Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis

Molecular profiling of single cells has advanced our knowledge of the molecular basis of development. However, current approaches mostly rely on dissociating cells from tissues, thereby losing the crucial spatial context of regulatory processes. Here, we apply an image-based single-cell transcriptomics method, sequential fluorescence in situ hybridization (seqFISH), to detect mRNAs for 387 target genes in tissue sections of mouse embryos at the 8-12 somite stage. By integrating spatial context and multiplexed transcriptional measurements with two single-cell transcriptome atlases, we characterize cell types across the embryo and demonstrate that spatially resolved expression of genes not profiled by seqFISH can be imputed. We use this high-resolution spatial map to characterize fundamental steps in the patterning of the midbrain-hindbrain boundary (MHB) and the developing gut tube. We uncover axes of cell differentiation that are not apparent from single-cell RNA-sequencing (scRNA-seq) data, such as early dorsal-ventral separation of esophageal and tracheal progenitor populations in the gut tube. Our method provides an approach for studying cell fate decisions in complex tissues and development.

Identification of a regeneration-organizing cell in the Xenopus tail

Unlike mammals, Xenopus laevis tadpoles have a high regenerative potential. To characterize this regenerative response, we performed single-cell RNA sequencing after tail amputation. By comparing naturally occurring regeneration-competent and -incompetent tadpoles, we identified a previously unrecognized cell type, which we term the regeneration-organizing cell (ROC). ROCs are present in the epidermis during normal tail development and specifically relocalize to the amputation plane of regeneration-competent tadpoles, forming the wound epidermis. Genetic ablation or manual removal of ROCs blocks regeneration, whereas transplantation of ROC-containing grafts induces ectopic outgrowths in early embryos. Transcriptional profiling revealed that ROCs secrete ligands associated with key regenerative pathways, signaling to progenitors to reconstitute lost tissue. These findings reveal the cellular mechanism through which ROCs form the wound epidermis and ensure successful regeneration.

Fermionic superradiance in a transversely pumped optical cavity

Following the experimental realization of Dicke superradiance in Bose gases coupled to cavity light fields, we investigate the behavior of ultracold fermions in a transversely pumped cavity. We focus on the equilibrium phase diagram of spinless fermions coupled to a single cavity mode and establish a zero temperature transition to a superradiant state. In contrast to the bosonic case, Pauli blocking leads to lattice commensuration effects that influence self-organization in the cavity light field. This includes a sequence of discontinuous transitions with increasing atomic density and tricritical superradiance. We discuss the implications for experiment.

Holographic superfluids and the dynamics of symmetry breaking

We explore the far-from-equilibrium response of a holographic superfluid using the AdS/CFT correspondence. We establish the dynamical phase diagram corresponding to quantum quenches of the order parameter source field. We find three distinct regimes of behavior that are related to the spectrum of black hole quasinormal modes. These correspond to damped oscillations of the order parameter and to overdamped approaches to the superfluid and normal states. The presence of three regimes, which includes an emergent dynamical temperature scale, is argued to occur more generally in time-reversal-invariant systems that display continuous symmetry breaking.

Ising deconfinement transition between Feshbach-resonant superfluids

We investigate the phase diagram of bosons interacting via Feshbach-resonant pairing interactions in a one-dimensional lattice. Using large scale density matrix renormalization group and field theory techniques we explore the atomic and molecular correlations in this low-dimensional setting. We provide compelling evidence for an Ising deconfinement transition occurring between distinct superfluids and extract the Ising order parameter and correlation length of this unusual superfluid transition. This is supported by results for the entanglement entropy which reveal both the location of the transition and critical Ising degrees of freedom on the phase boundary.

Collective dynamics of Bose-Einstein condensates in optical cavities

Experiments on Bose-Einstein condensates in optical cavities have observed a coherent state of the matter-light system-superradiance. The nature of these experiments demands consideration of collective dynamics. Including cavity leakage and the backreaction of the cavity field on the condensate, we find a rich phase diagram including multiphase coexistence regions, and persistent optomechanical oscillations. The proximity of the phase boundaries results in a critical slowing down of the decay of many-body oscillations, which can be enhanced by large cavity loss.

Feshbach resonance in optical lattices and the quantum Ising model

Motivated by experiments on heteronuclear Feshbach resonances in Bose mixtures, we investigate s-wave pairing of two species of bosons in an optical lattice. The zero temperature phase diagram supports a rich array of superfluid and Mott phases and a network of quantum critical points. This topology reveals an underlying structure that is succinctly captured by a two-component Landau theory. Within the second Mott lobe we establish a quantum phase transition described by the paradigmatic longitudinal and transverse field Ising model. This is confirmed by exact diagonalization of the 1D bosonic Hamiltonian. We also find this transition in the homonuclear case.

Repulsive atomic gas in a harmonic trap on the border of itinerant ferromagnetism

Alongside superfluidity, itinerant (Stoner) ferromagnetism remains one of the most well-characterized phases of correlated Fermi systems. A recent experiment has reported the first evidence for novel phase behavior on the repulsive side of the Feshbach resonance in a two-component ultracold Fermi gas. By adapting recent theoretical studies to the atomic trap geometry, we show that an adiabatic ferromagnetic transition would take place at a weaker interaction strength than is observed in experiment. This discrepancy motivates a simple nonequilibrium theory that takes account of the dynamics of magnetic defects and three-body losses. The formalism developed displays good quantitative agreement with experiment.

Inhomogeneous phase formation on the border of itinerant ferromagnetism

A variety of analytical techniques suggest that quantum fluctuations lead to a fundamental instability of the Fermi liquid that drives ferromagnetic transitions first order at low temperatures. We present both analytical and numerical evidence that, driven by the same quantum fluctuations, this first order transition is preempted by the formation of an inhomogeneous magnetic phase. This occurs in a manner that is closely analogous to the formation of the inhomogeneous superconducting Fulde-Ferrel-Larkin-Ovchinnikov state. We derive these results from a field-theoretical approach supplemented with numerical quantum Monte Carlo simulations.

Inhomogeneous magnetic phases: a Fulde-Ferrell-Larkin-Ovchinnikov-like phase in Sr3Ru2O7

The phase diagram of Sr3Ru2O7 contains a metamagnetic transition that bifurcates to enclose an anomalous phase with intriguing properties--a large resistivity with anisotropy that breaks the crystal-lattice symmetry. We propose that this is a magnetic analogue of the spatially inhomogeneous superconducting Fulde-Ferrel-Larkin-Ovchinnikov state. We show-through a Ginzburg-Landau expansion where the magnetization transverse to the applied field can become spatially inhomogeneous-that a Stoner model with electronic band dispersion can reproduce this phase diagram and transport behavior.

Polaritons and pairing phenomena in Bose-Hubbard mixtures

Motivated by recent experiments on cold atomic gases in ultrahigh finesse optical cavities, we consider the two-band Bose-Hubbard model coupled to quantum light. Photoexcitation promotes carriers between the bands, and we study the interplay between Mott insulating behavior and superfluidity. The model displays a U(1)xU(1) symmetry which supports the coexistence of Mott insulating and superfluid phases and yields a rich phase diagram with multicritical points. This symmetry is shared by several other problems of current experimental interest, including two-component Bose gases in optical lattices and the bosonic BEC-BCS crossover for atom-molecule mixtures induced by a Feshbach resonance. We corroborate our findings by numerical simulations.

Polarized Fermi condensates with unequal masses: tuning the tricritical point

We consider a two-component atomic Fermi gas within a mean-field, single-channel model, where both the mass and population of each component are unequal. We show that the tricritical point at zero temperature evolves smoothly from the BEC to BCS side of the resonance as a function of mass ratio r. We find that the interior gap state proposed by Liu and Wilczek is always unstable to phase separation, while the breached pair state with one Fermi surface for the excess fermions exhibits differences in its density of states and pair correlation functions depending on which side of the resonance it lies. Finally, we show that, when r greater, similar 3.95, the finite-temperature phase diagram of trapped gases at unitarity becomes topologically distinct from the equal mass system.

Phase bifurcation and quantum fluctuations in Sr3Ru2O7

The bilayer ruthenate Sr3Ru2O7 has been cited as a textbook example of itinerant metamagnetic quantum criticality. However, recent studies of the ultrapure system have revealed striking anomalies in magnetism and transport in the vicinity of the quantum critical point. Drawing on fresh experimental data, we show that the complex phase behavior reported here can be fully accommodated within the framework of a simple Landau theory. We discuss the potential physical mechanisms that underpin the phenomenology, and assess the capacity of the ruthenate system to realize quantum tricritial behavior.

Dynamics of the BCS-BEC crossover in a degenerate Fermi gas

We study the short-time dynamics of a degenerate Fermi gas positioned near a Feshbach resonance following an abrupt jump in the atomic interaction resulting from a change of magnetic field. We investigate the dynamics of the condensate order parameter and pair wave function for a range of field strengths. When the jump is sufficient to span the BCS to Bose-Einstein condensation crossover, we show that the rigidity of the momentum distribution precludes any atom-molecule oscillations in the entrance channel dominated resonances observed in 40K and 6Li. Focusing on material parameters tailored to the 40K Feshbach resonance at 202.1 G, we comment on the integrity of the fast sweep projection technique as a vehicle to explore the condensed phase in the crossover region.

Pattern formation as a signature of quantum degeneracy in a cold exciton system

The development of a Turing instability to a spatially modulated state in a photoexcited electron-hole system is proposed as a novel signature of exciton Bose statistics. We show that such an instability, driven by kinetics of exciton formation, can result from stimulated processes that build up near quantum degeneracy. The stability of an electron-hole interface which describes recently observed exciton rings is analyzed. Interface instability occurs below a critical temperature, with a periodic 1D pattern developing via a continuous (type II) transition, in a qualitative agreement with observations.

Formation mechanism and low-temperature instability of exciton rings

The macroscopic rings observed in the photoluminescence patterns of excitons in coupled quantum wells are explained by a mechanism of carrier imbalance, transport, and recombination. The rings originate from the spatial separation of p and n carriers, and occur at the interface of the p and n domains, where excitons are generated. We explore the states of excitons in the ring over a range of temperatures down to 380 mK and report a transition of the ring into a periodic array of aggregates, a new low-temperature ordered exciton state.

Universality of parametric spectral correlations: local versus extended perturbing potentials

We explore the influence of an arbitrary external potential perturbation V on the spectral properties of a weakly disordered conductor. In the framework of a statistical field theory of a nonlinear sigma-model type we find, depending on the range and the profile of the external perturbation, two qualitatively different universal regimes of parametric spectral statistics (i.e., cross correlations between the spectra of Hamiltonians H and H+V). We identify the translational invariance of the correlations in the space of Hamiltonians as the key indicator of universality, and find the connection between the coordinate system in this space which makes the translational invariance manifest, and the physically measurable properties of the system. In particular, in the case of localized perturbations, the latter turn out to be the eigenphases of the scattering matrix for scattering off the perturbing potential V. They also have a purely statistical interpretation in terms of the moments of the level velocity distribution. Finally, on the basis of this analysis, a set of results obtained recently by the authors using random matrix theory methods is shown to be applicable to a much wider class of disordered and chaotic structures.

Parametric statistics of individual energy levels in random Hamiltonians

We establish a general framework to explore parametric statistics of individual energy levels in disordered and chaotic quantum systems of unitary symmetry. The method is applied to the calculation of the universal intralevel parametric velocity correlation function and the distribution of level shifts under the influence of an arbitrary external perturbation.

Parametric spectral correlations in disordered and chaotic structures

We explore the influence of external perturbations on the energy levels of a Hamiltonian drawn at random from the Gaussian unitary distribution of Hermitian matrices. By deriving the joint distribution function of eigenvalues, we obtain the (n,m)-point parametric correlation function of the initial and the final density of states for perturbations of arbitrary rank and strength. A further generalization of these results allows for the incorporation of short-range spatial correlations in diffusive as well as ballistic chaotic structures.

Quantized adiabatic charge transport in a carbon nanotube

The coupling of a semimetallic carbon nanotube to a surface acoustic wave (SAW) is proposed as a vehicle to realize quantized adiabatic charge transport. We demonstrate that electron backscattering from a periodic SAW potential can be used to induce a miniband spectrum at energies near the Fermi level. Within the framework of Luttinger liquid theory, electron interaction is shown to enhance minigaps and thereby improve current quantization.

Preschool vision screening using the MTI-Photoscreener

Amblyopia is a condition that, if detected and treated early, can improve vision for most children. Thus, both pediatric and ophthalmologic groups have acknowledged the need for preschool vision screening. However, vision screening is the exception rather than the rule for preschoolers, since traditional methods of vision screening are often inappropriate for the preschool population and almost impossible for those children who are preverbal or nonverbal, developmentally delayed, and/or have chronic illnesses or disabilities. This study evaluated the use of a photoscreener to detect vision problems in a preschool population. Fifty-one children ages 3 to 5 years were evaluated using the MTI Photoscreener. Results were compared with a complete ophthalmologic examination, including cycloplegia. The sensitivity and specificity calculated for this study was 83% and 68%, respectively. Findings conclude that the MTI Photoscreener detected a broad range of vision problems, seemed to require less time, and seemed more acceptable to preschoolers when compared with the traditional vision screening methods performed by registered nurses. Although the sensitivity and specificity rates for this study were less than desired, it is likely that both could be improved with additional photo interpretation training.

Tail states in a superconductor with magnetic impurities

A field theoretic approach is developed to investigate the profile and spectrum of subgap states in a superconductor subject to a weak magnetic impurity potential. Such states are found to be associated with spatially inhomogeneous instanton configurations of the action.

Posterior fixation suture augmentation of full-tendon vertical rectus muscle transposition for abducens palsy

OBJECTIVE

To evaluate the effect of augmenting full-tendon vertical rectus transpositions with posterior fixation sutures in patients with complete or near-complete lateral rectus palsy.

METHODS

Transposition of the vertical recti to the lateral rectus muscle was performed in seven patients with unilateral lateral rectus palsy (the mean angle of preoperative horizontal deviation in primary gaze was 36.7 prism diopters (delta); range, 25-62delta of esotropia). A posterior fixation suture of 5.0 Mersilene (Ethicon, Somerville, NJ) was placed in sclera (14-16 mm posterior to the limbus) adjacent to the lateral rectus and incorporated 1/3 belly width of each transposed vertical rectus muscle.

RESULTS

The mean angle of postoperative horizontal deviation in primary gaze was 7.1delta (range, 0-20delta). The mean change in primary-position horizontal deviation postoperatively was 41.2delta (range, 37-72delta). Four patients were able to fuse without prism in primary gaze; three patients were orthophoric and one patient had a consecutive intermittent exotropia. The remaining three patients required prism correction to neutralize the postoperative gaze deviation. All patients had improvement in abduction. Mild limitation of adduction was noted in three patients (range, -0.5 to -2.0).

CONCLUSIONS

Augmenting full vertical rectus muscle transpositions with posterior fixation sutures improves the abducting effect of surgery without significant limitation of adduction.

Pediatric photoscreening for strabismus and refractive errors in a high-risk population

OBJECTIVE

To determine the accuracy of the MTI Photoscreener in detecting strabismus and refractive errors in children.

PARTICIPANTS

One hundred children underwent MTI photoscreening followed by complete ophthalmologic examination. Six observers graded the photographs for strabismus, according to the location of the corneal light reflexes, and for refractive error, according to the size and location of the light crescent.

RESULTS

The sensitivity of the MTI Photoscreener in detecting any amblyogenic factor was 80% to 91%, with a specificity of 20% to 67%. The sensitivity and specificity for particular amblyogenic factors varied widely among observers. The ranges were as follows: strabismus, sensitivity = 23% to 50%, specificity = 76% to 96%; myopia, sensitivity = 89%, specificity = 48% to 76%; hyperopia, sensitivity = 20% to 80%, specificity = 88% to 96%; and astigmatism, sensitivity = 46% to 77%, specificity = 79% to 89%.

CONCLUSIONS

These results suggest caution in relying on photoscreening to detect strabismus and refractive errors in children.

Surgical management of ocular motor cranial nerve palsies

This article reviews the various surgical treatment approaches currently used in the management of ocular motor cranial nerve palsies. Regardless of the approach, the final goal is improved alignment, especially in the primary and reading positions.

Surgical technique, visual outcome, and complications of pediatric intraocular lens implantation

PURPOSE

To evaluate retrospectively the surgical technique, visual outcome, and complications of pediatric cataract extraction (CE) and intraocular lens (IOL) implantation.

METHODS

Forty-three patients ages 2 to 12 underwent CE with IOL implantation with a minimum follow up of 1 month.

RESULTS

All IOLs were implanted in the posterior chamber with 17 (40%) in the bag, 25 (58%) sulcus fixated, and one (2%) partially in the bag (one haptic in the bag, one in the sulcus). Primary posterior capsulectomy was performed in 12 (28%) cases. A final visual acuity of at least 20/40 was achieved in 26 (60%) and at least 20/80 in 32 (74%). Posterior capsule opacification developed in 18 (42%) and pupillary capture in 7 (16%). Seventeen (40%) patients had postoperative visual acuity worse than 20/40. Of these, nine (53%) had this visual outcome as a result of presumed amblyopia.

CONCLUSIONS

Posterior chamber IOL implantation affords a safe and effective method of visual rehabilitation for cataractous children 2 years of age and older. Amblyopia and antecedent posterior segment trauma, rather than IOL-related or surgical complications, are the limiting factors in final visual outcome.

Calculation of relaxation rates from microscopic equations of motion

For classical systems with anharmonic forces, Newton's equations for particle trajectories are nonlinear, while Liouville's equation for the evolution of functions of position and momentum is linear and is solved by constructing a basis of functions in which the Liouvillian is a tridiagonal matrix, which is then diagonalized. For systems that are chaotic in the sense that neighboring trajectories diverge exponentially, the initial conditions determine the solution to Liouville's equation for short times; but for long times, the solutions decay exponentially at rates independent of the initial conditions. These are the relaxation rates of irreversible processes, and they arise in these calculations as the imaginary parts of the frequencies where there are singularities in the analytic continuations of solutions to Liouville's equation. These rates are calculated for two examples: the inverted oscillator, which can be solved both analytically and numerically, and a charged particle in a periodic magnetic field, which can only be solved numerically. In these systems, dissipation arises from traveling-wave solutions to Liouville's equation that couple low and high wave-number modes allowing energy to flow from disturbances that are coherent over large scales to disturbances on ever smaller scales finally becoming incoherent over microscopic scales. These results suggest that dissipation in large scale motion of the system is a consequence of chaos in the small scale motion.

Outcome of surgical management of superior oblique palsy: a study of 123 cases

PURPOSE

To determine the outcome of the surgical management of superior oblique palsy at our institution.

SUBJECTS AND METHODS

Retrospective review of 123 patients who underwent surgical correction of superior oblique paresis at Bascom Palmer Eye Institute from 1976 to 1996. Subject-Patients: 67% were male and 33% female. The mean age at surgery was 30.5 years (range, 2-78 years). Etiologies of the pareses were trauma (34%), congenital (33%), and acquired/non-traumatic (33%). The mean angle of preoperative vertical deviation in primary gaze was 14.0 delta (range, 0-45 delta).

SURGERY

109/123 (89%) patients underwent single muscle surgery. Of these 109, 57 had single oblique muscle surgery: a superior oblique tuck in 34/57 (60%); an inferior oblique weakening procedure in 22/57 (38%); and a Harada-Ito procedure in 1/57 (2%). The other 14 patients (11%) had bilateral surgery.

RESULTS

The final postoperative vertical deviation in primary gaze was < or =3 PD in 60% of patients and < or =7 PD in 80%. The mean change in primary position vertical deviation postoperatively was 10.4 PD for distance and 13.0 PD for near. An "excellent" outcome (final vertical deviation &le3 PD in primary and reading gazes) was achieved most frequently in those patients with congenital pareses and isolated oblique muscle surgery.

COMPLICATIONS

Clinically significant Brown's Syndrome occurred in 43/72 (60%) of those cases who had undergone a superior oblique tuck. The incidence of Brown's Syndrome was unrelated to tuck size. Reoperation was three times more likely to be necessary in traumatic cases than in congenital cases (35.0% vs 11.9%, p=0.02).

CONCLUSIONS

Based on these results we recommend oblique muscle surgery as the initial procedure to correct superior oblique palsy when appropriate.

A pars plana approach for cataract surgery in posterior lenticonus

PURPOSE

To report the management and outcome of cataract surgery and intraocular lens placement in a child with unilateral posterior lenticonus.

METHODS

Case report. A 7-year-old boy with a best-corrected visual acuity of RE, 20/200, posterior lenticonus, and cataract underwent a pars plana lensectomy, vitrectomy, posterior chamber intraocular lens insertion into the ciliary sulcus, and central anterior capsulotomy.

RESULT

At 2 years of follow-up, best-corrected visual acuity was RE, 20/40.

CONCLUSION

This technique allowed complete removal of the opaque posterior lenticonus plaque while preserving the peripheral anterior capsule for sulcus fixation of the posterior chamber intraocular lens.

Branch retinal vein occlusion. Axial length and other risk factors

OBJECTIVE

To determine the association between axial length, as a measurement of hyperopia, and branch retinal vein occlusion and to determine the clinical characteristics and other risk factors of patients with branch retinal vein occlusion.

METHODS

A case-control study was performed using 36 patients with branch retinal vein occlusion and 36 age- and sex-matched control patients selected from a list of subjects who had undergone cataract extraction.

RESULTS

There was essentially no difference in axial length between patients the disorder and control patients (23.55 mm versus 23.62 mm; P = 0.79). Although the intraocular pressure (IOP) among control eyes was somewhat higher than that in branch retinal vein occlusion eyes, the difference was not statistically significant (P = 0.32). Systemic hypertension was more common in patients with branch retinal vein occlusion (53%) than in control patients (42%) but the difference was not statistically significant (P = 0.35). Chronic open-angle glaucoma was present in 14% of patients with branch retinal vein occlusion and 22% of control patients (P = 0.37), but this difference was not statistically significant. Diabetes mellitus was two times more common in controls (28%) than in patients with branch retinal vein occlusion (14%). This difference, however, also did not reach statistical significance (P = 0.13).

CONCLUSIONS

Hyperopia as measured by axial length is not a risk factor for branch retinal vein occlusion. This study provides evidence that hypertension is a risk factor for branch retinal vein occlusion and that chronic open-angle glaucoma and diabetes mellitus are not risk factors for branch retinal vein occlusion.

The relation of surgery for prostatic hypertrophy to carcinoma of the prostate

The authors evaluated the risk of death from prostate cancer in Rhode Island men who had had surgery for prostatic hypertrophy during the years 1959-1970. The retrospective follow-up method was used. Among 4,853 men who had had either a transurethral resection or a prostatectomy, age- and time-standardized mortality from prostate cancer was 1.14 (95% confidence interval (CI) 0.93-1.33) times the rate in the general population of Rhode Island men. The age- and time-standardized mortality ratio was 1.01 (95% CI 0.77-1.31) for men who had had a suprapubic prostatectomy and 1.18 (95% CI 0.94-1.47) for men who had had a transurethral resection. The authors used the case-control method to relate the histologic features of prostatic hypertrophy to subsequent prostate cancer. The observed associations were weak and inconsistent. The results of this study suggest that surgically treated prostatic hypertrophy is not an important determinant of prostate cancer.