Analysis of Flow Competence in an Alluvial Gravel Bed Stream, Dupuyer Creek, Montana

Critical shear stress and unit discharge flow competence models were tested against coarse bed load data from Dupuyer Creek, Montana, United States. Maximum particle sizes sampled (Dmax) and D-50 to D-90 percentiles in the bed load grain size distribution were well correlated with both shear stress and unit discharge. Bed load grain sizes became coarser with increasing flow strength. For the D-max curve, Shields dimensionless parameter for the surface D-50 was estimated at 0.044, and the exponent for relative particle size (D-i/ D-50) was - 0.59. In the unit discharge criterion the critical flow to entrain the surface D50 was poorly predicted. Flow competence relationships based on D-max are prone to the influence of outliers and sample mass variability. The mean of the three largest particles, D-max ( 3), is more sensitive to changes in flow strength than the D-50 to D-90 bed load grain sizes, and may represent a good compromise

Complex Dynamics of Coral Gene Expression Responses to Low pH Across Species

Coral capacity to tolerate low pH affects coral community composition and, ultimately, reef ecosystem function. Low pH submarine discharges (‘Ojo’; Yucatán, México) represent a natural laboratory to study plasticity and acclimatization to low pH in relation to ocean acidification. A previous \u3e2‐year coral transplant experiment to ambient and low pH common garden sites revealed differential survivorship across species and sites, providing a framework to compare mechanistic responses to differential pH exposures. Here, we examined gene expression responses of transplants of three species of reef‐building corals (Porites astreoides, Porites porites and Siderastrea siderea) and their algal endosymbiont communities (Symbiodiniaceae) originating from low pH (Ojo) and ambient pH native origins (Lagoon or Reef). Transplant pH environment had the greatest effect on gene expression of Porites astreoides hosts and symbionts and P. porites hosts. Host P. astreoides Ojo natives transplanted to ambient pH showed a similar gene expression profile to Lagoon natives remaining in ambient pH, providing evidence of plasticity in response to ambient pH conditions. Although origin had a larger effect on host S. siderea gene expression due to differences in symbiont genera within Reef and Lagoon/Ojo natives, subtle effects of low pH on all origins demonstrated acclimatization potential. All corals responded to low pH by differentially expressing genes related to pH regulation, ion transport, calcification, cell adhesion and stress/immune response. This study demonstrates that the magnitude of coral gene expression responses to pH varies considerably among populations, species and holobionts, which could differentially affect acclimatization to and impacts of ocean acidification

Community dynamics of Pleistocene coral reefs during alternative climatic regimes

Reef ecosystems built during successive periods of Pleistocene sea level rise have shown remarkable persistence in coral community structure, but little is known of the ecological characteristics of reef communities during periods of low sea stands or sea level falls. We sampled the relative species abundance of coral, benthic foraminifera, and calcareous red algae communities from eight submerged coral reefs in the Huon Gulf, Papua New Guinea, which formed during successive sea level fall and lowstand periods over the past 416 kyr. We found that dissimilarity in coral species composition increased significantly with increasing time between reef-building events. However, neither coral diversity nor the taxonomic composition of benthic foraminifera and calcareous red algae assemblages varied significantly over time. The taxonomic composition of coral communities from lowstand reefs was significantly different from that of highstand reefs previously reported from the nearby Huon Peninsula. We interpret the community composition and temporal dynamics of lowstand reefs as a result of shifting energy regimes in the Huon Gulf, and differences between low and highstand reefs as a result of differences in the interaction between biotic and environmental factors between the Huon Gulf and Huon Peninsula. Regardless of the exact processes driving these trends, our study represents the first glimpse into the ecological dynamics of coral reefs during low sea level stands when climatic conditions for reef growth were much different and less optimal than during previously studied highstand periods. Copyright ESA. All rights reserved

Calcifying algae maintain settlement cues to larval abalone following algal exposure to extreme ocean acidification

Ocean acidification (OA) increasingly threatens marine systems, and is especially harmful to calcifying organisms. One important question is whether OA will alter species interactions. Crustose coralline algae (CCA) provide space and chemical cues for larval settlement. CCA have shown strongly negative responses to OA in previous studies, including disruption of settlement cues to corals. In California, CCA provide cues for seven species of harvested, threatened, and endangered abalone. We exposed four common CCA genera and a crustose calcifying red algae, Peyssonnelia (collectively CCRA) from California to three pCO levels ranging from 419-2,013 µatm for four months. We then evaluated abalone (Haliotis rufescens) settlement under ambient conditions among the CCRA and non-algal controls that had been previously exposed to the pCO treatments. Abalone settlement and metamorphosis increased from 11% in the absence of CCRA to 45-69% when CCRA were present, with minor variation among CCRA genera. Though all CCRA genera reduced growth during exposure to increased pCO , abalone settlement was unaffected by prior CCRA exposure to increased pCO . Thus, we find no impacts of OA exposure history on CCRA provision of settlement cues. Additionally, there appears to be functional redundancy in genera of CCRA providing cues to abalone, which may further buffer OA effects

Late glacial to deglacial variation of coralgal assemblages in the Great Barrier Reef, Australia

Integrated Ocean Drilling Program (IODP) Expedition 325 cored submerged reefs along the shelf edge of the Great Barrier Reef (GBR) to study sea-level and environmental changes and their impacts on reef communities and reef growth since the Last Glacial Maximum (LGM). Previous work defined five reef sequences (Reef 1–5) that span the last 30,000 years. Here we examined the variation in coralgal assemblages and their paleoenvironmental settings in late glacial to deglacial sequences from 23 holes cored seaward of the modern GBR in water depths from 46 to 131 m along four transects at three localities: Hydrographers Passage (HYD-01C and HYD-02A), Noggin Pass (NOG–01B), and Ribbon Reef (RIB-02A). We identified three coralline algal assemblages and eight coral assemblages indicating a broad range of reef settings from the shallow reef crest (0–5 m) to the deep forereef slope (>20 m). We document in detail for the first time the distribution and composition of reef communities that grew in the GBR during the LGM from 22,000–19,000 years ago. They included coral taxa that are major reef builders today: Isopora, Acropora gr. humilis, Dipsastraea gr. pallida, Porites, and Montipora. Prior to the fall in sea level to the maximum extent of the LGM, late glacial reef communities developed more proximally (landward) to the modern GBR along the shelf edge. Their distribution and composition reflect influences of the older Pleistocene basement depth and possible terrigenous sediment inputs. Post-LGM deglacial reef growth was vigorous in proximal sites and characterized by the accretion of a very shallow high-energy coralgal assemblage composed of medium to robustly branching Acropora, including A. gr. humilis, and thick algal crusts of Porolithon gr. onkodes associated with vermetid gastropods. More distally, reef growth was variably impacted by terrigenous input following deglacial reflooding of antecedent reef terraces. The coralgal succession and sedimentary facies in Noggin Pass indicate that an early drowning trend was linked to increased turbidity that was likely controlled by shelf morphology (narrow shelf, steep slope) and/or proximity to a paleo-river mouth. The deglacial succession in Ribbon Reef lacks typical shallow-water indicators, which may reflect influences of the particularly steep slope of the northern GBR shelf edge on reef zonation. A major sea-level jump at the onset of the Younger Dryas displaced reef habitats further upslope, forming a barrier reef system mainly composed of robustly branching acroporids distinct from the more distal sites. Our results highlight the importance of sedimentation and shelf morphology in addition to relative sea-level changes in controlling variations in reef community over centennial to millennial timescales. © 2019 Elsevier B.V.Australian Research Council-DP109400

Robust Single-view Cone-beam X-ray Pose Estimation with Neural Tuned Tomography (NeTT) and Masked Neural Radiance Fields (mNeRF)

Many tasks performed in image-guided, mini-invasive, medical procedures can be cast as pose estimation problems, where an X-ray projection is utilized to reach a target in 3D space. Expanding on recent advances in the differentiable rendering of optically reflective materials, we introduce new methods for pose estimation of radiolucent objects using X-ray projections, and we demonstrate the critical role of optimal view synthesis in performing this task. We first develop an algorithm (DiffDRR) that efficiently computes Digitally Reconstructed Radiographs (DRRs) and leverages automatic differentiation within TensorFlow. Pose estimation is performed by iterative gradient descent using a loss function that quantifies the similarity of the DRR synthesized from a randomly initialized pose and the true fluoroscopic image at the target pose. We propose two novel methods for high-fidelity view synthesis, Neural Tuned Tomography (NeTT) and masked Neural Radiance Fields (mNeRF). Both methods rely on classic Cone-Beam Computerized Tomography (CBCT); NeTT directly optimizes the CBCT densities, while the non-zero values of mNeRF are constrained by a 3D mask of the anatomic region segmented from CBCT. We demonstrate that both NeTT and mNeRF distinctly improve pose estimation within our framework. By defining a successful pose estimate to be a 3D angle error of less than 3 deg, we find that NeTT and mNeRF can achieve similar results, both with overall success rates more than 93%. However, the computational cost of NeTT is significantly lower than mNeRF in both training and pose estimation. Furthermore, we show that a NeTT trained for a single subject can generalize to synthesize high-fidelity DRRs and ensure robust pose estimations for all other subjects. Therefore, we suggest that NeTT is an attractive option for robust pose estimation using fluoroscopic projections

Natural and anthropogenic changes to mangrove distributions in the Pioneer River Estuary (QLD, Australia)

We analyzed a time series of aerial photographs and Landsat satellite imagery of the Pioneer River Estuary (near Mackay, Queensland, Australia) to document both natural and anthropogenic changes in the area of mangroves available to filter river runoff between 1948 and 2002. Over 54 years, there was a net loss of 137 ha (22%) of tidal mangroves during four successive periods that were characterized by different driving mechanisms: (1) little net change (1948– 1962); (2) net gain from rapid mangrove expansion (1962–1972); (3) net loss from clearing and tidal isolation (1972–1991); and (4) net loss from a severe species-specific dieback affecting over 50% of remaining mangrove cover (1991–2002). Manual digitization of aerial photographs was accurate for mapping changes in the boundaries of mangrove distributions, but this technique underestimated the total loss due to dieback. Regions of mangrove dieback were identified and mapped more accurately and efficiently after applying the Normalized Difference Vegetation Index (NDVI) to Landsat Thematic Mapper satellite imagery, and then monitoring changes to the index over time. These remote sensing techniques to map and monitor mangrove changes are important for identifying habitat degradation, both spatially and temporally, in order to prioritize restoration for management of estuarine and adjacent marine ecosystems

Quantifying the effectiveness of agri-environment schemes for a grassland butterfly using individual-based models

The intensification of agricultural practices throughout the twentieth century has had large detrimental effects on biodiversity and these are likely to increase as the human population rises, with consequent pressure on land. To offset these negative impacts, agri-environment schemes have been widely implemented, offering financial incentives for land-owners to create or maintain favourable habitats that enhance or maintain biodiversity. While some evidence is available on the resulting species richness and abundance for groups such as natural predators, pollinating insects including butterflies and moths, this is costly to obtain and it is difficult to predict the effects of specific habitat designs. To alleviate this problem we here develop an individual-based model (IBM), modelling the detailed movement behaviour, foraging, and energy budget of a grassland butterfly Maniola jurtina Linn. in patches of varying dimensions and quality. The IBM is successfully validated against data on M. jurtina densities, movement behaviour, resource use, fecundity and lifespan in habitats of varying quality. We use the IBM to quantify the benefits for life-history outcomes of M. jurtina of increasing the quantity and the quality of field margins within agricultural landscapes. We find that increasing the quantity of field margin habitat from 1 to 3 ha per 100 ha, as recommended in agri-environment schemes, increases the average number of eggs laid across a two-week period by 60% and adds an extra day to the average lifespan. Similar effects are reported for variation in the quality of field margins. We discuss the implications of the result for modelling butterfly responses to management scenarios

Conservation of pollinators in traditional agricultural landscapes – New challenges in Transylvania (Romania) posed by EU accession and recommendations for future research

Farmland biodiversity is strongly declining in most of Western Europe, but still survives in traditional low intensity agricultural landscapes in Central and Eastern Europe. Accession to the EU however intensifies agriculture, which leads to the vanishing of traditional farming. Our aim was to describe the pollinator assemblages of the last remnants of these landscapes, thus set the baseline of sustainable farming for pollination, and to highlight potential measures of conservation. In these traditional farmlands in the Transylvanian Basin, Romania (EU accession in 2007), we studied the major pollinator groups-wild bees, hoverflies and butterflies. Landscape scale effects of semi-natural habitats, land cover diversity, the effects of heterogeneity and woody vegetation cover and on-site flower resources were tested on pollinator communities in traditionally managed arable fields and grasslands. Our results showed: (i) semi-natural habitats at the landscape scale have a positive effect on most pollinators, especially in the case of low heterogeneity of the direct vicinity of the studied sites; (ii) both arable fields and grasslands hold abundant flower resources, thus both land use types are important in sustaining pollinator communities; (iii) thus, pollinator conservation can rely even on arable fields under traditional management regime. This has an indirect message that the tiny flower margins around large intensive fields in west Europe can be insufficient conservation measures to restore pollinator communities at the landscape scale, as this is still far the baseline of necessary flower resources. This hypothesis needs further study, which includes more traditional landscapes providing baseline, and exploration of other factors behind the lower than baseline level biodiversity values of fields under agri-environmental schemes (AES)

Effect of Hydrocortisone on Mortality and Organ Support in Patients With Severe COVID-19: The REMAP-CAP COVID-19 Corticosteroid Domain Randomized Clinical Trial.

Importance: Evidence regarding corticosteroid use for severe coronavirus disease 2019 (COVID-19) is limited. Objective: To determine whether hydrocortisone improves outcome for patients with severe COVID-19. Design, Setting, and Participants: An ongoing adaptive platform trial testing multiple interventions within multiple therapeutic domains, for example, antiviral agents, corticosteroids, or immunoglobulin. Between March 9 and June 17, 2020, 614 adult patients with suspected or confirmed COVID-19 were enrolled and randomized within at least 1 domain following admission to an intensive care unit (ICU) for respiratory or cardiovascular organ support at 121 sites in 8 countries. Of these, 403 were randomized to open-label interventions within the corticosteroid domain. The domain was halted after results from another trial were released. Follow-up ended August 12, 2020. Interventions: The corticosteroid domain randomized participants to a fixed 7-day course of intravenous hydrocortisone (50 mg or 100 mg every 6 hours) (n = 143), a shock-dependent course (50 mg every 6 hours when shock was clinically evident) (n = 152), or no hydrocortisone (n = 108). Main Outcomes and Measures: The primary end point was organ support-free days (days alive and free of ICU-based respiratory or cardiovascular support) within 21 days, where patients who died were assigned -1 day. The primary analysis was a bayesian cumulative logistic model that included all patients enrolled with severe COVID-19, adjusting for age, sex, site, region, time, assignment to interventions within other domains, and domain and intervention eligibility. Superiority was defined as the posterior probability of an odds ratio greater than 1 (threshold for trial conclusion of superiority >99%). Results: After excluding 19 participants who withdrew consent, there were 384 patients (mean age, 60 years; 29% female) randomized to the fixed-dose (n = 137), shock-dependent (n = 146), and no (n = 101) hydrocortisone groups; 379 (99%) completed the study and were included in the analysis. The mean age for the 3 groups ranged between 59.5 and 60.4 years; most patients were male (range, 70.6%-71.5%); mean body mass index ranged between 29.7 and 30.9; and patients receiving mechanical ventilation ranged between 50.0% and 63.5%. For the fixed-dose, shock-dependent, and no hydrocortisone groups, respectively, the median organ support-free days were 0 (IQR, -1 to 15), 0 (IQR, -1 to 13), and 0 (-1 to 11) days (composed of 30%, 26%, and 33% mortality rates and 11.5, 9.5, and 6 median organ support-free days among survivors). The median adjusted odds ratio and bayesian probability of superiority were 1.43 (95% credible interval, 0.91-2.27) and 93% for fixed-dose hydrocortisone, respectively, and were 1.22 (95% credible interval, 0.76-1.94) and 80% for shock-dependent hydrocortisone compared with no hydrocortisone. Serious adverse events were reported in 4 (3%), 5 (3%), and 1 (1%) patients in the fixed-dose, shock-dependent, and no hydrocortisone groups, respectively. Conclusions and Relevance: Among patients with severe COVID-19, treatment with a 7-day fixed-dose course of hydrocortisone or shock-dependent dosing of hydrocortisone, compared with no hydrocortisone, resulted in 93% and 80% probabilities of superiority with regard to the odds of improvement in organ support-free days within 21 days. However, the trial was stopped early and no treatment strategy met prespecified criteria for statistical superiority, precluding definitive conclusions. Trial Registration: ClinicalTrials.gov Identifier: NCT02735707