6 research outputs found

    Three-dimensional Segmentation of Trees Through a Flexible Multi-Class Graph Cut Algorithm (MCGC)

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    Developing a robust algorithm for automatic individual tree crown (ITC) detection from airborne laser scanning datasets is important for tracking the responses of trees to anthropogenic change. Such approaches allow the size, growth and mortality of individual trees to be measured, enabling forest carbon stocks and dynamics to be tracked and understood. Many algorithms exist for structurally simple forests including coniferous forests and plantations. Finding a robust solution for structurally complex, species-rich tropical forests remains a challenge; existing segmentation algorithms often perform less well than simple area-based approaches when estimating plot-level biomass. Here we describe a Multi-Class Graph Cut (MCGC) approach to tree crown delineation. This uses local three-dimensional geometry and density information, alongside knowledge of crown allometries, to segment individual tree crowns from airborne LiDAR point clouds. Our approach robustly identifies trees in the top and intermediate layers of the canopy, but cannot recognise small trees. From these three-dimensional crowns, we are able to measure individual tree biomass. Comparing these estimates to those from permanent inventory plots, our algorithm is able to produce robust estimates of hectare-scale carbon density, demonstrating the power of ITC approaches in monitoring forests. The flexibility of our method to add additional dimensions of information, such as spectral reflectance, make this approach an obvious avenue for future development and extension to other sources of three-dimensional data, such as structure from motion datasets.Jonathan Williams holds a NERC studentship [NE/N008952/1] which is a CASE partnership with support from Royal Society for the Protection of Birds (RSPB). David Coomes was supported by an International Academic Fellowship from the Leverhulme Trust. Carola-Bibiane Schoenlieb was supported by the RISE projects CHiPS and NoMADS, the Cantab Capital Institute for the Mathematics of Information and the Alan Turing Institute. We gratefully acknowledge the support of NVIDIA Corporation with the donation of a Quadro P6000 GPU used for this research

    Towards low vegetation identification: A new method for tree crown segmentation from LiDAR data based on a symmetrical structure detection algorithm (SSD)

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    Obtaining low vegetation data is important in order to quantify the structural characteristics of a forest. Dense three-dimensional (3D) laser scanning data can provide information on the vertical profile of a forest. However, most studies have focused on the dominant and subdominant layers of the forest, while few studies have tried to delineate the low vegetation. To address this issue, we propose a framework for individual tree crown (ITC) segmentation from laser data that focuses on both overstory and understory trees. The framework includes 1) a new algorithm (SSD) for 3D ITC segmentation of dominant trees, by detecting the symmetrical structure of the trees, and 2) removing points of dominant trees and mean shift clustering of the low vegetation. The framework was tested on a boreal forest in Sweden and the performance was compared 1) between plots with different stem density levels, vertical complexities, and tree species composition, and 2) using airborne laser scanning (ALS) data, terrestrial laser scanning (TLS) data, and merged ALS and TLS data (ALS + TLS data). The proposed framework achieved detection rates of 0.87 (ALS + TLS), 0.86 (TLS), and 0.76 (ALS) when validated with field inventory data (of trees with a diameter at breast height >= 4 cm). When validating the estimated number of understory trees by visual interpretation, the framework achieved 19%, 21%, and 39% root-mean-square error values with ALS + TLS, TLS, and ALS data, respectively. These results show that the SSD algorithm can successfully separate laser points of overstory and understory trees, ensuring the detection and segmentation of low vegetation in forest. The proposed framework can be used with both ALS and TLS data, and achieve ITC segmentation for forests with various structural attributes. The results also illustrate the potential of using ALS data to delineate low vegetation

    AmĂ©lioration de l’inventaire forestier Ă  l’aide de nuages de points Ă  haute densitĂ© acquis par drone lidar et lidar mobile : Ă©tude de cas en forĂȘts feuillues tempĂ©rĂ©es

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    Les exigences en matiĂšre d'inventaire forestier Ă©voluent rapidement pour rĂ©pondre Ă  un ensemble de normes Ă©conomiques, sociales et environnementales de plus en plus complexes en matiĂšre de gestion durable des ressources forestiĂšres. Le manque d'informations dĂ©taillĂ©es sur l'approvisionnement, c'est-Ă -dire la quantitĂ© et les caractĂ©ristiques des ressources forestiĂšres, constitue un obstacle important Ă  la satisfaction de ces exigences. Avec le dĂ©veloppement continu et la dĂ©mocratisation des capteurs de lidar sur drone (ULS) et de lidar mobile (MLS), de nouveaux types de nuages de points sont de plus en plus accessibles pour appuyer le niveau opĂ©rationnel de l’inventaire. Dans la prĂ©sente thĂšse, le potentiel et les limites de l’utilisation de nuages de points ULS et MLS pour la numĂ©risation des arbres feuillus en amont de la chaine d’approvisionnement ont Ă©tĂ© Ă©valuĂ©s. Des mĂ©thodes de traitement ont Ă©tĂ© dĂ©veloppĂ©es pour l’estimation d’attributs structuraux clefs tels que le diamĂštre Ă  hauteur de poitrine (DHP), la hauteur de l'arbre, les dimensions de la couronne et le volume de bois marchand. Dans le premier article, nous nous sommes concentrĂ©s sur le dĂ©veloppement et l'Ă©valuation de chaĂźnes de traitement automatiques pour la dĂ©tection et la segmentation des arbres individuels (ITD : Individual Tree Dectection and Delineation) et l'estimation de leurs attributs structuraux. Ceci, Ă  partir de donnĂ©es ULS acquises avec et sans feuilles dans un peuplement naturel hĂ©tĂ©rogĂšne de feuillus nordiques. Des comparaisons fines avec des nuages de points de lidar aĂ©rien (ALS) et terrestre (TLS) ont Ă©tĂ© rĂ©alisĂ©es pour mieux comprendre la configuration des donnĂ©es ULS et pour valider l'extraction d’attributs d’inventaire dĂ©rivĂ©s de l’ULS. Les meilleurs rĂ©sultats pour la segmentation des arbres et l’estimation de leurs attributs structuraux ont Ă©tĂ© obtenus hors feuilles via l’utilisation d’une approche de segmentation dite ascendante (« bottom-up »). Les performances globales des capteurs ULS, en termes d'ajustement cylindrique des tiges et de prĂ©cision gĂ©omĂ©trique des points le long de la tige, ne sont toutefois pas comparables Ă  celles du TLS. Les incertitudes sont encore trop Ă©levĂ©es au niveau de l'arbre individuel pour respecter les normes de l’inventaire terrain. L’acquisition hors feuilles de donnĂ©es ULS Ă  haute densitĂ© pourrait toutefois jouer un rĂŽle important dans le dĂ©veloppement de modĂšles allomĂ©triques locaux qui font gĂ©nĂ©ralement dĂ©faut dans les peuplements complexes de feuillus, ainsi que pour la caractĂ©risation des ressources et le soutien des opĂ©rations de foresterie de prĂ©cision. Dans le second article, nous proposons une mĂ©thode innovante pour extraire le volume de bois marchand Ă  partir des donnĂ©es MLS-SLAM (localisation et cartographie simultanĂ©es). Les approches actuelles pour prĂ©dire le volume de bois marchand reposent sur des Ă©quations allomĂ©triques qui sont indĂ©pendantes de la forme et de la gĂ©omĂ©trie de l'arbre. Il existe des biais et des erreurs connus associĂ©s Ă  cette simplification, en particulier pour les arbres feuillus. L'utilisation d'algorithmes de modĂšles structurels quantitatifs (QSM : Quantitative Structural Model) pour estimer le volume de bois Ă  partir de nuages de points 3D reprĂ©sente une alternative prometteuse aux mesures destructives et un fort potentiel pour amĂ©liorer les modĂšles allomĂ©triques. Les rĂ©sultats ont montrĂ© une grande similitude entre les donnĂ©es TLS et MLS pour l'estimation de la hauteur des arbres, des dimensions de la couronne et du DHP. L'application de QSMs sur des nuages de points MLS filtrĂ©s pour extraire le volume marchand du tronc principal des arbres feuillus n'a montrĂ© aucun biais significatif par rapport aux estimations TLS. NĂ©anmoins, les donnĂ©es MLS sont plus bruitĂ©es que les donnĂ©es TLS, ce qui a entraĂźnĂ© une surestimation du volume de bois des branches qui augmente avec l'ordre de ramification. Toutefois, ces erreurs ont Ă©tĂ© limitĂ©es du fait que les branches de 2Ăšme et de 3Ăšme ordre de ramification ne reprĂ©sentaient qu'une faible proportion du volume marchand total. Ces rĂ©sultats constituent une Ă©tape importante vers la prochaine gĂ©nĂ©ration d'inventaires forestiers amĂ©liorĂ©s par lidar mobiles au sol. Compte tenu de l'utilisation accrue des systĂšmes ULS et MLS dans la gestion forestiĂšre, nos dĂ©veloppements constituent des Ă©tapes importantes pour les futurs inventaires lidar Ă  l’échelle de l’arbre individuel. Nos rĂ©sultats dĂ©montrent des avancĂ©es significatives dans l'utilisation des configurations ULS et MLS pour l’estimation des paramĂštres biophysiques forestiers.Abstract : Forest inventory requirements are rapidly evolving to meet an increasingly complex set of economic, social and environmental standards for sustainable forest resource management. A significant obstacle to support this requirement is the lack of detailed information on the supply, i.e., the quantity and characteristics of forest resources. In recent decades, a substantial effort has been made to reduce the costs of forest inventories by minimizing labor-intensive field surveys and developing inventory systems enhanced by remote sensing. As such, the use of lidar technology in various aerial and terrestrial platforms, such as airborne laser scanning (ALS) and terrestrial laser scanning (TLS) has considerably increased to the point of becoming essential to improve the forest inventories beyond the existing photo-interpretation techniques. With the continuous development and the democratization of UAV-borne laser scanning (ULS) and mobile laser scanning (MLS) sensors, new types of point cloud are increasingly accessible for forest investigations. The level of detail of ULS and MLS point cloud is becoming comparable to that of TLS, decreasing the boundaries between ALS and TLS systems and providing new opportunities to characterize forest resources at the tree level. In the present thesis, the baselines of ULS and MLS point clouds in digitizing hardwood trees up the supply chain were benchmarked and methods were developed to extract critical structural attributes such as diameter at breast height (DBH), tree height, crown dimensions and merchantable wood volume. In the first article, we emphasized on the development and the evaluation of automatic workflows for the detection, the delineation and the estimation of tree structural attributes from leaf-on and leaf-off ULS data collection. These analyses were conducted in a complex heterogeneous natural stand of northern hardwoods. Co-registration process with ALS and TLS point clouds was achieved for a better understanding of ULS data configuration and to validate ULS retrieval of tree structural attributes. In leaf-on condition, no significant differences were observed between ALS and ULS-R raster-based ITD results, where crown delineation errors led to a poor prediction of individual tree DBH using allometry. In contrast, results in leaf-off condition using point cloud-based individual tree detection and delineation (ITD) algorithm outperformed the raster based ITD in terms of tree detection and tree delineation accuracy, revealing the full potential of high-resolution ULS data. DBH estimation from the “bottom-up” point cloud-based ITD also provided accurate results for both methods, namely allometry and cylinder fitting. The latter showed to be more efficient in dealing with forked trees. The overall performance, in terms of stem cylinder fitting and geometric accuracy of stem points from ULS sensors are not yet comparable to TLS. Uncertainties are still too high at the individual tree level to reach the standard of field inventories, but one might expect to get closer to operational requirements with narrower beams and higher ranging accuracy ULS sensors. In leaf-off condition, the use of bottom-up tree segmentation approaches presents a strong potential to overcome ITD limits currently encountered in hardwood stands. Applications requiring accurate tree location and crown size data could greatly benefit from this innovative approach. Leaf-off acquisition of high-density ULS data could play an important role in developing local allometric models that are typically lacking in complex hardwood stands, as well as for resource characterization and supporting precision forestry operations. In the second article, we propose an innovative method to extract merchantable wood volume from MLS data. Current approaches to predict merchantable wood volume rely on allometric equations that are independent of tree form and the geometry of the tree. There are known biases and errors associated with this simplification, particularly for hardwood trees. The use of quantitative structural model (QSM) algorithms to estimate wood volume from 3D point clouds represent a promising alternative to destructive measurement and a strong potential to improve allometric models. However, so far, they were mainly used on TLS point clouds, which are time-consuming to acquire in the field and complex to process. With the rapid technological progress of SLAM-based (simultaneous localization and mapping) MLS systems, new types of ground-based lidar points clouds are available for QSM analysis. SLAM-based MLS systems open new possibilities to support field inventory. In this study, we collected SLAM-based MLS data from a 1 ha leaf-off northern hardwood site and investigated its use for estimating tree structural attributes. Validation was performed on 26 trees using destructive field measurements and multi-scans TLS data. Results showed high similitude of TLS and MLS data for the estimation of the tree height, crown dimensions and DBH. The application of QSM on filtered MLS point clouds to extract the merchantable stem volume of hardwood trees showed no significant bias compared to the TLS estimates. Nevertheless, the MLS data are noisier than the TLS data, primarily due to the propagation of positioning errors and the greater divergence of the sensor beam. This resulted in an overestimation of the branching volume that increases with the branching order. However, these errors were limited by the fact that branches from the 2nd and 3rd branching order represented a small proportion of the total merchantable volume. These findings are an important step towards next generation of forest inventories enhanced by ground-based lidar. Considering the increased use of ULS and MLS systems in forest management, our developments are important steps forward for future individual-tree-based lidar inventories. We believe that our results demonstrate significant advances in the use of ULS and MLS configuration for the retrieval of forest biophysical parameters

    Volume 98 Issue 5, pp. 899-1054

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    ECOLOGY-EPIDEMIOLOGY-BEHAVIOR Increased Surfacing Behavior in Longnose Killifish Infected by Brain-Encysting Trematode. B. L. FREDENSBORG and A. N. LONGORIA - 899 Spatial Structure of Helminth Communities in the Golden Grey Mullet, Liza aurata (Actinopterygii: Mugilidae), From the Western Mediterranean. RAUL MIGUEZ-LOZANO, TRINIDAD V. PARDO-CARRANZA, ISABEL BLASCO-COSTA, and JUAN ANTONIO BALBUENA - 904 Hepatozoon Infection Prevalence in Four Snake Genera: Influence of Diet, Prey Parasitemia Levels, or Parasite Type? BEATRIZ TOME, JOAD P. M. C. MAIA, and D. JAMES HARRIS - 913 ECTOPARASITOLOGY Molecular Identification and Description of the Female of Nothoaspis reddelli (Ixodida: Argasidae) From a Cave in Southeastern Mexico. CARMEN GUZMAN-CORNEJO, RICARDO PAREDES-LEON, MARCELO B. LABRUNA, SANTIAGO NAVA, and JOSE M. VENZAL - 918 Prevalence of Hemoproteus iwa in Galapagos Great Frigatebirds (Fregata minor) and Their Obligate Fly Ectoparasite (01- Jersia spiniJera). IRIS I. LEVIN and PATRICIA G. PARKER - 924 Variable Microsatellite Loci for Population Genetic Analysis of Old World Monkey Lice (Pedicinus sp.). KATLYN SCHOLL, JULIE M. ALLEN, FABIAN H. LEENDERTZ, COLIN A. CHAPMAN, and DAVID L. REED - 930 FUNCTIONAL MORPHOLOGY Ultrastructural Study of Vitellogenesis of Aphallus tubarium (Rudolphi, 1819) Poche, 1926 (Digenea: Cryptogonimidae), an Intestinal Parasite of Dentex dentex (Pisces: Teleostei). SAMUEL GREANI, YANN QUILICHINI, JOSEPHINE FOATA, and BERNARD MARCHAND - 938 IMMUNOLOGY Seroprevalence of Toxoplasma gondii Infection in Domestic Horses in Durango State, Mexico. C. ALVARADO-ESQUIVEL, S. RODRIGUEZ-PENA, I. VILLENA, and J. P. DUBEY - 944 INVERTEBRATE-PARASITE RELATIONSHIPS Excystation Signals Do Not Isolate Gregarine Gene Pools: Experimental Excystation of Blabericola migrator Among 11 Species of Cockroaches. SHELBY M. STEELE, DEBRA T. CLOPTON, and RICHARD E. CLOPTON - 946 LIFE CYCLES-SURVEY A New Sarcocystis Species (Apicomplexa: Sarcocystidae) From the Rock Gecko Bunopus tuberculatus in Saudi Arabi. A. S. ABDEL-BAKI, H. M. ABDEL-HALEEM, and S. AL-QURAISHY - 951 A Retrospective Study of Abattoir Condemnation Due to Parasitic Infections: Economic Importance in Ahwaz, Southwestern Iran. HASSAN BORJI, MOHAMMAD AZIZZADEH, and MEHRAB KAMELLI - 954 Prevalence of Eimeria Infection in Yaks on the Qinghai-Tibet Plateau of China. HUI DONG, CHUNHUA LI, QIPING ZHAO, JING LI, HONGYU HAN, LIANLIAN JIANG, SHUNHAI ZHU, TING LI, CHUNLIN KONG, BING HUANG, and JINZHONG CAI - 958 Prevalence of Coccidial Infection in Dairy Cattle in Shanghai, China. HUI DONG, QIPING ZHAO, HONGYU HAN, LIANLIAN JIANG, SHUNHAI ZHU, TING LI, CHUNLIN KONG, and BING HUANG - 963 Genetic Sequence Data Identifies the Cercaria of Drepanocephalus spathans (Digenea: Echinostomatidae), a Parasite of the Double-Crested Cormorant (Phalacrocorax auritus), with Notes on Its Pathology in Juvenile Channel Catfish (Ictalurus punctatus). MATT J. GRIFFIN, LESTER H. KHOO, SYLVIE M. QUINIOU, MARY M. O\u27HEAR, LINDA M. POTE, TERRENCE E. GREENWAY, and DAVID J. WISE - 967 SYSTEMATICS-PHYLOGENETICS A New Species of Megalobatrachonema (Nematoda: Kathlaniidae) in Fojia bumui (Squamata: Scincidae) From Papua New Guinea. CHARLES R. BURSEY, STEPHEN R. GOLDBERG, and FRED KRAUS - 973 Two New Species of Schizorchis (Cestoda: Anoplocephalidae) From Leporids (Lagomorpha: Leporidae) in China. KUIZHENG CAI, JIALIN BAI, and SHIEN CHEN - 977 The Genus Guerrerostrongylus (Nematoda: Heligmonellidae) in Cricetid Rodents From the Atlantic Rain Forest of Misiones, Argentina: Emended Description of Guerrerostrongylus zetta (Travassos, 1937) and Description of a New Species. MARIA CELINA DIGIANI, JULIANA NOTARNICOLA, and GRACIELA T. NAVONE - 985 A New Microphallid (Digenea) Species From Lontra provocax (Mammalia: Mustelidae) From Freshwater Environments of Northwestern Patagonia (Argentina). VERONICA R. FLORES, NORMA L. BRUGNI, and CARLA M. POZZI - 992 Description of Riouxgolvania kapapkamui sp. n. (Nematoda: Muspiceoidea: Muspiceidae), a Peculiar Intradermal Parasite of Bats in Hokkaido, Japan. HIDEO HASEGAWA, MASAHIKO SATO, KISHIO MAEDA, and YOSHIKO MURAYAMA - 995 A New Species of Choleoeimeria (Apicomplexa: Eimeriidae) From Meller\u27s Chameleon, Trioceros melleri (Sauria: Chamaeleonidae). CHRIS T. McALLISTER - 1001 A New Species of Eimeria (Apicomplexa: Eimeriidae) From the Northern Myotis, Myotis septentrionalis (Chiroptera: Vespertilionidae), in Oklahoma. CHRIS T. McALLISTER, R. SCOTT SEVILLE, and ZACHARY P. ROEHRS - 1003 A New Spirurid (Nematoda) Parasite From Mormoopid Bats in Mexico. JORGE LUIS PERALTA-RODRIGUEZ, JUAN MANUEL CASPETA-MANDUJANO, and JOSE ANTONIO GUERRERO - 1006 THERAPEUTICS-DIAGNOSTICS Resistance of Rhipicephalus microplus to Amitraz and Cypermethrin in Tropical Cattle Farms in Veracruz, Mexico. AGUSTIN FERNANDEZ-SALAS, ROGER IVAN RODRIGUEZ-VIVAS, and MIGUEL ANGEL ALONSO-DIAZ - 1010 RESEARCH NOTES Seroprevalence Study on Theileria equi and Babesia caballi Antibodies in Horses From Central Province of Saudi Arabia. A. D. ALANAZI, M. S. ALYOUSIF, and M. M. HASSIEB - 1015 Influence of Rangelia vitalii (Apicomplexa: Piroplasmorida) on Copper, Iron and Zinc Bloodstream Levels in Experimentally Infected Dogs, ALEKSANDRO S, DA SILVA, RAQUELI T. FRANC;:A, MARCIO M. COSTA, CARLOS B. V. PAIM, FRANCINE C. PAIM, CLARISSA M. M. SANTOS, ERICO M. M. FLORES, TIAGO L. EILERS, CINTHIA M. MAZZANTI, SILVIA G. MONTEIRO, CARLOS H. DO AMARAL, and SONIA T. A. LOPES - 1018 Plagiorchis elegans (Trematoda) Induces Immune Response in an Incompatible Snail Host Biomphalaria glabrata (Pulmonata: Planorbidae). S. P. DAOUST, M. E. RAU, and J. D. McLAUGHLIN - 1021 Prevalence and Intensity of Fish-Borne Zoonotic Trematodes in Cultured Freshwater Fish From Rural and Urban Areas of Northern Vietnam. NGUYEN VAN DE, THANH HOA LE, and K. D. MURRELL - 1023 Details of the Paranephridial System of a Species of Prohyptiasmus (Cyclocoelidae: Hyptiasminae) From an American Coot, Fulica americana (Rallidae) in Oklahoma. NORMAN O. DRONEN, F. AGUSTIN JIMENEZ, and SCOTT L. GARDNER - 1026 Surface Ultrastructure of the Eggs of Malacopsylla grossiventris and Phthiropsylla agenoris (Siphonaptera: Malacopsyllidae). M. C. EZQUIAGA and M. LARES CHI - 1029 Prevalence of Ancylostoma braziliense in Cats in Three Northern Counties of Florida, United States. JANICE L. LIOTTA, KHUANCHAI N. KOOMPAPONG, JOSEPH P. YAROS, JOSEPH PRULLAGE, and DWIGHT D. BOWMAN - 1032 Obtaining an Isolate of Ancylostoma braziliense From Dogs Without the Need for Necropsy. JANICE L. LIOTTA, ALICE C. Y. LEE, SARP AKSEL, IBRAHIM ALKHALIFE, ALEJANDRO CRUZ-REYES, HEEJEONG YOUN, STEPHEN E. BIENHOFF, and DWIGHT D. BOWMAN - 1034 Obtaining an Isolate of Ancylostoma braziliense From Cats Without the Need for Necropsy. JANICE L. LIOTTA, ALICE C. Y. LEE, KHUANCHAI N. KOOMPAPONG, JOSEPH P. YAROS, JOSEPH PRULLAGE, MICHAEL A. ULRICH, and DWIGHT D. BOWMAN - 1037 Prevalence of Ancylostoma braziliense in Dogs From Alachua and Marion Counties, Florida, United States. JANICE L. LIOTTA, HEEJEONG YOUN, SARP AKSEL, STEPHEN E. BIENHOFF, and DWIGHT D. BOWMAN - 1039 Morphological Differentiation of Eggs of Ancylostoma caninum, Ancylostoma tubaeforme, and Ancylostoma braziliense From Dogs and Cats in the United States. ARACELI LUCIO-FORSTER, JANICE L. LIOTTA, JOSEPH P. YAROS, KAITLYN R. BRIGGS, HUSSNI O. MOHAMMED, and DWIGHT D. BOWMAN - 1041 Molecular and Immunological Characterization of a Novel 32-kDa Secreted Protein of Babesia microti. HIDEO OOKA, MOHAMAD A. TERKAWI, SHINUO CAO, GABRIEL ABOGE, YO UN-KYOUNG GOO, YUZI LUO, YAN LI, YOSHIFUMI NISHIKAWA, IKUO IGARASHI, and XUENAN XUAN - 1045 DNA Barcoding of Schistosome Cercariae Reveals a Novel Sub-Lineage within Schistosoma rodhaini From Ngamba Island Chimpanzee Sanctuary, Lake Victoria. C. J. STANDLEY and J. R. STOTHARD - 1049 Host Susceptibility Is Altered by Light Intensity After Exposure to Parasites. MICHELLE L. STEINAUER and KAITLIN M. BONNER - 1052 ANNOUNCEMENT: Change in Editorship - 903 ERRATUM - 91
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