Antillean manatee calves in captive rehabilitation change vocal behavior in anticipation of feeding.

Captive animals typically develop anticipatory behaviors, actions of increased frequency done in anticipation of an event such as feeding. Anticipatory behaviors can be an indicator of an animal's welfare. However, for rehabilitating animals that are expected to be reintroduced into the wild, these behaviors need to be extinguished to ensure successful release. Scheduled activities such as feeding occur daily and vocalizations could potentially be used to identify anticipatory behavior. Here, we tested the hypothesis that manatee calves modify their vocal production rate as a form of anticipatory behavior. Vocalizations of two Antillean manatee (Trichechus manatus manatus) calves were recorded for 10 min before, during, and after feeding sessions at Wildtracks, a manatee rehabilitation center in Belize. The number of calls were counted across recording sessions and three acoustic parameters were measured from calls including duration, frequency modulation, and center frequency. A repeated measures ANOVA comparing the number of calls across sessions indicated manatees produced significantly more calls before feeding sessions than during and after sessions. In addition, manatees increased the duration and lowered the frequency of calls before feeding sessions. This information can give further insight on ways to improve rehabilitation protocols and manage human interactions to increase the overall survival rate of rehabilitated manatees when released back into the wild.

Robustness and Flexibility of Neural Function through Dynamical Criticality.

In theoretical biology, robustness refers to the ability of a biological system to function properly even under perturbation of basic parameters (e.g., temperature or pH), which in mathematical models is reflected in not needing to fine-tune basic parameter constants; flexibility refers to the ability of a system to switch functions or behaviors easily and effortlessly. While there are extensive explorations of the concept of robustness and what it requires mathematically, understanding flexibility has proven more elusive, as well as also elucidating the apparent opposition between what is required mathematically for models to implement either. In this paper we address a number of arguments in theoretical neuroscience showing that both robustness and flexibility can be attained by systems that poise themselves at the onset of a large number of dynamical bifurcations, or dynamical criticality, and how such poising can have a profound influence on integration of information processing and function. Finally, we examine critical map lattices, which are coupled map lattices where the coupling is dynamically critical in the sense of having purely imaginary eigenvalues. We show that these map lattices provide an explicit connection between dynamical criticality in the sense we have used and "edge of chaos" criticality.

SEGGA: a toolset for rapid automated analysis of epithelial cell polarity and dynamics.

Epithelial remodeling determines the structure of many organs in the body through changes in cell shape, polarity and behavior and is a major area of study in developmental biology. Accurate and high-throughput methods are necessary to systematically analyze epithelial organization and dynamics at single-cell resolution. We developed SEGGA, an easy-to-use software for automated image segmentation, cell tracking and quantitative analysis of cell shape, polarity and behavior in epithelial tissues. SEGGA is free, open source, and provides a full suite of tools that allow users with no prior computational expertise to independently perform all steps of automated image segmentation, semi-automated user-guided error correction, and data analysis. Here we use SEGGA to analyze changes in cell shape, cell interactions and planar polarity during convergent extension in the Drosophila embryo. These studies demonstrate that planar polarity is rapidly established in a spatiotemporally regulated pattern that is dynamically remodeled in response to changes in cell orientation. These findings reveal an unexpected plasticity that maintains coordinated planar polarity in actively moving populations through the continual realignment of cell polarity with the tissue axes.

The Antillean manatee produces broadband vocalizations with ultrasonic frequencies.

Antillean manatees produce vocalizations reported to be important for communication, but their vocal behavior throughout their geographic range is poorly understood. A SoundTrap recorder (sample rates: 288/576 kHz) was deployed in Belize to record vocalizations of wild manatees in a seagrass channel and of a young rehabilitated and released manatee in a shallow lagoon. Spectral analysis revealed broadband vocalizations with frequencies up to 150 kHz and a high proportion of calls with ultrasonic components. Ultrasonic frequency components appear prevalent in their vocal repertoire and may be important to manatee communication.

Complex spatiotemporal behavior and coherent excitations in critically-coupled chains of neural circuits.

We investigate a critically-coupled chain of nonlinear oscillators, whose dynamics displays complex spatiotemporal patterns of activity, including regimes in which glider-like coherent excitations move about and interact. The units in the network are identical simple neural circuits whose dynamics is given by the Wilson-Cowan model and are arranged in space along a one-dimensional lattice with nearest neighbor interactions. The interactions follow an alternating sign rule, and hence the "synaptic matrix" M embodying them is tridiagonal antisymmetric and has purely imaginary (critical) eigenvalues. The model illustrates the interplay of two properties: circuits with a complex internal dynamics, such as multiple stable periodic solutions and period doubling bifurcations, and coupling with a "critical" synaptic matrix, i.e., having purely imaginary eigenvalues. In order to identify the dynamical underpinnings of these behaviors, we explored a discrete-time coupled-map lattice inspired by our system: the dynamics of the units is dictated by a chaotic map of the interval, and the interactions are given by allowing the critical coupling to act for a finite period τ , thus given by a unitary matrix U = exp ⁡ ( τ 2 M ) . It is now explicit that such critical couplings are volume-preserving in the sense of Liouville's theorem. We show that this map is also capable of producing a variety of complex spatiotemporal patterns including gliders, like our original chain of neural circuits. Our results suggest that if the units in isolation are capable of featuring multiple dynamical states, then local critical couplings lead to a wide variety of emergent spatiotemporal phenomena.

Loss of Consciousness Is Associated with Stabilization of Cortical Activity.

What aspects of neuronal activity distinguish the conscious from the unconscious brain? This has been a subject of intense interest and debate since the early days of neurophysiology. However, as any practicing anesthesiologist can attest, it is currently not possible to reliably distinguish a conscious state from an unconscious one on the basis of brain activity. Here we approach this problem from the perspective of dynamical systems theory. We argue that the brain, as a dynamical system, is self-regulated at the boundary between stable and unstable regimes, allowing it in particular to maintain high susceptibility to stimuli. To test this hypothesis, we performed stability analysis of high-density electrocorticography recordings covering an entire cerebral hemisphere in monkeys during reversible loss of consciousness. We show that, during loss of consciousness, the number of eigenmodes at the edge of instability decreases smoothly, independently of the type of anesthetic and specific features of brain activity. The eigenmodes drift back toward the unstable line during recovery of consciousness. Furthermore, we show that stability is an emergent phenomenon dependent on the correlations among activity in different cortical regions rather than signals taken in isolation. These findings support the conclusion that dynamics at the edge of instability are essential for maintaining consciousness and provide a novel and principled measure that distinguishes between the conscious and the unconscious brain. SIGNIFICANCE STATEMENT: What distinguishes brain activity during consciousness from that observed during unconsciousness? Answering this question has proven difficult because neither consciousness nor lack thereof have universal signatures in terms of most specific features of brain activity. For instance, different anesthetics induce different patterns of brain activity. We demonstrate that loss of consciousness is universally and reliably associated with stabilization of cortical dynamics regardless of the specific activity characteristics. To give an analogy, our analysis suggests that loss of consciousness is akin to depressing the damper pedal on the piano, which makes the sounds dissipate quicker regardless of the specific melody being played. This approach may prove useful in detecting consciousness on the basis of brain activity under anesthesia and other settings.

Stable encoding of sounds over a broad range of statistical parameters in the auditory cortex.

Natural auditory scenes possess highly structured statistical regularities, which are dictated by the physics of sound production in nature, such as scale-invariance. We recently identified that natural water sounds exhibit a particular type of scale invariance, in which the temporal modulation within spectral bands scales with the centre frequency of the band. Here, we tested how neurons in the mammalian primary auditory cortex encode sounds that exhibit this property, but differ in their statistical parameters. The stimuli varied in spectro-temporal density and cyclo-temporal statistics over several orders of magnitude, corresponding to a range of water-like percepts, from pattering of rain to a slow stream. We recorded neuronal activity in the primary auditory cortex of awake rats presented with these stimuli. The responses of the majority of individual neurons were selective for a subset of stimuli with specific statistics. However, as a neuronal population, the responses were remarkably stable over large changes in stimulus statistics, exhibiting a similar range in firing rate, response strength, variability and information rate, and only minor variation in receptive field parameters. This pattern of neuronal responses suggests a potentially general principle for cortical encoding of complex acoustic scenes: while individual cortical neurons exhibit selectivity for specific statistical features, a neuronal population preserves a constant response structure across a broad range of statistical parameters.

A phase transition in the first passage of a Brownian process through a fluctuating boundary with implications for neural coding.

Finding the first time a fluctuating quantity reaches a given boundary is a deceptively simple-looking problem of vast practical importance in physics, biology, chemistry, neuroscience, economics, and industrial engineering. Problems in which the bound to be traversed is itself a fluctuating function of time include widely studied problems in neural coding, such as neuronal integrators with irregular inputs and internal noise. We show that the probability p(t) that a Gauss-Markov process will first exceed the boundary at time t suffers a phase transition as a function of the roughness of the boundary, as measured by its Hölder exponent H. The critical value occurs when the roughness of the boundary equals the roughness of the process, so for diffusive processes the critical value is Hc = 1/2. For smoother boundaries, H > 1/2, the probability density is a continuous function of time. For rougher boundaries, H < 1/2, the probability is concentrated on a Cantor-like set of zero measure: the probability density becomes divergent, almost everywhere either zero or infinity. The critical point Hc = 1/2 corresponds to a widely studied case in the theory of neural coding, in which the external input integrated by a model neuron is a white-noise process, as in the case of uncorrelated but precisely balanced excitatory and inhibitory inputs. We argue that this transition corresponds to a sharp boundary between rate codes, in which the neural firing probability varies smoothly, and temporal codes, in which the neuron fires at sharply defined times regardless of the intensity of internal noise.

Human time-frequency acuity beats the Fourier uncertainty principle.

The time-frequency uncertainty principle states that the product of the temporal and frequency extents of a signal cannot be smaller than 1/(4 π). We study human ability to simultaneously judge the frequency and the timing of a sound. Our subjects often exceeded the uncertainty limit, sometimes by more than tenfold, mostly through remarkable timing acuity. Our results establish a lower bound for the nonlinearity and complexity of the algorithms employed by our brains in parsing transient sounds, rule out simple "linear filter" models of early auditory processing, and highlight timing acuity as a central feature in auditory object processing.

Modeling the resonant release of synaptic transmitter by hair cells as an example of biological oscillators with cooperative steps.

The initial synapses of the auditory system, which connect hair cells to afferent nerve fibers, display two unusual features. First, synaptic transmission occurs in a multiquantal fashion: the contents of multiple synaptic vesicles are discharged simultaneously. Second, synaptic transmission may be tuned to specific frequencies of stimulation. We developed a minimal theoretical model to explore the possibility that hair-cell synapses achieve both multiquantal release and frequency selectivity through a cooperative mechanism for the exocytotic release of neurotransmitter. We first characterized vesicle release as a four-step cycle at each release site, then generalized the result to an arbitrary number of steps. The cyclic process itself induces some degree of resonance, and may display a stable, underdamped fixed point of the release dynamics associated with a pair of complex eigenvalues. Cooperativity greatly enhances the frequency selectivity by moving the eigenvalues toward the imaginary axis; spontaneously oscillatory release can arise beyond a Hopf bifurcation. These phenomena occur both in the macroscopic limit, when the number of release sites involved is very large, and in the more realistic stochastic regime, when only a limited number of release sites participate at each synapse. It is thus possible to connect multiquantal release with frequency selectivity through the mechanism of cooperativity.

Genetic confirmation of Octopus insularis (Leite and Haimovici, 2008) in South Florida, United States using physical features and de novo genome assembly.

The distribution of octopuses within the Octopus vulgaris species complex remains inadequately understood. Species determination can be complex and involves characterizing a specimen's physical features and comparing its genetic makeup to other populations. In this study, we present the first genetic confirmation of Octopus insularis (Leite and Haimovici, 2008) inhabiting the coastal waters of the Florida Keys, United States. We employed visual observations to identify species-specific body patterns of three wild-caught octopuses and used de novo genome assembly to confirm their species. All three specimens exhibited a red/white reticulated pattern on their ventral arm surface. Two specimens displayed body pattern components of deimatic display (white eye encircled by a light ring, with darkening around the eye). All visual observations were consistent with distinguishing features of O. insularis. We then compared mitochondrial subunits COI, COIII, and 16S in these specimens across all available annotated octopod sequences, including Sepia apama (Hotaling et al., 2021) as a control outgroup taxon. For species exhibiting intraspecific genomic variation, we included multiple sequences from geographically distinct populations. Laboratory specimens consistently clustered into a single taxonomic node with O. insularis. These findings confirm O. insularis presence in South Florida and suggest a more extensive northern distribution than previously assumed. Whole genome Illumina sequencing of multiple specimens enabled taxonomic identification with well-established DNA barcodes while also generating the first de novo full assembly of O. insularis. Furthermore, constructing and comparing phylogenetic trees for multiple conserved genes is essential for confirming the presence and delineation of cryptic species in the Caribbean.

Vocalizations of wild West Indian manatee vary across subspecies and geographic location.

Geographic variation in the vocal behavior of manatees has been reported but is largely unexplored. Vocalizations of wild West Indian manatees (Trichechus manatus) were recorded with hydrophones in Florida from Florida manatees (Trichechus manatus latirostris), and in Belize and Panama from Antillean manatees (Trichechus manatus manatus) to determine if calls varied between subspecies and geographic regions. Calls were visually classified into five categories: squeaks, high squeaks, squeals, squeak-squeals, and chirps. From these five categories, only three call types (squeaks, high squeaks and squeals) were observed in all three populations. Six parameters from the temporal and frequency domains were measured from the fundamental frequency of 2878 manatee vocalizations. A repeated measures PERMANOVA found significant differences for squeaks and high squeaks between each geographic location and for squeals between Belize and Florida. Almost all measured frequency and temporal parameters of manatee vocalizations differed between and within subspecies. Variables that may have influenced the variation observed may be related to sex, body size, habitat and/or other factors. Our findings provide critical information of manatee calls for wildlife monitoring and highlight the need for further study of the vocal behavior of manatees throughout their range.

Enhancement of transport selectivity through nano-channels by non-specific competition.

The functioning of living cells requires efficient and selective transport of materials into and out of the cell, and between different cellular compartments. Much of this transport occurs through nano-scale channels that do not require large scale molecular re-arrangements (such as transition from a 'closed' to an 'open' state) and do not require a direct input of metabolic energy during transport. Nevertheless, these 'always open' channels are highly selective and pass only their cognate molecules, while efficiently excluding all others; indeed, these channels can efficiently transport specific molecules even in the presence of a vast excess of non-specific molecules. Such biological transporters have inspired the creation of artificial nano-channels. These channels can be used as nano-molecular sorters, and can also serve as testbeds for examining modes of biological transport. In this paper, we propose a simple kinetic mechanism that explains how the selectivity of such 'always open' channels can be based on the exclusion of non-specific molecules by specific ones, due to the competition for limited space inside the channel. The predictions of the theory account for the behavior of the nuclear pore complex and of artificial nanopores that mimic its function. This theory provides the basis for future work aimed at understanding the selectivity of various biological transport phenomena.

Is an eclipse described in the Odyssey?

Plutarch and Heraclitus believed a certain passage in the 20th book of the Odyssey ("Theoclymenus's prophecy") to be a poetic description of a total solar eclipse. In the late 1920s, Schoch and Neugebauer computed that the solar eclipse of 16 April 1178 B.C.E. was total over the Ionian Islands and was the only suitable eclipse in more than a century to agree with classical estimates of the decade-earlier sack of Troy around 1192-1184 B.C.E. However, much skepticism remains about whether the verses refer to this, or any, eclipse. To contribute to the issue independently of the disputed eclipse reference, we analyze other astronomical references in the Epic, without assuming the existence of an eclipse, and search for dates matching the astronomical phenomena we believe they describe. We use three overt astronomical references in the epic: to Boötes and the Pleiades, Venus, and the New Moon; we supplement them with a conjectural identification of Hermes's trip to Ogygia as relating to the motion of planet Mercury. Performing an exhaustive search of all possible dates in the span 1250-1115 B.C., we looked to match these phenomena in the order and manner that the text describes. In that period, a single date closely matches our references: 16 April 1178 B.C.E. We speculate that these references, plus the disputed eclipse reference, may refer to that specific eclipse.

Masks and distancing during COVID-19: a causal framework for imputing value to public-health interventions.

During the COVID-19 pandemic, the scientific community developed predictive models to evaluate potential governmental interventions. However, the analysis of the effects these interventions had is less advanced. Here, we propose a data-driven framework to assess these effects retrospectively. We use a regularized regression to find a parsimonious model that fits the data with the least changes in the [Formula: see text] parameter. Then, we postulate each jump in [Formula: see text] as the effect of an intervention. Following the do-operator prescriptions, we simulate the counterfactual case by forcing [Formula: see text] to stay at the pre-jump value. We then attribute a value to the intervention from the difference between true evolution and simulated counterfactual. We show that the recommendation to use facemasks for all activities would reduce the number of cases by 200,000 ([Formula: see text] CI 190,000-210,000) in Connecticut, Massachusetts, and New York State. The framework presented here might be used in any case where cause and effects are sparse in time.

The Relevance of Human Whistled Languages for the Analysis and Decoding of Dolphin Communication.

Humans use whistled communications, the most elaborate of which are commonly called "whistled languages" or "whistled speech" because they consist of a natural type of speech. The principle of whistled speech is straightforward: people articulate words while whistling and thereby transform spoken utterances by simplifying them, syllable by syllable, into whistled melodies. One of the most striking aspects of this whistled transformation of words is that it remains intelligible to trained speakers, despite a reduced acoustic channel to convey meaning. It constitutes a natural traditional means of telecommunication that permits spoken communication at long distances in a large diversity of languages of the world. Historically, birdsong has been used as a model for vocal learning and language. But conversely, human whistled languages can serve as a model for elucidating how information may be encoded in dolphin whistle communication. In this paper, we elucidate the reasons why human whistled speech and dolphin whistles are interesting to compare. Both are characterized by similar acoustic parameters and serve a common purpose of long distance communication in natural surroundings in two large brained social species. Moreover, their differences - e.g., how they are produced, the dynamics of the whistles, and the types of information they convey - are not barriers to such a comparison. On the contrary, by exploring the structure and attributes found across human whistle languages, we highlight that they can provide an important model as to how complex information is and can be encoded in what appears at first sight to be simple whistled modulated signals. Observing details, such as processes of segmentation and coarticulation, in whistled speech can serve to advance and inform the development of new approaches for the analysis of whistle repertoires of dolphins, and eventually other species. Human whistled languages and dolphin whistles could serve as complementary test benches for the development of new methodologies and algorithms for decoding whistled communication signals by providing new perspectives on how information may be encoded structurally and organizationally.

Damage and fluctuations induce loops in optimal transport networks.

Leaf venation is a pervasive example of a complex biological network, endowing leaves with a transport system and mechanical resilience. Transport networks optimized for efficiency have been shown to be trees, i.e., loopless. However, dicotyledon leaf venation has a large number of closed loops, which are functional and able to transport fluid in the event of damage to any vein, including the primary veins. Inspired by leaf venation, we study two possible reasons for the existence of a high density of loops in transport networks: resilience to damage and fluctuations in load. In the first case, we seek the optimal transport network in the presence of random damage by averaging over damage to each link. In the second case, we seek the network that optimizes transport when the load is sparsely distributed: at any given time most sinks are closed. We find that both criteria lead to the presence of loops in the optimum state.

A fast L(p) spike alignment metric.

The metrization of the space of neural responses is an ongoing research program seeking to find natural ways to describe, in geometrical terms, the sets of possible activities in the brain. One component of this program is spike metrics-notions of distance between two spike trains recorded from a neuron. Alignment spike metrics work by identifying "equivalent" spikes in both trains. We present an alignment spike metric having L(p) underlying geometrical structure; the L(2) version is Euclidean and is suitable for further embedding in Euclidean spaces by multidimensional scaling methods or related procedures. We show how to implement a fast algorithm for the computation of this metric based on bipartite graph matching theory.

Learning to localize sounds in a highly reverberant environment: Machine-learning tracking of dolphin whistle-like sounds in a pool.

Tracking the origin of propagating wave signals in an environment with complex reflective surfaces is, in its full generality, a nearly intractable problem which has engendered multiple domain-specific literatures. We posit that, if the environment and sensor geometries are fixed, machine learning algorithms can "learn" the acoustical geometry of the environment and accurately track signal origin. In this paper, we propose the first machine-learning-based approach to identifying the source locations of semi-stationary, tonal, dolphin-whistle-like sounds in a highly reverberant space, specifically a half-cylindrical dolphin pool. Our algorithm works by supplying a learning network with an overabundance of location "clues", which are then selected under supervised training for their ability to discriminate source location in this particular environment. More specifically, we deliver estimated time-difference-of-arrivals (TDOA's) and normalized cross-correlation values computed from pairs of hydrophone signals to a random forest model for high-feature-volume classification and feature selection, and subsequently deliver the selected features into linear discriminant analysis, linear and quadratic Support Vector Machine (SVM), and Gaussian process models. Based on data from 14 sound source locations and 16 hydrophones, our classification models yielded perfect accuracy at predicting novel sound source locations. Our regression models yielded better accuracy than the established Steered-Response Power (SRP) method when all training data were used, and comparable accuracy along the pool surface when deprived of training data at testing sites; our methods additionally boast improved computation time and the potential for superior localization accuracy in all dimensions with more training data. Because of the generality of our method we argue it may be useful in a much wider variety of contexts.

Virtual gating and nuclear transport: the hole picture.

The eukaryotic nucleus is surrounded by a protective nuclear envelope, which is perforated by trafficking machines termed nuclear pore complexes (NPCs). The NPCs are the sole mediators of exchange between the nucleus and the cytoplasm. Small molecules pass through the NPCs unchallenged; however, large macromolecules are excluded unless chaperoned across by transport factors. Here, we suggest a model, termed 'virtual gating', to explain the mechanism of this rapid and selective macromolecular trafficking.