Effects of preservation method on canine (Canis lupus familiaris) fecal microbiota.

Studies involving gut microbiome analysis play an increasing role in the evaluation of health and disease in humans and animals alike. Fecal sampling methods for DNA preservation in laboratory, clinical, and field settings can greatly influence inferences of microbial composition and diversity, but are often inconsistent and under-investigated between studies. Many laboratories have utilized either temperature control or preservation buffers for optimization of DNA preservation, but few studies have evaluated the effects of combining both methods to preserve fecal microbiota. To determine the optimal method for fecal DNA preservation, we collected fecal samples from one canine donor and stored aliquots in RNAlater, 70% ethanol, 50:50 glycerol:PBS, or without buffer at 25 °C, 4 °C, and -80 °C. Fecal DNA was extracted, quantified, and 16S rRNA gene analysis performed on Days 0, 7, 14, and 56 to evaluate changes in DNA concentration, purity, and bacterial diversity and composition over time. We detected overall effects on bacterial community of storage buffer (F-value = 6.87, DF = 3, P < 0.001), storage temperature (F-value=1.77, DF = 3, P = 0.037), and duration of sample storage (F-value = 3.68, DF = 3, P < 0.001). Changes in bacterial composition were observed in samples stored in -80 °C without buffer, a commonly used method for fecal DNA storage, suggesting that simply freezing samples may be suboptimal for bacterial analysis. Fecal preservation with 70% ethanol and RNAlater closely resembled that of fresh samples, though RNAlater yielded significantly lower DNA concentrations (DF = 8.57, P < 0.001). Although bacterial composition varied with temperature and buffer storage, 70% ethanol was the best method for preserving bacterial DNA in canine feces, yielding the highest DNA concentration and minimal changes in bacterial diversity and composition. The differences observed between samples highlight the need to consider optimized post-collection methods in microbiome research

Equilibrium vortex formation in ultrarapidly rotating two-component Bose-Einstein condensates

Equilibrium vortex formation in rotating binary Bose gases with a rotating frequency higher than the harmonic trapping frequency is investigated theoretically. We consider the system being evaporatively cooled to form condensates and a combined numerical scheme is applied to ensure the binary system being in an authentic equilibrium state. To keep the system stable against the large centrifugal force of ultrafast rotation, a quartic trapping potential is added to the existing harmonic part. Using the Thomas-Fermi approximation, a critical rotating frequency \Omega_c is derived, which characterizes the structure with or without a central density hole. Vortex structures are studied in detail with rotation frequency both above and below ?\Omega_c and with respect to the miscible, symmetrically separated, and asymmetrically separated phases in their nonrotating ground-state counterparts.Comment: 7 pages, 7 figure

Rigorous Derivation of the Gross-Pitaevskii Equation

The time dependent Gross-Pitaevskii equation describes the dynamics of initially trapped Bose-Einstein condensates. We present a rigorous proof of this fact starting from a many-body bosonic Schroedinger equation with a short scale repulsive interaction in the dilute limit. Our proof shows the persistence of an explicit short scale correlation structure in the condensate.Comment: 4 pages, 1 figur

Bending-wave Instability of a Vortex Ring in a Trapped Bose-Einstein Condensate

Based on a velocity formula derived by matched asymptotic expansion, we investigate the dynamics of a circular vortex ring in an axisymmetric Bose-Einstein condensate in the Thomas-Fermi limit. The trajectory for an axisymmetrically placed and oriented vortex ring is entirely determined, revealing that the vortex ring generally precesses in condensate. The linear instability due to bending waves is investigated both numerically and analytically. General stability boundaries for various perturbed wavenumbers are computed. In particular, the excitation spectrum and the absolutely stable region for the static ring are analytically determined.Comment: 4 pages, 4 figure

Stationary wave patterns generated by an impurity moving with supersonic velocity through a Bose-Einstein condensate

Formation of stationary 3D wave patterns generated by a small point-like impurity moving through a Bose-Einstein condensate with supersonic velocity is studied. Asymptotic formulae for a stationary far-field density distribution are obtained. Comparison with three-dimensional numerical simulations demonstrates that these formulae are accurate enough already at distances from the obstacle equal to a few wavelengths.Comment: 7 pages, 3 figure

Derivation of the Cubic Non-linear Schr\"odinger Equation from Quantum Dynamics of Many-Body Systems

We prove rigorously that the one-particle density matrix of three dimensional interacting Bose systems with a short-scale repulsive pair interaction converges to the solution of the cubic non-linear Schr\"odinger equation in a suitable scaling limit. The result is extended to $k$-particle density matrices for all positive integer $k$.Comment: 72 pages, 17 figures. Final versio

Transcritical flow of a stratified fluid over topography: analysis of the forced Gardner equation

Transcritical flow of a stratified fluid past a broad localised topographic obstacle is studied analytically in the framework of the forced extended Korteweg--de Vries (eKdV), or Gardner, equation. We consider both possible signs for the cubic nonlinear term in the Gardner equation corresponding to different fluid density stratification profiles. We identify the range of the input parameters: the oncoming flow speed (the Froude number) and the topographic amplitude, for which the obstacle supports a stationary localised hydraulic transition from the subcritical flow upstream to the supercritical flow downstream. Such a localised transcritical flow is resolved back into the equilibrium flow state away from the obstacle with the aid of unsteady coherent nonlinear wave structures propagating upstream and downstream. Along with the regular, cnoidal undular bores occurring in the analogous problem for the single-layer flow modeled by the forced KdV equation, the transcritical internal wave flows support a diverse family of upstream and downstream wave structures, including solibores, rarefaction waves, reversed and trigonometric undular bores, which we describe using the recent development of the nonlinear modulation theory for the (unforced) Gardner equation. The predictions of the developed analytic construction are confirmed by direct numerical simulations of the forced Gardner equation for a broad range of input parameters.Comment: 34 pages, 24 figure

Delocalization and Diffusion Profile for Random Band Matrices

We consider Hermitian and symmetric random band matrices $H = (h_{xy})$ in $d \geq 1$ dimensions. The matrix entries $h_{xy}$, indexed by x,y \in (\bZ/L\bZ)^d, are independent, centred random variables with variances s_{xy} = \E |h_{xy}|^2. We assume that $s_{xy}$ is negligible if $|x-y|$ exceeds the band width $W$. In one dimension we prove that the eigenvectors of $H$ are delocalized if $W\gg L^{4/5}$. We also show that the magnitude of the matrix entries \abs{G_{xy}}^2 of the resolvent $G=G(z)=(H-z)^{-1}$ is self-averaging and we compute \E \abs{G_{xy}}^2. We show that, as $L\to\infty$ and $W\gg L^{4/5}$, the behaviour of \E |G_{xy}|^2 is governed by a diffusion operator whose diffusion constant we compute. Similar results are obtained in higher dimensions

Spontaneous Crystallization of Skyrmions and Fractional Vortices in the Fast-rotating and Rapidly-quenched Spin-1 Bose-Einstein Condensates

We investigate the spontaneous generation of crystallized topological defects via the combining effects of fast rotation and rapid thermal quench on the spin-1 Bose-Einstein condensates. By solving the stochastic projected Gross-Pitaevskii equation, we show that, when the system reaches equilibrium, a hexagonal lattice of skyrmions, and a square lattice of half-quantized vortices can be formed in a ferromagnetic and antiferromagnetic spinor BEC, respetively, which can be imaged by using the polarization-dependent phase-contrast method

The ground state energy of a low density Bose gas: a second order upper bound

Consider $N$ bosons in a finite box \Lambda= [0,L]^3\subset \bR^3 interacting via a two-body nonnegative soft potential $V= \lambda \tilde V$ with $\tilde V$ fixed and $\lambda>0$ small. We will take the limit $L, N \to \infty$ by keeping the density $\varrho= N/L^{3}$ fixed and small. We construct a variational state which gives an upper bound on the ground state energy per particle \e \e \le 4\pi\varrho a \Big [1+ \frac{128}{15\sqrt{\pi}}(\varrho a^3)^{1/2}S_\lambda \Big ] + O(\varrho^2|\log\varrho|), \quad {as $\varrho\to 0$} with a constant satisfying $$1\leq S_\lambda \leq 1+C\lambda.$$ Here $a$ is the scattering length of $V$ and thus depends on $\lambda$. In comparison, the prediction by Lee-Yang \cite{LYang} and Lee-Huang-Yang \cite{LHY} asserts that $S_\lambda=1$ independent of $\lambda$.Comment: 10 pages, no figure