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orcAI: A machine learning tool to detect and classify acoustic signals of killer whales in audio recordings
Get PDFFunding: Eidgenössische Technische Hochschule Zurich; Icelandic Centre for Research. Grant Numbers: 120248042, 163060, 217519, 200229; Fundação para a Ciência e a Tecnologia. Grant Number: SFRH/BD/30303/2006; Earthwatch Institute; National Geographic Global Exploration Fund. Grant Number: GEFNE65-12; Russell Trust Award from the University of St Andrews; US Office of Naval Research. Grant Number: N00014-08-1-0984; US Living Marine Resources. Grant Number: 57; UK Defence Science and Technology Laboratory; French Direction Générale de l’Armement.Acoustic monitoring is an essential tool for investigating animal communication and behavior when visual contact is limited, but the scalability of bioacoustic projects is often limited by time‐intensive manual auditing of focal signals. To address this bottleneck, we introduce orcAI—a novel deep learning framework for the automated detection and classification of a broad acoustic repertoire of killer whales (Orcinus orca), including vocalizations (e.g., pulsed calls, whistles) and incidental sounds (e.g., breathing, tail slaps). orcAI combines a ResNet‐based Convolutional Neural Network (ResNet‐CNN) with Long Short‐Term Memory (LSTM) layers to capture both spatial features and temporal context, enabling the model to classify signals and to accurately determine their temporal boundaries in spectrograms. Trained on a comprehensive dataset from herring‐feeding killer whales off Iceland, the framework was designed to be adaptable to other populations upon training with equivalent data. Our final model achieves up to 98.2% accuracy on test data and is delivered as an open‐source tool with an easy‐to‐use command‐line interface. By providing a ready‐to‐use model that processes raw audio and outputs annotations, orcAI serves as a useful tool for advancing the study of killer whale vocal behavior and, more broadly, for understanding marine mammal communication and ecology.Peer reviewe
Structure of the NE Oman Mountains : a review of robust geochronological constraints for tectonic models of ophiolite obduction and continental subduction
Get PDFFunding: This research was supported by NSF (USA) Grant EAR-2120931 to J.M. Garber and A.J. Smye, NSF Grants EAR-1250522 and EAR-1650407 to M. Rioux, and funding from The Pennsylvania State University for J.M. Garber.The Late Cretaceous Semail ophiolite, Oman was emplaced onto the previously passive continental margin of Arabia. Recent geochronology from the ophiolite, its metamorphic sole, and associated high-pressure (HP) metamorphic rocks have resulted in a proliferation of new tectonic models explaining the sequence of events associated with ophiolite obduction and later continental subduction. These models have argued for (a) subduction initiation ∼8 Myr prior to Semail ophiolite formation, (b) two distinct HP metamorphic events, including HP subduction metamorphism before and after ophiolite emplacement, and (c) the presence of two separate, synchronous subduction zones operating during ophiolite formation and emplacement. We review published data and demonstrate that these new models are unsupported by robust geochronological and geological constraints; rather, the existing data are best explained by the initiation of a single NE-dipping subduction zone by ∼96.7 Ma, over which the ophiolite crystallized and along which the continental margin eventually subducted beneath it. The overlap between U-Pb zircon age dates on the Semail ophiolite crustal sequence (96.1–95.2 Ma), and U-Pb zircon (96.7–95.2 Ma) and internally consistent Lu-Hf garnet (97.9–93.0 Ma) dates from the metamorphic sole indicate synchronous Cenomanian ophiolite crystallization and sole metamorphism, consistent with ophiolite formation in a supra-subduction zone environment. By ∼79 Ma, the Oman continental margin reached the subduction zone, and Early Permian shelf carbonates and basement slices were dragged down to depths ∼90–100 km and metamorphosed to eclogite facies (≥20 kbar), which is recorded by Sm-Nd, U-Pb, and Rb-Sr ages from multiple phases (garnet, zircon, rutile, phengite).Peer reviewe
Insights into ACE2 dynamics and SARS-CoV-2 replicative mechanisms at the single-molecule level
No full textAbstract redacte
Highly transparent elastic optical microcavities for interferometric mapping of cell mechanics
Get PDFFunding: This study was financially supported by the Alexander von Humboldt Foundation (Humboldt Professorship to M.C.G.), the European Research Council (ERC) under the European Union’s Horizon Europe research and innovation program (CELL-FORCE, Grant Agreement No. 101113162), EPSRC (Doctoral Training grant EP/L505079/1 and grant EP/P030017/1), the European Research Council under the European Union’s Horizon 2020 Framework Programme (FP/2014-202) ERC grant agreement no. 640012 (ABLASE), and instrument funding by the Deutsche Forschungsgemeinschaft in cooperation with the Ministerium für Kunst und Wissenschaft of North Rhine-Westphalia (469988234, INST 216/1120-1 FUGG).Elastic resonator interference stress microscopy (ERISM) enables label-free, non-invasive measurements of cellular forces by detecting the cell-induced deformation of an optical microcavity using optical interference. Here, we present an improved microcavity design that utilizes a high-refractive-index elastomer, eliminating the need for the top metal layer required in traditional ERISM microcavities. This simplifies the fabrication process, offers improved control over mechanical properties, and enhances the resolution of ERISM measurements. The design is compatible with various bio-coatings, maintains long-term cell viability, and significantly improves optical transmission. This enables integrated and confocal fluorescence imaging with improved contrast over traditional ERISM microcavities.Peer reviewe
Abundance of the endangered Indus River dolphin Platanista minor
Get PDFFunding: International Whaling Commission, the Marine Conservation Action Fund (MCAF) of the New England Aquarium and the Small Grants Programme of WWF-Pakistan.Freshwater dolphins are among the world’s most endangered mammals, with all populations classified as Endangered or Critically Endangered on the IUCN Red List. The Indus River dolphin Platanista minor, functionally endemic to Pakistan, has one of the most restricted ranges of any cetacean and, due to fragmentation by irrigation dams, exists as 6 subpopulations. We estimated the abundance of the 3 largest subpopulations in 2011 and 2017 using Huggins conditional likelihood mark-recapture models applied to visual sightings from tandem survey vessels. Favourable survey conditions and the narrow river channel resulted in high detection rates: of 559 dolphin groups recorded across both years, 72.3% of groups and 83.3% of individuals were matched between vessels. The total species abundance was estimated at 1665 individuals in 2011 (CV = 17%, 95% CI = 1499-3017) and had increased to 1987 by 2017 (CV = 13%, 95% CI = 1886-3552)—a 19.4% rise over 6 yr. In 2017, subpopulation estimates were 188 (CV = 8%) between Chashma and Taunsa barrages, 660 (CV = 6%) between Taunsa and Guddu and 1139 (CV = 9%) between Guddu and Sukkur. Although abundance monitoring is resource intensive, even at 5 yr intervals, it is essential for assessing species status. The long-term dataset gained from continued multi-decade monitoring provides invaluable insight, with its value increasing over time. Given their continued isolation and vulnerability, sustained monitoring and conservation interventions remain critical to ensure the species’ long-term survival.Peer reviewe
Icons and paintings : differences in psychological distance, empathy, and the feeling of personal communication
Get PDFFunding: This work was supported by the Templeton Religion Trust (TRT-2021-10512).Background : There exists a long history of claimed qualitative differences between experiences of Western and Eastern religious art. Our study sought to examine empirically and quantitatively whether those reports are veridical and, if so, to what extent. We explored psychological distance, empathy, and the feeling of personal communication that humans experience when viewing Western paintings and Eastern icons. Method : We recruited three groups of self-identifying participants: Western Christians, Eastern Orthodox Christians, and non-believers. Participants viewed 15 digital images of artworks depicting events of the Gospels. Using self-report measures, we assessed temporal and spatial distance between participants and the depicted Gospel events, the feeling of personal communication, and cognitive and emotional empathy towards the depicted figures. Results : Across all participants, temporal and spatial distance were greater for Eastern icons compared to Western paintings. Cognitive and emotional empathy were higher for paintings compared to icons. No differences in the feeling of personal communication were found between icons and paintings. Among non-believers, temporal and spatial distance related to both icons and paintings were greater compared to Western and Eastern Christians. On the other hand, the feeling of personal communication was greater among Western and Eastern Christians, as well as emotional and cognitive empathy, compared to non-believers. Conclusions : Aesthetic properties of icons and paintings, as well as individual differences in religious backgrounds, influence the way viewers experience psychological distance, empathy, and the feeling of personal communication when observing religious art.Peer reviewe
Beyond the ‘jihadi bride’ : exploring British media and government complicity in racial and gendered constructions of ‘terrorism’
No full textThis thesis argues the British media and government’s racialised and gendered narratives about Shamima Begum demonstrate their complicity as institutions of the colonial state, and their role in upholding its continued coloniality and dominance. I argue that Shamima’s case not only demonstrates how these narratives are gendered and racialised, but that it is through that racialisation and gendering that the colonial state is reaffirmed by providing discourses and knowledge that justify state actions. The thesis is split into two core parts. The first part is the theoretical foundations of the thesis, wherein I firmly ground it in postcolonial, decolonial, and feminist theorisations, building on the work of Said, Fanon, Hall, Mahmood, Spivak, and Lugones. I bring together decolonial and postcolonial scholarship on coloniality, race, and gender to highlight how they are organising principles of our politics. I then demonstrate how the media is a political institution that is complicit in the functioning of the colonial state, particularly with regards to ‘terrorism.’ I complement this with the second part of the thesis: three chapters of empirical critical discourse analysis, based on primary data I collected including over 650 media headlines and 9 semi-structured interviews with relevant stakeholders. The empirical chapters bring together my analysis of this wealth of material to provide evidence for 1) how the constructions of Shamima are racist and gendered; 2) the role of these constructions in justifying state actions and further marginalisation of British Muslims; and 3) the complicit nature of the relationship between the media and the government in the UK. Together, these two parts of the thesis demonstrate how the British media and government’s complicity as institutions of the colonial state, and their role in upholding its continued coloniality and dominance, is evidenced through the racialised and gendered narratives around Shamima Begum."Thank you as well to the International Studies Association for the Dissertation Completion Fellowship that supported the completion of this thesis in my final year."--Fundin
Microrheology of the cumulus-oocyte matrix using optical tweezers
Get PDFFunding: K R D is supported by a Future Making Fellowship from the University of Adelaide. K D is supported by funding from the UK Engineering and Physical Sciences Research Council (EP/P030017/1) and the Australian Research Council (FL210100099 and DP220102303). The authors thank the Optofab node of the Australian National Fabrication Facility (ANFF) which is funded by both the Commonwealth and the South Australian State Government.Optical tweezers have emerged as a powerful, versatile approach for a range of studies in cellular and molecular biology. A particular highlight has been its use for microrheology measurements in miniscule sample volumes. In this study, we demonstrate the application of optical tweezers to investigate the viscosity of the extracellular matrix surrounding mammalian oocytes and determine whether this is associated with oocyte developmental potential. By analysing the motion of a trapped particle, we can quantify the mechanical properties of this matrix, thus overcoming limitations of traditional passive microrheology techniques that rely on free diffusion. We utilise two maturation methods—in vivo and in vitro—to generate oocytes with differing developmental potential. Our findings indicate that oocytes matured in vivo exhibit higher viability post-fertilisation compared to their in vitro counterparts and we establish a positive correlation between extracellular matrix viscosity and oocyte developmental potential. This work demonstrates that optical tweezers are a novel, non-invasive tool for assessing oocyte quality, contributing to valuable insights to the field of reproductive biology.Peer reviewe
[3+2] Cycloaddition to a chiral 5-methylene-1,3-dioxolan-4-one and pyrolysis of the spiro adducts
Get PDFFunding: The authors thank the School of Chemistry for a studentship to L.A.P.The [3+2] cycloaddition chemistry of (2S)-5-methylene-2-t-butyl-1,3-dioxolan-4-one, derived from lactic acid, has been examined and spiro adducts have been obtained with benzonitrile oxide, acetonitrile oxide, diazomethane and diphenyldiazomethane. The structure and absolute stereochemistry of the benzonitrile oxide adduct has been confirmed by X-ray diffraction and all the adducts have been fully characterised by 1H and 13C NMR. Attempted cycloaddition with a nitrile sulfide, a nitrile imine and azides failed. Pyrolysis results in a range of novel gas-phase reactions, with the nitrile oxide adducts giving pivalaldehyde, CO2, the nitrile and ketene, the diazomethane adduct losing only N2 to give a cyclopropane-fused dioxolanone, and the diphenylcyclopropane derived from diphenyldiazomethane giving mainly benzophenone in a sequence involving loss of pivalaldehyde and methyleneketene.Peer reviewe
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