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Deep Machine Learning Techniques for the Detection and Classification
www.nature.com/scientificreports Corrected: Publisher Correction OPEN Deep Machine Learning Techniques for the Detection and Classifcation of Sperm Whale Bioacoustics Received: 15 April 2019 Peter C. Bermant1, Michael M. Bronstein1,2,7, Robert J. Wood 3,4, Shane Gero 5 & Accepted: 15 August 2019 David F. Gruber 1,6 Published online: 29 August 2019 We implemented Machine Learning (ML) techniques to advance the study of sperm whale (Physeter macrocephalus) bioacoustics. This entailed employing Convolutional Neural Networks (CNNs) to construct an echolocation click detector designed to classify spectrograms generated from sperm whale acoustic data according to the presence or absence of a click. The click detector achieved 99.5% accuracy in classifying 650 spectrograms. The successful application of CNNs to clicks reveals the potential of future studies to train CNN-based architectures to extract fner-scale details from cetacean spectrograms. Long short-term memory and gated recurrent unit recurrent neural networks were trained to perform classifcation tasks, including (1) “coda type classifcation” where we obtained 97.5% accuracy in categorizing 23 coda types from a Dominica dataset containing 8,719 codas and 93.6% accuracy in categorizing 43 coda types from an Eastern Tropical Pacifc (ETP) dataset with 16,995 codas; (2) “vocal clan classifcation” where we obtained 95.3% accuracy for two clan classes from Dominica and 93.1% for four ETP clan types; and (3) “individual whale identifcation” where we obtained 99.4% accuracy using two Dominica sperm whales. These results demonstrate the feasibility of applying ML to sperm whale bioacoustics and establish the validity of constructing neural networks to learn meaningful representations of whale vocalizations. -
Advances in MARINE BIOLOGY
Advances in MARINE BIOLOGY VOLUME 46 ThisPageIntentionallyLeftBlank Advances in MARINE BIOLOGY Edited by A. J. SOUTHWARD Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, PL1 2PB, UK P. A. TYLER School of Ocean and Earth Science, University of Southampton, Southampton Oceanography Centre, European Way, Southampton, SO14 3ZH, UK C. M. YOUNG Oregon Institute of Marine Biology, University of Oregon P.O. Box 5389, Charleston, Oregon 97420, USA and L. A. FUIMAN Marine Science Institute, University of Texas at Austin, 750 Channel View Drive, Port Aransas, Texas 78373, USA Amsterdam – Boston – Heidelberg – London – New York – Oxford Paris – San Diego – San Francisco – Singapore – Sydney – Tokyo This book is printed on acid-free paper. ß 2003 Elsevier Science Ltd. All rights reserved. No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopy, recording, or any information storage and retrieval system, without permission in writing from the Publisher. The appearance of the code at the bottom of the first page of a chapter in this book indicates the Publisher’s consent that copies of the chapter may be made for personal or internal use of specific clients. This consent is given on the condition, however, that the copier pay the stated per copy fee through the Copyright Clearance Center, Inc. (222 Rosewood Drive, Danvers, Massachusetts 01923), for copying beyond that permitted by Sections 107 or 108 of the U.S. Copyright Law. This consent does not extend to other kinds of copying, such as copying for general distribution, for advertising or promotional purposes, for creating new collective works, or for resale. -
Publications Supported by NOAA's Office of Ocean Exploration And
1 Publications Supported by NOAA’s Office of Ocean Exploration and Research Compiled by Chris Belter, NOAA Central Library Accurate as of 17 April 2012 Journal Articles (n=454) Ahyong ST. 2008. Deepwater crabs from seamounts and chemosynthetic habitats off eastern New Zealand (Crustacea : Decapoda : Brachyura). Zootaxa(1708):1-72. Aig D, Haywood K. 2008. Through the Sea Snow: The Central Role of Videography in the Deep Gulf Wrecks Mission. International Journal of Historical Archaeology 12(2):133-145. doi:10.1007/s10761-008-0049-7 Andrews AH, Stone RP, Lundstrom CC, DeVogelaere AP. 2009. Growth rate and age determination of bamboo corals from the northeastern Pacific Ocean using refined Pb-210 dating. Marine Ecology-Progress Series 397:173-185. doi:10.3354/meps08193 Angel MV. 2010. Towards a full inventory of planktonic Ostracoda (Crustacea) for the subtropical Northwestern Atlantic Ocean. Deep-Sea Research Part Ii-Topical Studies in Oceanography 57(24-26):2173-2188. doi:10.1016/j.dsr2.2010.09.020 Arellano SM, Young CM. 2009. Spawning, Development, and the Duration of Larval Life in a Deep-Sea Cold-Seep Mussel. Biological Bulletin 216(2):149-162. Auster PJ. 2007. Linking deep-water corals and fish populations. Bulletin of Marine Science 81:93-99. Auster PJ, Gjerde K, Heupel E, Watling L, Grehan A, Rogers AD. 2011. Definition and detection of vulnerable marine ecosystems on the high seas: problems with the "move-on" rule. ICES Journal of Marine Science 68(2):254-264. doi:10.1093/icesjms/fsq074 Auster PJ, Watling L. 2010. Beaked whale foraging areas inferred by gouges in the seafloor. -
Biological Interactions Between Fish and Jellyfish in the Northwestern Mediterranean
Biological interactions between fish and jellyfish in the northwestern Mediterranean Uxue Tilves Barcelona 2018 Biological interactions between fish and jellyfish in the northwestern Mediterranean Interacciones biológicas entre meduas y peces y sus implicaciones ecológicas en el Mediterráneo Noroccidental Uxue Tilves Matheu Memoria presentada para optar al grado de Doctor por la Universitat Politècnica de Catalunya (UPC), Programa de doctorado en Ciencias del Mar (RD 99/2011). Tesis realizada en el Institut de Ciències del Mar (CSIC). Directora: Dra. Ana Maria Sabatés Freijó (ICM-CSIC) Co-directora: Dra. Verónica Lorena Fuentes (ICM-CSIC) Tutor/Ponente: Dr. Manuel Espino Infantes (UPC) Barcelona This student has been supported by a pre-doctoral fellowship of the FPI program (Spanish Ministry of Economy and Competitiveness). The research carried out in the present study has been developed in the frame of the FISHJELLY project, CTM2010-18874 and CTM2015- 68543-R. Cover design by Laura López. Visual design by Eduardo Gil. Thesis contents THESIS CONTENTS Summary 9 General Introduction 11 Objectives and thesis outline 30 Digestion times and predation potentials of Pelagia noctiluca eating CHAPTER1 fish larvae and copepods in the NW Mediterranean Sea 33 Natural diet and predation impacts of Pelagia noctiluca on fish CHAPTER2 eggs and larvae in the NW Mediterranean 57 Trophic interactions of the jellyfish Pelagia noctiluca in the NW Mediterranean: evidence from stable isotope signatures and fatty CHAPTER3 acid composition 79 Associations between fish and jellyfish in the NW CHAPTER4 Mediterranean 105 General Discussion 131 General Conclusion 141 Acknowledgements 145 Appendices 149 Summary 9 SUMMARY Jellyfish are important components of marine ecosystems, being a key link between lower and higher trophic levels. -
Aurelia Japonica: Molecular and Chromosomal Evidence A.V
Aurelia japonica: molecular and chromosomal evidence A.V. Kotova Institute of Cytology RAS, St. Petersburg, Russia, [email protected] L. S. Adonin Institute of Cytology RAS, St. Petersburg, Russia, [email protected] The genus Aurelia belongs to the family Ulmaridae, order Semaeostomeae, class Scyphozoa, type Cnidaria (Kramp, 1961). Mayer (1910) recorded 13 species of the genus Aurelia, after which Kramp (1961) mentioned only 7 and Russell (1970) reported only 2: A. aurita and A. limbata. At the end of the century again one of the species from «Synopsis of the medusae of the world” (Kramp, 1961), namely A. labiata, came back (Gershwin, 2001). Traditionally, the jellyfish Aurelia aurita was deemed cosmopolitan species. It was reported in a variety of coastal and shelf marine environments between 70°N and 40°S (Kramp, 1961). However, the molecular genetic approach suggests that A. aurita contains 11 cryptic species A.sp.1 – A.sp.11. The name Aurelia aurita was saved to the initial population described by Linnaeus at the European North coast (Dawson, 2001; Dawson, 2003; Dawson et al., 2005). Kishinouye (1891) described a form of Aurelia from Tokyo Bay as Aurelia japonica (Gershwin, 2001). This form of Aurelia was designated Aurelia sp. 1 and considered to be endemic to the western North Pacific and, therefore, dispersed globally from Japan (Dawson et al., 2005). In our previous study, the comparison of structural mesoglea protein mesoglein (Matveev et al., 2007, 2012) and its gene from three habitats White Sea (WsA), Black Sea (BsA), Japonic Sea (JsA) produced clear difference of two Aurelia populations. -
Life Cycle of Chrysaora Fuscescens (Cnidaria: Scyphozoa) and a Key to Sympatric Ephyrae1
Life Cycle of Chrysaora fuscescens (Cnidaria: Scyphozoa) and a Key to Sympatric Ephyrae1 Chad L. Widmer2 Abstract: The life cycle of the Northeast Pacific sea nettle, Chrysaora fuscescens Brandt, 1835, is described from gametes to the juvenile medusa stage. In vitro techniques were used to fertilize eggs from field-collected medusae. Ciliated plan- ula larvae swam, settled, and metamorphosed into scyphistomae. Scyphistomae reproduced asexually through podocysts and produced ephyrae by undergoing strobilation. The benthic life history stages of C. fuscescens are compared with benthic life stages of two sympatric species, and a key to sympatric scyphome- dusa ephyrae is included. All observations were based on specimens maintained at the Monterey Bay Aquarium jelly laboratory, Monterey, California. The Northeast Pacific sea nettle, Chry- tained at the Monterey Bay Aquarium, Mon- saora fuscescens Brandt, 1835, ranges from terey, California, for over a decade, with Mexico to British Columbia and generally ap- cultures started by F. Sommer, D. Wrobel, pears along the California and Oregon coasts B. B. Upton, and C.L.W. However the life in late summer through fall (Wrobel and cycle remained undescribed. Chrysaora fusces- Mills 1998). Relatively little is known about cens belongs to the family Pelagiidae (Gersh- the biology or ecology of C. fuscescens, but win and Collins 2002), medusae of which are when present in large numbers it probably characterized as having a central stomach plays an important role in its ecosystem giving rise to completely separated and because of its high biomass (Shenker 1984, unbranched radiating pouches and without 1985). Chrysaora fuscescens eats zooplankton a ring-canal. -
CNIDARIA Corals, Medusae, Hydroids, Myxozoans
FOUR Phylum CNIDARIA corals, medusae, hydroids, myxozoans STEPHEN D. CAIRNS, LISA-ANN GERSHWIN, FRED J. BROOK, PHILIP PUGH, ELLIOT W. Dawson, OscaR OcaÑA V., WILLEM VERvooRT, GARY WILLIAMS, JEANETTE E. Watson, DENNIS M. OPREsko, PETER SCHUCHERT, P. MICHAEL HINE, DENNIS P. GORDON, HAMISH J. CAMPBELL, ANTHONY J. WRIGHT, JUAN A. SÁNCHEZ, DAPHNE G. FAUTIN his ancient phylum of mostly marine organisms is best known for its contribution to geomorphological features, forming thousands of square Tkilometres of coral reefs in warm tropical waters. Their fossil remains contribute to some limestones. Cnidarians are also significant components of the plankton, where large medusae – popularly called jellyfish – and colonial forms like Portuguese man-of-war and stringy siphonophores prey on other organisms including small fish. Some of these species are justly feared by humans for their stings, which in some cases can be fatal. Certainly, most New Zealanders will have encountered cnidarians when rambling along beaches and fossicking in rock pools where sea anemones and diminutive bushy hydroids abound. In New Zealand’s fiords and in deeper water on seamounts, black corals and branching gorgonians can form veritable trees five metres high or more. In contrast, inland inhabitants of continental landmasses who have never, or rarely, seen an ocean or visited a seashore can hardly be impressed with the Cnidaria as a phylum – freshwater cnidarians are relatively few, restricted to tiny hydras, the branching hydroid Cordylophora, and rare medusae. Worldwide, there are about 10,000 described species, with perhaps half as many again undescribed. All cnidarians have nettle cells known as nematocysts (or cnidae – from the Greek, knide, a nettle), extraordinarily complex structures that are effectively invaginated coiled tubes within a cell. -
Researchers Unveil Rich World of Fish Biofluorescence
Media Inquiries: Kendra Snyder, Department of Communications 212-496-3419; [email protected] www.amnh.org _____________________________________________________________________________________ Wednesday, January 8, 2014 RESEARCHERS UNVEIL RICH WORLD OF FISH BIOFLUORESCENCE TECHNOLOGY-DRIVEN STUDY FINDS ABOUT 180 GLOWING SPECIES, HIGHLIGHTS NEW POTENTIAL SOURCE FOR BIOMEDICAL FLUORESCENT PROTEINS A team of researchers led by scientists from the American Museum of Natural History has released the first report of widespread biofluorescence in the tree of life of fishes, identifying more than 180 species that glow in a wide range of colors and patterns. Published today in PLOS ONE, the research shows that biofluorescence—a phenomenon by which organisms absorb light, transform it, and eject it as a different color—is common and variable among marine fish species, indicating its potential use in communication and mating. The report opens the door for the discovery of new fluorescent proteins that could be used in biomedical research. “We’ve long known about biofluorescence underwater in organisms like corals, jellyfish, and even in land animals like butterflies and parrots, but fish biofluorescence has been reported in only a few research publications,” said co-lead author John Sparks, a curator in the Museum’s Department of Ichthyology. “This paper is the first to look at the wide distribution of biofluorescence across fishes, and it opens up a number of new research areas.” Unlike the full-color environment that humans and other terrestrial animals inhabit, fishes live in a world that is predominantly blue because, with depth, water quickly absorbs the majority of the visible light spectrum. In recent years, the research team has discovered that many fishes absorb the remaining blue light and re-emit it in neon greens, reds, and oranges. -
Bibliography on the Scyphozoa with Selected References on Hydrozoa and Anthozoa
W&M ScholarWorks Reports 1971 Bibliography on the Scyphozoa with selected references on Hydrozoa and Anthozoa Dale R. Calder Virginia Institute of Marine Science Harold N. Cones Virginia Institute of Marine Science Edwin B. Joseph Virginia Institute of Marine Science Follow this and additional works at: https://scholarworks.wm.edu/reports Part of the Marine Biology Commons, and the Zoology Commons Recommended Citation Calder, D. R., Cones, H. N., & Joseph, E. B. (1971) Bibliography on the Scyphozoa with selected references on Hydrozoa and Anthozoa. Special scientific eporr t (Virginia Institute of Marine Science) ; no. 59.. Virginia Institute of Marine Science, William & Mary. https://doi.org/10.21220/V59B3R This Report is brought to you for free and open access by W&M ScholarWorks. It has been accepted for inclusion in Reports by an authorized administrator of W&M ScholarWorks. For more information, please contact [email protected]. BIBLIOGRAPHY on the SCYPHOZOA WITH SELECTED REFERENCES ON HYDROZOA and ANTHOZOA Dale R. Calder, Harold N. Cones, Edwin B. Joseph SPECIAL SCIENTIFIC REPORT NO. 59 VIRGINIA INSTITUTE. OF MARINE SCIENCE GLOUCESTER POINT, VIRGINIA 23012 AUGUST, 1971 BIBLIOGRAPHY ON THE SCYPHOZOA, WITH SELECTED REFERENCES ON HYDROZOA AND ANTHOZOA Dale R. Calder, Harold N. Cones, ar,d Edwin B. Joseph SPECIAL SCIENTIFIC REPORT NO. 59 VIRGINIA INSTITUTE OF MARINE SCIENCE Gloucester Point, Virginia 23062 w. J. Hargis, Jr. April 1971 Director i INTRODUCTION Our goal in assembling this bibliography has been to bring together literature references on all aspects of scyphozoan research. Compilation was begun in 1967 as a card file of references to publications on the Scyphozoa; selected references to hydrozoan and anthozoan studies that were considered relevant to the study of scyphozoans were included. -
Bioluminescent Flashes Drive Nighttime Schooling Behavior and Synchronized Swimming Dynamics in Flashlight Fish
University of Rhode Island DigitalCommons@URI Ocean Engineering Faculty Publications Ocean Engineering 8-14-2019 Bioluminescent flashes drive nighttime schooling behavior and synchronized swimming dynamics in flashlight fish David F. Gruber Brennan Phillips Rory O'Brien Vivek Boominathan Ashok Veeraraghavan See next page for additional authors Follow this and additional works at: https://digitalcommons.uri.edu/oce_facpubs Authors David F. Gruber, Brennan Phillips, Rory O'Brien, Vivek Boominathan, Ashok Veeraraghavan, Ganesh Vasan, Peter O'Brien, Vincent A. Pieribone, and John S. Sparks RESEARCH ARTICLE Bioluminescent flashes drive nighttime schooling behavior and synchronized swimming dynamics in flashlight fish 1,2,3 4 5 6 David F. GruberID *, Brennan T. PhillipsID , Rory O'Brien , Vivek BoominathanID , Ashok Veeraraghavan6, Ganesh Vasan5, Peter O'Brien5, Vincent A. Pieribone5, John S. Sparks3,7 1 Department of Natural Sciences, City University of New York, Baruch College, New York, New York, United States of America, 2 PhD Program in Biology, The Graduate Center, City University of New York, New York, a1111111111 New York, United States of America, 3 Sackler Institute for Comparative Genomics, American Museum of a1111111111 Natural History, New York, New York, United States of America, 4 Department of Ocean Engineering, a1111111111 University of Rhode Island, Narragansett, Rhode Island, United States of America, 5 Department of Cellular a1111111111 and Molecular Physiology, The John B. Pierce Laboratory, Yale University School of Medicine, New Haven, a1111111111 Connecticut, United States of America, 6 Rice University, Department of Electrical and Computer Engineering, Houston, Texas, United States of America, 7 Department of Ichthyology, Division of Vertebrate Zoology, American Museum of Natural History, New York, New York, United States of America * [email protected] OPEN ACCESS Citation: Gruber DF, Phillips BT, O'Brien R, Abstract Boominathan V, Veeraraghavan A, Vasan G, et al. -
A Review on Envenomation and Treatment in European Jellyfish
marine drugs Review To Pee, or Not to Pee: A Review on Envenomation and Treatment in European Jellyfish Species Louise Montgomery 1,2,*, Jan Seys 1 and Jan Mees 1,3 1 Flanders Marine Institute, InnovOcean Site, Wandelaarkaai 7, Ostende 8400, Belgium; [email protected] (J.S.); [email protected] (J.M.) 2 College of Medical, Veterinary & Life Sciences, Graham Kerr Building, University of Glasgow, Glasgow G12 8QQ, UK 3 Ghent University, Marine Biology Research Group, Krijgslaan 281, Campus Sterre-S8, Ghent B-9000, Belgium * Correspondence: [email protected]; Tel.: +32-059-342130; Fax: +32-059-342131 Academic Editor: Kirsten Benkendorff Received: 13 May 2016; Accepted: 30 June 2016; Published: 8 July 2016 Abstract: There is a growing cause for concern on envenoming European species because of jellyfish blooms, climate change and globalization displacing species. Treatment of envenomation involves the prevention of further nematocyst release and relieving local and systemic symptoms. Many anecdotal treatments are available but species-specific first aid response is essential for effective treatment. However, species identification is difficult in most cases. There is evidence that oral analgesics, seawater, baking soda slurry and 42–45 ˝C hot water are effective against nematocyst inhibition and giving pain relief. The application of topical vinegar for 30 s is effective on stings of specific species. Treatments, which produce osmotic or pressure changes can exacerbate the initial sting and aggravate symptoms, common among many anecdotal treatments. Most available therapies are based on weak evidence and thus it is strongly recommended that randomized clinical trials are undertaken. We recommend a vital increase in directed research on the effect of environmental factors on envenoming mechanisms and to establish a species-specific treatment. -
Pelagic Cnidaria of Mississippi Sound and Adjacent Waters
Gulf and Caribbean Research Volume 5 Issue 1 January 1975 Pelagic Cnidaria of Mississippi Sound and Adjacent Waters W. David Burke Gulf Coast Research Laboratory Follow this and additional works at: https://aquila.usm.edu/gcr Part of the Marine Biology Commons Recommended Citation Burke, W. 1975. Pelagic Cnidaria of Mississippi Sound and Adjacent Waters. Gulf Research Reports 5 (1): 23-38. Retrieved from https://aquila.usm.edu/gcr/vol5/iss1/4 DOI: https://doi.org/10.18785/grr.0501.04 This Article is brought to you for free and open access by The Aquila Digital Community. It has been accepted for inclusion in Gulf and Caribbean Research by an authorized editor of The Aquila Digital Community. For more information, please contact [email protected]. Gulf Research Reports, Vol. 5, No. 1, 23-38, 1975 PELAGIC CNIDARIA OF MISSISSIPPI SOUND AND ADJACENT WATERS’ W. DAVID BURKE Gulf Coast Research Laboratory, Ocean Springs, Mississippi 39564 ABSTRACT Investigations were made in Mississippi Sound and adjacent waters from March 1968 through March 1971 to record the occurrence and seasonality of planktonic cnidarians. About 700 plankton samples were taken from estuarine and oceanic areas. From these samples, 26 species of hydromedusae were identified, 12 of which were collected from Mis- sissippi Sound. In addition, 25 species of siphonophorae were identified from Mississippi waters, although only 6 species were collected in Mississippi Sound. From an examination of about 500 trawl samples taken during this period, 10 species of Scyphozoa were found in Mississippi waters, 6 of which occurred in Mississippi Sound. INTRODUCTION of coelenterates from Mississippi waters.