ORCA-SPY enables killer whale sound source simulation, detection, classification and localization using an integrated deep learning-based segmentation

Acoustic identification of vocalizing individuals opens up new and deeper insights into animal communications, such as individual-/group-specific dialects, turn-taking events, and dialogs. However, establishing an association between an individual animal and its emitted signal is usually non-trivial, especially for animals underwater. Consequently, a collection of marine species-, array-, and position-specific ground truth localization data is extremely challenging, which strongly limits possibilities to evaluate localization methods beforehand or at all. This study presents ORCA-SPY, a fully-automated sound source simulation, classification and localization framework for passive killer whale (Orcinus orca) acoustic monitoring that is embedded into PAMGuard, a widely used bioacoustic software toolkit. ORCA-SPY enables array- and position-specific multichannel audio stream generation to simulate real-world ground truth killer whale localization data and provides a hybrid sound source identification approach integrating ANIMAL-SPOT, a state-of-the-art deep learning-based orca detection network, followed by downstream Time-Difference-Of-Arrival localization. ORCA-SPY was evaluated on simulated multichannel underwater audio streams including various killer whale vocalization events within a large-scale experimental setup benefiting from previous real-world fieldwork experience. Across all 58,320 embedded vocalizing killer whale events, subject to various hydrophone array geometries, call types, distances, and noise conditions responsible for a signal-to-noise ratio varying from −14.2 dB to 3 dB, a detection rate of 94.0 % was achieved with an average localization error of 7.01∘. ORCA-SPY was field-tested on Lake Stechlin in Brandenburg Germany under laboratory conditions with a focus on localization. During the field test, 3889 localization events were observed with an average error of 29.19∘ and a median error of 17.54∘. ORCA-SPY was deployed successfully during the DeepAL fieldwork 2022 expedition (DLFW22) in Northern British Columbia, with a mean average error of 20.01∘ and a median error of 11.01∘ across 503 localization events. ORCA-SPY is an open-source and publicly available software framework, which can be adapted to various recording conditions as well as animal species

Preliminary design of the HEBT of IFMIF DONES

IFMIF-DONES (International Fusion Materials Irradiation Facility–DEMO Oriented Neutron Source) is currentlybeing developed in the frame of the EUROfusion Early Neutron Source work package (WPENS) and will be aninstallation for fusion material testing, that will generate aflux of neutrons of 1018m−2s−1with a broad peak at14 MeV by Li(d,xn) nuclear reactions thanks to a 40 MeV deuteron beam colliding on a liquid Liflow.The accelerator system is in charge of providing such high energy deuterons in order to produce the expectedneutronflux. The High Energy Beam Transport line (HEBT) is the last subsystem of the accelerator and its mainfunctions are to guide the deuteron beam towards the Lithium target and to shape it by the use of magneticelements to the reference beam footprint at the Lithium Target.The present work summarizes the current status of the HEBT design, including beam dynamics, vacuum,radioprotection, diagnostics and remote handling studies performed, along with the layout and integration of theline.This work has been carried out within the framework of the EUROfusion Consortium and has received funding from the Euratom research and training programme 2014–2018 and 2019–2020 under grant agreement No 633053. The work done by IREC has been supported by the CERCA Programme from Generalitat de Catalunya (Government of Catalonia).Peer reviewe

Commissioning Plan of the IFMIF-DONES Accelerator

IFMIF-DONES (International Fusion Materials Irradiation Facility- DEMO-Oriented Neutron Early Source) - a powerful neutron irradiation facility for studies and certification of materials to be used in fusion reactors - is planned as part of the European roadmap to fusion electricity. Its main goal will be to characterize and to qualify materials under irradiation in a neutron field similar to the one faced in a fusion reactor. The intense neutron source is produced by impinging deuterons, from high-power linear deuteron accelerator, on a liquid lithium curtain. The facility has accomplished the preliminary design phase and is currently in its detailed design phase. At the present stage, it is important to have a clear understanding of how the commissioning of the facility will be performed, especially the commissioning of a 5 MW CW deuteron beam, together with the lithium curtain and the beam optimization for the neutron irradiation. In this contribution, the present plans for the hardware and beam commissioning of the accelerator will be given, focusing on the most critical aspects of the tiered approach and on the integration of the procedure with the lithium and tests systems

Impact of infection on proteome-wide glycosylation revealed by distinct signatures for bacterial and viral pathogens

Mechanisms of infection and pathogenesis have predominantly been studied based on differential gene or protein expression. Less is known about posttranslational modifications, which are essential for protein functional diversity. We applied an innovative glycoproteomics method to study the systemic proteome-wide glycosylation in response to infection. The protein site-specific glycosylation was characterized in plasma derived from well-defined controls and patients. We found 3862 unique features, of which we identified 463 distinct intact glycopeptides, that could be mapped to more than 30 different proteins. Statistical analyses were used to derive a glycopeptide signature that enabled significant differentiation between patients with a bacterial or viral infection. Furthermore, supported by a machine learning algorithm, we demonstrated the ability to identify the causative pathogens based on the distinctive host blood plasma glycopeptide signatures. These results illustrate that glycoproteomics holds enormous potential as an innovative approach to improve the interpretation of relevant biological changes in response to infection

Relationship between molecular pathogen detection and clinical disease in febrile children across Europe: a multicentre, prospective observational study

BackgroundThe PERFORM study aimed to understand causes of febrile childhood illness by comparing molecular pathogen detection with current clinical practice.MethodsFebrile children and controls were recruited on presentation to hospital in 9 European countries 2016-2020. Each child was assigned a standardized diagnostic category based on retrospective review of local clinical and microbiological data. Subsequently, centralised molecular tests (CMTs) for 19 respiratory and 27 blood pathogens were performed.FindingsOf 4611 febrile children, 643 (14%) were classified as definite bacterial infection (DB), 491 (11%) as definite viral infection (DV), and 3477 (75%) had uncertain aetiology. 1061 controls without infection were recruited. CMTs detected blood bacteria more frequently in DB than DV cases for N. meningitidis (OR: 3.37, 95% CI: 1.92-5.99), S. pneumoniae (OR: 3.89, 95% CI: 2.07-7.59), Group A streptococcus (OR 2.73, 95% CI 1.13-6.09) and E. coli (OR 2.7, 95% CI 1.02-6.71). Respiratory viruses were more common in febrile children than controls, but only influenza A (OR 0.24, 95% CI 0.11-0.46), influenza B (OR 0.12, 95% CI 0.02-0.37) and RSV (OR 0.16, 95% CI: 0.06-0.36) were less common in DB than DV cases. Of 16 blood viruses, enterovirus (OR 0.43, 95% CI 0.23-0.72) and EBV (OR 0.71, 95% CI 0.56-0.90) were detected less often in DB than DV cases. Combined local diagnostics and CMTs respectively detected blood viruses and respiratory viruses in 360 (56%) and 161 (25%) of DB cases, and virus detection ruled-out bacterial infection poorly, with predictive values of 0.64 and 0.68 respectively.InterpretationMost febrile children cannot be conclusively defined as having bacterial or viral infection when molecular tests supplement conventional approaches. Viruses are detected in most patients with bacterial infections, and the clinical value of individual pathogen detection in determining treatment is low. New approaches are needed to help determine which febrile children require antibiotics.FundingEU Horizon 2020 grant 668303

Genomic investigations of unexplained acute hepatitis in children

Since its first identification in Scotland, over 1,000 cases of unexplained paediatric hepatitis in children have been reported worldwide, including 278 cases in the UK1. Here we report an investigation of 38 cases, 66 age-matched immunocompetent controls and 21 immunocompromised comparator participants, using a combination of genomic, transcriptomic, proteomic and immunohistochemical methods. We detected high levels of adeno-associated virus 2 (AAV2) DNA in the liver, blood, plasma or stool from 27 of 28 cases. We found low levels of adenovirus (HAdV) and human herpesvirus 6B (HHV-6B) in 23 of 31 and 16 of 23, respectively, of the cases tested. By contrast, AAV2 was infrequently detected and at low titre in the blood or the liver from control children with HAdV, even when profoundly immunosuppressed. AAV2, HAdV and HHV-6 phylogeny excluded the emergence of novel strains in cases. Histological analyses of explanted livers showed enrichment for T cells and B lineage cells. Proteomic comparison of liver tissue from cases and healthy controls identified increased expression of HLA class 2, immunoglobulin variable regions and complement proteins. HAdV and AAV2 proteins were not detected in the livers. Instead, we identified AAV2 DNA complexes reflecting both HAdV-mediated and HHV-6B-mediated replication. We hypothesize that high levels of abnormal AAV2 replication products aided by HAdV and, in severe cases, HHV-6B may have triggered immune-mediated hepatic disease in genetically and immunologically predisposed children