An optimization-based model of collective motion

Computational models of collective motion have yielded many insights about the way that groups of animals or simulated particles may move together and self-organize. Recent literature has compared predictions of models with large datasets of detailed observations of animal behavior, and found that there are important discrepancies, leading researchers to reexamine some of the most widely used assumptions. We introduce FlockOpt, an optimization-based, variable-speed, self-propelled particle model of collective motion that addresses important shortcomings of earlier models. In our model, each particle adjusts its velocity by performing a constrained optimization of a locally-defined objective function, which is computed at each time step over the kinematics of the particle and the relative position of neighboring particles. Our model explains how ordered motion can arise in the absence of an explicitly prescribed alignment term and simulations performed with our model exhibit a wide variety of patterns of motion, including several not possible with popular constant-speed models. Our model predicts that variations in speed and heading of particles are coupled due to costs associated with changes in relative position. We have found that a similar coupling effect may also be present in the flight of groups of gregarious bats. The Mexican Free-tailed bat (Tadarida brasiliensis) is a gregarious bat that forms large maternity colonies, containing hundreds of thousands to millions of individuals, in the southwestern United States in the summer. We have developed a protocol for calibrating cameras used in stereo videography and developed guidelines for data collection. Our field protocol can be deployed in a single afternoon, requiring only short video segments of light, portable calibration objects. These protocols have allowed us to reconstruct the three-dimensional flight trajectories of hundreds of thousands of bats in order to use their flight as a biological study system for our model

Perception and steering control in paired bat flight

Animals within groups need to coordinate their reactions to perceived environmental features and to each other in order to safely move from one point to another. This paper extends our previously published work on the flight patterns of Myotis velifer that have been observed in a habitat near Johnson City, Texas. Each evening, these bats emerge from a cave in sequences of small groups that typically contain no more than three or four individuals, and they thus provide ideal subjects for studying leader-follower behaviors. By analyzing the flight paths of a group of M. velifer, the data show that the flight behavior of a follower bat is influenced by the flight behavior of a leader bat in a way that is not well explained by existing pursuit laws, such as classical pursuit, constant bearing and motion camouflage. Thus we propose an alternative steering law based on virtual loom, a concept we introduce to capture the geometrical configuration of the leader-follower pair. It is shown that this law may be integrated with our previously proposed vision-enabled steering laws to synthesize trajectories, the statistics of which fit with those of the bats in our data set. The results suggest that bats use perceived information of both the environment and their neighbors for navigation.2018-08-0

Slower ship speed in the Bahamas due to COVID-19 produces a dramatic reduction in ocean sound levels

Funding for the purchase of SoundTrap hydrophones and associated field work came from Field School, Sabine and Reinhold Probst, M Rogers, The Devereux Ocean Foundation and The Bahamian Environment Protection Foundation.As underwater noise from ship traffic increases, profound effects on the marine environment highlight the need for improved mitigation measures. One measure, reduction in ship speed, has been shown to be one of the key drivers in reducing sound source levels of vessels. In 2017, a study began to assess the impacts of increasing commercial shipping traffic on sperm whales in Northwest Providence Channel, northern Bahamas, an international trade route that primarily serves the southeast US. Ship data were collected from an Automatic Identification System (AIS) station combined with recordings from an acoustic recorder to measure underwater sound levels and to detect the presence of sperm whales. Here we analyze a subset of these data to opportunistically investigate potential changes in ship traffic before and during the COVID-19 pandemic. These data span one calendar year from October 2019 to October 2020. A pre-COVID-19 dataset of 121 days, from a recorder approximately 2 km from the shipping route was compared to a 134-day dataset collected during COVID-19 from the same site, comprising 2900 and 3181 ten-minute recordings, respectively. A dramatic decrease in ocean noise levels concurrent with changes in shipping activity occurred during the pandemic. The mean pre-COVID-19 power density level in the 111–140 Hz 1/3-octave band was 88.81 dB re 1 μPa (range 81.38–100.90) and decreased to 84.27 dB re 1 μPa (range 78.60–99.51) during COVID-19, equating to a 41% reduction in sound pressure levels (SPL). After differences in seasonal changes in wind speed were accounted for, SPL decreased during the pandemic by 3.98 dB (37%). The most notable changes in ship activity were significantly reduced vessel speeds for all ship types and fewer ships using the area during the pandemic. Vessel speed was highly correlated to SPL and the only ship-based variable that predicted SPLs. Despite the opportunistic nature [i.e., not a standard before-after-control-impact (BACI) study], this study provides a unique opportunity to assess the effectiveness of ship traffic management strategies, such as slowing ships down, to mitigate impacts on marine life in the study area, including local sperm whale populations.Publisher PDFPeer reviewe

Perceptual modalities guiding bat flight in a native habitat

Flying animals accomplish high-speed navigation through fields of obstacles using a suite of sensory modalities that blend spatial memory with input from vision, tactile sensing, and, in the case of most bats and some other animals, echolocation. Although a good deal of previous research has been focused on the role of individual modes of sensing in animal locomotion, our understanding of sensory integration and the interplay among modalities is still meager. To understand how bats integrate sensory input from echolocation, vision, and spatial memory, we conducted an experiment in which bats flying in their natural habitat were challenged over the course of several evening emergences with a novel obstacle placed in their flight path. Our analysis of reconstructed flight data suggests that vision, echolocation, and spatial memory together with the possible exercise of an ability in using predictive navigation are mutually reinforcing aspects of a composite perceptual system that guides flight. Together with the recent development in robotics, our paper points to the possible interpretation that while each stream of sensory information plays an important role in bat navigation, it is the emergent effects of combining modalities that enable bats to fly through complex spaces

Optical flow sensing and the inverse perception problem for flying bats

The movements of birds, bats, and other flying species are governed by complex sensorimotor systems that allow the animals to react to stationary environmental features as well as to wind disturbances, other animals in nearby airspace, and a wide variety of unexpected challenges. The paper and talk will describe research that analyzes the three-dimensional trajectories of bats flying in a habitat in Texas. The trajectories are computed with stereoscopic methods using data from synchronous thermal videos that were recorded with high temporal and spatial resolution from three viewpoints. Following our previously reported work, we examine the possibility that bat trajectories in this habitat are governed by optical flow sensing that interpolates periodic distance measurements from echolocation. Using an idealized geometry of bat eyes, we introduce the concept of time-to-transit, and recall some research that suggests that this quantity is computed by the animals' visual cortex. Several steering control laws based on time-to-transit are proposed for an idealized flight model, and it is shown that these can be used to replicate the observed flight of what we identify as typical bats. Although the vision-based motion control laws we propose and the protocols for switching between them are quite simple, some of the trajectories that have been synthesized are qualitatively bat-like. Examination of the control protocols that generate these trajectories suggests that bat motions are governed both by their reactions to a subset of key feature points as well by their memories of where these feature points are located

Using collision cones to assess biological deconfliction methods

Biological systems consistently outperform autonomous systems governed by engineered algorithms in their ability to reactively avoid collisions. To better understand this discrepancy, a collision avoidance algorithm was applied to frames of digitized video trajectory data from bats, swallows and fish (Myotis velifer, Petrochelidon pyrrhonota and Danio aequipinnatus). Information available from visual cues, specifically relative position and velocity, was provided to the algorithm which used this information to define collision cones that allowed the algorithm to find a safe velocity requiring minimal deviation from the original velocity. The subset of obstacles provided to the algorithm was determined by the animal's sensing range in terms of metric and topological distance. The algorithmic calculated velocities showed good agreement with observed biological velocities, indicating that the algorithm was an informative basis for comparison with the three species and could potentially be improved for engineered applications with further study

SPE-44 Implements Sperm Cell Fate

The sperm/oocyte decision in the hermaphrodite germline of Caenorhabditis elegans provides a powerful model for the characterization of stem cell fate specification and differentiation. The germline sex determination program that governs gamete fate has been well studied, but direct mediators of cell-type-specific transcription are largely unknown. We report the identification of spe-44 as a critical regulator of sperm gene expression. Deletion of spe-44 causes sperm-specific defects in cytokinesis, cell cycle progression, and organelle assembly resulting in sterility. Expression of spe-44 correlates precisely with spermatogenesis and is regulated by the germline sex determination pathway. spe-44 is required for the appropriate expression of several hundred sperm-enriched genes. The SPE-44 protein is restricted to the sperm-producing germline, where it localizes to the autosomes (which contain sperm genes) but is excluded from the transcriptionally silent X chromosome (which does not). The orthologous gene in other Caenorhabditis species is similarly expressed in a sex-biased manner, and the protein likewise exhibits autosome-specific localization in developing sperm, strongly suggestive of an evolutionarily conserved role in sperm gene expression. Our analysis represents the first identification of a transcriptional regulator whose primary function is the control of gamete-type-specific transcription in this system

Multi-ancestry GWAS of the electrocardiographic PR interval identifies 202 loci underlying cardiac conduction

The electrocardiographic PR interval reflects atrioventricular conduction, and is associated with conduction abnormalities, pacemaker implantation, atrial fibrillation (AF), and cardiovascular mortality. Here we report a multi-ancestry (N=293,051) genome-wide association meta-analysis for the PR interval, discovering 202 loci of which 141 have not previously been reported. Variants at identified loci increase the percentage of heritability explained, from 33.5% to 62.6%. We observe enrichment for cardiac muscle developmental/contractile and cytoskeletal genes, highlighting key regulation processes for atrioventricular conduction. Additionally, 8 loci not previously reported harbor genes underlying inherited arrhythmic syndromes and/or cardiomyopathies suggesting a role for these genes in cardiovascular pathology in the general population. We show that polygenic predisposition to PR interval duration is an endophenotype for cardiovascular disease, including distal conduction disease, AF, and atrioventricular pre-excitation. These findings advance our understanding of the polygenic basis of cardiac conduction, and the genetic relationship between PR interval duration and cardiovascular disease. On the electrocardiogram, the PR interval reflects conduction from the atria to ventricles and also serves as risk indicator of cardiovascular morbidity and mortality. Here, the authors perform genome-wide meta-analyses for PR interval in multiple ancestries and identify 141 previously unreported genetic loci.Peer reviewe

Economic Evaluation of Lupus Nephritis in the Systemic Lupus International Collaborating Clinics Inception Cohort Using a Multistate Model Approach.

OBJECTIVE: Little is known about the long-term costs of lupus nephritis (LN). The costs were compared between patients with and without LN using multistate modeling. METHODS: Patients from 32 centers in 11 countries were enrolled in the Systemic Lupus International Collaborating Clinics inception cohort within 15 months of diagnosis and provided annual data on renal function, hospitalizations, medications, dialysis, and selected procedures. LN was diagnosed by renal biopsy or the American College of Rheumatology classification criteria. Renal function was assessed annually using the estimated glomerular filtration rate (GFR) or estimated proteinuria. A multistate model was used to predict 10-year cumulative costs by multiplying annual costs associated with each renal state by the expected state duration. RESULTS: A total of 1,545 patients participated; 89.3% were women, the mean ± age at diagnosis was 35.2 ± 13.4 years, 49% were white, and the mean followup duration was 6.3 ± 3.3 years. LN developed in 39.4% of these patients by the end of followup. Ten-year cumulative costs were greater in those with LN and an estimated glomerular filtration rate (GFR) 60 ml/minute) or with LN and estimated proteinuria >3 gm/day ($84,040 versus$20,499 if no LN and estimated proteinuria <0.25 gm/day). CONCLUSION: Patients with estimated GFR <30 ml/minute incurred 10-year costs 15-fold higher than those with normal estimated GFR. By estimating the expected duration in each renal state and incorporating associated annual costs, disease severity at presentation can be used to anticipate future health care costs. This is critical knowledge for cost-effectiveness evaluations of novel therapies

The 16th Data Release of the Sloan Digital Sky Surveys: First Release from the APOGEE-2 Southern Survey and Full Release of eBOSS Spectra

This paper documents the 16th data release (DR16) from the Sloan Digital Sky Surveys (SDSS), the fourth and penultimate from the fourth phase (SDSS-IV). This is the first release of data from the Southern Hemisphere survey of the Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2); new data from APOGEE-2 North are also included. DR16 is also notable as the final data release for the main cosmological program of the Extended Baryon Oscillation Spectroscopic Survey (eBOSS), and all raw and reduced spectra from that project are released here. DR16 also includes all the data from the Time Domain Spectroscopic Survey and new data from the SPectroscopic IDentification of ERosita Survey programs, both of which were co-observed on eBOSS plates. DR16 has no new data from the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey (or the MaNGA Stellar Library "MaStar"). We also preview future SDSS-V operations (due to start in 2020), and summarize plans for the final SDSS-IV data release (DR17)