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

Marine diatom proteorhodopsins and their potential role in coping with low iron availability

Proteorhodopsins (PR) are retinal-binding membrane proteins that function as light-driven proton pumps to generate energy for metabolism and growth. Recently PR-like genes have been identified in some marine eukaryotic protists, including diatoms, dinoflagellates, haptophytes and cryptophytes. These rhodopsins are homologous to green-light-absorbing, ATP-generating PRs present within bacteria. Here we show that in the oceanic diatom Pseudo-nitzschia granii, PR-like gene and protein expressions increase appreciably under iron limitation. In a survey of available transcriptomes, PR-like genes in diatoms are generally found in isolates from marine habitats where seasonal to chronic growth limitation by the micronutrient iron is prevalent, yet similar biogeographical patterns are not apparent in other phytoplankton taxa. We propose that rhodopsin-based phototrophy could account for a proportion of energy synthesis in marine eukaryotic photoautotrophs, especially when photosynthesis is compromised by low iron availability. This alternative ATP-generating pathway could have significant effects on plankton community structure and global ocean carbon cycling

Reduced nitrogenase efficiency dominates response of the globally important nitrogen fixer Trichodesmium to ocean acidification

工业革命以来，海洋吸收了约三分之一人为排放的CO2，以迄今3亿年来最快的速度酸化（CO2升高、pH下降），这势必影响海洋生态系统的关键过程和功能。研究团队创新性地从区分海洋酸化过程中CO2上升和pH下降的双重效应入手，揭示了海水CO2升高的正效应小于pH下降的负效应，故酸化的净效应为抑制束毛藻的固氮作用。这是因为酸化引起束毛藻胞质 pH下降，从而降低固氮酶效率、干扰胞内pH稳态、影响细胞产能。在上述研究工作的基础上，进一步系统地测定了固氮和光合系统蛋白的表达量及其含铁量，建立了一个束毛藻的“资源最优化分配”细胞模型。实现了实验数据和数值模型的紧密结合：实验数据是构筑模型的坚实基础，并提高了模型的预测水平；通过模型模拟，加深了对实验发现的认知，并对实验结论进行了时空拓展。 罗亚威博士和史大林博士为论文的共同第一作者和共同通讯作者，史大林课题组的洪海征教授、研究助理沈容和博士生张福婷为共同作者。论文的共同作者还包括美国佛罗里达州立大学助理教授Sven Kranz博士和乔治亚大学副教授Brian Hopkinson博士。【Abstract】The response of the prominent marine dinitrogen (N2)-fixing cyanobacteria Trichodesmium to ocean acidification (OA) is critical to understanding future oceanic biogeochemical cycles. Recent studies have reported conflicting findings on the effect of OA on growth and N2 fixation of Trichodesmium. Here, we quantitatively analyzed experimental data on how Trichodesmium reallocated intracellular iron and energy among key cellular processes in response to OA, and integrated the findings to construct an optimality-based cellular model. The model results indicate that Trichodesmium growth rate decreases under OA primarily due to reduced nitrogenase efficiency. The downregulation of the carbon dioxide (CO2)-concentrating mechanism under OA has little impact on Trichodesmium, and the energy demand of anti-stress responses to OA has a moderate negative effect. We predict that if anthropogenic CO2 emissions continue to rise, OA could reduce global N2 fixation potential of Trichodesmium by 27% in this century, with the largest decrease in iron-limiting regions.This work was funded by the National Key R&D Program of China (2016YFA0601404 and 2016YFA0601203), NSFC (41476093, 41721005, 41890802, 31861143022 and 41376116), and the MEL internal research fund (MELRI1502).本项研究得到了国家重点研发计划（2016YFA0601404 和2016YFA0601203）以及国家自然科学基金系列项目（41476093, 41721005, 41890802, 31861143022 和41376116）的资助

Mortality and pulmonary complications in patients undergoing surgery with perioperative SARS-CoV-2 infection: an international cohort study

Background: The impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on postoperative recovery needs to be understood to inform clinical decision making during and after the COVID-19 pandemic. This study reports 30-day mortality and pulmonary complication rates in patients with perioperative SARS-CoV-2 infection. Methods: This international, multicentre, cohort study at 235 hospitals in 24 countries included all patients undergoing surgery who had SARS-CoV-2 infection confirmed within 7 days before or 30 days after surgery. The primary outcome measure was 30-day postoperative mortality and was assessed in all enrolled patients. The main secondary outcome measure was pulmonary complications, defined as pneumonia, acute respiratory distress syndrome, or unexpected postoperative ventilation. Findings: This analysis includes 1128 patients who had surgery between Jan 1 and March 31, 2020, of whom 835 (74·0%) had emergency surgery and 280 (24·8%) had elective surgery. SARS-CoV-2 infection was confirmed preoperatively in 294 (26·1%) patients. 30-day mortality was 23·8% (268 of 1128). Pulmonary complications occurred in 577 (51·2%) of 1128 patients; 30-day mortality in these patients was 38·0% (219 of 577), accounting for 81·7% (219 of 268) of all deaths. In adjusted analyses, 30-day mortality was associated with male sex (odds ratio 1·75 [95% CI 1·28–2·40], p\textless0·0001), age 70 years or older versus younger than 70 years (2·30 [1·65–3·22], p\textless0·0001), American Society of Anesthesiologists grades 3–5 versus grades 1–2 (2·35 [1·57–3·53], p\textless0·0001), malignant versus benign or obstetric diagnosis (1·55 [1·01–2·39], p=0·046), emergency versus elective surgery (1·67 [1·06–2·63], p=0·026), and major versus minor surgery (1·52 [1·01–2·31], p=0·047). Interpretation: Postoperative pulmonary complications occur in half of patients with perioperative SARS-CoV-2 infection and are associated with high mortality. Thresholds for surgery during the COVID-19 pandemic should be higher than during normal practice, particularly in men aged 70 years and older. Consideration should be given for postponing non-urgent procedures and promoting non-operative treatment to delay or avoid the need for surgery. Funding: National Institute for Health Research (NIHR), Association of Coloproctology of Great Britain and Ireland, Bowel and Cancer Research, Bowel Disease Research Foundation, Association of Upper Gastrointestinal Surgeons, British Association of Surgical Oncology, British Gynaecological Cancer Society, European Society of Coloproctology, NIHR Academy, Sarcoma UK, Vascular Society for Great Britain and Ireland, and Yorkshire Cancer Research

Connecting real-world digital mobility assessment to clinical outcomes for regulatory and clinical endorsement–the Mobilise-D study protocol

Background: The development of optimal strategies to treat impaired mobility related to ageing and chronic disease requires better ways to detect and measure it. Digital health technology, including body worn sensors, has the potential to directly and accurately capture real-world mobility. Mobilise-D consists of 34 partners from 13 countries who are working together to jointly develop and implement a digital mobility assessment solution to demonstrate that real-world digital mobility outcomes have the potential to provide a better, safer, and quicker way to assess, monitor, and predict the efficacy of new interventions on impaired mobility. The overarching objective of the study is to establish the clinical validity of digital outcomes in patient populations impacted by mobility challenges, and to support engagement with regulatory and health technology agencies towards acceptance of digital mobility assessment in regulatory and health technology assessment decisions. Methods/design: The Mobilise-D clinical validation study is a longitudinal observational cohort study that will recruit 2400 participants from four clinical cohorts. The populations of the Innovative Medicine Initiative-Joint Undertaking represent neurodegenerative conditions (Parkinson’s Disease), respiratory disease (Chronic Obstructive Pulmonary Disease), neuro-inflammatory disorder (Multiple Sclerosis), fall-related injuries, osteoporosis, sarcopenia, and frailty (Proximal Femoral Fracture). In total, 17 clinical sites in ten countries will recruit participants who will be evaluated every six months over a period of two years. A wide range of core and cohort specific outcome measures will be collected, spanning patient-reported, observer-reported, and clinician-reported outcomes as well as performance-based outcomes (physical measures and cognitive/mental measures). Daily-living mobility and physical capacity will be assessed directly using a wearable device. These four clinical cohorts were chosen to obtain generalizable clinical findings, including diverse clinical, cultural, geographical, and age representation. The disease cohorts include a broad and heterogeneous range of subject characteristics with varying chronic care needs, and represent different trajectories of mobility disability. Discussion: The results of Mobilise-D will provide longitudinal data on the use of digital mobility outcomes to identify, stratify, and monitor disability. This will support the development of widespread, cost-effective access to optimal clinical mobility management through personalised healthcare. Further, Mobilise-D will provide evidence-based, direct measures which can be endorsed by regulatory agencies and health technology assessment bodies to quantify the impact of disease-modifying interventions on mobility. Trial registration: ISRCTN12051706

Internal carbonic anhydrase activity in three species of coral collected from the Florida Keys in August 2013

Dataset: Coral iCA ActivityInternal carbonic anhydrase activity in three species of coral collected from the Florida Keys in August 2013. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/794342NSF Emerging Frontiers Division (NSF EF) EF-131594

Modest increase in the C:N ratio of N-limited phytoplankton in the California Current in response to high CO2

Related Item links to supplementary material accompanying the article.In a fall 2008 cruise off the coast of California, on-deck incubations with surface seawater were conducted to compare the effect of increasing carbon dioxide (CO2) on nitrogen (N)-limited versus N-replete (+ NO3−) phytoplankton. Based on previous laboratory studies, we expected that under N-limitation C:N ratios would be more sensitive to CO2 availability. In particular, we wanted to test whether down-regulation of RuBisCO at high CO2 leads to an increased C:N ratio, since RuBisCO is thought to be a large pool of N in many autotrophs. In 4 out of 5 Nlimited experiments, the C:N ratio of phytoplankton biomass increased slightly from low to high CO2, and this increase was due chiefly to an increase in particulate organic carbon (POC), with little change in particulate organic nitrogen (PON). In contrast, the N-replete experiments did not show a change in C:N ratio, but some experiments exhibited higher rates of carbon fixation and growth at high CO2. In the one N-limited experiment that did not show a change in C:N ratio with CO2, the ambient population had a higher proportion of cyanobacteria compared with the other experiments. The concentration of RuBisCO decreased at high CO2 in several N-limited experiments, but this reduction only accounted for a minor proportion of the overall change in C:N ratio. An increase in C:N ratios at high CO2 in N-limited phytoplankton could provide negative feedback to increasing atmospheric CO2

Influence of Temperature and CO2 On Plasma‐membrane Permeability to CO2 and HCO3− in the Marine Haptophytes Emiliania huxleyi and Calcidiscus leptoporus (Prymnesiophyceae)

Membrane permeabilities to CO2 and HCO3− constrain the function of CO2 concentrating mechanisms that algae use to supply inorganic carbon for photosynthesis. In diatoms and green algae, plasma membranes are moderately to highly permeable to CO2 but effectively impermeable to HCO3−. Here, CO2 and HCO3− membrane permeabilities were measured using an 18O‐exchange technique on two species of haptophyte algae, Emiliania huxleyi and Calcidiscus leptoporus , which showed that the plasma membranes of these species are also highly permeable to CO2 (0.006–0.02 cm · s−1) but minimally permeable to HCO3−. Increased temperature and CO2 generally increased CO2 membrane permeabilities in both species, possibly due to changes in lipid composition or CO2 channel proteins. Changes in CO2 membrane permeabilities showed no association with the density of calcium carbonate coccoliths surrounding the cell, which could potentially impede passage of compounds. Haptophyte plasma‐membrane permeabilities to CO2 were somewhat lower than those of diatoms but generally higher than membrane permeabilities of green algae. One caveat of these measurements is that the model used to interpret 18O‐exchange data assumes that carbonic anhydrase, which catalyzes 18O‐exchange, is homogeneously distributed in the cell. The implications of this assumption were tested using a two‐compartment model with an inhomogeneous distribution of carbonic anhydrase to simulate 18O‐exchange data and then inferring plasma‐membrane CO2 permeabilities from the simulated data. This analysis showed that the inferred plasma‐membrane CO2 permeabilities are minimal estimates but should be quite accurate under most conditions.(© 2020 Phycological Society of America).ISSN:0022-3646ISSN:1529-881