Cross-Platform Comparison of Untargeted and Targeted Lipidomics Approaches on Aging Mouse Plasma.

Lipidomics - the global assessment of lipids - can be performed using a variety of mass spectrometry (MS)-based approaches. However, choosing the optimal approach in terms of lipid coverage, robustness and throughput can be a challenging task. Here, we compare a novel targeted quantitative lipidomics platform known as the Lipidyzer to a conventional untargeted liquid chromatography (LC)-MS approach. We find that both platforms are efficient in profiling more than 300 lipids across 11 lipid classes in mouse plasma with precision and accuracy below 20% for most lipids. While the untargeted and targeted platforms detect similar numbers of lipids, the former identifies a broader range of lipid classes and can unambiguously identify all three fatty acids in triacylglycerols (TAG). Quantitative measurements from both approaches exhibit a median correlation coefficient (r) of 0.99 using a dilution series of deuterated internal standards and 0.71 using endogenous plasma lipids in the context of aging. Application of both platforms to plasma from aging mouse reveals similar changes in total lipid levels across all major lipid classes and in specific lipid species. Interestingly, TAG is the lipid class that exhibits the most changes with age, suggesting that TAG metabolism is particularly sensitive to the aging process in mice. Collectively, our data show that the Lipidyzer platform provides comprehensive profiling of the most prevalent lipids in plasma in a simple and automated manner

Optimizing transport efficiency on scale-free networks through assortative or dissortative topology

We find that transport on scale-free random networks depends strongly on degree-correlated network topologies whereas transport on Erd$\ddot{o}$s-R$\acute{e}$nyi networks is insensitive to the degree correlation. An approach for the tuning of scale-free network transport efficiency through assortative or dissortative topology is proposed. We elucidate that the unique transport behavior for scale-free networks results from the heterogeneous distribution of degrees.Comment: 4 pages, 3 figure

Anderson transition on the Cayley tree as a traveling wave critical point for various probability distributions

For Anderson localization on the Cayley tree, we study the statistics of various observables as a function of the disorder strength $W$ and the number $N$ of generations. We first consider the Landauer transmission $T_N$. In the localized phase, its logarithm follows the traveling wave form $\ln T_N \simeq \bar{\ln T_N} + \ln t^*$ where (i) the disorder-averaged value moves linearly $\bar{\ln (T_N)} \simeq - \frac{N}{\xi_{loc}}$ and the localization length diverges as $\xi_{loc} \sim (W-W_c)^{-\nu_{loc}}$ with $\nu_{loc}=1$ (ii) the variable $t^*$ is a fixed random variable with a power-law tail $P^*(t^*) \sim 1/(t^*)^{1+\beta(W)}$ for large $t^*$ with $0<\beta(W) \leq 1/2$, so that all integer moments of $T_N$ are governed by rare events. In the delocalized phase, the transmission $T_N$ remains a finite random variable as $N \to \infty$, and we measure near criticality the essential singularity $\bar{\ln (T)} \sim - | W_c-W |^{-\kappa_T}$ with $\kappa_T \sim 0.25$. We then consider the statistical properties of normalized eigenstates, in particular the entropy and the Inverse Participation Ratios (I.P.R.). In the localized phase, the typical entropy diverges as $(W-W_c)^{- \nu_S}$ with $\nu_S \sim 1.5$, whereas it grows linearly in $N$ in the delocalized phase. Finally for the I.P.R., we explain how closely related variables propagate as traveling waves in the delocalized phase. In conclusion, both the localized phase and the delocalized phase are characterized by the traveling wave propagation of some probability distributions, and the Anderson localization/delocalization transition then corresponds to a traveling/non-traveling critical point. Moreover, our results point towards the existence of several exponents $\nu$ at criticality.Comment: 28 pages, 21 figures, comments welcom

Clustering properties of a generalised critical Euclidean network

Many real-world networks exhibit scale-free feature, have a small diameter and a high clustering tendency. We have studied the properties of a growing network, which has all these features, in which an incoming node is connected to its $i$th predecessor of degree $k_i$ with a link of length $\ell$ using a probability proportional to $k^\beta_i \ell^{\alpha}$. For $\alpha > -0.5$, the network is scale free at $\beta = 1$ with the degree distribution $P(k) \propto k^{-\gamma}$ and $\gamma = 3.0$ as in the Barab\'asi-Albert model ($\alpha =0, \beta =1$). We find a phase boundary in the $\alpha-\beta$ plane along which the network is scale-free. Interestingly, we find scale-free behaviour even for $\beta > 1$ for $\alpha < -0.5$ where the existence of a new universality class is indicated from the behaviour of the degree distribution and the clustering coefficients. The network has a small diameter in the entire scale-free region. The clustering coefficients emulate the behaviour of most real networks for increasing negative values of $\alpha$ on the phase boundary.Comment: 4 pages REVTEX, 4 figure

Quasi-stationary regime of a branching random walk in presence of an absorbing wall

A branching random walk in presence of an absorbing wall moving at a constant velocity $v$ undergoes a phase transition as the velocity $v$ of the wall varies. Below the critical velocity $v_c$, the population has a non-zero survival probability and when the population survives its size grows exponentially. We investigate the histories of the population conditioned on having a single survivor at some final time $T$. We study the quasi-stationary regime for $v<v_c$ when $T$ is large. To do so, one can construct a modified stochastic process which is equivalent to the original process conditioned on having a single survivor at final time $T$. We then use this construction to show that the properties of the quasi-stationary regime are universal when $v\to v_c$. We also solve exactly a simple version of the problem, the exponential model, for which the study of the quasi-stationary regime can be reduced to the analysis of a single one-dimensional map.Comment: 2 figures, minor corrections, one reference adde

Last passage percolation and traveling fronts

We consider a system of N particles with a stochastic dynamics introduced by Brunet and Derrida. The particles can be interpreted as last passage times in directed percolation on {1,...,N} of mean-field type. The particles remain grouped and move like a traveling wave, subject to discretization and driven by a random noise. As N increases, we obtain estimates for the speed of the front and its profile, for different laws of the driving noise. The Gumbel distribution plays a central role for the particle jumps, and we show that the scaling limit is a L\'evy process in this case. The case of bounded jumps yields a completely different behavior

On the black hole content and initial mass function of 47 Tuc

The globular cluster (GC) 47 Tuc has recently been proposed to host an intermediate-mass black hole (IMBH) or a population of stellar-mass black holes (BHs). To shed light on its dark content, we present an application of self-consistent multimass models with a varying mass function and content of stellar remnants, which we fit to various observational constraints. Our best-fitting model successfully matches the observables and correctly predicts the radial distribution of millisecond pulsars and their gravitational accelerations inferred from long-term timing observations. The data favours a population of BHs with a total mass of $430^{+386}_{-301}$ $M_{\odot}$, but the most likely model has very few BHs. Since our models do not include a central IMBH and accurately reproduce the observations, we conclude that there is currently no need to invoke the presence of an IMBH in 47 Tuc. The global present-day mass function inferred is significantly depleted in low-mass stars (power-law slope $\alpha=-0.52^{+0.17}_{-0.16}$). Given the orbit and predicted mass-loss history of this massive GC, the dearth of low-mass stars is difficult to explain with a standard initial mass function (IMF) followed by long-term preferential escape of low-mass stars driven by two-body relaxation, and instead suggests that 47 Tuc may have formed with a bottom-light IMF. We discuss alternative evolutionary origins for the flat mass function and ways to reconcile this with the low BH retention fraction. Finally, by capturing the effect of dark remnants, our method offers a new way to probe the IMF in a GC above the current main-sequence turn-off mass, for which we find a slope of $-2.49\pm0.08$.Comment: 16 pages, 7 figures, accepted to MNRAS after minor revisio

Role of hindbrain in inner ear morphogenesis: Analysis of Noggin knockout mice

AbstractSignaling from rhombomeres 5 and 6 of the hindbrain is thought to be important for inner ear patterning. In Noggin −/− embryos, the gross anatomy of the inner ear is distorted and malformed, with cochlear duct outgrowth and coiling most affected. We attributed these defects to a caudal shift of the rhombomeres caused by the shortened body axis and the kink in the neural tube. To test the hypothesis that a caudal shift of the rhombomeres affects inner ear development, we surgically generated chicken embryos in which rhombomeres 5 and 6 were similarly shifted relative to the position of the inner ears, as in Noggin mutants. All chicken embryos with shifted rhombomeres showed defects in cochlear duct formation indicating that signaling from rhombomeres 5 and 6 is important for cochlear duct patterning in both chicken and mice. In addition, the size of the otic capsule is increased in Noggin −/− mutants, which most likely is due to unopposed BMP signaling for chondrogenesis in the peri-otic mesenchyme

Free-energy distribution of the directed polymer at high temperature

We study the directed polymer of length $t$ in a random potential with fixed endpoints in dimension 1+1 in the continuum and on the square lattice, by analytical and numerical methods. The universal regime of high temperature $T$ is described, upon scaling 'time' $t \sim T^5/\kappa$ and space $x = T^3/\kappa$ (with $\kappa=T$ for the discrete model) by a continuum model with $\delta$-function disorder correlation. Using the Bethe Ansatz solution for the attractive boson problem, we obtain all positive integer moments of the partition function. The lowest cumulants of the free energy are predicted at small time and found in agreement with numerics. We then obtain the exact expression at any time for the generating function of the free energy distribution, in terms of a Fredholm determinant. At large time we find that it crosses over to the Tracy Widom distribution (TW) which describes the fixed $T$ infinite $t$ limit. The exact free energy distribution is obtained for any time and compared with very recent results on growth and exclusion models.Comment: 6 pages, 3 figures large time limit corrected and convergence to Tracy Widom established, 1 figure changed