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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
SPORTS PARTICIPATION AND QUALITY OF LIFE IN ADOLESCENTS AND YOUNG ADULTS WITH CONGENITAL HEART DISEASE (SQUAD STUDY)
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)
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