Publications

Consistent estimation of associations in microbial genomic survey count data is fundamental to microbiome research. Technical limitations, including compositionality, low sample sizes, and technical variability, obstruct standard application of association measures and require data normalization prior to estimating associations. Here, we investigate the interplay between data normalization and microbial association estimation by a comprehensive analysis of statistical consistency. Leveraging the large sample size of the American Gut Project (AGP), we assess the consistency of the two prominent linear association estimators, correlation and proportionality, under different sample scenarios and data normalization schemes, including RNA-seq analysis work flows and log-ratio transformations. We show that shrinkage estimation, a standard technique in high-dimensional statistics, can universally improve the quality of association estimates for microbiome data. We find that large-scale association patterns in the AGP data can be grouped into five normalization-dependent classes. Using microbial association network construction and clustering as examples of exploratory data analysis, we show that variance-stabilizing and log-ratio approaches provide for the most consistent estimation of taxonomic and structural coherence. Taken together, the findings from our reproducible analysis workflow have important implications for microbiome studies in multiple stages of analysis, particularly when only small sample sizes are available.

With biomedical research transitioning into data-rich science, machine learning provides a powerful toolkit for extracting knowledge from large-scale biological data sets. The increasing availability of comprehensive kidney omics compendia (transcriptomics, proteomics, metabolomics, and genome sequencing), as well as other data modalities such as electronic health records, digital nephropathology repositories, and radiology renal images, makes machine learning approaches increasingly essential for analyzing human kidney data sets. Here, we discuss how machine learning approaches can be applied to the study of kidney disease, with a particular focus on how they can be used for understanding the relationship between genotype and phenotype.

Hermann Bondi's 1952 paper "On spherically symmetrical accretion" is recognized as one of the foundations of accretion theory. Although Bondi later remarked that it was "not much more than an examination exercise", his mathematical analysis of spherical accretion on to a point mass has found broad use across fields of astrophysics that were embryonic or non-existent at the time of the paper's publication. In this non-technical review, I describe the motivations for Bondi's work, and briefly discuss some of the applications of Bondi accretion in high energy astrophysics, galaxy formation, and star formation.

Dirac fermions with highly dispersive linear bands are usually considered weakly correlated due to the relatively large bandwidths (W) compared to Coulomb interactions (U). With the discovery of nodal-line semimetals, the notion of the Dirac point has been extended to lines and loops in momentum space. The anisotropy associated with nodal-line structure gives rise to greatly reduced kinetic energy along the line. However, experimental evidence for the anticipated enhanced correlations in nodal-line semimetals is sparse. Here, we report on prominent correlation effects in a nodal-line semimetal compound, ZrSiSe, through a combination of optical spectroscopy and density functional theory calculations. We observed two fundamental spectroscopic hallmarks of electronic correlations: strong reduction (1/3) of the free-carrier Drude weight and also the Fermi velocity compared to predictions of density functional band theory. The renormalization of Fermi velocity can be further controlled with an external magnetic field. ZrSiSe therefore offers the rare opportunity to investigate correlation-driven physics in a Dirac system.

Over the last few years, extraordinary advances in experimental and theoretical tools have allowed us to monitor and control matter at short time and atomic scales with a high degree of precision. An appealing and challenging route toward engineering materials with tailored properties is to find ways to design or selectively manipulate materials, especially at the quantum level. To this end, having a state-of-the-art ab initio computer simulation tool that enables a reliable and accurate simulation of light-induced changes in the physical and chemical properties of complex systems is of utmost importance. The first principles real-space-based Octopus project was born with that idea in mind, i.e., to provide a unique framework that allows us to describe non-equilibrium phenomena in molecular complexes, low dimensional materials, and extended systems by accounting for electronic, ionic, and photon quantum mechanical effects within a generalized time-dependent density functional theory. This article aims to present the new features that have been implemented over the last few years, including technical developments related to performance and massive parallelism. We also describe the major theoretical developments to address ultrafast light-driven processes, such as the new theoretical framework of quantum electrodynamics density-functional formalism for the description of novel light–matter hybrid states. Those advances, and others being released soon as part of the Octopus package, will allow the scientific community to simulate and characterize spatial and time-resolved spectroscopies, ultrafast phenomena in molecules and materials, and new emergent states of matter (quantum electrodynamical-materials).

In the course of doing astronomy, one often encounters plots of densities, for example probability densities, flux densities, and mass functions. Quite frequently the ordinate of these diagrams is plotted logarithmically to accommodate a large dynamic range. In this situation, I argue that it is critical to adjust the density appropriately, rather than simply setting the x-scale to `log' in your favorite plotting code. I will demonstrate the basic issue with a pedagogical example, then mention a few common plots where this may arise, and finally some possible exceptions to the rule.

The occurrence of coiled or helical morphologies is common in nature, from plant roots to DNA packaging into viral capsids, as well as in applications such as oil drilling processes. In many examples, chiral structures result from the buckling of a straight fibre either with intrinsic twist or to which end moments have been applied in addition to compression forces. Here, we elucidate a generic way to form regular helicoidal shapes from achiral straight filaments transported in viscous flows with free ends. Through a combination of experiments using fluorescently labelled actin filaments in microfluidic divergent flows and two distinct sets of numerical simulations, we demonstrate the robustness of helix formation. A nonlinear stability analysis is performed, and explains the emergence of such chiral structures from the nonlinear interaction of perpendicular planar buckling modes, an effect that solely requires a strong compressional flow, independent of the exact nature of the fibre or type of flow field. The fundamental mechanism for the uncovered morphological transition and characterization of the emerging conformations advance our understanding of several biological and industrial processes and can also be exploited for the controlled microfabrication of chiral objects.

It is imperative that useful quantum computers be very difficult to simulate classically; otherwise classical computers could be used for the applications envisioned for the quantum ones. Perfect quantum computers are unarguably exponentially difficult to simulate: the classical resources required grow exponentially with the number of qubits N or the depth D of the circuit. Real quantum computing devices, however, are characterized by an exponentially decaying fidelity F∼(1−ϵ)ND with an error rate ϵ per operation as small as ~1% for current devices. In this work, we demonstrate that real quantum computers can be simulated at a tiny fraction of the cost that would be needed for a perfect quantum computer. Our algorithms compress the representations of quantum wavefunctions using matrix product states (MPS), which capture states with low to moderate entanglement very accurately. This compression introduces a finite error rate ϵ so that the algorithms closely mimic the behavior of real quantum computing devices. The computing time of our algorithm increases only linearly with N and D. We illustrate our algorithms with simulations of random circuits for qubits connected in both one and two dimensional lattices. We find that ϵ can be decreased at a polynomial cost in computing power down to a minimum error ϵ∞. Getting below ϵ∞ requires computing resources that increase exponentially with ϵ∞/ϵ. For a two dimensional array of N=54 qubits and a circuit with Control-Z gates, error rates better than state-of-the-art devices can be obtained on a laptop in a few hours. For more complex gates such as a swap gate followed by a controlled rotation, the error rate increases by a factor three for similar computing time.

More than 80 loss-of-function (LOF) mutations in the SLC6A8 creatine transporter (hCRT1) are responsible for cerebral creatine deficiency syndrome (CCDS), which gives rise to a spectrum of neurological defects, including intellectual disability, epilepsy, and autism spectrum disorder. To gain insight into the nature of the molecular defects caused by these mutations, we quantitatively profiled the cellular processing, trafficking, expression, and function of eight pathogenic CCDS variants in relation to the wild type (WT) and one neutral isoform. All eight CCDS variants exhibit measurable proteostatic deficiencies that likely contribute to the observed LOF. However, the magnitudes of their specific effects on the expression and trafficking of hCRT1 vary considerably, and we find that the LOF associated with two of these variants primarily arises from the disruption of the substrate-binding pocket. In conjunction with an analysis of structural models of the transporter, we use these data to suggest mechanistic classifications for these variants. To evaluate potential avenues for therapeutic intervention, we assessed the sensitivity of these variants to temperature and measured their response to the proteostasis regulator 4-phenylbutyrate (4-PBA). Only one of the tested variants (G132V) is sensitive to temperature, though its response to 4-PBA is negligible. Nevertheless, 4-PBA significantly enhances the activity of WT hCRT1 in HEK293T cells, which suggests it may be worth evaluating as a therapeutic for female intellectual disability patients carrying a single CCDS mutation. Together, these findings reveal that pathogenic SLC6A8 mutations cause a spectrum of molecular defects that should be taken into consideration in future efforts to develop CCDS therapeutics.

Optogenetic perturbations, live imaging, and time-resolved ChIP-seq assays in Drosophila embryos were used to dissect the ERK-dependent control of the HMG-box repressor Capicua (Cic), which plays critical roles in development and is deregulated in human spinocerebellar ataxia and cancers. We established that Cic target genes are activated before significant downregulation of nuclear localization of Cic and demonstrated that their activation is preceded by fast dissociation of Cic from the regulatory DNA. We discovered that both Cic-DNA binding and repression are rapidly reinstated in the absence of ERK activation, revealing that inductive signaling must be sufficiently sustained to ensure robust transcriptional response. Our work provides a quantitative framework for the mechanistic analysis of dynamics and control of transcriptional repression in development.