Publications

Developing oocytes need large supplies of macromolecules and organelles. A conserved strategy for accumulating these products is to pool resources of oocyte-associated germline nurse cells. In Drosophila, these cells grow more than 100-fold to boost their biosynthetic capacity. No previously known mechanism explains how nurse cells coordinate growth collectively. Here, we report a cell cycle-regulating mechanism that depends on bidirectional communication between the oocyte and nurse cells, revealing the oocyte as a critical regulator of germline cyst growth. Transcripts encoding the cyclin-dependent kinase inhibitor, Dacapo, are synthesized by the nurse cells and actively localized to the oocyte. Retrograde movement of the oocyte-synthesized Dacapo protein to the nurse cells generates a network of coupled oscillators that controls the cell cycle of the nurse cells to regulate cyst growth. We propose that bidirectional nurse cell-oocyte communication establishes a growth-sensing feedback mechanism that regulates the quantity of maternal resources loaded into the oocyte.

This paper presents the gravitational-wave measurement of the Hubble constant (H0) using the detections from the first and second observing runs of the Advanced LIGO and Virgo detector network. The presence of the transient electromagnetic counterpart of the binary neutron star GW170817 led to the first standard-siren measurement of H0. Here we additionally use binary black hole detections in conjunction with galaxy catalogs and report a joint measurement. Our updated measurement is H0=68.7+17.0−7.8 km/s/Mpc (68.3\% of the highest density posterior interval with a flat-in-log prior) which is an improvement by a factor of 1.04 (about 4\%) over the GW170817-only value of 68.7+17.5−8.3 km/s/Mpc. A significant additional contribution currently comes from GW170814, a loud and well-localized detection from a part of the sky thoroughly covered by the Dark Energy Survey. With numerous detections anticipated over the upcoming years, an exhaustive understanding of other systematic effects are also going to become increasingly important. These results establish the path to cosmology using gravitational-wave observations with and without transient electromagnetic counterparts.

Standard workflows for analyzing microbiomes often include the creation and curation of phylogenetic trees. Here we present EMPress, an interactive web tool for visualizing trees in the context of microbiome, metabolome, and other community data scalable to trees with well over 500,000 nodes. EMPress provides novel functionality—including ordination integration and animations—alongside many standard tree visualization features and thus simplifies exploratory analyses of many forms of ‘omic data.

Sedimentation in active fluids has come into focus due to the ubiquity of swimming micro-organisms in natural and industrial processes. Here, we investigate sedimentation dynamics of passive particles in a fluid as a function of bacteria E. coli concentration. Results show that the presence of swimming bacteria significantly reduces the speed of the sedimentation front even in the dilute regime, in which the sedimentation speed is expected to be independent of particle concentration. Furthermore, bacteria increase the dispersion of the passive particles, which determines the width of the sedimentation front. For short times, particle sedimentation speed has a linear dependence on bacterial concentration. Mean square displacement data shows, however, that bacterial activity decays over long experimental (sedimentation) times. An advection-diffusion equation coupled to bacteria population dynamics seems to capture concentration profiles relatively well. A single parameter, the ratio of single particle speed to the bacteria flow speed can be used to predict front sedimentation speed.

Convolutional neural networks (CNNs) have become a standard for analysis of biological sequences. Tuning of network architectures is essential for a CNN’s performance, yet it requires substantial knowledge of machine learning and commitment of time and effort. This process thus imposes a major barrier to broad and effective application of modern deep learning in genomics. Here we present Automated Modelling for Biological Evidence-based Research (AMBER), a fully automated framework to efficiently design and apply CNNs for genomic sequences. AMBER designs optimal models for user-specified biological questions through the state-of-the-art neural architecture search (NAS). We applied AMBER to the task of modelling genomic regulatory features and demonstrated that the predictions of the AMBER-designed model are significantly more accurate than the equivalent baseline non-NAS models and match or even exceed published expert-designed models. Interpretation of AMBER architecture search revealed its design principles of utilizing the full space of computational operations for accurately modelling genomic sequences. Furthermore, we illustrated the use of AMBER to accurately discover functional genomic variants in allele-specific binding and disease heritability enrichment. AMBER provides an efficient automated method for designing accurate deep learning models in genomics.

We numerically study a model of interacting spin-$1/2$ electrons with random exchange coupling on a fully connected lattice. This model hosts a quantum critical point separating two distinct metallic phases as a function of doping: a Fermi liquid with a large Fermi surface volume and a low-doping phase with local moments ordering into a spin-glass. We show that this quantum critical point has non-Fermi liquid properties characterized by $T$-linear Planckian
behaviour, $\omega/T$ scaling and slow spin dynamics of the Sachdev-Ye-Kitaev (SYK) type. The $\omega/T$ scaling function associated with the electronic self-energy is found to have an intrinsic particle-hole asymmetry, a hallmark of a `skewed' non-Fermi liquid.

The scattering of cosmic microwave background (CMB) photons off the free-electron gas in galaxies and clusters leaves detectable imprints on high resolution CMB maps: the thermal and kinematic Sunyaev-Zel'dovich effects (tSZ and kSZ respectively). We use combined microwave maps from the Atacama Cosmology Telescope (ACT) DR5 and Planck in combination with the CMASS and LOWZ galaxy catalogs from the Baryon Oscillation Spectroscopic Survey (BOSS DR10 and DR12), to study the gas associated with these galaxy groups. Using individual reconstructed velocities, we perform a stacking analysis and reject the no-kSZ hypothesis at 6.5σ, the highest significance to date. This directly translates into a measurement of the electron number density profile, and thus of the gas density profile. Despite the limited signal to noise, the measurement shows at high significance that the gas density profile is more extended than the dark matter density profile, for any reasonable baryon abundance (formally >90σ for the cosmic baryon abundance). We simultaneously measure the tSZ signal, i.e. the electron thermal pressure profile of the same CMASS objects, and reject the no-tSZ hypothesis at 10σ. We combine tSZ and kSZ measurements to estimate the electron temperature to 20% precision in several aperture bins, and find it comparable to the virial temperature. In a companion paper, we analyze these measurements to constrain the gas thermodynamics and the properties of feedback inside galaxy groups. We present the corresponding LOWZ measurements in this paper, ruling out a null kSZ (tSZ) signal at 2.9 (13.9)σ, and leave their interpretation to future work. Our stacking software ThumbStack is publicly available at \href{https://github.com/EmmanuelSchaan/ThumbStack}{this https URL} and directly applicable to future Simons Observatory and CMB-S4 data.

The thermal and kinematic Sunyaev-Zel'dovich effects (tSZ, kSZ) probe the thermodynamic properties of the circumgalactic and intracluster medium (CGM and ICM) of galaxies, groups, and clusters, since they are proportional, respectively, to the integrated electron pressure and momentum along the line-of-sight. We present constraints on the gas thermodynamics of CMASS galaxies in the Baryon Oscillation Spectroscopic Survey (BOSS) using new measurements of the kSZ and tSZ signals obtained in a companion paper. Combining kSZ and tSZ measurements, we measure within our model the amplitude of energy injection ϵM⋆c2, where M⋆ is the stellar mass, to be ϵ=(40±9)×10−6, and the amplitude of the non-thermal pressure profile to be αNth<0.2 (2σ), indicating that less than 20% of the total pressure within the virial radius is due to a non-thermal component. We estimate the effects of including baryons in the modeling of weak-lensing galaxy cross-correlation measurements using the best-fit density profile from the kSZ measurement. Our estimate reduces the difference between the original theoretical model and the weak-lensing galaxy cross-correlation measurements in arXiv:1611.08606 by half but does not fully reconcile it. Comparing the tSZ measurements to cosmological simulations, we find that simulations underestimate the CGM pressure at large radii while they fare better in comparison with the kSZ measurements. This suggests that the energy injected via feedback models in the simulations that we compared against does not sufficiently heat the gas at these radii. We do not find significant disagreement at smaller radii. These measurements provide novel tests of current and future simulations. This work demonstrates the power of joint, high signal-to-noise kSZ and tSZ observations, upon which future cross-correlation studies will improve.

One of the central features of deep learning is the generalization abilities of neural networks, which seem to improve relentlessly with over-parametrization. In this work, we investigate how properties of data impact the test error as a function of the number of training examples and number of training parameters; in other words, how the structure of data shapes the "generalization phase space". We first focus on the random features model trained in the teacher-student scenario. The synthetic input data is composed of independent blocks, which allow us to tune the saliency of low-dimensional structures and their relevance with respect to the target function. Using methods from statistical physics, we obtain an analytical expression for the train and test errors for both regression and classification tasks in the high-dimensional limit. The derivation allows us to show that noise in the labels and strong anisotropy of the input data play similar roles on the test error. Both promote an asymmetry of the phase space where increasing the number of training examples improves generalization further than increasing the number of training parameters. Our analytical insights are confirmed by numerical experiments involving fully-connected networks trained on MNIST and CIFAR10.

Broken symmetries induce strong even-order nonlinear optical responses in materials and at interfaces. Unlike conventional covalently bonded nonlinear crystals, van der Waals (vdW) heterostructures feature layers that can be stacked at arbitrary angles, giving complete control over the presence or lack of inversion symmetry at a crystal interface. Here, we report highly tunable second harmonic generation (SHG) from nanomechanically rotatable stacks of bulk hexagonal boron nitride (BN) crystals and introduce the term twistoptics to describe studies of optical properties in twistable vdW systems. By suppressing residual bulk effects, we observe SHG intensity modulated by a factor of more than 50, and polarization patterns determined by moiré interface symmetry. Last, we demonstrate greatly enhanced conversion efficiency in vdW vertical superlattice structures with multiple symmetry-broken interfaces. Our study paves the way for compact twistoptics architectures aimed at efficient tunable frequency conversion and demonstrates SHG as a robust probe of buried vdW interfaces.