Automated classification of three-dimensional reconstructions of coral reefs using convolutional neural networks

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Hopkinson, B. M., King, A. C., Owen, D. P., Johnson-Roberson, M., Long, M. H., & Bhandarkar, S. M. Automated classification of three-dimensional reconstructions of coral reefs using convolutional neural networks. PLoS One, 15(3), (2020): e0230671, doi: 10.1371/journal.pone.0230671.Coral reefs are biologically diverse and structurally complex ecosystems, which have been severally affected by human actions. Consequently, there is a need for rapid ecological assessment of coral reefs, but current approaches require time consuming manual analysis, either during a dive survey or on images collected during a survey. Reef structural complexity is essential for ecological function but is challenging to measure and often relegated to simple metrics such as rugosity. Recent advances in computer vision and machine learning offer the potential to alleviate some of these limitations. We developed an approach to automatically classify 3D reconstructions of reef sections and assessed the accuracy of this approach. 3D reconstructions of reef sections were generated using commercial Structure-from-Motion software with images extracted from video surveys. To generate a 3D classified map, locations on the 3D reconstruction were mapped back into the original images to extract multiple views of the location. Several approaches were tested to merge information from multiple views of a point into a single classification, all of which used convolutional neural networks to classify or extract features from the images, but differ in the strategy employed for merging information. Approaches to merging information entailed voting, probability averaging, and a learned neural-network layer. All approaches performed similarly achieving overall classification accuracies of ~96% and >90% accuracy on most classes. With this high classification accuracy, these approaches are suitable for many ecological applications.This study was funded by grants from the Alfred P. Sloan Foundation (BMH, BR2014-049; https://sloan.org), and the National Science Foundation (MHL, OCE-1657727; https://www.nsf.gov). The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript

Measurements at low energies of the polarization-transfer coefficient Kyy' for the reaction 3H(p,n)3He at 0 degrees

Measurements of the transverse polarization coefficient Kyy' for the reaction 3H(p,n)3He are reported for outgoing neutron energies of 1.94, 5.21, and 5.81 MeV. This reaction is important both as a source of polarized neutrons for nuclear physics experiments, and as a test of theoretical descriptions of the nuclear four-body system. Comparison is made to previous measurements, confirming the 3H(p,n)3He reaction can be used as a polarized neutron source with the polarization known to an accuracy of approximately 5%. Comparison to R-matrix theory suggests that the sign of the 3F3 phase-shift parameter is incorrect. Changing the sign of this parameter dramatically improves the agreement between theory and experiment.Comment: 12 pages, RevTeX, 5 eps figures, submitted to Phys. Rev.

Measurements of the Total Cross Section for the Scattering of Polarized Neutrons from Polarized 3^3He

Measurements of polarized neutron--polarized $^3$He scattering are reported. The target consisted of cryogenically-polarized solid $^3$He, thickness 0.04 atom/b and polarization 40%. The longitudinal and transverse total cross-section differences $\Delta\sigma_L$ and $\Delta\sigma_T$ were measured for incident neutron energies 2-8 MeV. The results are compared to phase-shift predictions based on four different analyses of n-$^3$He scattering. The best agreement is obtained with a recent R-matrix analysis of A=4 scattering and reaction data, lending strong suport to the $^4$He level scheme obtained in that analysis.Comment: 19 pages RevTeX style, 5 postscript figures, excepted for publication in the Aug96 issue of Phys. Rev. C. Revised version includes correct version of 1 postscript figur

DNA methylation associated with postpartum depressive symptoms overlaps findings from a genome-wide association meta-analysis of depression

Background Perinatal depressive symptoms have been linked to adverse maternal and infant health outcomes. The etiology associated with perinatal depressive psychopathology is poorly understood, but accumulating evidence suggests that understanding inter-individual differences in DNA methylation (DNAm) patterning may provide insight regarding the genomic regions salient to the risk liability of perinatal depressive psychopathology. Results Genome-wide DNAm was measured in maternal peripheral blood using the Infinium MethylationEPIC microarray. Ninety-two participants (46% African-American) had DNAm samples that passed all quality control metrics, and all participants were within 7 months of delivery. Linear models were constructed to identify differentially methylated sites and regions, and permutation testing was utilized to assess significance. Differentially methylated regions (DMRs) were defined as genomic regions of consistent DNAm change with at least two probes within 1 kb of each other. Maternal age, current smoking status, estimated cell-type proportions, ancestry-relevant principal components, days since delivery, and chip position served as covariates to adjust for technical and biological factors. Current postpartum depressive symptoms were measured using the Edinburgh Postnatal Depression Scale. Ninety-eight DMRs were significant (false discovery rate \u3c 5%) and overlapped 92 genes. Three of the regions overlap loci from the latest Psychiatric Genomics Consortium meta-analysis of depression. Conclusions Many of the genes identified in this analysis corroborate previous allelic, transcriptomic, and DNAm association results related to depressive phenotypes. Future work should integrate data from multi-omic platforms to understand the functional relevance of these DMRs and refine DNAm association results by limiting phenotypic heterogeneity and clarifying if DNAm differences relate to the timing of onset, severity, duration of perinatal mental health outcomes of the current pregnancy or to previous history of depressive psychopathology

Parity Nonconservation in 106Pd and 108Pd Neutron Resonances

Parity nonconservation (PNC) has been studied in the neutron p-wave resonances of 106Pd and 108Pd in the energy range of 20 to 2000 eV. Longitudinal asymmetries in p-wave capture cross sections are measured using longitudinally polarized neutrons incident on ∼20-g metal-powder targets at LANSCE. A CsI γ-ray detector array measures capture cross section asymmetries as a function of neutron energy which is determined by the neutron time-of-flight method. A total of 21 p-wave resonances in 106Pd and 21 p-wave resonances in 108Pd were studied. One statistically significant PNC effect was observed in106Pd, and no effects were observed in 108Pd. For 106Pd a weak spreading width of Γw=34-28+47×10-7 eV was obtained. For 108Pd an upper limit on the weak spreading width of Γw\u3c12×10-7 eV was determined at the 68% confidence level

Parity Violation in Neutron Resonances in 107,109Ag

Parity nonconservation (PNC) was studied in p-wave resonances in Ag by measuring the helicity dependence of the neutron total cross section. Transmission measurements on natural Ag were performed in the energy range 32 to 422 eV with the time-of-flight method at the Manuel Lujan Neutron Scattering Center at Los Alamos National Laboratory. A total of 15 p-wave neutron resonances were studied in 107Ag and ninep-wave resonances in 109Ag. Statistically significant asymmetries were observed for eight resonances in 107Ag and for four resonances in109Ag. An analysis treating the PNC matrix elements as random variables yields a weak spreading width of Γw=(2.67-1.21+2.65)×10-7 eV for107Ag and Γw=(1.30-0.74+2.49)×10-7 eV for 109Ag

Neutron Resonance Spectroscopy of 106Pd, and 108Pd from 20–2000 eV

Parity nonconserving asymmetries have been measured in p-wave resonances of 106Pd and 108Pd. The data analysis requires knowledge of the neutron resonance parameters. Transmission and capture γ-ray yields were measured for En=20–2000 eV with the time-of-flight method at the Los Alamos Neutron Science Center (LANSCE). A total of 28 resonances in 106Pd and 32 resonances in 108Pd were studied. The resonance parameters for 106Pd are new for all except one resonance. In 108Pd six new resonances were observed and the precision improved for many of the resonance parameters. A Bayesian analysis was used to assign orbital angular momentum for the resonances studied

Parity Nonconservation in Neutron Resonances in 232Th,

Parity nonconservation (PNC) was measured for 24 p-wave resonances from 8 to 300 eV in 232Th by measuring the helicity dependence of the total neutron cross section for epithermal neutrons with an improved experimental system. Ten resonances show statistically significant parity violation. For these ten resonances the analyzing powers are all positive, thus confirming the previously observed sign correlation. The data are fit to the sum of two terms, a constant asymmetry and a fluctuating asymmetry. With this ansatz the root-mean-square PNC matrix element M=1.12 meV, which corresponds to a weak spreading widthΓw=4.7×10-7 eV. For the neighboring nuclide 238U there is no constant offset, suggesting that the sign correlation is specific to 232Th

Parity Violation in 232Th Neutron Resonances Above 250 eV

The analysis of parity nonconservation (PNC) measurements performed on 232Th by the TRIPLE Collaboration has been extended to include the neutron energy range of 250 to 1900 eV. Below 250 eV all ten statistically significant parity violations have the same sign. However, at higher energies PNC effects of both signs were observed in the transmission of longitudinally polarized neutrons through a thick thorium target. Although the limited experimental energy resolution precluded analysis in terms of the longitudinal asymmetry, parity violations were observed and the cross section differences for positive and negative neutron helicities were obtained. For comparison, a similar analysis was performed on the data below 250 eV, for which longitudinal asymmetries were obtained previously. For energies below 250 eV, the p-wave neutron strength functions for the J=1/2 and J=3/2 states were extracted: S1/21=(1.68±0.61)×10-4 and S3/21=(0.75±0.18)×10-4. The data provide constraints on the properties of local doorway states proposed to explain the PNC sign effect in thorium

Prospective Longitudinal Study of the Pregnancy DNA Methylome: The US Pregnancy, Race, Environment, Genes (PREG) Study

Purpose The goal of the Pregnancy, Race, Environment, Genes study was to understand how social and environmental determinants of health (SEDH), pregnancy-specific environments (PSE) and biological processes influence the timing of birth and account for the racial disparity in preterm birth. The study followed a racially diverse longitudinal cohort throughout pregnancy and included repeated measures of PSE and DNA methylation (DNAm) over the course of gestation and up to 1 year into the postpartum period. Participants All women were between 18 and 40 years of age with singleton pregnancies and no diagnosis of diabetes or indication of assisted reproductive technology. Both mother and father had to self-identify as either African-American (AA) or European-American (EA). Maternal peripheral blood samples along with self-report questionnaires measuring SEDH and PSE factors were collected at four pregnancy visits, and umbilical cord blood was obtained at birth. A subset of participants returned for two additional postpartum visits, during which additional questionnaires and maternal blood samples were collected. The pregnancy and postpartum extension included n=240 (AA=126; EA=114) and n=104 (AA=50; EA=54), respectively. Findings to date One hundred seventy-seven women (AA=89, EA=88) met full inclusion criteria out of a total of 240 who were initially enrolled. Of the 63 participants who met exclusion criteria after enrolment, 44 (69.8%) were associated with a medical reason. Mean gestational age at birth was significantly shorter for the AA participants by 5.1 days (M=272.5 (SD=10.5) days vs M=277.6 (SD=8.3)). Future plans Future studies will focus on identifying key environmental factors that influence DNAm change across pregnancy and account for racial differences in preterm birth