bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structure-Based Comparative Analysis and Prediction of N-Linked Glycosylation Sites in Evolutionarily Distant Eukaryotes
Authors: Lam Phuc Vinh Nguyen , Goldman Radoslav , Karagiannis Konstantinos , Narsule Tejas , Simonyan Vahan , Soika Valerii , Mazumder Raja 
Published: March 2013

Abstract
The asparagine-X-serine/threonine (NXS/T) motif, where X is any amino acid except proline, is the consensus motif for N-linked glycosylation. Significant numbers of high-resolution crystal structures of glycosylated proteins allow us to carry out structural analysis of the N-linked glycosylation sites (NGS). Our analysis shows that there is enough structural information from diverse glycoproteins to allow the development of rules which can be used to predict NGS. A Python-based tool was developed to investigate asparagines implicated in N-glycosylation in five species: Homo sapiens, Mus musculus, Drosophila melanogaster, Arabidopsis thaliana and Saccharomyces cerevisiae. Our analysis shows that 78% of all asparagines of NXS/T motif involved in N-glycosylation are localized in the loop/turn conformation in the human proteome. Similar distribution was revealed for all the other species examined. Comparative analysis of the occurrence of NXS/T motifs not known to be glycosylated and their reverse sequence (S/TXN) shows a similar distribution across the secondary structural elements, indicating that the NXS/T motif in itself is not biologically relevant. Based on our analysis, we have defined rules to determine NGS. Using machine learning methods based on these rules we can predict with 93% accuracy if a particular site will be glycosylated. If structural information is not available the tool uses structural prediction results resulting in 74% accuracy. The tool was used to identify glycosylation sites in 108 human proteins with structures and 2247 proteins without structures that have acquired NXS/T site/s due to non-synonymous variation. The tool, Structure Feature Analysis Tool (SFAT), is freely available to the public at http://hive.biochemistry.gwu.edu/tools/sfat.
High expression of microRNA‐625‐3p is associated with poor response to first‐line oxaliplatin based treatment of metastatic colorectal cancer
Authors: Rasmussen Mads H. , Jensen Niels F. , Tarpgaard Line S. , Qvortrup Camilla , Rømer Maria U. , Stenvang Jan , Hansen Tine P. , Christensen Lise L. , Lindebjerg Jan , Hansen Flemming , Jensen Benny V. , Hansen Torben F. , Pfeiffer Per , Brünner Nils , Ørntoft Torben F. , Andersen Claus L. 
Published: March 2013

The backbone of current cytotoxic treatment of metastatic colorectal cancer (mCRC) consists of a fluoropyrimidine together with either oxaliplatin (XELOX/FOLFOX) or irinotecan (XELIRI/FOLFIRI). With an overall objective response rate of approximately 50% for either treatment combination, a major unsolved problem is that no predictors of response to these treatments are available. To address this issue, we profiled 742 microRNAs in laser‐capture microdissected cancer cells from responding and non‐responding patients receiving XELOX/FOLFOX as first‐line treatment for mCRC, and identified, among others, high expression of miR‐625‐3p, miR‐181b and miR‐27b to be associated with poor clinical response. In a validation cohort of 94 mCRC patients treated first‐line with XELOX, high expression of miR‐625‐3p was confirmed to be associated with poor response (OR = 6.25, 95%CI [1.8; 21.0]). Independent analyses showed that miR‐625‐3p was not dysregulated between normal and cancer samples, nor was its expression associated with recurrence of stage II or III disease, indicating that miR‐625‐3p solely is a response marker. Finally, we also found that these miRNAs were up‐regulated in oxaliplatin resistant HCT116/oxPt (miR‐625‐3p, miR‐181b and miR‐27b) and LoVo/oxPt (miR‐181b) colon cancer cell lines as compared with their isogenic parental cells. Altogether, our results suggest an association between miR‐625‐3p and response to first‐line oxaliplatin based chemotherapy of mCRC.
Quillen's work on formal group laws and complex cobordism theory
Authors: Ravenel Douglas C. 
Published: March 2013

AbstractIn 1969 Quillen discovered a deep connection between complex cobordism and formal group laws which he announced in [Qui69]. Algebraic topology has never been the same since. We will describe the content of [Qui69] and then discuss its impact on the field. This paper is a writeup of a talk on the same topic given at the Quillen Conference at MIT in October 2012. Slides for that talk are available on the author's home page.
Stochastic dynamics and model reduction of amplifier flows: the backward facing step flow
Authors: Dergham G. , Sipp D. , Robinet J.-Ch. 
Published: March 2013

AbstractMethods for investigating and approximating the linear dynamics of amplifier flows are examined in this paper. The procedures are derived for incompressible flow over a two-dimensional backward-facing step. First, the singular value decomposition of the resolvent is performed over a frequency range in order to identify the optimal and suboptimal harmonic forcing and responses of the flow. These forcing/responses are shown to be organized into two categories: the first accounting for the Orr and Kelvin–Helmholtz instabilities in the shear layer and the second for the advection and diffusion of perturbations in the free stream. Next, we investigate the dynamics of the flow when excited by a white in space and time noise. We compute the predominant patterns of the random flow which optimally account for the sustained variance, the empirical orthogonal functions (EOFs), as well as the predominant forcing structures which optimally contribute to the sustained variance, the stochastic optimals (SOs). The leading EOFs and SOs are expressed as a linear combination of the suboptimal forcing and responses of the flow and are related to particular instability mechanisms and/or frequency intervals. Finally, we use the leading EOFs, SOs and balanced modes (obtained from balanced truncation) to build low-order models of the flow dynamics. These models are shown to accurately recover the time propagator and resolvent of the original dynamical system. In other words, such models capture the entire flow response from any forcing and may be used in the design of efficient closed-loop controllers for amplifier flows.
Steady base states for non-Newtonian granular hydrodynamics
Authors: Vega Reyes Francisco , Santos Andrés , Garzó Vicente 
Published: March 2013

AbstractWe study in this work steady laminar flows in a low-density granular gas modelled as a system of identical smooth hard spheres that collide inelastically. The system is excited by shear and temperature sources at the boundaries, which consist of two infinite parallel walls. Thus, the geometry of the system is the same that yields the planar Fourier and Couette flows in standard gases. We show that it is possible to describe the steady granular flows in this system, even at large inelasticities, by means of a (non-Newtonian) hydrodynamic approach. All five types of Couette–Fourier granular flows are systematically described, identifying the different types of hydrodynamic profiles. Excellent agreement is found between our classification of flows and simulation results. Also, we obtain the corresponding nonlinear transport coefficients by following three independent and complementary methods: (i) an analytical solution obtained from Grad’s 13-moment method applied to the inelastic Boltzmann equation; (ii) a numerical solution of the inelastic Boltzmann equation obtained by means of the direct simulation Monte Carlo method; and (iii) event-driven molecular dynamics simulations. We find that, while Grad’s theory does not describe quantitatively well all transport coefficients, the three procedures yield the same general classification of planar Couette–Fourier flows for the granular gas.
Vortex-induced vibration of a neutrally buoyant tethered sphere
Authors: Lee H. , Hourigan K. , Thompson M. C. 
Published: March 2013

AbstractA combined numerical and experimental study examining vortex-induced vibration (VIV) of a neutrally buoyant tethered sphere has been undertaken. The study covered the Reynolds-number range $50\leq \mathit{Re}\lesssim 12\hspace{0.167em} 000$, with the numerical ($50\leq \mathit{Re}\leq 800$) and experimental ($370\leqslant \mathit{Re}\lesssim 12\hspace{0.167em} 000$) ranges overlapping. Neutral buoyancy was chosen to eliminate one parameter, i.e. the influence of gravity, on the VIV behaviour, although, of course, the effect of added mass remains. The tether length was also chosen to be sufficiently long so that, to a good approximation, the sphere was constrained to move within a plane. Seven broad but relatively distinct sphere oscillation and wake states could be distinguished. For regime I, the wake is steady and axisymmetric, and it undergoes transition to a steady two-tailed wake in regime II at $\mathit{Re}= 210$. Those regimes are directly analogous to those of a fixed sphere. Once the sphere begins to vibrate at $\mathit{Re}\simeq 270$ in regime III, the wake behaviour is distinct from the fixed-sphere wake. Initially the vibration frequency of the sphere is half the shedding frequency in the wake, with the latter consistent with the fixed-sphere wake frequency. The sphere vibration is not purely periodic but modulated over several base periods. However, at slightly higher Reynolds numbers ($\mathit{Re}\simeq 280$), planar symmetry is broken, and the vibration shifts to the planar normal (or azimuthal) direction, and becomes completely azimuthal at the start of regime IV at $\mathit{Re}= 300$. In comparison, for a fixed sphere, planar symmetry is broken at a much higher Reynolds number of $\mathit{Re}\simeq 375$. Interestingly, planar symmetry returns to the wake for $\mathit{Re}\gt 330$, in regime V, for which the oscillations are again radial, and is maintained until $\mathit{Re}= 450$ or higher. At the same time, the characteristic vortex loops in the wake become symmetrical, i.e. two-sided. For $\mathit{Re}\gt 500$, in regime VI, the trajectory of the sphere becomes irregular, possibly chaotic. That state is maintained over the remaining Reynolds-number range simulated numerically ($\mathit{Re}\leq 800$). Experiments overlapping this Reynolds-number range confirm the amplitude radial oscillations in regime V and the chaotic wandering for regime VI. At still higher Reynolds numbers of $\mathit{Re}\gt 3000$, in regime VII, the trajectories evolve to quasi-circular orbits about the neutral point, with the orbital radius increasing as the Reynolds number is increased. At $\mathit{Re}= 12\hspace{0.167em} 000$, the orbital diameter reaches approximately one sphere diameter. Of interest, this transition sequence is distinct from that for a vertically tethered heavy sphere, which undergoes transition to quasi-circular orbits beyond $\mathit{Re}= 500$.
Convective shutdown in a porous medium at high Rayleigh number
Authors: Hewitt Duncan R. , Neufeld Jerome A. , Lister John R. 
Published: March 2013

AbstractConvection in a closed domain driven by a dense buoyancy source along the upper boundary soon starts to wane owing to the increase of the average interior density. In this paper, theoretical and numerical models are developed of the subsequent long period of shutdown of convection in a two-dimensional porous medium at high Rayleigh number $\mathit{Ra}$. The aims of this paper are twofold. Firstly, the relationship between this slowly evolving ‘one-sided’ shutdown system and the statistically steady ‘two-sided’ Rayleigh–Bénard (RB) cell is investigated. Numerical measurements of the Nusselt number $\mathit{Nu}$ from an RB cell (Hewitt et al., Phys. Rev. Lett., vol. 108, 2012, 224503) are very well described by the simple parametrization $\mathit{Nu}= 2. 75+ 0. 0069\mathit{Ra}$. This parametrization is used in theoretical box models of the one-sided shutdown system and found to give excellent agreement with high-resolution numerical simulations of this system. The dynamical structure of shutdown can also be accurately predicted by measurements from an RB cell. Results are presented for a general power-law equation of state. Secondly, these ideas are extended to model more complex physical systems, which comprise two fluid layers with an equation of state such that the solution that forms at the (moving) interface is more dense than either layer. The two fluids are either immiscible or miscible. Theoretical box models compare well with numerical simulations in the case of a flat interface between the fluids. Experimental results from a Hele-Shaw cell and numerical simulations both show that interfacial deformation can dramatically enhance the convective flux. The applicability of these results to the convective dissolution of geologically sequestered ${\mathrm{CO} }_{2} $ in a saline aquifer is discussed.
Highly focused supersonic microjets: numerical simulations
Authors: Peters Ivo R. , Tagawa Yoshiyuki , Oudalov Nikolai , Sun Chao , Prosperetti Andrea , Lohse Detlef , van der Meer Devaraj 
Published: March 2013

AbstractBy focusing a laser pulse inside a capillary partially filled with liquid, a vapour bubble is created that emits a pressure wave. This pressure wave travels through the liquid and creates a fast, focused axisymmetric microjet when it is reflected at the meniscus. We numerically investigate the formation of this microjet using axisymmetric boundary integral simulations, where we model the pressure wave as a pressure pulse applied on the bubble. We find a good agreement between the simulations and experimental results in terms of the time evolution of the jet and on all parameters that can be compared directly. We present a simple analytical model that accurately predicts the velocity of the jet after the pressure pulse and its maximum velocity.
Nonlinear energy transfer between fluid sloshing and vessel motion
Authors: Turner M. R. , Bridges T. J. 
Published: March 2013

AbstractThis paper examines the dynamic coupling between a sloshing fluid and the motion of the vessel containing the fluid. A mechanism is identified that leads to an energy exchange between the vessel dynamics and fluid motion. It is based on a 1:1 resonance in the linearized equations, but nonlinearity is essential for the energy transfer. For definiteness, the theory is developed for Cooker’s pendulous sloshing experiment. The vessel has a rectangular cross-section, is partially filled with a fluid and is suspended by two cables. A nonlinear normal form is derived close to an internal 1:1 resonance, with the energy transfer manifested by a heteroclinic connection, which connects the purely symmetric sloshing modes to the purely antisymmetric sloshing modes. Parameter values where this pure energy transfer occurs are identified. In practice, this energy transfer can lead to sloshing-induced destabilization of fluid-carrying vessels.
Explicit filtering to obtain grid-spacing-independent and discretization-order-independent large-eddy simulation of two-phase volumetrically dilute flow with evaporation
Authors: Radhakrishnan Senthilkumaran , Bellan Josette 
Published: March 2013

AbstractPredictions from conventional large-eddy simulation (LES) are known to be grid-spacing and spatial-discretization-order dependent. In a previous article (Radhakrishnan & Bellan,J. Fluid Mech., vol. 697, 2012a, pp. 399–435), we reformulated LES for compressible single-phase flow by explicitly filtering the nonlinear terms in the governing equations so as to render the solution grid-spacing and discretization-order independent. Having shown in Radhakrishnan & Bellan (2012a) that the reformulated LES, which we call EFLES, yields grid-spacing-independent and discretization-order-independent solutions for compressible single-phase flow, we explore here the potential of EFLES for evaporating two-phase flow where the small scales have an additional origin compared to single-phase flow. Thus, we created a database through direct numerical simulation (DNS) that when filtered serves as a template for comparisons with both conventional LES and EFLES. Both conventional LES and EFLES are conducted with two gas-phase SGS models; the drop-field SGS model is the same in all these simulations. For EFLES, we also compared simulations performed with the same SGS model for the gas phase but two different drop-field SGS models. Moreover, to elucidate the influence of explicit filtering versus gas-phase SGS modelling, EFLES with two drop-field SGS models but no gas-phase SGS models were conducted. The results from all these simulations were compared to those from DNS and from the filtered DNS (FDNS). Similar to the single-phase flow findings, the conventional LES method yields solutions which are both grid-spacing and spatial-discretization-order dependent. The EFLES solutions are found to be grid-spacing independent for sufficiently large filter-width to grid-spacing ratio, although for the highest discretization order this ratio is larger in the two-phase flow compared to the single-phase flow. For a sufficiently fine grid, the results are also discretization-order independent. The absence of a gas-phase SGS model leads to build-up of energy near the filter cut-off indicating that while explicit filtering removes energy above the filter width, it does not provide the correct dissipation at the scales smaller than this width. A wider viewpoint leads to the conclusion that although the minimum filter-width to grid-spacing ratio necessary to obtain the unique grid-independent solution might be different for various discretization-order schemes, the grid-independent solution thus obtained is also discretization-order independent.
Rogue wave occurrence and dynamics by direct simulations of nonlinear wave-field evolution
Authors: Xiao Wenting , Liu Yuming , Wu Guangyu , Yue Dick K. P. 
Published: March 2013

AbstractWe study the occurrence and dynamics of rogue waves in three-dimensional deep water using phase-resolved numerical simulations based on a high-order spectral (HOS) method. We obtain a large ensemble of nonlinear wave-field simulations ($M= 3$ in HOS method), initialized by spectral parameters over a broad range, from which nonlinear wave statistics and rogue wave occurrence are investigated. The HOS results are compared to those from the broad-band modified nonlinear Schrödinger (BMNLS) equations. Our results show that for (initially) narrow-band and narrow directional spreading wave fields, modulational instability develops, resulting in non-Gaussian statistics and a probability of rogue wave occurrence that is an order of magnitude higher than linear theory prediction. For longer times, the evolution becomes quasi-stationary with non-Gaussian statistics, a result not predicted by the BMNLS equations (without consideration of dissipation). When waves spread broadly in frequency and direction, the modulational instability effect is reduced, and the statistics and rogue wave probability are qualitatively similar to those from linear theory. To account for the effects of directional spreading on modulational instability, we propose a new modified Benjamin–Feir index for effectively predicting rogue wave occurrence in directional seas. For short-crested seas, the probability of rogue waves based on number frequency is imprecise and problematic. We introduce an area-based probability, which is well defined and convergent for all directional spreading. Based on a large catalogue of simulated rogue wave events, we analyse their geometry using proper orthogonal decomposition (POD). We find that rogue wave profiles containing a single wave can generally be described by a small number of POD modes.
The electrophoretic mobility of rod-like particles
Authors: Yariv Ehud , Schnitzer Ory 
Published: March 2013

AbstractAt finite Dukhin numbers, where Smoluchowski’s formula is inapplicable to thin-double-layer electrophoresis, the mobility of non-spherical particles is generally anisotropic. We consider bodies of revolution of otherwise arbitrary shape, where a uniformly applied electric field results in a rectilinear motion in the plane spanned by the field direction and the particle symmetry axis, as well as (for particles lacking fore–aft symmetry) rigid-body rotation about an axis perpendicular to that plane. Focusing upon slender particles, where the ratio $\epsilon $ of cross-sectional and longitudinal scales is asymptotically small, the translational and rotational mobilities are obtained as quadratures which depend upon the lengthwise distribution of the scaled cross-sectional width and the force densities associated with rigid-body motion. These mobility expressions approach finite limits as $\epsilon \rightarrow 0$, yielding closed-form expressions for specific particle geometries.
Wake and thrust of an angularly reciprocating plate
Authors: Lee Jeongsu , Park Yong-Jai , Jeong Useok , Cho Kyu-Jin , Kim Ho-Young 
Published: March 2013

AbstractAs one of the most important force production mechanisms of swimming and flying animals, the fluid dynamics of flapping has been intensively studied. However, these efforts have been mainly directed toward animals in forward motion or locomotive appendages undergoing linear translation. Here we seek to complement the existing knowledge of the flapping mechanism by studying angularly reciprocating flat plates without a free stream velocity, under a so-called ‘bollard pull’ condition. We visualize the flow field around the flat plate to find that two independent vortical structures are formed per half-cycle, resulting in the separation of two distinct vortex pairs at sharp edges rather than a single vortex loop which is typical of a starting–stopping vortex paradigm in flows with free streams. Based on our observations, we derive a scaling law to predict the thrust of the flapping plate; this is the first experimentally validated theoretical model for the thrust of angularly reciprocating plates without a prescribed background flow.
Axisymmetric travelling waves in annular sliding Couette flow at finite and asymptotically large Reynolds number
Authors: Deguchi K. , Walton A. G. 
Published: March 2013

AbstractThe relationship between numerical finite-amplitude equilibrium solutions of the full Navier–Stokes equations and nonlinear solutions arising from a high-Reynolds-number asymptotic analysis is discussed for a Tollmien–Schlichting wave-type two-dimensional vortical flow structure. The specific flow chosen for this purpose is that which arises from the mutual axial sliding of co-axial cylinders for which nonlinear axisymmetric travelling-wave solutions have been discovered recently by Deguchi & Nagata (J. Fluid Mech., vol. 678, 2011, pp. 156–178). We continue this solution branch to a Reynolds number $R= 1{0}^{8} $ and confirm that the behaviour of its so-called lower branch solutions, which typically produce a smaller modification to the laminar state than the other solution branches, quantitatively agrees with the axisymmetric asymptotic theory developed in this paper. We further find that this asymptotic structure breaks down when the disturbance wavelength is comparable with $R$. The new structure which replaces it is investigated and the governing equations are derived and solved. The flow visualization of the resultant solutions reveals that they possess a streamwise localized structure, with the trend agreeing qualitatively with full Navier–Stokes solutions for relatively long-wavelength disturbances.