Analogue gravity in nonlocal fluids of light

Analogue gravity designates the study of curved spacetime in a laboratory environment and allows to test concepts of General Relativity. This analogy is established via a conformal identity between the flow of curved spacetime and inhomogeneous flows in hydrodynamics, which predicts that small waves on a fluid behave exactly as scalar fields in a curved spacetime metric. Atomic quantum fluids such as Bose-Einstein Condensates (BEC) are a widespread workbench for studying artificial black holes and many-body physics but face considerably large experimental challenges. In recent years, quantum fluids of light became a promising alternative at less technical expense, where the many-body dynamics in a laser beam are established via photon-photon interactions mediated through an optical nonlinearity. Whereas recent works considered strongly confined laser fields in microcavities, this work presents a photon fluid in a propagating geometry, i.e. a paraxially propagating laser beam in a bulk nonlinear medium. In this scenario, the propagating direction maps onto a time coordinate and the photon fluid is established in the transverse beam profile. The thermal nonlinearity is excited through heating of the absorbed laser power that introduces a nonlocal response of the medium and adds another level of complexity. It is experimentally shown that the dynamics of small amplitude excitations are governed by the Bogoliubov dispersion relation and allows to observe superfluidity at sufficiently large wavelengths. This is confirmed by the onset of persistent currents and the nucleation of quantized vortices in sub- and supercritical flows around an extended obstacle, which is a direct observation of superfluidity in a room-temperature system. The superfluid regime is a requirement for building analogue spacetime metrics and is thus of paramount importance. The spacetime of a rotating black and white whole was then created by shaping the topology of the spatial phase using diffractive phase masks. The experimental measurements of the inhomogeneous flows revealed, for the first time conclusive evidence of a (2+1) dimensional acoustic horizon and ergosphere. Such a system promises to study Penrose superradiance, where first experimental and numerical results for its observation are presented. Finally, nonlinear wave dynamics such as self-steepening and shock formation are studied where the dynamics can be interpreted in terms of a self-induced spacetime. Furthermore, the dynamics of a sea of incoherent waves is studied with respect to the long-range interactions provided by the nonlocality, where a novel transition from individual dispersive shock waves towards a collective giant shock wave is observed

Experimental characterization of nonlocal photon fluids

Quantum gases of atoms and exciton-polaritons are now well-established theoretical and experimental tools for fundamental studies of quantum many-body physics and suggest promising applications to quantum computing. Given their technological complexity, it is of paramount interest to devise other systems where such quantum many-body physics can be investigated at lesser technological expense. Here we examine a relatively well-known system of laser light propagating through thermo-optical defocusing media: based on a hydrodynamic description of light as a quantum fluid of interacting photons, we investigate such systems as a valid room-temperature alternative to atomic or exciton–polariton condensates for studies of many-body physics. First, we show that by using a technique traditionally used in oceanography it is possible to perform a direct measurement of the single-particle part of the dispersion relation of the elementary excitations on top of the photon fluid and to detect its global flow. Then, using a pump-and-probe setup, we investigate the dispersion of excitation modes of the fluid: for very long wavelengths, a sonic, dispersionless propagation is observed that we interpret as a signature of superfluid behavior

Optical analogues of the Newton–Schrödinger equation and boson star evolution

Many gravitational phenomena that lie at the core of our understanding of the Universe have not yet been directly observed. An example in this sense is the boson star that has been proposed as an alternative to some compact objects currently interpreted as being black holes. In the weak field limit, these stars are governed by the Newton–Schrodinger equation. Here we present an optical system that, under appropriate conditions, identically reproduces such equation in two dimensions. A rotating boson star is experimentally and numerically modelled by an optical beam propagating through a medium with a positive thermal nonlinearity and is shown to oscillate in time while also stable up to relatively high densities. For higher densities, instabilities lead to an apparent breakup of the star, yet coherence across the whole structure is maintained. These results show that optical analogues can be used to shed new light on inaccessible gravitational objects

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment