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https://www.readbyqxmd.com/read/28239851/sawfishes-stealth-revealed-using-computational-fluid-dynamics
#1
D R Bradney, A Davidson, S P Evans, B E Wueringer, D L Morgan, P D Clausen
Detailed computational fluid dynamics simulations for the rostrum of three species of sawfish (Pristidae) revealed that negligible turbulent flow is generated from all rostra during lateral swipe prey manipulation and swimming. These results suggest that sawfishes are effective stealth hunters that may not be detected by their teleost prey's lateral line sensory system during pursuits. Moreover, during lateral swipes, the rostra were found to induce little velocity into the surrounding fluid. Consistent with previous data of sawfish feeding behaviour, these data indicate that the rostrum is therefore unlikely to be used to stir up the bottom to uncover benthic prey...
February 27, 2017: Journal of Fish Biology
https://www.readbyqxmd.com/read/28239722/transient-inhomogeneous-flow-patterns-in-supercooled-liquids-under-shear
#2
Ingo Fuereder, Patrick Ilg
Supercooled liquids and other soft glassy systems show characteristic spatial inhomogeneities in their local dynamical properties. Using detailed molecular dynamics simulations, we find that for sufficiently low temperatures and sufficiently high shear rates supercooled liquids also show transient inhomogeneous flow patterns (shear banding) in the start-up of steady shear flow, similar to what has already been observed for many other soft glassy systems. We verify that the onset of transient shear banding coincides quite well with the appearance of a stress overshoot for temperatures in the supercooled regime...
February 27, 2017: Soft Matter
https://www.readbyqxmd.com/read/28239715/clustering-in-vibrated-monolayers-of-granular-rods
#3
M González-Pinto, F Borondo, Y Martínez-Ratón, E Velasco
We investigate the ordering properties of vertically-vibrated monolayers of granular cylinders in a circular container at high packing fraction. In line with previous works by other groups, we identify liquid-crystalline ordering behaviour similar to that of two-dimensional hard rectangular particles subject to thermal equilibrium fluctuations. However, due to dissipation, there is a much stronger tendency for particles to cluster into parallel arrangements in the granular system. These clusters behave as a polydisperse mixture of long life-time 'superparticles', and some aspects of the system behaviour can be understood by applying mean-field theories for equilibrium hard rectangles, based on two-body correlations, to these 'superparticles'...
February 27, 2017: Soft Matter
https://www.readbyqxmd.com/read/28239705/chemical-communication-and-dynamics-of-droplet-emulsions-in-networks-of-belousov-zhabotinsky-micro-oscillators-produced-by-microfluidics
#4
Kristian Torbensen, Federico Rossi, Sandra Ristori, Ali Abou-Hassan
Chemical communication leading to synchronization and collective behaviour of dynamic elements, such as cell colonies, is a widespread phenomenon with biological, physical and chemical importance. Such synchronization between elements proceeds via chemical communication by emmision, interdiffusion and reception of specific messenger molecules. On a lab scale, these phenomena can be modeled by encapsulating an oscillating chemical reaction, which serves as a signal (information) sender/receiver element, inside microcompartments such as droplet emulsions, liposomes and polymersomes...
February 27, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28239661/klf2-and-klf4-control-endothelial-identity-and-vascular-integrity
#5
Panjamaporn Sangwung, Guangjin Zhou, Lalitha Nayak, E Ricky Chan, Sandeep Kumar, Dong-Won Kang, Rongli Zhang, Xudong Liao, Yuan Lu, Keiki Sugi, Hisashi Fujioka, Hong Shi, Stephanie D Lapping, Chandra C Ghosh, Sarah J Higgins, Samir M Parikh, Hanjoong Jo, Mukesh K Jain
Maintenance of vascular integrity in the adult animal is needed for survival, and it is critically dependent on the endothelial lining, which controls barrier function, blood fluidity, and flow dynamics. However, nodal regulators that coordinate endothelial identity and function in the adult animal remain poorly characterized. Here, we show that endothelial KLF2 and KLF4 control a large segment of the endothelial transcriptome, thereby affecting virtually all key endothelial functions. Inducible endothelial-specific deletion of Klf2 and/or Klf4 reveals that a single allele of either gene is sufficient for survival, but absence of both (EC-DKO) results in acute death from myocardial infarction, heart failure, and stroke...
February 23, 2017: JCI Insight
https://www.readbyqxmd.com/read/28239442/integral-projection-models-for-host-parasite-systems-with-an-application-to-amphibian-chytrid-fungus
#6
Mark Q Wilber, Kate E Langwig, A Marm Kilpatrick, Hamish I McCallum, Cheryl J Briggs
Host parasite models are typically constructed under either a microparasite or macroparasite paradigm. However, this has long been recognized as a false dichotomy because many infectious disease agents, including most fungal pathogens, have attributes of both microparasites and macroparasites.We illustrate how Integral Projection Models (IPM)s provide a novel, elegant modeling framework to represent both types of pathogens. We build a simple host-parasite IPM that tracks both the number of susceptible and infected hosts and the distribution of parasite burdens in infected hosts...
October 2016: Methods in Ecology and Evolution
https://www.readbyqxmd.com/read/28239424/non-covalent-interactions-in-controlling-ph-responsive-behaviors-of-self-assembled-nanosystems
#7
Yang Li, Zhaohui Wang, Qi Wei, Min Luo, Gang Huang, Baran D Sumer, Jinming Gao
Self-assembly and associated dynamic and reversible non-covalent interactions are the basis of protein biochemistry (e.g., protein folding) and development of sophisticated nanomaterial systems that can respond to and amplify biological signals. In this study, we report a systematic investigation of non-covalent interactions that affect the pH responsive behaviors and resulting supramolecular self-assembly of a series of ultra-pH sensitive (UPS) block copolymers. Increase of hydrophobic and π-π stacking interactions led to the decrease of pKa values...
October 14, 2016: Polymer Chemistry
https://www.readbyqxmd.com/read/28239411/reliable-measurement-of-e-coli-single-cell-fluorescence-distribution-using-a-standard-microscope-set-up
#8
Marilisa Cortesi, Lucia Bandiera, Alice Pasini, Alessandro Bevilacqua, Alessandro Gherardi, Simone Furini, Emanuele Giordano
BACKGROUND: Quantifying gene expression at single cell level is fundamental for the complete characterization of synthetic gene circuits, due to the significant impact of noise and inter-cellular variability on the system's functionality. Commercial set-ups that allow the acquisition of fluorescent signal at single cell level (flow cytometers or quantitative microscopes) are expensive apparatuses that are hardly affordable by small laboratories. METHODS: A protocol that makes a standard optical microscope able to acquire quantitative, single cell, fluorescent data from a bacterial population transformed with synthetic gene circuitry is presented...
2017: Journal of Biological Engineering
https://www.readbyqxmd.com/read/28239346/parallel-steps-large-scale-stochastic-spatial-reaction-diffusion-simulation-with-high-performance-computers
#9
Weiliang Chen, Erik De Schutter
Stochastic, spatial reaction-diffusion simulations have been widely used in systems biology and computational neuroscience. However, the increasing scale and complexity of models and morphologies have exceeded the capacity of any serial implementation. This led to the development of parallel solutions that benefit from the boost in performance of modern supercomputers. In this paper, we describe an MPI-based, parallel operator-splitting implementation for stochastic spatial reaction-diffusion simulations with irregular tetrahedral meshes...
2017: Frontiers in Neuroinformatics
https://www.readbyqxmd.com/read/28239224/ice-sheet-dynamics-through-the-quaternary-on-the-mid-norwegian-continental-margin-inferred-from-3d-seismic-data
#10
A Montelli, J A Dowdeswell, D Ottesen, S E Johansen
Reconstructing the evolution of ice sheets is critical to our understanding of the global environmental system, but most detailed palaeo-glaciological reconstructions have hitherto focused on the very recent history of ice sheets. Here, we present a three-dimensional (3D) reconstruction of the changing nature of ice-sheet derived sedimentary architecture through the Quaternary Ice Age of almost 3 Ma. An extensive geophysical record documents a marine-terminating, calving Fennoscandian Ice Sheet (FIS) margin present periodically on the mid-Norwegian shelf since the beginning of the Quaternary...
February 2017: Marine and Petroleum Geology
https://www.readbyqxmd.com/read/28238809/in-situ-protein-determination-to-monitor-contamination-in-a-centrifugal-partition-chromatograph
#11
Feriel Bouiche, Karine Faure
Centrifugal partition chromatography (CPC) works with biphasic liquid systems including aqueous two-phase systems. Metallic rotors are able to retain an aqueous stationary phase able to purify proteins. But the adhesion of proteins to solid surface may pose a cross-contamination risk during downstream processes. So it is of utmost importance to ensure the cleanliness of the equipment and detect possible protein contamination in a timely manner. Thereby, a direct method that allows the determination of the effective presence of proteins and the extent of contamination in the metallic CPC rotors was developed...
February 23, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/28238662/coordination-by-cdc42-of-actin-contractility-and-adhesion-for-melanoblast-movement-in-mouse-skin
#12
Emma F Woodham, Nikki R Paul, Benjamin Tyrrell, Heather J Spence, Karthic Swaminathan, Michelle R Scribner, Evangelos Giampazolias, Ann Hedley, William Clark, Frieda Kage, Daniel J Marston, Klaus M Hahn, Stephen W G Tait, Lionel Larue, Cord H Brakebusch, Robert H Insall, Laura M Machesky
The individual molecular pathways downstream of Cdc42, Rac, and Rho GTPases are well documented, but we know surprisingly little about how these pathways are coordinated when cells move in a complex environment in vivo. In the developing embryo, melanoblasts originating from the neural crest must traverse the dermis to reach the epidermis of the skin and hair follicles. We previously established that Rac1 signals via Scar/WAVE and Arp2/3 to effect pseudopod extension and migration of melanoblasts in skin...
February 18, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28238422/a-reduced-order-model-for-wall-shear-stress-in-abdominal-aortic-aneurysms-by-proper-orthogonal-decomposition
#13
Gary Han Chang, Clemens M Schirmer, Yahya Modarres-Sadeghi
In this paper, we introduce a method to construct a Reduced-Order Model (ROM) to study the physiological flow and the Wall Shear Stress (WSS) conditions in Abdominal Aortic Aneurysms (AAA). We start the process by running a training case using Computational Fluid Dynamics (CFD) simulations with time-varying flow parameters, such that these parameters cover the range of parameters that we would like to consider in our ROM. We use the inflow angle as the variable parameter in the current study. Then we use the snapshot Proper Orthogonal Decomposition (POD) to construct the reduced-order bases, which are subsequently enhanced using a QR-factorization technique to satisfy the relevant fluid boundary conditions...
February 2, 2017: Journal of Biomechanics
https://www.readbyqxmd.com/read/28238392/quantitative-representation-of-eustachian-tube-component-movements-during-swallowing
#14
Selma Cetin, Miriam S Teixeira, Cuneyt M Alper
OBJECTIVE: Describes a method of dynamic video-endoscopy of the Eustachian tube (ET) orifice at the nasopharynx to quantitatively represent ET component movements during swallowing using a graphic function and analyze their importance to its opening mechanics. METHODS: This was a pilot study of relational event capture using a polar coordinate system applied to trans-nasal video-endoscopic recordings of the ET during 3 swallows in 5 adults. After topical anesthesia of the nose, a 45° telescope was introduced unilaterally and focused on the ipsilateral ET orifice...
February 18, 2017: Auris, Nasus, Larynx
https://www.readbyqxmd.com/read/28238327/population-dynamics-of-the-rock-shell-reishia-clavigera-associated-with-different-degrees-of-organotin-contamination-in-hong-kong
#15
Kevin K Y Ho, Kenneth M Y Leung
Application of organotins in antifouling systems on ship hulls has been globally prohibited by the International Maritime Organization since September 2008. It is, therefore, anticipated that there is a recovery of imposex-affected gastropod populations worldwide. We studied the population dynamics of the rock shell Reishia clavigera in six locations around Hong Kong's coastal waters, covering different degrees of organotin contamination for 25months (2011-2013). Abundance and density of R. clavigera were higher in clean sites, while they tended to grow faster in polluted sites...
February 18, 2017: Marine Pollution Bulletin
https://www.readbyqxmd.com/read/28238048/dynamics-of-the-rr-interval-versus-blood-pressure-relationship-at-exercise-onset-in-humans
#16
Aurélien Bringard, Alessandra Adami, Nazzareno Fagoni, Timothée Fontolliet, Frédéric Lador, Christian Moia, Enrico Tam, Guido Ferretti
PURPOSE: The dynamics of the postulated phenomenon of exercise baroreflex resetting is poorly understood, but can be investigated using closed-loop procedures. To shed light on some mechanisms and temporal relationships participating in the resetting process, we studied the time course of the relationship between the R-R interval (RRi) and arterial pressure with a closed-loop approach. METHODS: On ten young volunteers at rest and during light exercise in supine and upright position, we continuously determined, on single-beat basis, RRi (electrocardiography), and arterial pressure (non-invasive finger pressure cuff)...
February 25, 2017: European Journal of Applied Physiology
https://www.readbyqxmd.com/read/28237707/study-of-fluid-dynamics-reveals-direct-communications-between-lymphatic-vessels-and-venous-blood-vessels-at-lymph-nodes-of-mice
#17
Kazu Takeda, Shiro Mori, Tetsuya Kodama
Cancer cells metastasize to lymph nodes, with distant metastasis resulting in poor prognosis. The role of lymph node metastasis (LNM) in the spread of cancer to distant organs remain incompletely characterized. The visualization of flow dynamics in the lymphatic and blood vessels of MXH10/Mo-lpr/lpr mice, which develop systemic swelling of lymph nodes up to 10mm in diameter, has revealed that lymph nodes have the potential to be a direct source of systemic metastasis. However, it is not known whether these fluid dynamics characteristics are universal phenomena present in other strains of laboratory mice...
February 22, 2017: Journal of Immunological Methods
https://www.readbyqxmd.com/read/28237668/mathematical-modeling-of-hiv-like-particle-assembly-in-vitro
#18
Yuewu Liu, Xiufen Zou
In vitro, the recombinant HIV-1 Gag protein can generate spherical particles with a diameter of 25-30 nm in a fully defined system. It has approximately 80 building blocks, and its intermediates for assembly are abundant in geometry. Accordingly, there are a large number of nonlinear equations in the classical model. Therefore, it is difficult to compute values of geometry parameters for intermediates and make the mathematical analysis using the model. In this work, we develop a new model of HIV-like particle assembly in vitro by using six-fold symmetry of HIV-like particle assembly to decrease the number of geometry parameters...
February 22, 2017: Mathematical Biosciences
https://www.readbyqxmd.com/read/28237667/identifiability-of-large-scale-non-linear-dynamic-network-models-applied-to-the-adm1-case-study
#19
Philippe Nimmegeers, Joost Lauwers, Dries Telen, Filip Logist, Jan Van Impe
In this work, both the structural and practical identifiability of the Anaerobic Digestion Model no. 1 (ADM1) is investigated, which serves as a relevant case study of large non-linear dynamic network models. The structural identifiability is investigated using the probabilistic algorithm, adapted to deal with the specifics of the case study (i.e., a large-scale non-linear dynamic system of differential and algebraic equations). The practical identifiability is analyzed using a Monte Carlo parameter estimation procedure for a 'non-informative' and 'informative' experiment, which are heuristically designed...
February 22, 2017: Mathematical Biosciences
https://www.readbyqxmd.com/read/28237665/modeling-the-population-dynamics-and-community-impacts-of-ambystoma-tigrinum-a-case-study-of-phenotype-plasticity
#20
Maeve L McCarthy, Dorothy Wallace, Howard H Whiteman, Evan T Rheingold, Ann M Dunham, Olivia Prosper, Michelle Chen, Eileen Hu-Wang
Phenotypic plasticity is the ability of an organism to change its phenotype in response to changes in the environment. General mathematical descriptions of the phenomenon rely on an abstract measure of "viability" that, in this study, is instantiated in the case of the Tiger Salamander, Ambystoma tigrinum. This organism has a point in its development when, upon maturing, it may take two very different forms. One is a terrestrial salamander (metamorph)that visits ponds to reproduce and eat, while the other is an aquatic form (paedomorph) that remains in the pond to breed and which consumes a variety of prey including its own offspring...
February 22, 2017: Mathematical Biosciences
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