ACOUSTIC METHODS FOR MAPPING AND CHARACTERIZING SUBMERGED AQUATIC VEGETATION USING A MULTIBEAM ECHOSOUNDER

Submerged aquatic vegetation (SAV) is an important component of many temperate global coastal ecosystems. SAV monitoring programs using optical remote sensing are limited by water clarity and attenuation with depth. Here underwater acoustics is used to analyze the water volume above the bottom to detect, map and characterize SAV. In particular, this dissertation developed and applied new methods for analyzing the full time series of acoustic intensity data (e.g., water column data) collected by a multibeam echosounder. This dissertation is composed of three separate but related studies. In the first study, novel methods for detecting and measuring the canopy height of eelgrass beds are developed and used to map eelgrass in a range of different environments throughout the Great Bay Estuary, New Hampshire, and Cape Cod Bay, Massachusetts. The results of this study validated these methods by showing agreement between boundaries of eelgrass beds in acoustic and aerial datasets more in shallow water than at the deeper edges, where the acoustics were able to detect eelgrass more easily and at lower densities. In the second study, the methods developed for measuring canopy height in the first study are used to delineate between kelp-dominated and non-kelp-dominated habitat at several shallow rocky subtidal sites on the Maine and New Hampshire coast. The kelp detection abilities of these methods are first tested and confirmed at a pilot site with detailed diver quadrat macroalgae data, and then these methods are used to successfully extrapolate kelp- and non-kelp-dominated percent coverages derived from video photomosaic data. The third study examines the variability of the acoustic signature and acoustically-derived canopy height under different tidal currents. Submerged aquatic canopies are known to bend to accommodate the drag they generate in response to hydrodynamic forcing, and, in turn, the canopy height measured by acoustics will not be a perfect representation of canopy height as defined by common seagrass monitoring protocols, which is usually measured as the length of the blade of seagrass. Additionally, the bending of the canopy affects how the blades of seagrass are distributed within the footprint of the sonar, changing the acoustic signature of the seagrass canopy. For this study, a multibeam echosounder, a current profiler and an HD video camera were deployed on a stationary frame in a single eelgrass bed over 2 tidal cycles. Acoustic canopy heights varied by as much as 30 cm over the experiment, and although acoustic canopy height was correlated to current magnitude, the relationship did not follow the predictive flexible vegetation reconfiguration model of Luhar and Nepf (2011). Results indicate that there are significant differences in the shape of the return from a deflected (i.e., bent-over) canopy and an upright canopy, and that these differences in shape have implications for the accuracy of bottom detection using the maximum amplitude of a beam time series. These three studies clearly show the potential for using multibeam water column backscatter data for mapping coastal submerged aquatic vegetation while also testing the natural variability in acoustic canopy height measurements in the field

Para-infectious brain injury in COVID-19 persists at follow-up despite attenuated cytokine and autoantibody responses

To understand neurological complications of COVID-19 better both acutely and for recovery, we measured markers of brain injury, inflammatory mediators, and autoantibodies in 203 hospitalised participants; 111 with acute sera (1–11 days post-admission) and 92 convalescent sera (56 with COVID-19-associated neurological diagnoses). Here we show that compared to 60 uninfected controls, tTau, GFAP, NfL, and UCH-L1 are increased with COVID-19 infection at acute timepoints and NfL and GFAP are significantly higher in participants with neurological complications. Inflammatory mediators (IL-6, IL-12p40, HGF, M-CSF, CCL2, and IL-1RA) are associated with both altered consciousness and markers of brain injury. Autoantibodies are more common in COVID-19 than controls and some (including against MYL7, UCH-L1, and GRIN3B) are more frequent with altered consciousness. Additionally, convalescent participants with neurological complications show elevated GFAP and NfL, unrelated to attenuated systemic inflammatory mediators and to autoantibody responses. Overall, neurological complications of COVID-19 are associated with evidence of neuroglial injury in both acute and late disease and these correlate with dysregulated innate and adaptive immune responses acutely

Dimethyl fumarate in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial

Dimethyl fumarate (DMF) inhibits inflammasome-mediated inflammation and has been proposed as a treatment for patients hospitalised with COVID-19. This randomised, controlled, open-label platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]), is assessing multiple treatments in patients hospitalised for COVID-19 (NCT04381936, ISRCTN50189673). In this assessment of DMF performed at 27 UK hospitals, adults were randomly allocated (1:1) to either usual standard of care alone or usual standard of care plus DMF. The primary outcome was clinical status on day 5 measured on a seven-point ordinal scale. Secondary outcomes were time to sustained improvement in clinical status, time to discharge, day 5 peripheral blood oxygenation, day 5 C-reactive protein, and improvement in day 10 clinical status. Between 2 March 2021 and 18 November 2021, 713 patients were enroled in the DMF evaluation, of whom 356 were randomly allocated to receive usual care plus DMF, and 357 to usual care alone. 95% of patients received corticosteroids as part of routine care. There was no evidence of a beneficial effect of DMF on clinical status at day 5 (common odds ratio of unfavourable outcome 1.12; 95% CI 0.86-1.47; p = 0.40). There was no significant effect of DMF on any secondary outcome

Dimethyl fumarate in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial

Dimethyl fumarate (DMF) inhibits inflammasome-mediated inflammation and has been proposed as a treatment for patients hospitalised with COVID-19. This randomised, controlled, open-label platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]), is assessing multiple treatments in patients hospitalised for COVID-19 (NCT04381936, ISRCTN50189673). In this assessment of DMF performed at 27 UK hospitals, adults were randomly allocated (1:1) to either usual standard of care alone or usual standard of care plus DMF. The primary outcome was clinical status on day 5 measured on a seven-point ordinal scale. Secondary outcomes were time to sustained improvement in clinical status, time to discharge, day 5 peripheral blood oxygenation, day 5 C-reactive protein, and improvement in day 10 clinical status. Between 2 March 2021 and 18 November 2021, 713 patients were enroled in the DMF evaluation, of whom 356 were randomly allocated to receive usual care plus DMF, and 357 to usual care alone. 95% of patients received corticosteroids as part of routine care. There was no evidence of a beneficial effect of DMF on clinical status at day 5 (common odds ratio of unfavourable outcome 1.12; 95% CI 0.86-1.47; p = 0.40). There was no significant effect of DMF on any secondary outcome

The commentariat and discourse failure: language and atrocity in Cool Britannia

Recent terrorist events in the UK, such as the security alerts at British airports in August 2006 and the London bombings of July 2005 gained extensive media and academic analysis. This study contends, however, that much of the commentary demonstrated a wide degree of failure among government agencies, academic and analytic experts and the wider media, about the nature of the threat and continues to distort comprehension of the extant danger. The principal failure, this argument maintains, was, and continues to be, one of an asymmetry of comprehension that mistakes the still relatively limited means of violent jihadist radicals with limited political ends. The misapprehension often stems from the language that surrounds the idea of 'terrorism', which increasingly restricts debate to an intellectually redundant search for the 'root causes' that give rise to the politics of complacency. In recent times this outlook has consistently underestimated the level of the threat to the security of the UK. This article argues that a more realistic appreciation of the current security condition requires abandoning the prevailing view that the domestic threat is best prosecuted as a criminal conspiracy. It demands instead a total strategy to deal with a totalizing threat. The empirical evidence demonstrates the existence of a physical threat, not merely the political fear of threat. The implementation of a coherent set of social policies for confronting the threat at home recognizes that securing state borders and maintaining internal stability are the first tasks of government. Fundamentally, this requires a return to an understanding of the Hobbesian conditions for sovereignty, which, despite the delusions of post-Cold War cosmopolitan multiculturalism, never went away

Thousands of small, novel genes predicted in global phage genomes

Fremin BJ, Bhatt AS, Kyrpides NC, et al. Thousands of small, novel genes predicted in global phage genomes. Cell Reports. 2022;39(12): 110984

Thousands of small, novel genes predicted in global phage genomes.

Small genes (<150 nucleotides) have been systematically overlooked in phage genomes. We employ a large-scale comparative genomics approach to predict >40,000 small-gene families in ∼2.3 million phage genome contigs. We find that small genes in phage genomes are approximately 3-fold more prevalent than in host prokaryotic genomes. Our approach enriches for small genes that are translated in microbiomes, suggesting the small genes identified are coding. More than 9,000 families encode potentially secreted or transmembrane proteins, more than 5,000 families encode predicted anti-CRISPR proteins, and more than 500 families encode predicted antimicrobial proteins. By combining homology and genomic-neighborhood analyses, we reveal substantial novelty and diversity within phage biology, including small phage genes found in multiple host phyla, small genes encoding proteins that play essential roles in host infection, and small genes that share genomic neighborhoods and whose encoded proteins may share related functions