Processes and products of turbidity currents entering soft muddy substrates

New laboratory experiments reveal that cohesionless turbidity currents are able to enter cohesive soft muddy substrates without losing their shape. These intrabed currents are driven by bed shear stress exceeding bed cohesive strength, and by flow density exceeding bed den - sity. The flows produce unique turbidites with internal mud layers, mixed cohesive-nonco - hesive sediment layers, and flame and load structures. A depositional model for intrabed (I) turbidites is proposed, comprising, from base to top: I1�sand-bearing mud, with a scoured base, dispersed mud, and mud clasts; I2�muddy sand from the intrabed portion of the tur - bidity current; I3�sandy mud with a speckled appearance; and I4�mud-poor sand from the suprabed portion of the flow. Complete I1�I4 turbidites are inferred to dominate loca - tions in nature where the currents mix with the bed and deep erosional scours form, filled with deformed or chaotic sand-mud mixtures. Further downflow, base-missing I2�I4 and I4 sequences signify gradual deceleration, loss of erosivity, and termination of intrabed flo

Sediment Composition Influences Spatial Variation in the Abundance of Human Pathogen Indicator Bacteria within an Estuarine Environment

Faecal contamination of estuarine and coastal waters can pose a risk to human health, particularly in areas used for shellfish production or recreation. Routine microbiological water quality testing highlights areas of faecal indicator bacteria (FIB) contamination within the water column, but fails to consider the abundance of FIB in sediments, which under certain hydrodynamic conditions can become resuspended. Sediments can enhance the survival of FIB in estuarine environments, but the influence of sediment composition on the ecology and abundance of FIB is poorly understood. To determine the relationship between sediment composition (grain size and organic matter) and the abundance of pathogen indicator bacteria (PIB), sediments were collected from four transverse transects of the Conwy estuary, UK. The abundance of culturable Escherichia coli, total coliforms, enterococci, Campylobacter, Salmonella and Vibrio spp. in sediments was determined in relation to sediment grain size, organic matter content, salinity, depth and temperature. Sediments that contained higher proportions of silt and/or clay and associated organic matter content showed significant positive correlations with the abundance of PIB. Furthermore, the abundance of each bacterial group was positively correlated with the presence of all other groups enumerated. Campylobacter spp. were not isolated from estuarine sediments. Comparisons of the number of culturable E. coli, total coliforms and Vibrio spp. in sediments and the water column revealed that their abundance was 281, 433 and 58-fold greater in sediments (colony forming units (CFU)/100 g) when compared with the water column (CFU/100 ml), respectively. These data provide important insights into sediment compositions that promote the abundance of PIB in estuarine environments, with important implications for the modelling and prediction of public health risk based on sediment resuspension and transport

Transport of branched tetraether lipids from the Tagus River basin to the coastal ocean of the Portuguese margin: consequences for the interpretation of the MBT’/CBT paleothermometer

Branched glycerol dialkyl glycerol tetraethers (brGDGTs), which are transported from soil to marine sediment by rivers, have been used to reconstruct the mean annual air temperature (MAAT) and soil pH of the drainage basin using the methylation index of branched tetraethers (MBT, recently refined as MBT') and cyclization index of branched tetraethers (CBT) from coastal marine sediment records. In this study we are tracing the brGDGTs from source to sink in the Tagus River basin, the longest river system on the Iberian Peninsula, by determining their concentration and distribution in soils, river suspended particulate matter (SPM), riverbank sediments, marine SPM, and marine surface sediments. The concentrations of brGDGTs in river SPM were substantially higher and their distributions were different compared to those of the drainage basin soils. This indicates that brGDGTs are mainly produced in the river itself. In the marine environment, the brGDGT concentrations rapidly decreased with increasing distance from the Tagus estuary. At the same time, the brGDGT distributions in marine sediments also changed, indicating that marine in-situ production also takes place. These results show that there are various problems that complicate the use of the MBT'/CBT for paleoreconstructions using coastal marine sediments in the vicinity of a river. However, if the majority of brGDGTs are produced in the river, it might be possible to reconstruct the environmental (temperature and pH) conditions of the river water using appropriate aquatic calibrations, provided that marine core locations are chosen in such a way that the brGDGTs in their sediments are predominantly derived from riverine in-situ production

Sticky stuff : redefining bedform prediction in modern and ancient environments

This work was funded by the UK Natural Environment Research Council (NERC) under the COHBED project (NE/1027223/1). Paterson was funded by the Marine Alliance for Science and Technology for Scotland (MASTS).The dimensions and dynamics of subaqueous bedforms are well known for cohesionless sediments. However, the effect of physical cohesion imparted by cohesive clay within mixed sand-mud substrates has not been examined, despite its recognized influence on sediment stability. Here we present a series of controlled laboratory experiments to establish the influence of substrate clay content on subaqueous bedform dynamics within mixtures of sand and clay exposed to unidirectional flow. The results show that bedform dimensions and steepness decrease linearly with clay content, and comparison with existing predictors of bedform dimensions, established within cohesionless sediments, reveals significant over-prediction of bedform size for all but the lowermost clay contents examined. The profound effect substrate clay content has on bedform dimensions has a number of important implications for interpretation in a range of modern and ancient environments, including reduced roughness and bedform heights in estuarine systems and the often cited lack of large dune cross-sets in turbidites. The results therefore offer a step change in our understanding of bedform formation and dynamics in these, and many other, sedimentary environments.Publisher PDFPeer reviewe

Estimating non-response bias in family studies: application to mental health and lifestyle.

Non-response to mailed surveys reduces the effective sample size and may introduce bias. Non-response has been studied by (1) comparison to available data in population based registers, (2) directly contacting non-respondents by telephone or single-item reply cards, and (3) longitudinal repetition of the survey. The goal of this paper was to propose an additional method to study non-response bias: when the variable of interest has a familial component, data from respondents can be used as proxy for the data from their non-responding family members. This approach was used with data on smoking, alcohol consumption, physical activity, coffee- and tea-use, education, body mass index, religion, burnout, life events, personality and mental health in large number of siblings and DZ twins registered with the Netherlands Twin Register. In addition, for smoking behavior, we also used the second strategy by sending a reply card. Results show that scores of members from less cooperative families or incomplete twin pairs tended to be more unfavorable than the scores from highly cooperative families or complete twin pairs. For example, family members from less cooperative families cycled less often and scored higher on anxious depression and neuroticism. For smoking, both the results of the reply card and the results of the additional method suggested a higher percentage smokers among the non-respondents but this was only significant with reply card method. In general, differences between highly/less cooperative families and complete/incomplete DZ twins were small. Results suggest that, even for studies with moderate response rates, data collected on health, personality and lifestyle are relatively unbiased

Alteration of the Exhaled Volatile Organic Compound Pattern in Colorectal Cancer Patients after Intentional Curative Surgery—A Prospective Pilot Study

As current follow-up modalities for colorectal carcinoma (CRC) have restricted sensitivity, novel diagnostic tools are needed. The presence of CRC changes the endogenous metabolism, resulting in the release of a specific volatile organic compounds (VOC) pattern that can be detected with an electronic nose or AeonoseTM. To evaluate the use of an electronic nose in the follow-up of CRC, we studied the effect of curative surgery on the VOC pattern recognition using AeonoseTM. A prospective cohort study was performed, in which 47 patients diagnosed with CRC were included, all of whom underwent curative surgical resection. Breath testing was performed before and after surgery using the AeonoseTM. A machine learning model was developed by discerning between the 94 pre-and postoperative breath samples. The training model differentiated between the pre-and postoperative CRC breath samples with a sensitivity and specificity of 0.78 (95%CI 0.61–0.90) and 0.73 (95%CI 0.56–0.86), respectively, with an accuracy of 0.76 (95%CI 0.66–0.85), and an area under the curve of 0.79 (95%CI 0.68–0.89). The internal validation of the test set resulted in an accuracy of 0.75 (95%CI 0.51–0.91) and AUC of 0.82 (95%CI 0.61–1). In conclusion, our results suggest that the VOC pattern of CRC patients is altered by curative surgery in a short period, indicating that the exhaled VOCs might be closely related to the presence of CRC. However, to use AeonoseTM as a potential diagnostic tool in the clinical follow-up of CRC patients, the performance of the models needs to be improved through further large-scale prospective research.</p

Variant type and position predict two distinct limb phenotypes in patients with GLI3-mediated polydactyly syndromes

Introduction: Pathogenic DNA variants in the GLI-Kruppel family member 3 (GLI3) gene are known to cause multiple syndromes: for example, Greig syndrome, preaxial polydactyly-Type 4 (PPD4) and Pallister-Hall syndrome. Out of these, Pallister-Hall is a different entity, but the distinction between Greig syndrome and PPD4 is less evident. Using latent class analysis (LCA), our study aimed to investigate the correlation between reported limb anomalies and the reported GLI3 variants in these GLI3-mediated polydactyly syndromes. We identified two subclasses of limb anomalies that relate to the underlying variant. Methods: Both local and published cases were included for analysis. The presence of individual limb phenotypes was dichotomised and an exploratory LCA was performed. Distribution of phenotypes and genotypes over the classes were explored and subsequently the key predictors of latent class membership were correlated to the different clustered genotypes. Results: 297 cases were identified with 127 different variants in the GLI3 gene. A two-class model was fitted revealing two subgroups of patients with anterior versus posterior anomalies. Posterior anomalies were observed in cases with truncating variants in the activator domain (postaxial polydactyly; hand, OR: 12.7; foot, OR: 33.9). Multivariate analysis supports these results (Beta: 1.467, p=0.013 and Beta: 2.548, p<0.001, respectively). Corpus callosum agenesis was significantly correlated to these variants (OR: 8.8, p<0.001). Conclusion: There are two distinct phenotypes within the GLI3-mediated polydactyly population: Anteriorly and posteriorly orientated. Variants that likely produce haploinsufficiency are associated with anterior phenotypes. Posterior phenotypes are associated with truncating variants in the activator domain. Patients with these truncating variants have a greater risk for corpus callosum anomalies

Current- and Wave-Generated Bedforms on Mixed Sand–Clay Intertidal Flats: A New Bedform Phase Diagram and Implications for Bed Roughness and Preservation Potential

The effect of bedforms on frictional roughness felt by the overlying flow is crucial to the regional modelling of estuaries and coastal seas. Bedforms are also a key marker of palaeoenvironments. Experiments have shown that even modest biotic and abiotic cohesion in sand inhibits bedform formation, modifies bedform size, and slows bedform development, but this has rarely been tested in nature. The present study used a comprehensive dataset recorded over a complete spring–neap cycle on an intertidal flat to investigate bedform dynamics controlled by a wide range of wave and current conditions, including the effects of wave–current angle and bed cohesion. A detailed picture of different bedform types and their relationship to the flow, be they equilibrium, non-equilibrium, or relict, was produced, and captured in a phase diagram that integrates wave-dominated, current-dominated, and combined wave–current bedforms. This bedform phase diagram incorporates a substantially wider range of flow conditions than previous phase diagrams, including bedforms related to near-orthogonal wave–current angles, such as ladderback ripples. Comparison with laboratory-derived bedform phase diagrams indicates that washed-out ripples, lunate interference ripples and upper-stage plane beds replace the subaqueous dune field; such bedform distributions may be a key characteristic of intertidal flats. The field data also provide a means of predicting the dimensions of these bedforms, which can be transferred to other areas and grain sizes. We show that an equation for the prediction of equilibrium bedform size is sufficient to predict the roughness, even though the bedforms are highly variable in character and only in equilibrium with the flow for approximately half the time. Whilst the effect of cohesive clay is limited under more active spring conditions, clay does play a role in reducing the bedform dimensions under more quiescent neap conditions. We also investigated which combinations of waves, currents, and bed clay contents in the intertidal zone have the highest potential for bedform preservation in the geological record. This shows that combined wave–current bedforms have the lowest preservation potential and equilibrium current ripples have the highest preservation potential, even in the presence of moderate and storm waves. Hence, the absence of wave ripples and combined-flow bedforms and their primary stratification in sedimentary successions cannot be taken as evidence that waves were absent at the time of deposition