A Novel, Generic Approach To Simulate Bank Retreat In Alluvial River Channels

Despite the importance of bank erosion in rivers, most computational fluid dynamics (CFD) models have limited capacity to examine bank retreat and channel-floodplain interactions, as they lack bank stability algorithms and ignore vegetation effects. This research seeks to develop a numerical model to improve our understanding of key properties of bank material and vegetation cover with respect to lateral erosion in river meanders at intermediate spatial (5−10 meander bends) and temporal (2−3 years) scales. Following a comparison of six different morphodynamic models for three sinuous laboratory configurations, the CFD model TELEMAC-2D was chosen to receive a newly developed bank retreat module that respects geotechnical principles and integrates spatial analysis concepts. It was tested against morphological datasets from two contrasted river reaches, the semi-alluvial Medway Creek (Ontario) and alluvial St. François River (Quebec). Statistical analysis, combined with the use of machine learning algorithms, demonstrate that the coupled model is able to fit observed bank retreat location and extent. Some local disagreement with observations along Medway Creek seems associated with the heterogeneity of soil material and stratigraphy, and in vegetation cover present at the field site. The coupled model was also used to identify key geotechnical parameters and optimal parameter values for the studied reaches. An epistemological reflection on the purpose of modelling in fluvial geomorphology leads to the conclusion that the primary model strength lies in its ability to provide explanations on bank retreat mechanisms. Further research should seek to test more thoroughly morphodynamic modelling in complex geomorphological environments

Comparing the Sensitivity of Bank Retreat to Changes in Biophysical Conditions between Two Contrasting River Reaches Using a Coupled Morphodynamic Model

Morphodynamic models of river meandering patterns and dynamics are based on the premise that the integration of biophysical processes matching those operating in natural rivers should result in a better fit with observations. Only a few morphodynamic models have been applied to natural rivers, typically along short reaches, and the relative importance of biophysical parameters remains largely unknown in these cases. Here, a series of numerical simulations were run using the hydrodynamic solver TELEMAC-2D, coupled to an advanced physics-based geotechnical module, to verify if sensitivity to key biophysical conditions differs substantially between two natural meandering reaches of different scale and geomorphological context. The model was calibrated against observed measurements of bank retreat for a 1.5 km semi-alluvial meandering reach incised into glacial till (Medway Creek, Ontario, Canada) and an 8.6 km long sinuous alluvial reach of the St. François River (Quebec, Canada). The two river reaches have contrasting bed and bank composition, and they differ in width by one order of magnitude. Calibration was performed to quantify and contrast the contribution of key geotechnical parameters, such as bank cohesion, to bank retreat. Results indicate that the sensitivity to key geotechnical parameters is dependent on the biophysical context and highly variable at the sub-reach scale. The homogeneous sand-bed St. François River is less sensitive to cohesion and friction angle than the more complex Medway Creek, flowing through glacial-till deposits. The latter highlights the limits of physics-based models for practical purposes, as the amount and spatial resolution of biophysical parameters required to improve the agreement between simulation results and observations may justify the use of a reduced complexity modelling approach

Assessment of Management Strategies for a Lowland Straightened Agricultural Stream

Channel straightening and dredging were extensively used in the 20th century to enhance agricultural drainage and facilitate crop maintenance and harvest. Although the adverse geomorphological and ecological effects of channelization are widely acknowledged, the use of alternative management strategies remains marginal in Southwestern Québec. Bank stabilisation projects are often carried out to mitigate local erosion problems with little assessment of their effects at the reach and watershed scales and with insufficient guidance on suitable designs. The objective of this research is to assess the impacts of various management strategies by studying a case of straightened agricultural stream. Field measurements in the Richer stream, which drains a small agricultural watershed in the St. Lawrence Lowlands, were used to parameterise a hydro-morphological model at the watershed scale and a 3D computational fluid dynamics model at the reach scale. The increase in stream power associated with the loss in sinuosity since the 1930s has resulted in noteworthy erosion problems in the studied watershed, in particular near residential development where there is limited space available to establish riparian strips. The tested management strategies at the watershed scale are the recreation of meanders and the installation of backwater ponds whereas, at the reach scale, stream barbs and bed weirs are tested. These management strategies are also assessed through a cost-benefit analysis which also takes into account environmental and practical implementation aspects. Results indicate that both the addition of ponds and re-meandering can markedly reduce unit stream power, thus the potential for erosion. Hydraulic structures such as stream barbs and V-shaped bed weirs re-align the flow towards channel centre, thus reducing near-bank velocities. The re-meandering approach involving natural vegetation regeneration has the highest overall effectiveness at the watershed scale whilst V-shaped weirs are found to be moderately effective at the reach scale. The diversification of flow conditions and channel morphologies associated with these approaches were important factors contributing to their higher suitability compared to other potential solutions. The modelling methodology used in this study can help limit the uncertainty surrounding restoration activities by better predicting the efficiency of proposed stabilisation techniques prior to their implementation while considering specific stream and watershed characteristics as well as ecological factors

Sensitivity of simulated flow fields and bathymetries in meandering channels to the choice of a morphodynamic model

Morphodynamic models are used by river practitioners and scientists to simulate geomorphic change in natural and artificial river channels. It has long been recognized that these models are sensitive to the choice of parameter values, and proper calibration is now common practice. This paper investigates the less recognized impact of the choice of the model itself. All morphodynamic models purport to simulate the same flow and sediment dynamics, often relying on the same governing equations. Yet in solving these equations, the models have different underlying assumptions, for example regarding spatial discretization, turbulence, sediment inflow, lateral friction, and bed load transport. These differences are not always considered by the average model user, who might expect similar predictions from calibrated models. Here, a series of numerical simulations in meandering channels was undertaken to test whether six morphodynamic codes (BASEMENT, CCHE-2D, NAYS, SSIIM-1, TELEMAC-2D and TELEMAC-3D) would yield significantly different equilibrium bathymetries if subjected to identical, initial flow conditions. We found that, despite producing moderately similar velocity patterns on a fixed-flat bed (regression coefficient r of 0.77 ± 0.20), the codes disagree substantially with respect to simulated bathymetries (r = 0.49 ± 0.31). We relate these discrepancies to differences in the codes' assumptions. Results were configuration specific, i.e. codes that perform well for a given channel configuration do not necessarily perform well with higher or lower sinuosity configurations. Finally, limited correlation is found between accuracy and code complexity; the inclusion of algorithms that explicitly account for the effects of local bed slope and channel curvature effects on transport magnitude and direction does not guarantee accuracy. The range of solutions obtained from the evaluated codes emphasises the need for carefully considering the choice of code. We recommend the creation of a central repository providing universal validation cases and documentation of recognized fluvial codes in commonly studied fluvial settings. This article is protected by copyright. All rights reserved

Diminishing returns on labour in the global marine food system

Technological advances over the past century have greatly reduced the proportion of human labour required to produce the world’s food. On land, these advances have continually increased yields, feeding a growing human population even as the number of farmers has fallen. It has long been recognized that technological advances do not necessarily increase fishery yields in the same way; since the natural productivity of wild fish stocks puts a strong limit on capture fisheries, high labour inputs can lead to overfishing. However, the global evolution of labour in marine fisheries has not been assessed, leaving the overall interactions among technology, fishers and catches unknown. Here we reconstruct the global number of marine fishers from 1950 to 2015 and show that the total number of fishers grew with no sign of reversal despite mechanization, as large increases in lower- and middle-income countries overwhelmed an ~60% decrease in higher-income countries. As a result, the wild fish catch per fisher has declined since the 1990s despite major technological advances—a stark contrast to the 70% increase of the production per farmer over the same period. Our results show that, globally averaged, fisheries displayed diminishing—or even negative—returns on labour over 1950–2015, which has been detrimental for food production efficiency, marine ecosystems and fishing communities.acceptedVersio

Serum Markers of Hepatocyte Death and Apoptosis Are Non Invasive Biomarkers of Severe Fibrosis in Patients with Alcoholic Liver Disease

BACKGROUND: Quantification of hepatocyte death is useful to evaluate the progression of alcoholic liver diseases. Our aims were to quantify and correlate the circulating levels of Cytokeratin 18 (CK18) and its caspases-generated fragment to disease severity in heavy alcoholics. METHODOLOGY/PRINCIPAL FINDINGS: CK18 and CK18-fragment were evaluated in the serum of 143 heavy alcoholics. Serum levels of markers of hepatocyte death (CK18), apoptosis (CK18 fragment) and necrosis (CK18 -CK18 fragment) increased in patients with severe fibrosis compared to patients with mild fibrosis. These markers strongly correlated with Mallory-Denk bodies, hepatocyte ballooning, fibrosis and with hepatic TNFα and TGFβ assessed in the liver of 24 patients. Elevated levels of serum hepatocyte death and apoptotic markers were independent risk factors in predicting severe fibrosis in a model combining alkaline phosphatase, bilirubin, prothrombin index, hyaluronate, hepatocyte death and apoptotic markers. The level of markers of hepatocyte death and apoptosis had an area under the receiving operator curve that predicted severe fibrosis of 0.84 and 0.76, respectively. CONCLUSION/SIGNIFICANCE: Death of hepatocytes can be easily evaluated with serum markers and correlated with severe fibrosis in heavy alcohol drinkers. These biomarkers could be useful to rapidly evaluate liver injuries and the efficacy of therapies

Near-Fatal Multiple Organ Dysfunction Syndrome Induced by Plasmodium malariae

International audienc

Widespread anti-CRISPR proteins in virulent bacteriophages inhibit a range of Cas9 proteins

International audienceCRISPR-Cas systems are bacterial anti-viral systems, and bacterial viruses (bacteriophages, phages) can carry anti-CRISPR (Acr) proteins to evade that immunity. Acrs can also fine-tune the activity of CRISPR-based genome-editing tools. While Acrs are prevalent in phages capable of lying dormant in a CRISPR-carrying host, their orthologs have been observed only infrequently in virulent phages. Here we identify AcrIIA6, an Acr encoded in 33% of virulent Streptococcus thermophilus phage genomes. The X-ray structure of AcrIIA6 displays some features unique to this Acr family. We compare the activity of AcrIIA6 to those of other Acrs, including AcrIIA5 (also from S. thermophilus phages), and characterize their effectiveness against a range of CRISPR-Cas systems. Finally, we demonstrate that both Acr families from S. thermophilus phages inhibit Cas9-mediated genome editing of human cells