comprising the catalytic triad differ from previously-characterized fungal homologs, and resolves three large loop regions that are unique to this bacterial sub-clade. The catalytic triad of the bacterial CE15, which includes Asp 332 as its third member, closely resembles that of family 1 carbohydrate esterases (CE1), despite the overall lower structural similarity with members of this family...
December 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29221989/differential-targeting-of-membrane-lipid-domains-by-caffeic-acid-and-its-ester-derivatives
#8
Hugo A L Filipe, Carla Sousa, Joaquim T Marquês, Diogo Vila-Viçosa, António de Granada Flor, Ana S Viana, M Soledade C S Santos, Miguel Machuqueiro, Rodrigo F M de Almeida
Phenolic acids have been associated to a wide range of important health benefits underlain by a common molecular mechanism of action. Considering that significant membrane permeation is prevented by their hydrophilic character, we hypothesize that their main effects result from the interplay with cell membrane surface. This hypothesis was tested using the paradigmatic caffeic acid (CA) and two of its ester derivatives, rosmarinic (RA) and chlorogenic (CGA) acids, for which we predict, based on molecular dynamics simulations, a shallow location in phospholipid bilayers dependent on the protonation-state...
December 5, 2017: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/29221091/raman-lidar-for-hydrogen-gas-concentration-monitoring-and-future-radioactive-waste-management
#9
Anasthase Liméry, Nicolas Cézard, Didier Fleury, Didier Goular, Christophe Planchat, Johan Bertrand, Alain Hauchecorne
A multi-channel Raman lidar has been developed, allowing for the first time simultaneous and high-resolution profiling of hydrogen gas and water vapor. The lidar measures vibrational Raman scattering in the UV (355 nm) domain. It works in a high-bandwidth photon counting regime using fast SiPM detectors and takes into account the spectral overlap between hydrogen and water vapor Raman spectra. Measurement of concentration profiles of H2 and H2O are demonstrated along a 5-meter-long open gas cell with 1-meter resolution at 85 meters...
November 27, 2017: Optics Express
https://www.readbyqxmd.com/read/29221080/integrated-pillar-scatterers-for-speeding-up-classification-of-cell-holograms
#10
Alessio Lugnan, Joni Dambre, Peter Bienstman
The computational power required to classify cell holograms is a major limit to the throughput of label-free cell sorting based on digital holographic microscopy. In this work, a simple integrated photonic stage comprising a collection of silica pillar scatterers is proposed as an effective nonlinear mixing interface between the light scattered by a cell and an image sensor. The light processing provided by the photonic stage allows for the use of a simple linear classifier implemented in the electric domain and applied on a limited number of pixels...
November 27, 2017: Optics Express
https://www.readbyqxmd.com/read/29220769/influence-of-urban-pattern-on-inundation-flow-in-floodplains-of-lowland-rivers
#11
M Bruwier, A Mustafa, D G Aliaga, P Archambeau, S Erpicum, G Nishida, X Zhang, M Pirotton, J Teller, B Dewals
The objective of this paper is to investigate the respective influence of various urban pattern characteristics on inundation flow. A set of 2000 synthetic urban patterns were generated using an urban procedural model providing locations and shapes of streets and buildings over a square domain of 1×1km2. Steady two-dimensional hydraulic computations were performed over the 2000 urban patterns with identical hydraulic boundary conditions. To run such a large amount of simulations, the computational efficiency of the hydraulic model was improved by using an anisotropic porosity model...
December 5, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29220306/improving-spiking-dynamical-networks-accurate-delays-higher-order-synapses-and-time-cells
#12
Aaron R Voelker, Chris Eliasmith
Researchers building spiking neural networks face the challenge of improving the biological plausibility of their model networks while maintaining the ability to quantitatively characterize network behavior. In this work, we extend the theory behind the neural engineering framework (NEF), a method of building spiking dynamical networks, to permit the use of a broad class of synapse models while maintaining prescribed dynamics up to a given order. This theory improves our understanding of how low-level synaptic properties alter the accuracy of high-level computations in spiking dynamical networks...
December 8, 2017: Neural Computation
https://www.readbyqxmd.com/read/29220305/spiking-neural-classifier-with-lumped-dendritic-nonlinearity-and-binary-synapses-a-current-mode-vlsi-implementation-and-analysis
#13
Aritra Bhaduri, Amitava Banerjee, Subhrajit Roy, Sougata Kar, Arindam Basu
We present a neuromorphic current mode implementation of a spiking neural classifier with lumped square law dendritic nonlinearity. It has been shown previously in software simulations that such a system with binary synapses can be trained with structural plasticity algorithms to achieve comparable classification accuracy with fewer synaptic resources than conventional algorithms. We show that even in real analog systems with manufacturing imperfections (CV of 23.5% and 14.4% for dendritic branch gains and leaks respectively), this network is able to produce comparable results with fewer synaptic resources...
December 8, 2017: Neural Computation
https://www.readbyqxmd.com/read/29220175/a-spectroscopic-signature-for-stable-%C3%AE-amyloid-fibrils-versus-%C3%AE-sheet-rich-oligomers
#14
Justin P Lomont, Kacie L Rich, Michał Maj, Jia-Jung Ho, Joshua S Ostrander, Martin T Zanni
We use 2D IR spectroscopy to explore fibril formation for the two predominant isoforms of the β-amyloid (Aβ1-40 and Aβ1-42) protein associated with Alzheimer's disease. 2D IR spectra resolve a transition at 1610 cm-1 in Aβ fibrils that does not appear in other Aβ aggregates, even those with predominantly β-sheet structure like oligomers. This transition is not resolved in linear IR spectroscopy, because it lies under the broad band centered at 1625 cm-1 that is the traditional infrared signature for amy-loid fibrils...
December 8, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29219034/measuring-relative-coupling-strength-in-circadian-systems
#15
Christoph Schmal, Erik D Herzog, Hanspeter Herzel
Modern imaging techniques allow the monitoring of circadian rhythms of single cells. Coupling between these single cellular circadian oscillators can generate coherent periodic signals on the tissue level that subsequently orchestrate physiological outputs. The strength of coupling in such systems of oscillators is often unclear. In particular, effects on coupling strength by varying cell densities, by knockouts, and by inhibitor applications are debated. In this study, we suggest to quantify the relative coupling strength via analyzing period, phase, and amplitude distributions in ensembles of individual circadian oscillators...
December 1, 2017: Journal of Biological Rhythms
https://www.readbyqxmd.com/read/29218993/energy-landscape-of-the-substrate-translocation-equilibrium-of-plasma-membrane-glutamate-transporters
#16
Jiali Wang, Thomas Albers, Christof T Grewer
Glutamate transporters maintain a large glutamate concentration gradient across synaptic membranes and are, thus, critical for functioning of the excitatory synapse. Mammalian glutamate transporters concentrate glutamate inside cells through energetic coupling of glutamate flux to the transmembrane concentration gradient of Na+. Structural models based on an archeal homologue of mammalian glutamate transporters, GltPh, suggest an elevator-like carrier mechanism. However, the energetic determinants of this carrier-based movement are not well understood...
December 8, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29218592/mathematical-modeling-of-the-effects-of-tumor-heterogeneity-on-the-efficiency-of-radiation-treatment-schedule
#17
Farinaz Forouzannia, Heiko Enderling, Mohammad Kohandel
Radiotherapy uses high doses of energy to eradicate cancer cells and control tumors. Various treatment schedules have been developed and tried in clinical trials, yet significant obstacles remain to improving the radiotherapy fractionation. Genetic and non-genetic cellular diversity within tumors can lead to different radiosensitivity among cancer cells that can affect radiation treatment outcome. We propose a minimal mathematical model to study the effect of tumor heterogeneity and repair in different radiation treatment schedules...
December 7, 2017: Bulletin of Mathematical Biology
https://www.readbyqxmd.com/read/29218591/model-based-phenotypic-signatures-governing-the-dynamics-of-the-stem-and-semi-differentiated-cell-populations-in-dysplastic-colonic-crypts
#18
Svetoslav Nikolov, Guido Santos, Olaf Wolkenhauer, Julio Vera
Mathematical modeling of cell differentiated in colonic crypts can contribute to a better understanding of basic mechanisms underlying colonic tissue organization, but also its deregulation during carcinogenesis and tumor progression. Here, we combined bifurcation analysis to assess the effect that time delay has in the complex interplay of stem cells and semi-differentiated cells at the niche of colonic crypts, and systematic model perturbation and simulation to find model-based phenotypes linked to cancer progression...
December 7, 2017: Bulletin of Mathematical Biology
https://www.readbyqxmd.com/read/29218016/synergistic-anti-arrhythmic-effects-in-human-atria-with-combined-use-of-sodium-blockers-and-acacetin
#19
Haibo Ni, Dominic G Whittaker, Wei Wang, Wayne R Giles, Sanjiv M Narayan, Henggui Zhang
Atrial fibrillation (AF) is the most common cardiac arrhythmia. Developing effective and safe anti-AF drugs remains an unmet challenge. Simultaneous block of both atrial-specific ultra-rapid delayed rectifier potassium (K+) current (IKur) and the Na+ current (INa) has been hypothesized to be anti-AF, without inducing significant QT prolongation and ventricular side effects. However, the antiarrhythmic advantage of simultaneously blocking these two channels vs. individual block in the setting of AF-induced electrical remodeling remains to be documented...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/29218000/synapse-specific-regulation-revealed-at-single-synapses-is-concealed-when-recording-multiple-synapses
#20
Justin Lines, Ana Covelo, Ricardo Gómez, Lan Liu, Alfonso Araque
Synaptic transmission and its activity-dependent modulation, known as synaptic plasticity, are fundamental processes in nervous system function. Neurons may receive thousands of synaptic contacts, but synaptic regulation may occur only at individual or discrete subsets of synapses, which may have important consequences on the spatial extension of the modulation of synaptic information. Moreover, while several electrophysiological methods are used to assess synaptic transmission at different levels of observation, i...
2017: Frontiers in Cellular Neuroscience
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