Systematics, Natural History, and Conservation: Field Biologists Must Fight a Public-Image Problem

Organismic and Evolutionary Biolog

A Smooth Representation of Belief over SO(3) for Deep Rotation Learning with Uncertainty

Accurate rotation estimation is at the heart of robot perception tasks such as visual odometry and object pose estimation. Deep neural networks have provided a new way to perform these tasks, and the choice of rotation representation is an important part of network design. In this work, we present a novel symmetric matrix representation of the 3D rotation group, SO(3), with two important properties that make it particularly suitable for learned models: (1) it satisfies a smoothness property that improves convergence and generalization when regressing large rotation targets, and (2) it encodes a symmetric Bingham belief over the space of unit quaternions, permitting the training of uncertainty-aware models. We empirically validate the benefits of our formulation by training deep neural rotation regressors on two data modalities. First, we use synthetic point-cloud data to show that our representation leads to superior predictive accuracy over existing representations for arbitrary rotation targets. Second, we use image data collected onboard ground and aerial vehicles to demonstrate that our representation is amenable to an effective out-of-distribution (OOD) rejection technique that significantly improves the robustness of rotation estimates to unseen environmental effects and corrupted input images, without requiring the use of an explicit likelihood loss, stochastic sampling, or an auxiliary classifier. This capability is key for safety-critical applications where detecting novel inputs can prevent catastrophic failure of learned models.Comment: In Proceedings of Robotics: Science and Systems (RSS'20), Corvallis , Oregon, USA, Jul. 12-16, 202

The Sloan Digital Sky Survey Reverberation Mapping Project: Velocity Shifts of Quasar Emission Lines

Quasar emission lines are often shifted from the systemic velocity due to various dynamical and radiative processes in the line-emitting region. The level of these velocity shifts depends both on the line species and on quasar properties. We study velocity shifts for the line peaks of various narrow and broad quasar emission lines relative to systemic using a sample of 849 quasars from the Sloan Digital Sky Survey Reverberation Mapping (SDSS-RM) project. The coadded (from 32 epochs) spectra of individual quasars have sufficient signal-to-noise ratio (SNR) to measure stellar absorption lines to provide reliable systemic velocity estimates, as well as weak narrow emission lines. The sample also covers a large dynamic range in quasar luminosity (~2 dex), allowing us to explore potential luminosity dependence of the velocity shifts. We derive average line peak velocity shifts as a function of quasar luminosity for different lines, and quantify their intrinsic scatter. We further quantify how well the peak velocity can be measured for various lines as a function of continuum SNR, and demonstrate there is no systematic bias in the line peak measurements when the spectral quality is degraded to as low as SNR~3 per SDSS pixel. Based on the observed line shifts, we provide empirical guidelines on redshift estimation from [OII]3728, [OIII]5008, [NeV]3426, MgII, CIII], HeII1640, broad Hbeta, CIV, and SiIV, which are calibrated to provide unbiased systemic redshifts in the mean, but with increasing intrinsic uncertainties of 46, 56, 119, 205, 233, 242, 400, 415, and 477 km/s, in addition to the measurement uncertainties. These more realistic redshift uncertainties are generally much larger than the formal uncertainties reported by the redshift pipelines for spectroscopic quasar surveys, and demonstrate the infeasibility of measuring quasar redshifts to better than ~200 km/s with only broad lines.Comment: matched to the published version; minor changes and conclusions unchange

Constraining properties of the black hole population using LISA

LISA should detect gravitational waves from tens to hundreds of systems containing black holes with mass in the range from 10 thousand to 10 million solar masses. Black holes in this mass range are not well constrained by current electromagnetic observations, so LISA could significantly enhance our understanding of the astrophysics of such systems. In this paper, we describe a framework for combining LISA observations to make statements about massive black hole populations. We summarise the constraints that LISA observations of extreme-mass-ratio inspirals might be able to place on the mass function of black holes in the LISA range. We also describe how LISA observations can be used to choose between different models for the hierarchical growth of structure in the early Universe. We consider four models that differ in their prescription for the initial mass distribution of black hole seeds, and in the efficiency of accretion onto the black holes. We show that with as little as 3 months of LISA data we can clearly distinguish between these models, even under relatively pessimistic assumptions about the performance of the detector and our knowledge of the gravitational waveforms.Comment: 12 pages, 3 figures, submitted to Class. Quantum Grav. for proceedings of 8th LISA Symposium; v2 minor changes for consistency with accepted versio

In vivo monitoring of fetoplacental Vegfr2 gene activity in a murine pregnancy model using a Vegfr2-luc reporter gene and bioluminescent imaging

<p>Abstract</p> <p>Background</p> <p>Vascular endothelial growth factor receptor-2 (VEGFR2) plays a pivotal role in angiogenesis by eliciting vascular endothelial cell growth when bound to VEGF, a powerful pro-angiogenic ligand. While Vegf and Vegfr2 are expressed throughout gestation, the latter third of gestation in mice is characterized by a marked increase in fetoplacental angiogenesis. Thus, the objective of this study was to determine the feasibility of monitoring fetoplacental Vegfr2 gene activity non-invasively using a Vegfr2-luc reporter transgenic mouse and bioluminescent imaging.</p> <p>Methods</p> <p>Imaging parameters were optimized using two wild-type (WT) females, bearing Vegfr2-luc fetuses. Then, seven WT females, bred to Vegfr2-luc males, were imaged from gestational day (GD) 12 to 18 to determine the usefulness of the Vegfr2-luc mouse as a model for studying fetoplacental Vegfr2 activity during pregnancy. Semi-quantitative RT-PCR of Vegfr2 was also performed on whole fetoplacental units during this time. Additionally, resultant neonates were imaged at postnatal day (PND) 7, 14 and 21 to monitor Vegfr2 activity during post-natal development.</p> <p>Results</p> <p>Fetoplacental Vegfr2 gene activity was detected as light emissions beginning on GD 12 of gestation and increased throughout the imaging period (P < 0.05), and this paralleled the Vegfr2 mRNA data obtained from RT-PCR analysis. A decline in fetoplacental light emissions was associated with a poor pregnancy outcome in one pregnancy, indicating that this approach has potential use for studies monitoring pregnancy well being. Additionally, neonatal Vegfr2 activity was detected at PND 7, 14 and 21 but declined with time (P < 0.0001).</p> <p>Conclusions</p> <p><it>In utero </it>fetoplacental Vegfr2 gene activity was monitored longitudinally in a quantitative manner using a luciferase reporter gene and bioluminescent imaging during the latter third of gestation. This study demonstrates the feasibility of using the Vegfr2-luc mouse to monitor late gestation fetoplacental angiogenic activity under normal and experimental conditions. Additionally, neonatal Vegfr2 gene activity was monitored for three weeks postpartum, allowing continuous monitoring of Vegfr2 activity during the latter third of gestation and postnatal development within the same animals.</p

The Sloan Digital Sky Survey Reverberation Mapping Project: No Evidence for Evolution in the M-sigma Relation to z~1

We present host stellar velocity dispersion measurements for a sample of 88 broad-line quasars at 0.10.6) from the Sloan Digital Sky Survey Reverberation Mapping (SDSS-RM) project. High signal-to-noise ratio coadded spectra (average S/N~30 per 69 km/s pixel) from SDSS-RM allowed decomposition of the host and quasar spectra, and measurement of the host stellar velocity dispersions and black hole (BH) masses using the single-epoch (SE) virial method. The large sample size and dynamic range in luminosity (L5100=10^(43.2-44.7) erg/s) lead to the first clear detection of a correlation between SE virial BH mass and host stellar velocity dispersion far beyond the local universe. However, the observed correlation is significantly flatter than the local relation, suggesting that there are selection biases in high-z luminosity-threshold quasar samples for such studies. Our uniform sample and analysis enable an investigation of the redshift evolution of the M-sigma relation free of caveats by comparing different samples/analyses at disjoint redshifts. We do not observe evolution of the M-sigma relation in our sample, up to z~1, but there is an indication that the relation flattens towards higher redshifts. Coupled with the increasing threshold luminosity with redshift in our sample, this again suggests certain selection biases are at work, and simple simulations demonstrate that a constant M-sigma relation is favored to z~1. Our results highlight the scientific potential of deep coadded spectroscopy from quasar monitoring programs, and offer a new path to probe the co-evolution of BHs and galaxies at earlier times.Comment: replaced with the accepted version (minor changes and updated references); ApJ in press; changed title to highlight the main resul

A reference database for tumor-related genes co-expressed with interleukin-8 using genome-scale in silico analysis

BACKGROUND: The EST database provides a rich resource for gene discovery and in silico expression analysis. We report a novel computational approach to identify co-expressed genes using EST database, and its application to IL-8. RESULTS: IL-8 is represented in 53 dbEST cDNA libraries. We calculated the frequency of occurrence of all the genes represented in these cDNA libraries, and ranked the candidates based on a Z-score. Additional analysis suggests that most IL-8 related genes are differentially expressed between non-tumor and tumor tissues. To focus on IL-8's function in tumor tissues, we further analyzed and ranked the genes in 16 IL-8 related tumor libraries. CONCLUSIONS: This method generated a reference database for genes co-expressed with IL-8 and could facilitate further characterization of functional association among genes

Developmental changes in the organization of functional connections between the basal ganglia and cerebral cortex

The basal ganglia (BG) comprise a set of subcortical nuclei with sensorimotor, cognitive, and limbic subdivisions, indicative of functional organization. BG dysfunction in several developmental disorders suggests the importance of the healthy maturation of these structures. However, few studies have investigated the development of BG functional organization. Using resting-state functional connectivity MRI (rs-fcMRI), we compared human child and adult functional connectivity of the BG with rs-fcMRI-defined cortical systems. Because children move more than adults, customized preprocessing, including volume censoring, was used to minimize motion-induced rsfcMRI artifact. Our results demonstrated functional organization in the adult BG consistent with subdivisions previously identified in anatomical tracing studies. Group comparisons revealed a developmental shift in bilateral posterior putamen/pallidum clusters from preferential connectivity with the somatomotor “face” system in childhood to preferential connectivity with control/attention systems (frontoparietal, ventral attention) in adulthood. This shift was due to a decline in the functional connectivity of these clusters with the somatomotor face system over development, and no change with control/attention systems. Applying multivariate pattern analysis, we were able to reliably classify individuals as children or adults based on BG–cortical system functional connectivity. Interrogation of the features driving this classification revealed, in addition to the somatomotor face system, contributions by the orbitofrontal, auditory, and somatomotor hand systems. These results demonstrate that BG–cortical functional connectivity evolves over development, and may lend insight into developmental disorders that involve BG dysfunction, particularly those involving motor systems (e.g., Tourette syndrome)

Developmental Changes in the Organization of Functional Connections between the Basal Ganglia and Cerebral Cortex

The basal ganglia (BG) comprise a set of subcortical nuclei with sensorimotor, cognitive, and limbic subdivisions, indicative of functional organization. BG dysfunction in several developmental disorders suggests the importance of the healthy maturation of these structures. However, few studies have investigated the development of BG functional organization. Using resting-state functional connectivity MRI (rs-fcMRI), we compared human child and adult functional connectivity of the BG with rs-fcMRI-defined cortical systems. Because children move more than adults, customized preprocessing, including volume censoring, was used to minimize motion-induced rsfcMRI artifact. Our results demonstrated functional organization in the adult BG consistent with subdivisions previously identified in anatomical tracing studies. Group comparisons revealed a developmental shift in bilateral posterior putamen/pallidum clusters from preferential connectivity with the somatomotor “face” system in childhood to preferential connectivity with control/attention systems (frontoparietal, ventral attention) in adulthood. This shift was due to a decline in the functional connectivity of these clusters with the somatomotor face system over development, and no change with control/attention systems. Applying multivariate pattern analysis, we were able to reliably classify individuals as children or adults based on BG–cortical system functional connectivity. Interrogation of the features driving this classification revealed, in addition to the somatomotor face system, contributions by the orbitofrontal, auditory, and somatomotor hand systems. These results demonstrate that BG–cortical functional connectivity evolves over development, and may lend insight into developmental disorders that involve BG dysfunction, particularly those involving motor systems (e.g., Tourette syndrome)