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1. Genetic identification of three CITES-listed sharks using a paper-based Lab-on-a-Chip (LOC).

Author

Guuske P Tiktak, Alexandria Gabb, Margarita Brandt, Fernando R Diz, Karla Bravo-Vásquez, César Peñaherrera-Palma, Jonathan Valdiviezo-Rivera, Aaron Carlisle, Louise M Melling, Bradley Cain, David Megson, Richard Preziosi, and Kirsty J Shaw

Subjects
Medicine, Science
Abstract

Threatened shark species are caught in large numbers by artisanal and commercial fisheries and traded globally. Monitoring both which shark species are caught and sold in fisheries, and the export of CITES-restricted products, are essential in reducing illegal fishing. Current methods for species identification rely on visual examination by experts or DNA barcoding techniques requiring specialist laboratory facilities and trained personnel. The need for specialist equipment and/or input from experts means many markets are currently not monitored. We have developed a paper-based Lab-on-a-Chip (LOC) to facilitate identification of three threatened and CITES-listed sharks, bigeye thresher (Alopias superciliosus), pelagic thresher (A. pelagicus) and shortfin mako shark (Isurus oxyrinchus) at market source. DNA was successfully extracted from shark meat and fin samples and combined with DNA amplification and visualisation using Loop Mediated Isothermal Amplification (LAMP) on the LOC. This resulted in the successful identification of the target species of sharks in under an hour, with a working positive and negative control. The LOC provided a simple "yes" or "no" result via a colour change from pink to yellow when one of the target species was present. The LOC serves as proof-of-concept (PoC) for field-based species identification as it does not require specialist facilities. It can be used by non-scientifically trained personnel, especially in areas where there are suspected high frequencies of mislabelling or for the identification of dried shark fins in seizures.

Published
2024
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2. Using pseudo-absence models to test for environmental selection in marine movement ecology: the importance of sample size and selection strength

Author

Jérôme Pinti, Matthew Shatley, Aaron Carlisle, Barbara A. Block, and Matthew J. Oliver

Subjects
Movement ecology, Null models, Brownian motion, Random walks, Biotelemetry, Habitat selection, Biology (General), QH301-705.5
Abstract

Abstract Background Understanding the selection of environmental conditions by animals requires knowledge of where they are, but also of where they could have been. Presence data can be accurately estimated by direct sampling, sightings, or through electronic tag deployments. However, absence data are harder to determine because absences are challenging to measure in an uncontrolled setting. To address this problem, ecologists have developed different methods for generating pseudo-absence data relying on theoretical movement models. These null models represent the movement of environmentally naive individuals, creating a set of locations that animals could have been if they were not exhibiting environmental selection. Methods Here, we use four different kinds of null animal movement models—Brownian motion, Lévy walks, Correlated random walks, and Joint correlated random walks to test the ability and power of each of these null movement models to serve as appropriate animal absence models. We use Kolmogorov-Smirnov tests to detect environmental selection using two data sets, one of simulated animal tracks biased towards warmer sea surface temperatures, and one of 57 observed blue shark tracks of unknown sea surface temperature selection. Results The four different types of movement models showed minimal difference in the ability to serve as appropriate null models for environmental selection studies. Selection strength and sample size were more important in detecting true environmental selection. We show that this method can suffer from high false positive rates, especially in the case where animals are not selecting for specific environments. We provide estimates of test accuracy at different sample sizes and selection strengths to avoid false positives when using this method. Conclusion We show how movement models can be used to generate pseudo-absences and test for habitat selection in marine organisms. While this approach efficiently detects environmental selection in marine organisms, it cannot detect the underlying mechanisms driving this selection.

Published
2022
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3. Design and Conduct of Randomized Clinical Trials Evaluating Surgical Innovations in Ophthalmology: A Systematic Review

Author

Augusto Azuara-Blanco, Aaron Carlisle, Matthew O'Donnell, Hari Jayaram, Gus Gazzard, Daniel F.P. Larkin, Louisa Wickham, and Noemi Lois

Subjects
surgery, Ophthalmology, systematic review, Randomized clinical trial
Abstract

PurposeSurgical innovations are necessary to improve patient care. After an initial exploratory phase novel surgical technique should be compared with alternative options or standard care in randomized clinical trials (RCTs). However surgical RCTs have unique methodological challenges. Our study sought to investigate key aspects of the design, conduct and reporting of RCTs of novel surgeries.DesignSystematic ReviewMethodsThe protocol was prospectively registered in PROSPERO (CRD42021253297). RCTs evaluating novel surgeries for cataract, vitreoretinal, glaucoma and corneal diseases were included. Medline, EMBASE, Cochrane Library and Clinicaltrials.gov were searched. The search period was January 1, 2016, to June 16, 2021.ResultsFifty-two ophthalmic surgery RCTs were identified in the fields of glaucoma (n=12), vitreoretinal surgery (n=5) cataract (n=19) and cornea (n=16). A description defining the surgeon's experience or level of expertise was reported in 30 RCTs (57%); and was presented in both, control and intervention groups, in eleven (21%). Specification of number of cases performed in the particular surgical innovation being assessed prior to the trial was reported in 10 RCTs (19%); and an evaluation of quality of the surgical intervention in seven (13%). Prospective trial registration was recorded in 12 RCTs (23%), retrospective registration in 13 (25%) and there was no registration record in the remaining 28 (53%) studies.ConclusionImportant aspects of the study design such as surgical learning curve, surgeon's previous experience, quality assurance, and trial registration details were often missing in novel ophthalmic surgical procedures. The IDEAL framework aims to improve the quality of study design.

Published
2023

9. Diving into the vertical dimension of elasmobranch movement ecology

Author

Samantha Andrzejaczek, Tim C.D. Lucas, Maurice C. Goodman, Nigel E. Hussey, Amelia J. Armstrong, Aaron Carlisle, Daniel M. Coffey, Adrian C. Gleiss, Charlie Huveneers, David M. P. Jacoby, Mark G. Meekan, Johann Mourier, Lauren R. Peel, Kátya Abrantes, André S. Afonso, Matthew J. Ajemian, Brooke N. Anderson, Scot D. Anderson, Gonzalo Araujo, Asia O. Armstrong, Pascal Bach, Adam Barnett, Mike B. Bennett, Natalia A. Bezerra, Ramon Bonfil, Andre M. Boustany, Heather D. Bowlby, Ilka Branco, Camrin D. Braun, Edward J. Brooks, Judith Brown, Patrick J. Burke, Paul Butcher, Michael Castleton, Taylor K. Chapple, Olivier Chateau, Maurice Clarke, Rui Coelho, Enric Cortes, Lydie I. E. Couturier, Paul D. Cowley, Donald A. Croll, Juan M. Cuevas, Tobey H. Curtis, Laurent Dagorn, Jonathan J. Dale, Ryan Daly, Heidi Dewar, Philip D. Doherty, Andrés Domingo, Alistair D. M. Dove, Michael Drew, Christine L. Dudgeon, Clinton A. J. Duffy, Riley G. Elliott, Jim R. Ellis, Mark V. Erdmann, Thomas J. Farrugia, Luciana C. Ferreira, Francesco Ferretti, John D. Filmalter, Brittany Finucci, Chris Fischer, Richard Fitzpatrick, Fabien Forget, Kerstin Forsberg, Malcolm P. Francis, Bryan R. Franks, Austin J. Gallagher, Felipe Galvan-Magana, Mirta L. García, Troy F. Gaston, Bronwyn M. Gillanders, Matthew J. Gollock, Jonathan R. Green, Sofia Green, Christopher A. Griffiths, Neil Hammerschlag, Abdi Hasan, Lucy A. Hawkes, Fabio Hazin, Matthew Heard, Alex Hearn, Kevin J. Hedges, Suzanne M. Henderson, John Holdsworth, Kim N. Holland, Lucy A. Howey, Robert E. Hueter, Nicholas E. Humphries, Melanie Hutchinson, Fabrice R. A. Jaine, Salvador J. Jorgensen, Paul E. Kanive, Jessica Labaja, Fernanda O. Lana, Hugo Lassauce, Rebecca S. Lipscombe, Fiona Llewellyn, Bruno C. L. Macena, Ronald Mambrasar, Jaime D. McAllister, Sophy R. McCully Phillips, Frazer McGregor, Matthew N. McMillan, Lianne M. McNaughton, Sibele A. Mendonça, Carl G. Meyer, Megan Meyers, John A. Mohan, John C. Montgomery, Gonzalo Mucientes, Michael K. Musyl, Nicole Nasby-Lucas, Lisa J. Natanson, John B. O’Sullivan, Paulo Oliveira, Yannis P. Papastamtiou, Toby A. Patterson, Simon J. Pierce, Nuno Queiroz, Craig A. Radford, Andy J. Richardson, Anthony J. Richardson, David Righton, Christoph A. Rohner, Mark A. Royer, Ryan A. Saunders, Matthias Schaber, Robert J. Schallert, Michael C. Scholl, Andrew C. Seitz, Jayson M. Semmens, Edy Setyawan, Brendan D. Shea, Rafid A. Shidqi, George L. Shillinger, Oliver N. Shipley, Mahmood S. Shivji, Abraham B. Sianipar, Joana F. Silva, David W. Sims, Gregory B. Skomal, Lara L. Sousa, Emily J. Southall, Julia L. Y. Spaet, Kilian M. Stehfest, Guy Stevens, Joshua D. Stewart, James A. Sulikowski, Ismail Syakurachman, Simon R. Thorrold, Michele Thums, David Tickler, Mariana T. Tolloti, Kathy A. Townsend, Paulo Travassos, John P. Tyminski, Jeremy J. Vaudo, Drausio Veras, Laurent Wantiez, Sam B. Weber, R.J. David Wells, Kevin C. Weng, Bradley M. Wetherbee, Jane E. Williamson, Matthew J. Witt, Serena Wright, Kelly Zilliacus, Barbara A. Block, David J. Curnick, Andrzejaczek, Samantha [0000-0002-9929-7312], Lucas, Tim CD [0000-0003-4694-8107], Goodman, Maurice C [0000-0002-6874-2313], Hussey, Nigel E [0000-0002-9050-6077], Armstrong, Amelia J [0000-0001-8103-4314], Carlisle, Aaron [0000-0003-0796-6564], Coffey, Daniel M [0000-0001-5983-0146], Huveneers, Charlie [0000-0001-8937-1358], Jacoby, David MP [0000-0003-2729-3811], Meekan, Mark G [0000-0002-3067-9427], Mourier, Johann [0000-0001-9019-1717], Peel, Lauren R [0000-0001-6960-5663], Abrantes, Kátya [0000-0001-7430-8428], Afonso, André S [0000-0001-9129-278X], Ajemian, Matthew J [0000-0002-2725-4030], Anderson, Brooke N [0000-0003-4299-3496], Araujo, Gonzalo [0000-0002-4708-3638], Armstrong, Asia O [0000-0002-9307-0598], Barnett, Adam [0000-0001-7430-8428], Bennett, Mike B [0000-0001-8051-0040], Bezerra, Natalia A [0000-0002-4203-8408], Bonfil, Ramon [0000-0002-5753-464X], Boustany, Andre M [0000-0001-5501-7190], Bowlby, Heather D [0000-0002-2532-3725], Branco, Ilka [0000-0001-8136-2596], Braun, Camrin D [0000-0002-9317-9489], Brooks, Edward J [0000-0001-5206-7133], Burke, Patrick J [0000-0002-7217-0215], Butcher, Paul [0000-0001-7338-6037], Castleton, Michael [0000-0001-9639-6967], Chapple, Taylor K [0000-0002-0357-0223], Chateau, Olivier [0000-0003-1153-6284], Coelho, Rui [0000-0003-3813-5157], Cortes, Enric [0000-0001-6001-2482], Couturier, Lydie IE [0000-0002-3885-3397], Cuevas, Juan M [0000-0003-0086-5963], Curtis, Tobey H [0000-0003-0164-7335], Dale, Jonathan J [0000-0001-8565-3841], Daly, Ryan [0000-0002-4409-6951], Dewar, Heidi [0000-0002-8202-1387], Doherty, Philip D [0000-0001-7561-3731], Domingo, Andrés [0000-0002-1793-7663], Dove, Alistair DM [0000-0003-3239-4772], Drew, Michael [0000-0002-5109-7792], Dudgeon, Christine L [0000-0001-5059-7886], Duffy, Clinton AJ [0000-0002-3352-1609], Elliott, Riley G [0000-0003-0234-5953], Erdmann, Mark V [0000-0002-3644-8347], Farrugia, Thomas J [0000-0001-9052-8826], Ferreira, Luciana C [0000-0001-6755-2799], Ferretti, Francesco [0000-0001-9510-3552], Finucci, Brittany [0000-0003-1315-2946], Forget, Fabien [0000-0002-4845-4277], Forsberg, Kerstin [0000-0002-1233-9381], Franks, Bryan R [0000-0003-4016-9225], Gallagher, Austin J [0000-0003-1515-3440], García, Mirta L [0000-0003-0143-7397], Gaston, Troy F [0000-0003-0049-0831], Gillanders, Bronwyn M [0000-0002-7680-2240], Green, Jonathan R [0000-0001-7671-6716], Green, Sofia [0000-0002-2878-5984], Griffiths, Christopher A [0000-0001-7203-0426], Hammerschlag, Neil [0000-0001-9002-9082], Hawkes, Lucy A [0000-0002-6696-1862], Hearn, Alex [0000-0002-4986-098X], Hedges, Kevin J [0000-0002-2219-2360], Holland, Kim N [0000-0003-4663-7026], Howey, Lucy A [0000-0001-7381-4871], Humphries, Nicholas E [0000-0003-3741-1594], Hutchinson, Melanie [0000-0001-7042-0658], Jaine, Fabrice RA [0000-0002-9304-5034], Jorgensen, Salvador J [0000-0002-4331-1648], Kanive, Paul E [0000-0003-2430-6920], Labaja, Jessica [0000-0001-6916-7050], Lana, Fernanda O [0000-0001-7235-069X], Lassauce, Hugo [0000-0001-9636-6522], Lipscombe, Rebecca S [0000-0001-9602-643X], Llewellyn, Fiona [0000-0003-4309-8311], Macena, Bruno CL [0000-0001-5010-8560], McCully Phillips, Sophy R [0000-0003-3110-5916], McGregor, Frazer [0000-0002-7441-4404], McMillan, Matthew N [0000-0001-6348-184X], Mendonça, Sibele A [0000-0002-1981-5950], Mohan, John A [0000-0002-2758-163X], Mucientes, Gonzalo [0000-0001-6650-3020], Musyl, Michael K [0000-0003-4719-9259], Nasby-Lucas, Nicole [0000-0001-8355-9392], Natanson, Lisa J [0000-0002-2903-6037], O'Sullivan, John B [0000-0002-1689-2141], Oliveira, Paulo [0000-0001-7697-2111], Papastamtiou, Yannis P [0000-0002-6091-6841], Patterson, Toby A [0000-0002-7150-9205], Pierce, Simon J [0000-0002-9375-5175], Queiroz, Nuno [0000-0002-3860-7356], Radford, Craig A [0000-0001-7949-9497], Richardson, Andy J [0000-0003-2598-5080], Richardson, Anthony J [0000-0002-9289-7366], Righton, David [0000-0001-8643-3672], Rohner, Christoph A [0000-0001-8760-8972], Royer, Mark A [0000-0002-6938-7536], Schaber, Matthias [0000-0003-1032-4626], Schallert, Robert J [0000-0002-3584-2668], Scholl, Michael C [0000-0002-6014-1759], Semmens, Jayson M [0000-0003-1742-6692], Setyawan, Edy [0000-0001-6629-5997], Shea, Brendan D [0000-0001-7771-0586], Shillinger, George L [0000-0001-5168-4551], Shipley, Oliver N [0000-0001-5163-3471], Sianipar, Abraham B [0000-0003-4049-3893], Silva, Joana F [0000-0002-2897-1410], Sims, David W [0000-0002-0916-7363], Sousa, Lara L [0000-0002-4392-3572], Southall, Emily J [0000-0001-7246-278X], Spaet, Julia LY [0000-0001-8703-1472], Stevens, Guy [0000-0002-2056-9830], Sulikowski, James A [0000-0002-3646-5200], Thums, Michele [0000-0002-8669-8440], Tickler, David [0000-0001-7722-0771], Tolloti, Mariana T [0000-0001-6895-2479], Townsend, Kathy A [0000-0002-2581-2158], Travassos, Paulo [0000-0001-8667-5292], Tyminski, John P [0000-0001-8251-7385], Vaudo, Jeremy J [0000-0002-6826-3822], Veras, Drausio [0000-0001-5627-6848], Wantiez, Laurent [0000-0001-5024-2057], Weber, Sam B [0000-0003-1447-4082], Wells, RJ David [0000-0002-1306-0614], Weng, Kevin C [0000-0002-7069-7152], Wetherbee, Bradley M [0000-0002-3753-8950], Williamson, Jane E [0000-0003-3627-4508], Witt, Matthew J [0000-0002-9498-5378], Zilliacus, Kelly [0000-0001-9166-5611], Block, Barbara A [0000-0001-5181-3616], Curnick, David J [0000-0002-3093-1282], Apollo - University of Cambridge Repository, Zoological Society of London - ZSL (UNITED KINGDOM), Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), and Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)

Subjects
Multidisciplinary, [SDV]Life Sciences [q-bio], Violacea Bonaparte, 3103 Ecology, Pelagic stingray, Scalloped hammerhead shark, 41 Environmental Sciences, Western North Pacific, Reproductive-biology, Habitat Use, Carcharhinus-falciformis, Galeocerdo-cuvier, Sexual segregation, Sphyna-lewini, 31 Biological Sciences
Abstract

20 pages, 3 tables, 5 figures.-- Samantha Andrzejaczek ... et al.-- Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC), Knowledge of the three-dimensional movement patterns of elasmobranchs is vital to understand their ecological roles and exposure to anthropogenic pressures. To date, comparative studies among species at global scales have mostly focused on horizontal movements. Our study addresses the knowledge gap of vertical movements by compiling the first global synthesis of vertical habitat use by elasmobranchs from data obtained by deployment of 989 biotelemetry tags on 38 elasmobranch species. Elasmobranchs displayed high intra- and interspecific variability in vertical movement patterns. Substantial vertical overlap was observed for many epipelagic elasmobranchs, indicating an increased likelihood to display spatial overlap, biologically interact, and share similar risk to anthropogenic threats that vary on a vertical gradient. We highlight the critical next steps toward incorporating vertical movement into global management and monitoring strategies for elasmobranchs, emphasizing the need to address geographic and taxonomic biases in deployments and to concurrently consider both horizontal and vertical movements, Data analysis was funded by the Bertarelli Foundation through the Marine Science program through grants to D.J.C., B.A.B., and S.A. D.J.C. is also funded through Research England, UK. S.A. and B.A.B. thank the Moore Foundation and the Packard Foundation. F.G.-M. thanks the Instituto Politecnico Nacional for fellowships (COFAA, EDI). S.B.W. thanks funding from the Darwin Initiative (DPLUS046). A.D.M.D. acknowledges funding from the Research and Conservation Budget at Georgia Aquarium, including philanthropic gifts from several anonymous donors. K.F. acknowledges funding from the Rolex Awards for Enterprise and the Whitley Fund for Nature

Published
2022

11. Do Ophthalmology Residents Know How to Check the Calibration of a Goldmann Applanation Tonometer?

Author

Aaron Carlisle, Sofia Habib, Zhiheng Lin, Jared Ching, and Nuwan Niyadurupola

Abstract

Purpose: A observational study to determine if ophthalmology residents know how to check Goldmann Applanation Tonometer (GAT) calibration.Methods: The step-by-step technique for checking the calibration of a GAT was taken from the manufacturer’s manual and developed into a mark sheet. Ophthalmology residents in years 2-8 of training from ten hospitals were individually observed and assessed checking calibration of a GAT. Participation was voluntary. Contact between participants was minimised to prevent communication about the study. Results: 74% (n = 20) of eligible ophthalmology residents (years 2-8) from 10 hospitals (2 teaching hospitals and 8 local general hospitals) were observed checking GAT calibration. Only 45% (n=9; CI: 26-66%) of ophthalmology residents were able to correctly check GAT calibration. Failure to mount the prism in the prism holder accounted for most cases of failure to correctly check GAT calibration. Conclusions: Most ophthalmology residents were unable to correctly check GAT calibration. Although better than previously published results, this observational study shows that further training and assessment is required for ophthalmology residents to learn the technique of checking GAT calibration.

Published
2022

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