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

Reasons for current E -cigarette use among U.S. adults

E-cigarette use has increased rapidly among U.S. adults. However, reasons for use among adults are unclear. We assessed reasons for e-cigarette use among a national sample of U.S. adults. Data were collected via online surveys among U.S. adults aged 18 or older from April through June 2014. Descriptive and multivariate regression analyses were conducted to assess reasons for e-cigarette use among 2448 current e-cigarette users, by sociodemographic characteristics and product type. Assessed reasons included cessation/health, consideration of others, convenience, cost, curiosity, flavoring, and simulation of conventional cigarettes. Among current e-cigarette users, 93% were also current cigarette smokers. The most common reasons for e-cigarette use were cessation/health (84.5%), consideration of others (71.5%), and convenience (56.7%). The prevalence of citing convenience (adjusted prevalence ratio [aPR] = 1.49) and curiosity (aPR = 1.54) as reasons for e-cigarette use were greater among current cigarette smokers than nonsmokers (P < 0.05). The prevalence of citing flavoring as a reason for use was greater among adults aged 18 to 24 (aPR = 2.02) than 55 or older (P < 0.05). Tank use was associated with greater prevalence of citing every assessed reason except convenience and curiosity. Cessation- and health-related factors are primary reasons cited for e-cigarette use among adults, and flavorings are more commonly cited by younger adults. Efforts are warranted to provide consumers with accurate information on the health effects of e-cigarettes and to ensure that flavoring and other unregulated features do not promote nicotine addiction, particularly among young adults

THE EFFECT OF JUMP DIRECTION AND PLANNING ON DROP LANDING MECHANICS IN FEMALE ATHLETES

The purpose of this study was to assess differences in landing and jump kinematics during a drop landing task in female athletes. Participants (n=18) with previous athletic experience (i.e., jumping sports) volunteered for the study and performed planned and unplanned jumps in three different directions (left, straight, right). Kinematic and kinetic data were analyzed from initial ground contact and toe off. Preferential weight distribution toward the right side was found during the bilateral drop landing task which was supported by larger peak ground reaction forces (GRFPeak)on the right limb. Jump direction significantly altered total plate time (p\u3c0.05), GRFPeak (p\u3c0.001), mean GRF symmetry (p\u3c 0.01), and knee path distance (p\u3c0.05). Based on these findings, off-center jumps, but not anticipation, altered landing and jumping kinematics in a manner that may relate to knee injury risk

Zapiola Gyre, velocities and mixing, new Argo insights

The Zapiola Gyre is a large, full-depth, bottom-intensified, anticyclonic recirculation in the Argentine Basin. It rotates around the Zapiola Drift, a sedimentary rise standing a few hundred meters above the abyssal plain, tall enough to create closed contours of planetary potential vorticity. Hence the gyre has been posited to be an eddy-driven free mode that is damped primarily by the bottom Ekman layer. It describes approximately a zonally elongated ellipse with a zonal semi-major axis of ∼440 km and a meridional semi-minor axis of ∼125 km. Its volume transport is estimated here at ∼110 (±25) × 106 m3 s−1. It has peak depth-averaged meridional velocities of ∼0.06 and ∼0.08 m s−1, and peak depth-averaged zonal velocities of ∼0.11 and ∼0.12 m s−1. Peak surface velocities are ∼57% of peak bottom velocities, consistent with the dynamics of a bottom-intensified Taylor column in a stratified flow. Deep and Core Argo float trajectories follow the gyre, with a couple of Core Argo floats with 1000-dbar parking depths executing more than three anticyclonic rotations around it, and Core Argo floats that approach within ∼75 km of the gyre center executing on average ∼1.7 circumnavigations. Deep Argo temperature-salinity profiles combined with historical shipboard CTD profile data afford maps newly illuminating the advective swirling of water-mass signatures around the gyre at the density of the North Atlantic Deep Water salinity maximum. Their patterns are consistent with a Peclet number of ∼30 estimated here using previously published lateral eddy diffusivities in the region

Is Your Neighborhood Designed to Support Physical Activity? A Brief Streetscape Audit Tool.

INTRODUCTION:Macro level built environment factors (eg, street connectivity, walkability) are correlated with physical activity. Less studied but more modifiable microscale elements of the environment (eg, crosswalks) may also affect physical activity, but short audit measures of microscale elements are needed to promote wider use. This study evaluated the relation of a 15-item neighborhood environment audit tool with a full version of the tool to assess neighborhood design on physical activity in 4 age groups. METHODS:From the 120-item Microscale Audit of Pedestrian Streetscapes (MAPS) measure of street design, sidewalks, and street crossings, we developed the 15-item version (MAPS-Mini) on the basis of associations with physical activity and attribute modifiability. As a sample of a likely walking route, MAPS-Mini was conducted on a 0.25-mile route from participant residences toward the nearest nonresidential destination for children (n = 758), adolescents (n = 897), younger adults (n = 1,655), and older adults (n = 367). Active transportation and leisure physical activity were measured with age-appropriate surveys, and accelerometers provided objective physical activity measures. Mixed-model regressions were conducted for each MAPS item and a total environment score, adjusted for demographics, participant clustering, and macrolevel walkability. RESULTS:Total scores of MAPS-Mini and the 120-item MAPS correlated at r = .85. Total microscale environment scores were significantly related to active transportation in all age groups. Items related to active transport in 3 age groups were presence of sidewalks, curb cuts, street lights, benches, and buffer between street and sidewalk. The total score was related to leisure physical activity and accelerometer measures only in children. CONCLUSION:The MAPS-Mini environment measure is short enough to be practical for use by community groups and planning agencies and is a valid substitute for the full version that is 8 times longer

Arsenal of plant cell wall degrading enzymes reflects host preference among plant pathogenic fungi

<p>Abstract</p> <p>Background</p> <p>The discovery and development of novel plant cell wall degrading enzymes is a key step towards more efficient depolymerization of polysaccharides to fermentable sugars for the production of liquid transportation biofuels and other bioproducts. The industrial fungus <it>Trichoderma reesei </it>is known to be highly cellulolytic and is a major industrial microbial source for commercial cellulases, xylanases and other cell wall degrading enzymes. However, enzyme-prospecting research continues to identify opportunities to enhance the activity of <it>T. reesei </it>enzyme preparations by supplementing with enzymatic diversity from other microbes. The goal of this study was to evaluate the enzymatic potential of a broad range of plant pathogenic and non-pathogenic fungi for their ability to degrade plant biomass and isolated polysaccharides.</p> <p>Results</p> <p>Large-scale screening identified a range of hydrolytic activities among 348 unique isolates representing 156 species of plant pathogenic and non-pathogenic fungi. Hierarchical clustering was used to identify groups of species with similar hydrolytic profiles. Among moderately and highly active species, plant pathogenic species were found to be more active than non-pathogens on six of eight substrates tested, with no significant difference seen on the other two substrates. Among the pathogenic fungi, greater hydrolysis was seen when they were tested on biomass and hemicellulose derived from their host plants (commelinoid monocot or dicot). Although <it>T. reesei </it>has a hydrolytic profile that is highly active on cellulose and pretreated biomass, it was less active than some natural isolates of fungi when tested on xylans and untreated biomass.</p> <p>Conclusions</p> <p>Several highly active isolates of plant pathogenic fungi were identified, particularly when tested on xylans and untreated biomass. There were statistically significant preferences for biomass type reflecting the monocot or dicot host preference of the pathogen tested. These highly active fungi are promising targets for identification and characterization of novel cell wall degrading enzymes for industrial applications.</p

Effects of β2 Agonists, Corticosteroids, and Novel Therapies on Rhinovirus-Induced Cytokine Release and Rhinovirus Replication in Primary Airway Fibroblasts

Rhinovirus-(RV-) induced asthma exacerbations account for high asthma-related health costs and morbidity in Australia. The cellular mechanism underlying this pathology is likely the result of RV-induced nuclear-factor-kappa-B-(NF-κB-) dependent inflammation. NF-κB may also be important in RV replication as inhibition of NF-κB inhibits replication of other viruses such as human immunodeficiency virus and cytomegalovirus. To establish the role of NF-κB inhibitors in RV-induced IL- 6 and IL-8 and RV replication, we used pharmacological inhibitors of NF-κB, and steroids and/or β2 agonists were used for comparison. Primary human lung fibroblasts were infected with RV-16 in the presence of NF-κB inhibitors: BAY-117085 and dimethyl fumarate; β2 agonist: salmeterol; and/or corticosteroids: dexamethasone; fluticasone. RV-induced IL-6 and IL-8 and RV replication were assessed using ELISAs and virus titration assays. RV replicated and increased IL-6 and IL-8 release. Salmeterol increased, while dexamethasone and fluticasone decreased RV-induced IL-6 and IL-8 (P<0.05). The NF-κB inhibitor BAY-117085 inhibited only RV-induced IL-6 (P<0.05) and dimethyl fumarate did not alter RV-induced IL-6 and IL-8. Dimethylfumarate increased RV replication whilst other drugs did not alter RV replication. These data suggest that inhibition of NF-κB alone is unlikely to be an effective treatment compared to current asthma therapeutics

Promoting inclusivity and equity in information and communications technology for food, land, and water systems

Food, land, and water systems underpin the health of societies and the environment, yet they are facing pressure from climate change, population growth, urbanization, and the overexploitation of natural resources. Information and Communication Technologies (ICTs) have the potential to support food, land, and water systems in response to these challenges. This report explores issues of inclusivity and equity of ICTs and how these technologies might be better used to their full potential

Religious Identity, Religious Attendance, and Parental Control

Using a national sample of adolescents aged 10–18 years and their parents (N = 5,117), this article examines whether parental religious identity and religious participation are associated with the ways in which parents control their children. We hypothesize that both religious orthodoxy and weekly religious attendance are related to heightened levels of three elements of parental control: monitoring activities, normative regulations, and network closure. Results indicate that an orthodox religious identity for Catholic and Protestant parents and higher levels of religious attendance for parents as a whole are associated with increases in monitoring activities and normative regulations of American adolescents