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

Fortilin Binds IRE1α and Prevents ER Stress from Signaling Apoptotic Cell Death

The endoplasmic reticulum, the cytoplasmic organelle that matures a massive amount of nascent secretory polypeptides, is particularly sensitive to stress. Endoplasmic reticulum stress causes unfolded proteins to populate the organelle, eliciting the unfolded protein response. During the unfolded protein response, GRP78—an endoplasmic reticulum master stress regulator—detaches from three endoplasmic reticulum stress sensors (IRE1α, PERK, and ATF6) and allows them to activate the apoptotic signaling pathway. Fortilin, a pro-survival molecule, is known to inhibit apoptosis by binding and inhibiting p53, but its role in endoplasmic reticulum stress-induced apoptosis remains unknown. Here, we report that fortilin directly interacts with the cytoplasmic domain of IRE1α, inhibits both kinase and endoribonuclease (RNase) activities of the stress sensor, and protects cells against apoptotic cell death at both cellular and whole animal levels. Our data support a role of fortilin in the unfolded protein response and its potential participation in human diseases caused by unfolded protein response

Progress report on the EAVI BCI toolkit for music: musical applications of algorithms for use with consumer brain computer interfaces

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A Business Plan for The Fitzgerald Institute

This piece seeks to develop a business strategy for the University of Akron\u27s Fitzgerald Institute for Entrepreneurship. The recommendations given were developed utilizing research on entrepreneurial education and the desires of students at the university

MAGICCARPET: Verified Detection and Recovery for Hardware-based Exploits

Abstract—MAGICCARPET is a new approach to defending systems against exploitable processor bugs. MAGICCARPET uses hardware to detect violations of invariants involving security-critical processor state and uses firmware to correctly push software’s state past the violations. The invariants are specified at run time. MAGICCARPET focuses on dynamically validating updates to security-critical processor state. In this work, (1) we generate correctness proofs for both MAGICCARPET hardware and firmware; (2) we prove that processor state and events never violate our security invariants at runtime; and (3) we show that MAGICCARPET copes with hardware-based exploits discovered post-fabrication using a combination of verified reconfigurations of invariants in the fabric and verified recoveries via reprogrammable software. We implement MAGICCARPET inside a popular open source processor on an FPGA platform. We evaluate MAGICCARPET using a diverse set of hardware-based attacks based on escaped and exploitable commercial processor bugs. MAGICCARPET is able to detect and recover from all tested attacks with no software run-time overhead in the attack-free case

Optimization of strength and ductility in nanotwinned ultra-fine grained Ag: Twin density and grain orientations

Nanotwinned ultrafine grained Ag thick films with different twin densities and orientations have been synthesized by magnetron sputtering with a wide-range of deposition rates. The twin boundary (TB) spacings and orientations as well as the grain size for the different deposition conditions have been characterized by both synchrotron X-ray scattering and transmission electron microscopy (TEM). Structural characterization combined with uniaxial tensile tests of the free-standing films reveals a large increase in the yield strength for films deposited at high deposition rates without any accompanying change in the TB spacing – a behavior that is not reported in the literature. We find that films deposited at lower deposition rates exhibit more randomly oriented grains with a lower overall twin density (averaged over all the grains) than the more heavily twinned grains with strong 〈1 1 1〉 fiber texture in the films deposited at higher deposition rates. The TB spacing in the twinned grains, however, does not show any significant dependence on the deposition rate. The dependence of the strength and ductility on the twin density and orientations can be described by two different soft deformation modes: (1) untwinned grains and (2) nanowinned grains that are not oriented with 〈1 1 1〉 along the growth direction. The untwinned grains provide relatively low resistance to slip, and thus decreased strength, while the nanotwinned grains that are not oriented with 〈1 1 1〉 along the growth direction are softer than nanotwinned grains that are oriented with 〈1 1 1〉 along the growth direction. We have revealed that an ultrafine-grained (150–200 nm) structure consisting of a mixture of nanotwinned (∼8–12 nm spacing) and untwined grains yields the best combination of high strength and uniform tensile ductility

Porcine brachial artery tortuosity for in vivo evaluation of neuroendovascular devices

We report a novel model of arterial tortuosity in the porcine brachial artery for testing of endovascular devices in the flexed forelimb position. This provides an ideal vascular territory for an in vivo assessment of guidewires, microcatheters, and endovascular implants because it closely mimics the challenging curvature at the carotid siphon

Testing metallicity indicators at z~1.4 with the gravitationally lensed galaxy CASSOWARY 20

We present X-shooter observations of CASSOWARY 20 (CSWA 20), a star-forming (SFR ~6 Msol/yr) galaxy at z=1.433, magnified by a factor of 11.5 by the gravitational lensing produced by a massive foreground galaxy at z=0.741. We analysed the integrated physical properties of the HII regions of CSWA 20 using temperature- and density-sensitive emission lines. We find the abundance of oxygen to be ~1/7 of solar, while carbon is ~50 times less abundant than in the Sun. The unusually low C/O ratio may be an indication of a particularly rapid timescale of chemical enrichment. The wide wavelength coverage of X-shooter gives us access to five different methods for determining the metallicity of CSWA 20, three based on emission lines from HII regions and two on absorption features formed in the atmospheres of massive stars. All five estimates are in agreement, within the factor of ~2 uncertainty of each method. The interstellar medium of CSWA 20 only partially covers the star-forming region as viewed from our direction; in particular, absorption lines from neutrals and first ions are exceptionally weak. We find evidence for large-scale outflows of the interstellar medium (ISM) with speeds of up 750 km/s, similar to the values measured in other high-z galaxies sustaining much higher rates of star formation.Comment: 18 pages, 11 figures, accepted for publication in MNRA

Intergroup Dialogue in a High School Classroom

In this paper, we share our work using Intergroup Dialogue (IGD) for increasing group understanding, building relationships across difference, and enhancing understanding of social inequities. IGD is an emerging area of research in K–12 settings and with adolescents. Taking this into consideration, we used this well-developed critical pedagogy in higher education–related settings to design a qualitative case study that explored its use in a high school classroom. We worked with ninth- and tenth-grade students in their sociology class to examine how IGD affected their understanding of gender and society. We found evidence that IGD enhances empathy across different lived experiences, backgrounds, and perspectives. Furthermore, findings show IGD’s impact on improving intergroup understanding and relationships