Experimental Realization of a Fermionic Spin-Momentum Lattice.

We experimentally realize a spin-momentum lattice with a homogeneously trapped Fermi gas. The lattice is created via cyclically rotated atom-laser couplings between three bare atomic spin states, and are such that they form a triangular lattice in a synthetic spin-momentum space. We demonstrate the lattice and explore its dynamics with spin- and momentum-resolved absorption imaging. This platform will provide new opportunities for synthetic spin systems and the engineering of topological bands. In particular, the use of three spin states in two spatial dimensions would allow the simulation of synthetic magnetic fields of high spatial uniformity, which would lead to ultranarrow Chern bands that support robust fractional quantum Hall states.

Many-Body Decay of the Gapped Lowest Excitation of a Bose-Einstein Condensate.

We study the decay mechanism of the gapped lowest-lying axial excitation of a quasipure atomic Bose-Einstein condensate confined in a cylindrical box trap. Owing to the absence of accessible lower-energy modes, or direct coupling to an external bath, this excitation is protected against one-body (linear) decay, and the damping mechanism is exclusively nonlinear. We develop a universal theoretical model that explains this fundamentally nonlinear damping as a process whereby two quanta of the gapped lowest excitation mode couple to a higher-energy mode, which subsequently decays into a continuum. We find quantitative agreement between our experiments and the predictions of this model. Finally, by strongly driving the system below its (lowest) resonant frequency, we observe third-harmonic generation, a hallmark of nonlinear behavior.

seekCRIT: Detecting and characterizing differentially expressed circular RNAs using high-throughput sequencing data.

Over the past two decades, researchers have discovered a special form of alternative splicing that produces a circular form of RNA. Although these circular RNAs (circRNAs) have garnered considerable attention in the scientific community for their biogenesis and functions, the focus of current studies has been on the tissue-specific circRNAs that exist only in one tissue but not in other tissues or on the disease-specific circRNAs that exist in certain disease conditions, such as cancer, but not under normal conditions. This approach was conducted in the relative absence of methods that analyze a group of common circRNAs that exist in both conditions, but are more abundant in one condition relative to another (differentially expressed). Studies of differentially expressed circRNAs (DECs) between two conditions would serve as a significant first step in filling this void. Here, we introduce a novel computational tool, seekCRIT (seek for differentially expressed CircRNAs In Transcriptome), that identifies the DECs between two conditions from high-throughput sequencing data. Using rat retina RNA-seq data from ischemic and normal conditions, we show that over 74% of identifiable circRNAs are expressed in both conditions and over 40 circRNAs are differentially expressed between two conditions. We also obtain a high qPCR validation rate of 90% for DECs with a FDR of < 5%. Our results demonstrate that seekCRIT is a novel and efficient approach to detect DECs using rRNA depleted RNA-seq data. seekCRIT is freely downloadable at https://github.com/UofLBioinformatics/seekCRIT. The source code is licensed under the MIT License. seekCRIT is developed and tested on Linux CentOS-7.

Compression asphyxia and other clinicopathological findings from the Hillsborough Stadium disaster.

Ninety-six people died following a crowd crush at the Hillsborough Football Stadium, Sheffield, UK in 1989. The cause of death in nearly all cases was compression asphyxia. The clinical and pathological features of deaths encountered in crowds are discussed with a particular focus on the Hillsborough disaster.

Choice of library size normalization and statistical methods for differential gene expression analysis in balanced two-group comparisons for RNA-seq studies.

BACKGROUND: High-throughput RNA sequencing (RNA-seq) has evolved as an important analytical tool in molecular biology. Although the utility and importance of this technique have grown, uncertainties regarding the proper analysis of RNA-seq data remain. Of primary concern, there is no consensus regarding which normalization and statistical methods are the most appropriate for analyzing this data. The lack of standardized analytical methods leads to uncertainties in data interpretation and study reproducibility, especially with studies reporting high false discovery rates. In this study, we compared a recently developed normalization method, UQ-pgQ2, with three of the most frequently used alternatives including RLE (relative log estimate), TMM (Trimmed-mean M values) and UQ (upper quartile normalization) in the analysis of RNA-seq data. We evaluated the performance of these methods for gene-level differential expression analysis by considering the factors, including: 1) normalization combined with the choice of a Wald test from DESeq2 and an exact test/QL (Quasi-likelihood) F-Test from edgeR; 2) sample sizes in two balanced two-group comparisons; and 3) sequencing read depths. RESULTS: Using the MAQC RNA-seq datasets with small sample replicates, we found that UQ-pgQ2 normalization combined with an exact test can achieve better performance in term of power and specificity in differential gene expression analysis. However, using an intra-group analysis of false positives from real and simulated data, we found that a Wald test performs better than an exact test when the number of sample replicates is large and that a QL F-test performs the best given sample sizes of 5, 10 and 15 for any normalization. The RLE, TMM and UQ methods performed similarly given a desired sample size. CONCLUSION: We found the UQ-pgQ2 method combined with an exact test/QL F-test is the best choice in order to control false positives when the sample size is small. When the sample size is large, UQ-pgQ2 with a QL F-test is a better choice for the type I error control in an intra-group analysis. We observed read depths have a minimal impact for differential gene expression analysis based on the simulated data.

Long-Range Coherence and Multiple Steady States in a Lossy Qubit Array.

We show that a simple experimental setting of a locally pumped and lossy array of two-level quantum systems can stabilize states with strong long-range coherence. Indeed, by explicit analytic construction, we show there is an extensive set of steady-state density operators, from minimally to maximally entangled, despite this being an interacting open many-body problem. Such nonequilibrium steady states arise from a hidden symmetry that stabilizes Bell pairs over arbitrarily long distances, with unique experimental signatures. We demonstrate a protocol by which one can selectively prepare these states using dissipation. Our findings are accessible in present-day experiments.

Tenfold Way for Quadratic Lindbladians.

We uncover a topological classification applicable to open fermionic systems governed by a general class of Lindblad master equations. These "quadratic Lindbladians" can be captured by a non-Hermitian single-particle matrix which describes internal dynamics as well as system-environment coupling. We show that this matrix must belong to one of ten non-Hermitian Bernard-LeClair symmetry classes which reduce to the Altland-Zirnbauer classes in the closed limit. The Lindblad spectrum admits a topological classification, which we show results in gapless edge excitations with finite lifetimes. Unlike previous studies of purely Hamiltonian or purely dissipative evolution, these topological edge modes are unconnected to the form of the steady state. We provide one-dimensional examples where the addition of dissipators can either preserve or destroy the closed classification of a model, highlighting the sensitivity of topological properties to details of the system-environment coupling.

Sample size calculations for the differential expression analysis of RNA-seq data using a negative binomial regression model.

High throughput RNA sequencing (RNA-seq) technology is increasingly used in disease-related biomarker studies. A negative binomial distribution has become the popular choice for modeling read counts of genes in RNA-seq data due to over-dispersed read counts. In this study, we propose two explicit sample size calculation methods for RNA-seq data using a negative binomial regression model. To derive these new sample size formulas, the common dispersion parameter and the size factor as an offset via a natural logarithm link function are incorporated. A two-sided Wald test statistic derived from the coefficient parameter is used for testing a single gene at a nominal significance level 0.05 and multiple genes at a false discovery rate 0.05. The variance for the Wald test is computed from the variance-covariance matrix with the parameters estimated from the maximum likelihood estimates under the unrestricted and constrained scenarios. The performance and a side-by-side comparison of our new formulas with three existing methods with a Wald test, a likelihood ratio test or an exact test are evaluated via simulation studies. Since other methods are much computationally extensive, we recommend our M1 method for quick and direct estimation of sample sizes in an experimental design. Finally, we illustrate sample sizes estimation using an existing breast cancer RNA-seq data.

Urinary levels of the acrolein conjugates of carnosine are associated with inhaled toxicants.

OBJECTIVE: The inhalation of air-borne toxicants is associated with adverse health outcomes which can be somewhat mitigated by enhancing endogenous anti-oxidant capacity. Carnosine is a naturally occurring dipeptide (ß-alanine-L-histidine), present in high abundance in skeletal and cardiac muscle. This multi-functional dipeptide has anti-oxidant properties, can buffer intracellular pH, chelate metals, and sequester aldehydes such as acrolein. Due to these chemical properties, carnosine may be protective against inhaled pollutants which can contain metals and aldehydes and can stimulate the generation of electrophiles in exposed tissues. Thus, assessment of carnosine levels, or levels of its acrolein conjugates (carnosine-propanal and carnosine-propanol) may inform on level of exposure and risk assessment. METHODS: We used established mass spectroscopy methods to measure levels of urinary carnosine (n = 605) and its conjugates with acrolein (n = 561) in a subset of participants in the Louisville Healthy Heart Study (mean age = 51 ± 10; 52% male). We then determined associations between these measures and air pollution exposure and smoking behavior using statistical modeling approaches. RESULTS: We found that higher levels of non-conjugated carnosine, carnosine-propanal, and carnosine-propanol were significantly associated with males (p < 0.02) and those of Caucasian ethnicity (p < 0.02). Levels of carnosine-propanol were significantly higher in never-smokers (p = 0.001) but lower in current smokers (p = 0.037). This conjugate also demonstrated a negative association with mean-daily particulate air pollution (PM2.5) levels (p = 0.01). CONCLUSIONS: These findings suggest that urinary levels of carnosine-propanol may inform as to risk from inhaled pollutants.

Critical Response of a Quantum van der Pol Oscillator.

Classical dynamical systems close to a critical point are known to act as efficient sensors due to a strongly nonlinear response. We explore such systems in the quantum regime by modeling a quantum version of a driven van der Pol oscillator. We find the classical response survives down to one excitation quantum. At very weak drives, genuine quantum features arise, including diverging and negative susceptibilities. Further, the linear response is greatly enhanced by using a strong incoherent pump. These results are largely generic and can be probed in current experimental platforms suited for quantum sensing.

Topology of One-Dimensional Quantum Systems Out of Equilibrium.

We study the topological properties of one-dimensional systems undergoing unitary time evolution. We show that symmetries possessed both by the initial wave function and by the Hamiltonian at all times may not be present in the time-dependent wave function-a phenomenon which we dub "dynamically induced symmetry breaking." This leads to the possibility of a time-varying bulk index after quenching within noninteracting gapped topological phases. The consequences are observable experimentally through particle transport measurements. With reference to the entanglement spectrum, we explain how the topology of the wave function can change out of equilibrium, both for noninteracting fermions and for symmetry-protected topological phases protected by antiunitary symmetries.

Theory of the Josephson Junction Laser.

We develop an analytic theory for the recently demonstrated Josephson junction laser [M. C. Cassidy et al., Science 355, 939 (2017)SCIEAS0036-807510.1126/science.aah6640]. By working in the time-domain representation (rather than the frequency domain), a single nonlinear equation is obtained for the dynamics of the device, which is fully solvable in some regimes of operation. The nonlinear drive is seen to lead to mode-locked output, with a period set by the round-trip time of the resonant cavity.

Anomalous de Haas-van Alphen Effect in InAs/GaSb Quantum Wells.

The de Haas-van Alphen effect describes the periodic oscillation of the magnetization in a material as a function of an inverse applied magnetic field. It forms the basis of a well established procedure for measuring Fermi surface properties, and its observation is typically taken as a direct signature of a system being metallic. However, certain insulators can show similar oscillations of the magnetization from quantization of the energies of electron states in filled bands. Recently, the theory of such an anomalous dHvAE (AdHvAE) was worked out, but there has not yet been a clear experimental observation. Here, we show that the inverted narrow gap regime of InAs/GaSb quantum wells is an ideal platform for the observation of the AdHvAE. From our microscopic calculations, we make quantitative predictions for the relevant magnetic field and temperature regimes, and we describe unambiguous experimental signatures.

Excitons in topological Kondo insulators: Theory of thermodynamic and transport anomalies in SmB_{6}.

Kondo insulating materials lie outside the usual dichotomy of weakly versus correlated-band versus Mott-insulators. They are metallic at high temperatures but resemble band insulators at low temperatures because of the opening of an interaction-induced band gap. The first discovered Kondo insulator (KI) SmB_{6} has been predicted to form a topological KI (TKI). However, since its discovery thermodynamic and transport anomalies have been observed that have defied a theoretical explanation. Enigmatic signatures of collective modes inside the charge gap are seen in specific heat, thermal transport, and quantum oscillation experiments in strong magnetic fields. Here, we show that TKIs are susceptible to the formation of excitons and magnetoexcitons. These charge neutral composite particles can account for long-standing anomalies in SmB_{6}.

Synthetic Spin-Orbit Coupling in an Optical Lattice Clock.

We propose the use of optical lattice clocks operated with fermionic alkaline-earth atoms to study spin-orbit coupling (SOC) in interacting many-body systems. The SOC emerges naturally during the clock interrogation, when atoms are allowed to tunnel and accumulate a phase set by the ratio of the "magic" lattice wavelength to the clock transition wavelength. We demonstrate how standard protocols such as Rabi and Ramsey spectroscopy that take advantage of the sub-Hertz resolution of state-of-the-art clock lasers can perform momentum-resolved band tomography and determine SOC-induced s-wave collisions in nuclear-spin-polarized fermions. With the use of a second counterpropagating clock beam, we propose a method for engineering controlled atomic transport and study how it is modified by p- and s-wave interactions. The proposed spectroscopic probes provide clean and well-resolved signatures at current clock operating temperatures.

Dynamics of Cochlear Nonlinearity.

Dynamic aspects of cochlear mechanical compression were studied by recording basilar membrane (BM) vibrations evoked by tone pairs ("beat stimuli") in the 11-19 kHz region of the gerbil cochlea. The frequencies of the stimulus components were varied to produce a range of "beat rates" at or near the characteristic frequency (CF) of the BM site under study, and the amplitudes of the components were balanced to produce near perfect periodic cancellations, visible as sharp notches in the envelope of the BM response. We found a compressive relation between instantaneous stimulus intensity and BM response magnitude that was strongest at low beat rates (e.g., 10-100 Hz). At higher beat rates, the amount of compression reduced progressively (i.e. the responses became linearized), and the rising and falling flanks of the response envelope showed increasing amounts of hysteresis; the rising flank becoming steeper than the falling flank. This hysteresis indicates that cochlear mechanical compression is not instantaneous, and is suggestive of a gain control mechanism having finite attack and release times. In gain control terms, the linearization that occurs at higher beat rates occurs because the instantaneous gain becomes smoothened, or low-pass filtered, with respect to the magnitude fluctuations in the stimulus. In terms of peripheral processing, the linearization corresponds to an enhanced coding, or decompression, of rapid amplitude modulations. These findings are relevant both to those who wish to understand the underlying mechanisms and those who need a realistic model of nonlinear processing by the auditory periphery.

Quantum Oscillations without a Fermi Surface and the Anomalous de Haas-van Alphen Effect.

The de Haas-van Alphen effect (dHvAE), describing oscillations of the magnetization as a function of magnetic field, is commonly assumed to be a definite sign for the presence of a Fermi surface (FS). Indeed, the effect forms the basis of a well-established experimental procedure for accurately measuring FS topology and geometry of metallic systems, with parameters commonly extracted by fitting to the Lifshitz-Kosevich (LK) theory based on Fermi liquid theory. Here we show that, in contrast to this canonical situation, there can be quantum oscillations even for band insulators of certain types. We provide simple analytic formulas describing the temperature dependence of the quantum oscillations in this setting, showing strong deviations from LK theory. We draw connections to recent experiments and discuss how our results can be used in future experiments to accurately determine, e.g., hybridization gaps in heavy-fermion systems.

Fractional Chern Insulators in Harper-Hofstadter Bands with Higher Chern Number.

The Harper-Hofstadter model provides a fractal spectrum containing topological bands of any integer Chern number C. We study the many-body physics that is realized by interacting particles occupying Harper-Hofstadter bands with |C|>1. We formulate the predictions of Chern-Simons or composite fermion theory in terms of the filling factor ν, defined as the ratio of particle density to the number of single-particle states per unit area. We show that this theory predicts a series of fractional quantum Hall states with filling factors ν=r/(r|C|+1) for bosons, or ν=r/(2r|C|+1) for fermions. This series includes a bosonic integer quantum Hall state in |C|=2 bands. We construct specific cases where a single band of the Harper-Hofstadter model is occupied. For these cases, we provide numerical evidence that several states in this series are realized as incompressible quantum liquids for bosons with contact interactions.

Signatures of fractional exclusion statistics in the spectroscopy of quantum Hall droplets.

We show how spectroscopic experiments on a small Laughlin droplet of rotating bosons can directly demonstrate Haldane fractional exclusion statistics of quasihole excitations. The characteristic signatures appear in the single-particle excitation spectrum. We show that the transitions are governed by a "many-body selection rule" which allows one to relate the number of allowed transitions to the number of quasihole states on a finite geometry. We illustrate the theory with numerically exact simulations of small numbers of particles.

Dynamic Optical Lattices of Subwavelength Spacing for Ultracold Atoms.

We propose a scheme for realizing lattice potentials of subwavelength spacing for ultracold atoms. It is based on spin-dependent optical lattices with a time-periodic modulation. We show that the atomic motion is well described by the combined action of an effective, time-independent lattice of small spacing, together with a micromotion associated with the time modulation. A numerical simulation shows that an atomic gas can be adiabatically loaded into the effective lattice ground state, for time scales comparable to the ones required for adiabatic loading of standard optical lattices. We generalize our scheme to a two-dimensional geometry, leading to Bloch bands with nonzero Chern numbers. The realization of lattices of subwavelength spacing allows for the enhancement of energy scales, which could facilitate the achievement of strongly correlated (topological) states.