Publications

Background
The abundance and diversity of antibiotic resistance genes (ARGs) in the human respiratory microbiome remain poorly characterized. In the context of influenza virus infection, interactions between the virus, the host, and resident bacteria with pathogenic potential are known to complicate and worsen disease, resulting in coinfection and increased morbidity and mortality of infected individuals. When pathogenic bacteria acquire antibiotic resistance, they are more difficult to treat and of global health concern. Characterization of ARG expression in the upper respiratory tract could help better understand the role antibiotic resistance plays in the pathogenesis of influenza-associated bacterial secondary infection.

Results
Thirty-seven individuals participating in the Household Influenza Transmission Study (HITS) in Managua, Nicaragua, were selected for this study. We performed metatranscriptomics and 16S rRNA gene sequencing analyses on nasal and throat swab samples, and host transcriptome profiling on blood samples. Individuals clustered into two groups based on their microbial gene expression profiles, with several microbial pathways enriched with genes differentially expressed between groups. We also analyzed antibiotic resistance gene expression and determined that approximately 25% of the sequence reads that corresponded to antibiotic resistance genes mapped to Streptococcus pneumoniae and Staphylococcus aureus. Following construction of an integrated network of ARG expression with host gene co-expression, we identified several host key regulators involved in the host response to influenza virus and bacterial infections, and host gene pathways associated with specific antibiotic resistance genes.

Conclusions
This study indicates the host response to influenza infection could indirectly affect antibiotic resistance gene expression in the respiratory tract by impacting the microbial community structure and overall microbial gene expression. Interactions between the host systemic responses to influenza infection and antibiotic resistance gene expression highlight the importance of viral-bacterial co-infection in acute respiratory infections like influenza.

Although a wide variety of quantum computers are currently being developed, actual computational results have been largely restricted to contrived, artificial tasks. Finding ways to apply quantum computers to useful, real-world computational tasks remains an active research area. Here we describe our mapping of the protein design problem to the D-Wave quantum annealer. We present a system whereby Rosetta, a state-of-the-art protein design software suite, interfaces with the D-Wave quantum processing unit to find amino acid side chain identities and conformations to stabilize a fixed protein backbone. Our approach, which we call the QPacker, uses a large side-chain rotamer library and the full Rosetta energy function, and in no way reduces the design task to a simpler format. We demonstrate that quantum annealer-based design can be applied to complex real-world design tasks, producing designed molecules comparable to those produced by widely adopted classical design approaches. We also show through large-scale classical folding simulations that the results produced on the quantum annealer can inform wet-lab experiments. For design tasks that scale exponentially on classical computers, the QPacker achieves nearly constant runtime performance over the range of problem sizes that could be tested. We anticipate better than classical performance scaling as quantum computers mature.

We introduce a sparse scattering deep convolutional neural network, which provides a simple model to analyze properties of deep representation learning for classification. Learning a single dictionary matrix with a classifier yields a higher classification accuracy than AlexNet over the ImageNet 2012 dataset. The network first applies a scattering transform that linearizes variabilities due to geometric transformations such as translations and small deformations. A sparse $\ell^1$ dictionary coding reduces intra-class variability while preserving class separation through projections over unions of linear spaces. It is implemented in a deep convolutional network with a homotopy algorithm having an exponential convergence. A convergence proof is given in a general framework that includes ALISTA. Classification results are analyzed on ImageNet.

Topological defects determine the structure and function of physical and biological matter over a wide range of scales, from the turbulent vortices in planetary atmospheres, oceans or quantum fluids to bioelectrical signalling in the heart1,2,3 and brain4, and cell death5. Many advances have been made in understanding and controlling the defect dynamics in active6,7,8,9 and passive9,10 non-equilibrium fluids. Yet, it remains unknown whether the statistical laws that govern the dynamics of defects in classical11 or quantum fluids12,13,14 extend to the active matter7,15,16 and information flows17,18 in living systems. Here, we show that a defect-mediated turbulence underlies the complex wave propagation patterns of Rho-GTP signalling protein on the membrane of starfish egg cells, a process relevant to cytoskeletal remodelling and cell proliferation19,20. Our experiments reveal that the phase velocity field extracted from Rho-GTP concentration waves exhibits vortical defect motions and annihilation dynamics reminiscent of those seen in quantum systems12,13, bacterial turbulence15 and active nematics7. Several key statistics and scaling laws of the defect dynamics can be captured by a minimal Helmholtz–Onsager point vortex model21 as well as a generic complex Ginzburg–Landau22 continuum theory, suggesting a close correspondence between the biochemical signal propagation on the surface of a living cell and a widely studied class of two-dimensional turbulence23 and wave22 phenomena.

We study a many-server queueing model with server vacations, where the population size dynamics of servers and customers are coupled: a server may leave for vacation only when no customers await, and the capacity available to customers is directly affected by the number of servers on vacation. We focus on scaling regimes in which server dynamics and queue dynamics fluctuate at matching time scales, so that their limiting dynamics are coupled. Specifically, we argue that interesting coupled dynamics occur in (a) the Halfin-Whitt regime, (b) the nondegenerate slowdown regime, and (c) the intermediate, near Halfin-Whitt regime; whereas the dynamics asymptotically decouple in the other heavy traffic regimes. We characterize the limiting dynamics, which are different for each scaling regime. We consider relevant respective performance measures for regimes (a) and (b) --- namely, the probability of wait and the slowdown. While closed form formulas for these performance measures have been derived for models that do not accommodate server vacations, it is difficult to obtain closed form formulas for these performance measures in the setting with server vacations. Instead, we propose formulas that approximate these performance measures, and depend on the steady-state mean number of available servers and previously derived formulas for models without server vacations. We test the accuracy of these formulas numerically.

Multisite protein phosphorylation plays a critical role in cell regulation [1, 2, 3]. It is widely appreciated that the functional capabilities of multisite phosphorylation depend on the order and kinetics of phosphorylation steps, but kinetic aspects of multisite phosphorylation remain poorly understood [4, 5, 6]. Here, we focus on what appears to be the simplest scenario, when a protein is phosphorylated on only two sites in a strict, well-defined order. This scenario describes the activation of ERK, a highly conserved cell-signaling enzyme. We use Bayesian parameter inference in a structurally identifiable kinetic model to dissect dual phosphorylation of ERK by MEK, a kinase that is mutated in a large number of human diseases [7, 8, 9, 10, 11, 12]. Our results reveal how enzyme processivity and efficiencies of individual phosphorylation steps are altered by pathogenic mutations. The presented approach, which connects specific mutations to kinetic parameters of multisite phosphorylation mechanisms, provides a systematic framework for closing the gap between studies with purified enzymes and their effects in the living organism.

Multisite protein phosphorylation plays a critical role in cell regulation [1, 2, 3]. It is widely appreciated that the functional capabilities of multisite phosphorylation depend on the order and kinetics of phosphorylation steps, but kinetic aspects of multisite phosphorylation remain poorly understood [4, 5, 6]. Here, we focus on what appears to be the simplest scenario, when a protein is phosphorylated on only two sites in a strict, well-defined order. This scenario describes the activation of ERK, a highly conserved cell-signaling enzyme. We use Bayesian parameter inference in a structurally identifiable kinetic model to dissect dual phosphorylation of ERK by MEK, a kinase that is mutated in a large number of human diseases [7, 8, 9, 10, 11, 12]. Our results reveal how enzyme processivity and efficiencies of individual phosphorylation steps are altered by pathogenic mutations. The presented approach, which connects specific mutations to kinetic parameters of multisite phosphorylation mechanisms, provides a systematic framework for closing the gap between studies with purified enzymes and their effects in the living organism.

Principles that predict reactions or properties of materials define the discipline of chemistry. In this work, we derive chemical rules, based on atomic distances and chemical bond character, which predict topological materials in compounds that feature the structural motif of a square-net. Using these rules, we identify over 300 potential new topological materials. We show that simple chemical heuristics can be a powerful tool to characterize topological matter. In contrast to previous database-driven materials’ categorization, our approach allows us to identify candidates that are alloys, solid-solutions, or compounds with statistical vacancies. While previous material searches relied on density functional theory, our approach is not limited by this method and could also be used to discover magnetic and statistically disordered topological semimetals.

Gravitational wave echoes have been proposed as a smoking-gun signature of exotic compact objects with near-horizon structure. Recently there have been observational claims that echoes are indeed present in stretches of data from Advanced LIGO and Advanced Virgo immediately following gravitational wave signals from presumed binary black hole mergers, as well as a binary neutron star merger. In this paper we deploy a morphology-independent search algorithm for echoes introduced in Tsang et al., Phys. Rev. D 98, 024023 (2018), which (a) is able to accurately reconstruct a possible echoes signal with minimal assumptions about their morphology, and (b) computes Bayesian evidences for the hypotheses that the data contain a signal, an instrumental glitch, or just stationary, Gaussian noise. Here we apply this analysis method to all the significant events in the first Gravitational Wave Transient Catalog (GWTC-1), which comprises the signals from binary black hole and binary neutron star coalescences found during the first and second observing runs of Advanced LIGO and Advanced Virgo. In all cases, the ratios of evidences for signal versus noise and signal versus glitch do not rise above their respective "background distributions" obtained from detector noise, the smallest p-value being 3% (for event GW170823). Hence we find no statistically significant evidence for echoes in GWTC-1.