Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics.

BackgroundSingle-cell transcriptomics allows researchers to investigate complex communities of heterogeneous cells. It can be applied to stem cells and their descendants in order to chart the progression from multipotent progenitors to fully differentiated cells. While a variety of statistical and computational methods have been proposed for inferring cell lineages, the problem of accurately characterizing multiple branching lineages remains difficult to solve.ResultsWe introduce Slingshot, a novel method for inferring cell lineages and pseudotimes from single-cell gene expression data. In previously published datasets, Slingshot correctly identifies the biological signal for one to three branching trajectories. Additionally, our simulation study shows that Slingshot infers more accurate pseudotimes than other leading methods.ConclusionsSlingshot is a uniquely robust and flexible tool which combines the highly stable techniques necessary for noisy single-cell data with the ability to identify multiple trajectories. Accurate lineage inference is a critical step in the identification of dynamic temporal gene expression

The Diversity of Terrestrial Mammals Surrounding Waterfall at Billy Barquedier National Park

Billy Barquedier is a National Park located in the Stann Creek district of Belize that contains Neotropical vegetation and wildlife. This study was performed to provide a baseline inventory and appearance frequency patterns of the terrestrial mammals located within Zone 1 of the park near a waterfall and to gain a greater understanding of the biodiversity and activity patterns of terrestrial mammals within the park. The methods included camera traps, small Sherman live traps, large live traps, and tracking methods. A non-random sampling method of placing camera traps and live traps on or near human-made or animal-made trails was used to identify the maximum amount of species possible within the eight-week study period. Bait including the local fruit Mamey Apple (Pouteria sapota) was used to attract wildlife to the study area. The hypothesis was at least eight species would be identified during the eight-week study period. The results indicated eleven species were identified, therefore the null hypothesis less than eight species would be identified was rejected and the alternative hypothesis that at least eight species would be identified was accepted. The non- random sampling method introduced bias into the data. Consequently, definite conclusions about relative density and abundance of animals in the area cannot be drawn by this study alone. However, chi-squared tests revealed statistically significant evidence animals appeared more frequently in the central region of the study site, during the first three days the cameras were set out, and during the nighttime hours (2000 to 0459)

Issues on Generating Primordial Anisotropies at the End of Inflation

We revisit the idea of generating primordial anisotropies at the end of inflation in models of inflation with gauge fields. To be specific we consider the charged hybrid inflation model where the waterfall field is charged under a U(1) gauge field so the surface of end of inflation is controlled both by inflaton and the gauge fields. Using delta N formalism properly we find that the anisotropies generated at the end of inflation from the gauge field fluctuations are exponentially suppressed on cosmological scales. This is because the gauge field evolves exponentially during inflation while in order to generate appreciable anisotropies at the end of inflation the spectator gauge field has to be frozen and scale invariant. We argue that this is a generic feature, that is, one can not generate observable anisotropies at the end of inflation within an FRW background.Comment: V3: new references added, JCAP published versio

Slow Roll during the Waterfall Regime: The Small Coupling Window for SUSY Hybrid Inflation

It has recently been pointed out that a substantial amount of e-folds can occur during the waterfall regime of hybrid inflation. Moreover, Kodama et.al. have derived analytic approximations for the trajectories of the inflaton and of the waterfall fields. Based on these, we derive here the consequences for F- and D-term SUSY hybrid inflation: A substantial amount of e-folds may occur in the waterfall regime, provided kappa << M^2/M_P^2, where kappa is the superpotential coupling, M the scale of symmetry breaking and M_P the reduced Planck mass. When this condition is amply fulfilled, a number of e-folds much larger than N_e\approx60 can occur in the waterfall regime and the scalar spectral index is then given by the expression found by Kodama et.al. n_s=1-4/N_e. This value may be increased up to unity, if only about N_e e-folds occur during the waterfall regime, such that the largest observable scale leaves the horizon close to the critical point of hybrid inflation, what can be achieved for kappa\approx10^(-13) and M\approx5x10^(12) GeV in F-term inflation. Imposing the normalization of the power spectrum leads to a lower bound on the scale of symmetry breaking.Comment: 14 pages, 4 figures, minor corrections, references added, accepted for publication in Phys.Rev.

Ambient Sound Provides Supervision for Visual Learning

The sound of crashing waves, the roar of fast-moving cars -- sound conveys important information about the objects in our surroundings. In this work, we show that ambient sounds can be used as a supervisory signal for learning visual models. To demonstrate this, we train a convolutional neural network to predict a statistical summary of the sound associated with a video frame. We show that, through this process, the network learns a representation that conveys information about objects and scenes. We evaluate this representation on several recognition tasks, finding that its performance is comparable to that of other state-of-the-art unsupervised learning methods. Finally, we show through visualizations that the network learns units that are selective to objects that are often associated with characteristic sounds.Comment: ECCV 201

Non-Gaussianities and Curvature Perturbations from Hybrid Inflation

For the original hybrid inflation as well as the supersymmetric F-term and D-term hybrid models, we calculate the level of non-gaussianities and the power spectrum of curvature perturbations generated during the waterfall, taking into account the contribution of entropic modes. We focus on the regime of mild waterfall, in which inflation continues for more than about 60 e-folds N during the waterfall. We find that the associated f_nl parameter goes typically from f_nl \simeq -1 / N_exit in the regime with N >> 60, where N_exit is the number of e-folds between the time of Hubble exit of a pivot scale and the end of inflation, down to f_nl ~-0.3 when N \gtrsim 60, i.e. much smaller in magnitude than the current bound from Planck. Considering only the adiabatic perturbations, the power spectrum is red, with a spectral index n_s = 1 - 4 / N_exit, in the case N >> 60, whereas in the case N \gtrsim 60, it increases up to unity. Including the contribution of entropic modes does not change the observable predictions in the first case. However, in the second case, they are a relevant source for the power spectrum of curvature perturbations, of which the amplitude increases by several orders of magnitudes and can lead to black hole formation. We conclude that due to the important contribution of entropic modes, the parameter space leading to a mild waterfall phase is excluded by CMB observations for all the considered models.Comment: 17 pages, 5 figures, Phys.Rev.D versio