Observed and modelled tidal bar sedimentology reveals preservation bias against mud in estuarine stratigraphy

Mud plays a pivotal role in estuarine ecology and morphology. However, field data on the lateral and vertical depositional record of mud are rare. Furthermore, numerical morphodynamic models often ignore mud due to long computational times and simplifications of mixed depositional processes. This study aims to understand the spatial distribution, formative conditions and preservation of mud deposits in the intertidal zone of bars in high-energy sand-dominated estuaries, and to elucidate the effects of mud on morphology, ecology and stratigraphic architecture. To meet these objectives, field data (historic bathymetry, bio-morphological maps and sediment cores of the shoal of Walsoorden, Western Scheldt estuary, the Netherlands) were combined with complementary hydro-morphodynamic numerical modelling (Delft3D). Based on the field observations, two types of mud deposits were distinguished: (1) mudflat deposits, which are thick (>10 cm) mud beds at the surface associated with high elevations and low accumulation rates; and (2) mud drapes, which are thin (millimetre to centimetre) buried laminae that form and preserve at a wide range of elevations and energy conditions. Model results show that deposition on mudflats occurs just after high-tide slack water in areas shielded from high flood velocities, suggesting that mud accumulation is mostly controlled by elevation, flow velocity and flow direction. Mud accumulation increases shoal elevation, sometimes to supratidal levels. This reduces flow over the shoal, which in turn reduces chute channel formation, stabilises bar morphology and decreases local tidal prism. These effects further promote mud deposition and vegetation settling. Although observations show that mud cover at the surface is relatively high (20%–40% of the intertidal area), mud constitutes only a small percentage of the total estuary volume (ca 5%) revealing that only a small fraction is preserved in the stratigraphy. Due to this mismatch between surface and subsurface expression of mud, interpretations of estuarine stratigraphy risk underestimating the influence of mud at the surface on morphodynamics and habitats

Interviews for the assessment of long-term incapacity for work: a study on adherence to protocols and principles

<p>Abstract</p> <p>Background</p> <p>Assessments for long-term incapacity for work are performed by Social Insurance Physicians (SIPs) who rely on interviews with claimants as an important part of the process. These interviews are susceptible to bias. In the Netherlands three protocols have been developed to conduct these interviews. These protocols are expert- and practice-based. We studied to what extent these protocols are adhered to by practitioners.</p> <p>Methods</p> <p>We compared the protocols with one another and with the ICF and the biopsychosocial approach. The protocols describe semi-structured interviews with comparable but not identical topics. All protocols prescribe that the client's opinion on his capacity for work, and his arguments, need to be determined and assessed. We developed a questionnaire to elicit the adherence SIPs have to the protocols, their underlying principles and topics. We conducted a survey among one hundred fifty-five experienced SIPs in the Netherlands.</p> <p>Results</p> <p>Ninety-eight SIPs responded (64%). All respondents used some form of protocol, either one of the published protocols or their own mix. We found no significant relation between training and the use of a particular protocol. Ninety percent use a semi-structured interview. Ninety-five percent recognise having to verify what the claimant says and eighty-three percent feel the need to establish a good relation (p = 0.019). Twelve topics are basically always addressed by over eighty percent of the respondents. The claimant's opinion of being fit for his own work or other work, and his claim of incapacity and his health arguments for that claim, reach a hundred percent. Description of claimants' previous work reaches ninety-nine percent.</p> <p>Conclusion</p> <p>Our study shows professional consensus among experienced Dutch SIPs about the principle of assessment on arguments, the principle of conducting a semi-structured interview and the most crucial interview topics. This consensus can be used to further develop a protocol for interviewing in the assessment of incapacity for work in social insurance. Such a protocol can improve the quality of the assessments in terms of transparency and reproducibility, as well as by enabling clients to better prepare themselves for the assessments.</p

Identifying potential survival strategies of HIV-1 through virus-host protein interaction networks

Background: The National Institute of Allergy and Infectious Diseases has launched the HIV-1 Human Protein Interaction Database in an effort to catalogue all published interactions between HIV-1 and human proteins. In order to systematically investigate these interactions functionally and dynamically, we have constructed an HIV-1 human protein interaction network. This network was analyzed for important proteins and processes that are specific for the HIV life-cycle. In order to expose viral strategies, network motif analysis was carried out showing reoccurring patterns in virus-host dynamics.Results: Our analyses show that human proteins interacting with HIV form a densely connected and central sub-network within the total human protein interaction network. The evaluation of this sub-network for connectivity and centrality resulted in a set of proteins essential for the HIV life-cycle. Remarkably, we were able to associate proteins involved in RNA polymerase II transcription with hubs and proteasome formation with bottlenecks. Inferred network motifs show significant over-representation of positive and negative feedback patterns between virus and host. Strikingly, such patterns have never been reported in combined virus-host systems.Conclusions: HIV infection results in a reprioritization of cellular processes reflected by an increase in the relative importance of transcriptional machinery and proteasome formation. We conclude that during the evolution of HIV, some patterns of interaction have been selected for resulting in a system where virus proteins preferably interact with central human proteins for direct control and with proteasomal proteins for indirect control over the cellular processes. Finally, the patterns described by network motifs illustrate how virus and host interact with one another

Archimetrics: a quantitative tool to predict three-dimensional meander belt sandbody heterogeneity

Fluvial meander belt sediments form some of the most architecturally complex reservoirs in hydrocarbon fields due to multiple scales of heterogeneity inherent in their deposition. Currently, characterization of meander belt bodies largely relies on idealized vertical profiles and a limited number of analogue models that naively infer architecture from active river dimensions. Three-dimensional architectural data are needed to quantify scales of grain-size heterogeneity, spatial patterns of sedimentation and bar preservation in a direct relationship with the relevant length scales of active river channels. In this study, three large flume experiments and a numerical model were used to characterize and construct the architecture (referred to as ‘archimetrics’) and sedimentology of meander belt deposits, while taking reworking and partial preservation into account. Meander belt sandbody width-to-thickness ratios between 100 and 200 were observed, which are consistent with reported values of natural meander belts. For the first time, the relief of the base of a meander belt is quantified, enabling improved estimates of connectedness of amalgamated meander belts. A key observation is that the slope and number of lateral-accretion packages within natural point bar deposits can be well predicted from fairly basic observables, a finding subsequently tested on several natural systems. Probability curves of preserved architectural characteristics for three dimensions were quantified allowing estimates of bar dimensions, baffle and barrier spacing distributions and container dimensions. Based on this, a set of rules were identified for combining reservoir parameters with the identified probability curves on sandbody dimensions and character, to help create more realistic geomodels for estimating exploration success on the basis of seismic and core data

Archimetrics: a quantitative tool to predict three-dimensional meander belt sandbody heterogeneity

Fluvial meander belt sediments form some of the most architecturally complex reservoirs in hydrocarbon fields due to multiple scales of heterogeneity inherent in their deposition. Currently, characterization of meander belt bodies largely relies on idealized vertical profiles and a limited number of analogue models that naively infer architecture from active river dimensions. Three-dimensional architectural data are needed to quantify scales of grain-size heterogeneity, spatial patterns of sedimentation and bar preservation in a direct relationship with the relevant length scales of active river channels. In this study, three large flume experiments and a numerical model were used to characterize and construct the architecture (referred to as ‘archimetrics’) and sedimentology of meander belt deposits, while taking reworking and partial preservation into account. Meander belt sandbody width-to-thickness ratios between 100 and 200 were observed, which are consistent with reported values of natural meander belts. For the first time, the relief of the base of a meander belt is quantified, enabling improved estimates of connectedness of amalgamated meander belts. A key observation is that the slope and number of lateral-accretion packages within natural point bar deposits can be well predicted from fairly basic observables, a finding subsequently tested on several natural systems. Probability curves of preserved architectural characteristics for three dimensions were quantified allowing estimates of bar dimensions, baffle and barrier spacing distributions and container dimensions. Based on this, a set of rules were identified for combining reservoir parameters with the identified probability curves on sandbody dimensions and character, to help create more realistic geomodels for estimating exploration success on the basis of seismic and core data

Alluvial connectivity in multi-channel networks in rivers and estuaries

Channels in rivers and estuaries are the main paths of fluvial and tidal currents that transport sediment through the system. While network representations of multi-channel systems and their connectivity are quite useful for characterisation of braiding patterns and dynamics, the recognition of channels and their properties is complicated because of the large bed elevation variations, such as shallow shoals and bed steps that render channels visually disconnected. We present and analyse two mathematically rigorous methods to identify channel networks from a terrain model of the river bed. Both methods construct a dense network of locally steepest-descent channels from saddle points on the terrain, and select a subset of channels with a certain minimum sediment volume between them. This is closely linked to the main mechanism of channel formation and change by displacement of sediment volume. The two methods differ in how they compute these sediment volumes: either globally through the entire length of the river, or locally. We compare the methods for the measured bathymetry of the Western Scheldt estuary, The Netherlands, over the past decades. The global method is overly sensitive to small changes elsewhere in the network compared to the local method. We conclude that the local method works best conceptually and for stability reasons. The associated concept of alluvial connectivity between channels in a network is thus the inverse of the volume of sediment that must be displaced to merge the channels. Our method opens up possibilities for new analyses as shown in two examples. First, it shows a clear pattern of scale dependence on volume of the total network length and of the number of nodes by a power law relation, showing that the smaller channels are relatively much shorter. Second, channel bifurcations were found to be predominantly mildly asymmetrical, which is unexpected from fluvial bifurcation theory

Alluvial connectivity in multi-channel networks in rivers and estuaries

Channels in rivers and estuaries are the main paths of fluvial and tidal currents that transport sediment through the system. While network representations of multi-channel systems and their connectivity are quite useful for characterisation of braiding patterns and dynamics, the recognition of channels and their properties is complicated because of the large bed elevation variations, such as shallow shoals and bed steps that render channels visually disconnected. We present and analyse two mathematically rigorous methods to identify channel networks from a terrain model of the river bed. Both methods construct a dense network of locally steepest-descent channels from saddle points on the terrain, and select a subset of channels with a certain minimum sediment volume between them. This is closely linked to the main mechanism of channel formation and change by displacement of sediment volume. The two methods differ in how they compute these sediment volumes: either globally through the entire length of the river, or locally. We compare the methods for the measured bathymetry of the Western Scheldt estuary, The Netherlands, over the past decades. The global method is overly sensitive to small changes elsewhere in the network compared to the local method. We conclude that the local method works best conceptually and for stability reasons. The associated concept of alluvial connectivity between channels in a network is thus the inverse of the volume of sediment that must be displaced to merge the channels. Our method opens up possibilities for new analyses as shown in two examples. First, it shows a clear pattern of scale dependence on volume of the total network length and of the number of nodes by a power law relation, showing that the smaller channels are relatively much shorter. Second, channel bifurcations were found to be predominantly mildly asymmetrical, which is unexpected from fluvial bifurcation theory

Empirical assessment tool for bathymetry, flow velocity and salinity in estuaries based on tidal amplitude and remotely-sensed imagery

Hydromorphological data for many estuaries worldwide is scarce and usually limited to offshore tidal amplitude and remotely-sensed imagery. In many projects, information about morphology and intertidal area is needed to assess the effects of human interventions and rising sea-level on the natural depth distribution and on changing habitats. Habitat area depends on the spatial pattern of intertidal area, inundation time, peak flow velocities and salinity. While numerical models can reproduce these spatial patterns fairly well, their data need and computational costs are high and for each case a new model must be developed. Here, we present a Python tool that includes a comprehensive set of relations that predicts the hydrodynamics, bed elevation and the patterns of channels and bars in mere seconds. Predictions are based on a combination of empirical relations derived from natural estuaries, including a novel predictor for cross-sectional depth distributions, which is dependent on the along-channel width profile. Flow velocity, an important habitat characteristic, is calculated with a new correlation between depth below high water level and peak tidal flow velocity, which was based on spatial numerical modelling. Salinity is calculated from estuarine geometry and flow conditions. The tool only requires an along-channel width profile and tidal amplitude, making it useful for quick assessments, for example of potential habitat in ecology, when only remotely-sensed imagery is available