The need for calcium imaging in nonhuman primates: New motor neuroscience and brain-machine interfaces

A central goal of neuroscience is to understand how populations of neurons coordinate and cooperate in order to give rise to perception, cognition, and action. Nonhuman primates (NHPs) are an attractive model with which to understand these mechanisms in humans, primarily due to the strong homology of their brains and the cognitively sophisticated behaviors they can be trained to perform. Using electrode recordings, the activity of one to a few hundred individual neurons may be measured electrically, which has enabled many scientific findings and the development of brain-machine interfaces. Despite these successes, electrophysiology samples sparsely from neural populations and provides little information about the genetic identity and spatial micro-organization of recorded neurons. These limitations have spurred the development of all-optical methods for neural circuit interrogation. Fluorescent calcium signals serve as a reporter of neuronal responses, and when combined with post-mortem optical clearing techniques such as CLARITY, provide dense recordings of neuronal populations, spatially organized and annotated with genetic and anatomical information. Here, we advocate that this methodology, which has been of tremendous utility in smaller animal models, can and should be developed for use with NHPs. We review here several of the key opportunities and challenges for calcium-based optical imaging in NHPs. We focus on motor neuroscience and brain-machine interface design as representative domains of opportunity within the larger field of NHP neuroscience

Holographic View on Quantum Correlations and Mutual Information between Disjoint Blocks of a Quantum Critical System

In (d+1) dimensional Multiscale Entanglement Renormalization Ansatz (MERA) networks, tensors are connected so as to reproduce the discrete, (d + 2) holographic geometry of Anti de Sitter space (AdSd+2) with the original system lying at the boundary. We analyze the MERA renormalization flow that arises when computing the quantum correlations between two disjoint blocks of a quantum critical system, to show that the structure of the causal cones characteristic of MERA, requires a transition between two different regimes attainable by changing the ratio between the size and the separation of the two disjoint blocks. We argue that this transition in the MERA causal developments of the blocks may be easily accounted by an AdSd+2 black hole geometry when the mutual information is computed using the Ryu-Takayanagi formula. As an explicit example, we use a BTZ AdS3 black hole to compute the MI and the quantum correlations between two disjoint intervals of a one dimensional boundary critical system. Our results for this low dimensional system not only show the existence of a phase transition emerging when the conformal four point ratio reaches a critical value but also provide an intuitive entropic argument accounting for the source of this instability. We discuss the robustness of this transition when finite temperature and finite size effects are taken into account.Comment: 21 pages, 5 figures. Abstract and Figure 1 has been modified. Minor modifications in Section 1 and Section

Holographic Superconductor/Insulator Transition at Zero Temperature

We analyze the five-dimensional AdS gravity coupled to a gauge field and a charged scalar field. Under a Scherk-Schwarz compactification, we show that the system undergoes a superconductor/insulator transition at zero temperature in 2+1 dimensions as we change the chemical potential. By taking into account a confinement/deconfinement transition, the phase diagram turns out to have a rich structure. We will observe that it has a similarity with the RVB (resonating valence bond) approach to high-Tc superconductors via an emergent gauge symmetry.Comment: 25 pages, 23 figures; A new subsection on a concrete string theory embedding added, references added (v2); Typos corrected, references added (v3

Modelling informative time points: an evolutionary process approach

Real time series sometimes exhibit various types of "irregularities": missing observations, observations collected not regularly over time for practical reasons, observation times driven by the series itself, or outlying observations. However, the vast majority of methods of time series analysis are designed for regular time series only. A particular case of irregularly spaced time series is that in which the sampling procedure over time depends also on the observed values. In such situations, there is stochastic dependence between the process being modelled and the times of the observations. In this work, we propose a model in which the sampling design depends on all past history of the observed processes. Taking into account the natural temporal order underlying available data represented by a time series, then a modelling approach based on evolutionary processes seems a natural choice. We consider maximum likelihood estimation of the model parameters. Numerical studies with simulated and real data sets are performed to illustrate the benefits of this model-based approach.- The authors acknowledge Foundation FCT (FundacAo para a Ciencia e Tecnologia) as members of the research project PTDC/MAT-STA/28243/2017 and Center for Research & Development in Mathematics and Applications of Aveiro University within project UID/MAT/04106/2019

Dimensionality and dynamics in the behavior of C. elegans

A major challenge in analyzing animal behavior is to discover some underlying simplicity in complex motor actions. Here we show that the space of shapes adopted by the nematode C. elegans is surprisingly low dimensional, with just four dimensions accounting for 95% of the shape variance, and we partially reconstruct "equations of motion" for the dynamics in this space. These dynamics have multiple attractors, and we find that the worm visits these in a rapid and almost completely deterministic response to weak thermal stimuli. Stimulus-dependent correlations among the different modes suggest that one can generate more reliable behaviors by synchronizing stimuli to the state of the worm in shape space. We confirm this prediction, effectively "steering" the worm in real time.Comment: 9 pages, 6 figures, minor correction

Superfluid behaviour of a two-dimensional Bose gas

Two-dimensional (2D) systems play a special role in many-body physics. Because of thermal fluctuations, they cannot undergo a conventional phase transition associated to the breaking of a continuous symmetry. Nevertheless they may exhibit a phase transition to a state with quasi-long range order via the Berezinskii-Kosterlitz-Thouless (BKT) mechanism. A paradigm example is the 2D Bose fluid, such as a liquid helium film, which cannot Bose-condense at non-zero temperature although it becomes superfluid above a critical phase space density. Ultracold atomic gases constitute versatile systems in which the 2D quasi-long range coherence and the microscopic nature of the BKT transition were recently explored. However, a direct observation of superfluidity in terms of frictionless flow is still missing for these systems. Here we probe the superfluidity of a 2D trapped Bose gas with a moving obstacle formed by a micron-sized laser beam. We find a dramatic variation of the response of the fluid, depending on its degree of degeneracy at the obstacle location. In particular we do not observe any significant heating in the central, highly degenerate region if the velocity of the obstacle is below a critical value.Comment: 5 pages, 3 figure

Positivity, entanglement entropy, and minimal surfaces

The path integral representation for the Renyi entanglement entropies of integer index n implies these information measures define operator correlation functions in QFT. We analyze whether the limit $n\rightarrow 1$, corresponding to the entanglement entropy, can also be represented in terms of a path integral with insertions on the region's boundary, at first order in $n-1$. This conjecture has been used in the literature in several occasions, and specially in an attempt to prove the Ryu-Takayanagi holographic entanglement entropy formula. We show it leads to conditional positivity of the entropy correlation matrices, which is equivalent to an infinite series of polynomial inequalities for the entropies in QFT or the areas of minimal surfaces representing the entanglement entropy in the AdS-CFT context. We check these inequalities in several examples. No counterexample is found in the few known exact results for the entanglement entropy in QFT. The inequalities are also remarkable satisfied for several classes of minimal surfaces but we find counterexamples corresponding to more complicated geometries. We develop some analytic tools to test the inequalities, and as a byproduct, we show that positivity for the correlation functions is a local property when supplemented with analyticity. We also review general aspects of positivity for large N theories and Wilson loops in AdS-CFT.Comment: 36 pages, 10 figures. Changes in presentation and discussion of Wilson loops. Conclusions regarding entanglement entropy unchange

Inductively guided circuits for ultracold dressed atoms

Recent progress in optics, atomic physics and material science has paved the way to study quantum effects in ultracold atomic alkali gases confined to non-trivial geometries. Multiply connected traps for cold atoms can be prepared by combining inhomogeneous distributions of DC and radio-frequency electromagnetic fields with optical fields that require complex systems for frequency control and stabilization. Here we propose a flexible and robust scheme that creates closed quasi-one-dimensional guides for ultracold atoms through the ‘dressing’ of hyperfine sublevels of the atomic ground state, where the dressing field is spatially modulated by inductive effects over a micro-engineered conducting loop. Remarkably, for commonly used atomic species (for example, 7Li and 87Rb), the guide operation relies entirely on controlling static and low-frequency fields in the regimes of radio-frequency and microwave frequencies. This novel trapping scheme can be implemented with current technology for micro-fabrication and electronic control

The space group classification of topological band insulators

Topological band insulators (TBIs) are bulk insulating materials which feature topologically protected metallic states on their boundary. The existing classification departs from time-reversal symmetry, but the role of the crystal lattice symmetries in the physics of these topological states remained elusive. Here we provide the classification of TBIs protected not only by time-reversal, but also by crystalline symmetries. We find three broad classes of topological states: (a) Gamma-states robust against general time-reversal invariant perturbations; (b) Translationally-active states protected from elastic scattering, but susceptible to topological crystalline disorder; (c) Valley topological insulators sensitive to the effects of non-topological and crystalline disorder. These three classes give rise to 18 different two-dimensional, and, at least 70 three-dimensional TBIs, opening up a route for the systematic search for new types of TBIs.Comment: Accepted in Nature Physic

Lipids Regulate Lck Protein Activity through Their Interactions with the Lck Src Homology 2 Domain.

Lymphocyte-specific protein-tyrosine kinase (Lck) plays an essential role in T cell receptor (TCR) signaling and T cell development, but its activation mechanism is not fully understood. To explore the possibility that plasma membrane (PM) lipids control TCR signaling activities of Lck, we measured the membrane binding properties of its regulatory Src homology 2 (SH2) and Src homology 3 domains. The Lck SH2 domain binds anionic PM lipids with high affinity but with low specificity. Electrostatic potential calculation, NMR analysis, and mutational studies identified the lipid-binding site of the Lck SH2 domain that includes surface-exposed basic, aromatic, and hydrophobic residues but not the phospho-Tyr binding pocket. Mutation of lipid binding residues greatly reduced the interaction of Lck with the chain in the activated TCR signaling complex and its overall TCR signaling activities. These results suggest that PM lipids, including phosphatidylinositol 4,5-bisphosphate and phosphatidylinositol 3,4,5-trisphosphate, modulate interaction of Lck with its binding partners in the TCR signaling complex and its TCR signaling activities in a spatiotemporally specific manner via its SH2 domain.1175Ysciescopu