Classification of Southern Ocean krill and icefish echoes using random forests

Acknowledgements The authors thank the crews, fishers, and scientists who conducted the various surveys from which data were obtained. This work was supported by the Government of South Georgia and South Sandwich Islands. Additional logistical support provided by The South Atlantic Environmental Research Institute, with thanks to Paul Brickle. PF receives funding from the MASTS pooling initiative (TheMarine Alliance for Science and Technology for Scotland), and their support is gratefully acknowledged. MASTS is funded by the Scottish Funding Council (grant reference HR09011) and contributing institutions. SF is funded by the Natural Environment Research Council, and data were provided from the British Antarctic Survey Ecosystems Long-term Monitoring and Surveys programme as part of the BAS Polar Science for Planet Earth Programme. The authors also thank the anonymous referees for their helpful suggestions on an earlier version of this manuscript.Peer reviewedPostprin

Assessing consistency of fish survey data : uncertainties in the estimation of mackerel icefish (Champsocephalus gunnari) abundance at South Georgia

Acknowledgments The authors wish to thank the crews, fishermen and scientists who conducted the various surveys from which data were obtained, and Mark Belchier and Simeon Hill for their contributions. This work was supported by the Government of South Georgia and South Sandwich Islands. Additional logistical support provided by The South Atlantic Environmental Research Institute with thanks to Paul Brickle. Thanks to Stephen Smith of Fisheries and Oceans Canada (DFO) for help in constructing bootstrap confidence limits. Paul Fernandes receives funding from the MASTS pooling initiative (The Marine Alliance for Science and Technology for Scotland), and their support is gratefully acknowledged. MASTS is funded by the Scottish Funding Council (grant reference HR09011) and contributing institutions. We also wish to thank two anonymous referees for their helpful suggestions on earlier versions of this manuscript.Peer reviewedPostprin

FIS workshop on Global synthesis of climate impacts on fish distribution and growth and implications for Scottish fisheries : FIS028

All workshop attendees and remote participants (identified in Table 1) are thanked for their contributions to presentations, discussion and this report. A. Audzijonyte, R. Allman, B. Bogstad, C. Champion, T. Essington, M. Haltuch, A. Haynie, T. Helser, E. Hjörleifsson, J. Morrongiello, M. Peck, G. Pecl, J. Pinnegar, M. Pinsky, C. Stawitz, B. Townhill, J. Thorson, and P.D. van Denderen contributed text to this report. George R. West is thanked for his participation in the public event. Jens Rasmussen assisted in the development of recommendations for future research. The assistance of Mindfully Wired Communications (Harriet Yates and Ginny Russell) is gratefully acknowledged.Publisher PD

Can the Common Fisheries Policy achieve Good Environmental Status in exploited ecosystems : the west of Scotland demersal fisheries example

Alan R. Baudron, Niall G. Fallon and Paul G. Fernandes were funded by the Horizon 2020 European research project MareFrame (grant No. 613571). Natalia Serpetti and Johanna J. Heymans were funded by the Natural Environment Research Council and Department for Environment, Food and Rural Affairs under the Marine Ecosystems Research Programme (MERP) (grant No. NE/L003279/1). We thank two anonymous reviewers for their insightful comments.Peer reviewedPostprintPostprintPostprintPostprin

Participatory planning and decision support for ecosystem based fisheries management of the west coast of Scotland

Mixed fisheries and the marine ecosystems that sustain them are complex entities and involve multiple and potentially conflicting management objectives and stakeholder interests. The presence of multiple trade-offs complicates the identification of strategies that satisfy various policy requirements while being acceptable to affected stakeholder groups. This creates a demand for tools and processes that support learning, cooperation and planning. We report on the application of decision support methodology used in combination with a co-creation approach to scenario based planning for the demersal fisheries of the West coast of Scotland. These fisheries face significant challenges, such as the depletion of key stocks and increased predation by seals. In collaboration with stakeholders we identified generic management alternatives and indicators to evaluate their performance in a structured evaluation using Multi Criteria Analysis. We identify the potential and limitations of this approach and suggest how it can contribute to Ecosystem Based Fisheries Management (EBFM). This approach does not provide tactical management advice, but stimulates learning and creates an opportunity for stakeholders to search for strategic and policy relevant solutions in an EBFM context.Peer reviewe

Characterisation of the pro-inflammatory cytokine signature in severe COVID-19

Clinical outcomes from infection with SARS-CoV-2, the cause of the COVID-19 pandemic, are remarkably variable ranging from asymptomatic infection to severe pneumonia and death. One of the key drivers of this variability is differing trajectories in the immune response to SARS-CoV-2 infection. Many studies have noted markedly elevated cytokine levels in severe COVID-19, although results vary by cohort, cytokine studied and sensitivity of assay used. We assessed the immune response in acute COVID-19 by measuring 20 inflammatory markers in 118 unvaccinated patients with acute COVID-19 (median age: 70, IQR: 58-79 years; 48.3% female) recruited during the first year of the pandemic and 44 SARS-CoV-2 naïve healthy controls. Acute COVID-19 was associated with marked elevations in nearly all pro-inflammatory markers, whilst eleven markers (namely IL-1β, IL-2, IL-6, IL-10, IL-18, IL-23, IL-33, TNF-α, IP-10, G-CSF and YKL-40) were associated with disease severity. We observed significant correlations between nearly all markers elevated in those infected with SARS-CoV-2 consistent with widespread immune dysregulation. Principal component analysis highlighted a pro-inflammatory cytokine signature (with strongest contributions from IL-1β, IL-2, IL-6, IL-10, IL-33, G-CSF, TNF-α and IP-10) which was independently associated with severe COVID-19 (aOR: 1.40, 1.11-1.76, p=0.005), invasive mechanical ventilation (aOR: 1.61, 1.19-2.20, p=0.001) and mortality (aOR 1.57, 1.06-2.32, p = 0.02). Our findings demonstrate elevated cytokines and widespread immune dysregulation in severe COVID-19, adding further evidence for the role of a pro-inflammatory cytokine signature in severe and critical COVID-19

A novel role for von Willebrand factor in the pathogenesis of experimental cerebral malaria

Plasmodium falciparum malaria infection is associated with an early marked increase in plasma VWF levels, together with a pathological accumulation of hyper-reactive ultra-large VWF (UL-VWF) multimers. Given the established critical role of platelets in malaria pathogenesis, these increases in plasma VWF raise the intriguing possibility that VWF may play a direct role in modulating malaria pathogenesis. To address this hypothesis, we utilized an established murine model of experimental cerebral malaria (ECM), in which wild type (WT) C57BL/6J mice were infected with Plasmodium berghei ANKA. In keeping with findings in children with P. falciparum malaria, acute endothelial cell activation was an early and consistent feature in the murine model of CM, resulting in significantly increased plasma VWF levels. Despite the fact that murine plasma ADAMTS13 levels were not significantly reduced, pathological UL-VWF multimers were also observed in murine plasma following P. berghei infection. To determine whether VWF plays a role in modulating the pathogenesis of CM in vivo, we further investigated P. berghei infection in VWF(-/-) C57BL/6J mice. Clinical ECM progression was delayed and overall survival was significantly prolonged in VWF(-/-) mice compared to wild type controls. Despite this protection against ECM, no significant differences in platelet counts, or blood parasitaemia levels, were observed between VWF(-/-) and WT mice. Interestingly however, the degree of ECM-associated enhanced blood brain barrier permeability was significantly attenuated in VWF(-/-) mice compared to WT controls. Given the significant morbidity and mortality associated with CM, these novel data may have direct translational significance

Dimethyl fumarate and 4-octyl itaconate are anticoagulants that suppress Tissue Factor in macrophages via inhibition of Type I Interferon

Abstract Excessive inflammation-associated coagulation is a feature of infectious diseases, occurring in such conditions as bacterial sepsis and COVID-19. It can lead to disseminated intravascular coagulation, one of the leading causes of mortality worldwide. Recently, type I interferon (IFN) signaling has been shown to be required for tissue factor (TF; gene name F3) release from macrophages, a critical initiator of coagulation, providing an important mechanistic link between innate immunity and coagulation. The mechanism of release involves type I IFN-induced caspase-11 which promotes macrophage pyroptosis. Here we find that F3 is a type I IFN-stimulated gene. Furthermore, F3 induction by lipopolysaccharide (LPS) is inhibited by the anti-inflammatory agents dimethyl fumarate (DMF) and 4-octyl itaconate (4-OI). Mechanistically, inhibition of F3 by DMF and 4-OI involves suppression of Ifnb1 expression. Additionally, they block type I IFN- and caspase-11-mediated macrophage pyroptosis, and subsequent TF release. Thereby, DMF and 4-OI inhibit TF-dependent thrombin generation. In vivo, DMF and 4-OI suppress TF-dependent thrombin generation, pulmonary thromboinflammation, and lethality induced by LPS, E. coli, and S. aureus, with 4-OI additionally attenuating inflammation-associated coagulation in a model of SARS-CoV-2 infection. Our results identify the clinically approved drug DMF and the pre-clinical tool compound 4-OI as anticoagulants that inhibit TF-mediated coagulopathy via inhibition of the macrophage type I IFN-TF axis