A novel 3D volumetric method for directly quantifying porosity and pore space morphology in flocculated suspended sediments.

Flocculated suspended sediments (flocs) are found in a variety of environments globally, and their transport and behavior bear substantial importance to several industries including fisheries, aquaculture, and shipping. Additionally, the modelling of their behavior is important for estuarine and coastal flood prediction and defence, and the process of flocculation occurs in other unrelated industries such as paper and chemical production. Floc porosity is conventionally assessed using inferential indirect or proxy data approaches. These methods underestimate floc porosity % by c. 30% and cannot measure the micro-scale complexity of these pore spaces and networks, rendering inputs to models sub-optimal. This study introduces a novel 3D porosity and pore space quantification protocol, that produces directly quantified porosity % and pore space data.•3D floc data from micro-CT scanning is segmented volumetrically•This segmented volume is quantified to extract porosity and several pore space parameters from the floc structure.

Quantification of 3-dimensional structure and properties of flocculated natural suspended sediment.

Natural sediment flocs are fragile and highly heterogeneous aggregates of biogenic and minerogenic material typically with high porosity and low density. In aquatic environments dominated by fine, cohesive or mixed sediments they can dominate suspended sediment flux. Consequently, monitoring and modelling the behaviour, transport and distribution of flocs is very important for many aquatic industries, maintenance of waterways and conservation and management of aquatic waterbodies. Mathematical models that predict the behaviour of flocs rely on the accurate assessments of the size, shape, density, porosity and fractal dimension of flocs. These inherently 3-dimensional (3D) characteristics are typically derived from 2-dimensional (2D) data, largely due to the challenges associated with sampling, capturing, imaging and quantifying these fragile aggregates. We have developed new volumetric microscopy techniques which can quantify 3D internal and external structures and characteristics of sediment flocs. Here, these techniques were applied to quantify the 3D size (volume), shape and fractal dimension of natural and artificial sediment flocs and compare them to standard 2D approaches. Our study demonstrates that 2D approaches are under-estimating shape complexity and over-estimating the size and mass settling flux of flocs by up to two orders of magnitude, and the discrepancy between 2D and 3D is most marked for natural, organic rich macroflocs. Our study has significant implications for estimations of sediment flux at local to global scales within in aquatic environments. These new data and approaches offer the potential to improve the current parameterisation of sediment transport models and to improve the accuracy of current field-monitoring techniques.

Time to Surgery Following Short-Course Radiotherapy in Rectal Cancer and its Impact on Postoperative Outcomes. A Population-Based Study Across the English National Health Service, 2009-2014.

AIMS: Preoperative short-course radiotherapy (SCRT) is an important treatment option for rectal cancer. The length of time between completing SCRT and surgery may influence postoperative outcomes, but the evidence available to determine the optimal interval is limited and often conflicting. MATERIALS AND METHODS: Information was extracted from a colorectal cancer data repository (CORECT-R) on all surgically treated rectal cancer patients who received SCRT in the English National Health Service between April 2009 and December 2014. The time from radiotherapy to surgery was described across the population. Thirty-day postoperative mortality, returns to theatre, length of stay and 1-year survival were investigated in relation to the interval between radiotherapy and surgery. RESULTS: Within the cohort of 3469 patients, the time to surgery was 0-7 days for 76% of patients, 8-14 days for 19% of patients and 15-27 days for 5% of patients. There was a clear variation in relation to different patient characteristics. There was, however, no evidence of differences in postoperative outcomes in relation to interval length. CONCLUSIONS: This study suggests that the time interval between SCRT and surgery does not influence postoperative outcomes up to a year after surgery. The study provides population-level, real-world evidence to complement that from clinical trials.

Replication of genetic loci for ages at menarche and menopause in the multi-ethnic Population Architecture using Genomics and Epidemiology (PAGE) study.

STUDY QUESTION: Do genetic associations identified in genome-wide association studies (GWAS) of age at menarche (AM) and age at natural menopause (ANM) replicate in women of diverse race/ancestry from the Population Architecture using Genomics and Epidemiology (PAGE) Study? SUMMARY ANSWER: We replicated GWAS reproductive trait single nucleotide polymorphisms (SNPs) in our European descent population and found that many SNPs were also associated with AM and ANM in populations of diverse ancestry. WHAT IS KNOWN ALREADY: Menarche and menopause mark the reproductive lifespan in women and are important risk factors for chronic diseases including obesity, cardiovascular disease and cancer. Both events are believed to be influenced by environmental and genetic factors, and vary in populations differing by genetic ancestry and geography. Most genetic variants associated with these traits have been identified in GWAS of European-descent populations. STUDY DESIGN, SIZE, DURATION: A total of 42 251 women of diverse ancestry from PAGE were included in cross-sectional analyses of AM and ANM. MATERIALS, SETTING, METHODS: SNPs previously associated with ANM (n = 5 SNPs) and AM (n = 3 SNPs) in GWAS were genotyped in American Indians, African Americans, Asians, European Americans, Hispanics and Native Hawaiians. To test SNP associations with ANM or AM, we used linear regression models stratified by race/ethnicity and PAGE sub-study. Results were then combined in race-specific fixed effect meta-analyses for each outcome. For replication and generalization analyses, significance was defined at P < 0.01 for ANM analyses and P < 0.017 for AM analyses. MAIN RESULTS AND THE ROLE OF CHANCE: We replicated findings for AM SNPs in the LIN28B locus and an intergenic region on 9q31 in European Americans. The LIN28B SNPs (rs314277 and rs314280) were also significantly associated with AM in Asians, but not in other race/ethnicity groups. Linkage disequilibrium (LD) patterns at this locus varied widely among the ancestral groups. With the exception of an intergenic SNP at 13q34, all ANM SNPs replicated in European Americans. Three were significantly associated with ANM in other race/ethnicity populations: rs2153157 (6p24.2/SYCP2L), rs365132 (5q35/UIMC1) and rs16991615 (20p12.3/MCM8). While rs1172822 (19q13/BRSK1) was not significant in the populations of non-European descent, effect sizes showed similar trends. LIMITATIONS, REASONS FOR CAUTION: Lack of association for the GWAS SNPs in the non-European American groups may be due to differences in locus LD patterns between these groups and the European-descent populations included in the GWAS discovery studies; and in some cases, lower power may also contribute to non-significant findings. WIDER IMPLICATIONS OF THE FINDINGS: The discovery of genetic variants associated with the reproductive traits provides an important opportunity to elucidate the biological mechanisms involved with normal variation and disorders of menarche and menopause. In this study we replicated most, but not all reported SNPs in European descent populations and examined the epidemiologic architecture of these early reported variants, describing their generalizability and effect size across differing ancestral populations. Such data will be increasingly important for prioritizing GWAS SNPs for follow-up in fine-mapping and resequencing studies, as well as in translational research.

A novel tracer technique for the assessment of fine sediment dynamics in urban water management systems.

Urban storm water run off can reduce the quality of receiving waters due to high sediment load and associated sediment-bound contaminants. Consequently, urban water management systems, such as detention ponds, that both modify water quantity through storage and improve water quality through sediment retention are frequently-used best management practices. To manage such systems effectively and to improve their efficiency, there is a need to understand the dynamics (transport and settling) of sediment, and in particular the fine sediment fraction (<63 µm) and its associated contaminants within urban storm water management systems. This can be difficult to achieve, as modelling the transport behaviour of fine-grained and cohesive sediment is problematic and field-based measurements can be costly, time-consuming and unrepresentative. The aim of this study was to test the application of a novel cohesive sediment tracer and to determine fine sediment transport dynamics within a storm water detention pond. The cohesive sediment tracer used was a holmium labelled montmorillonite clay which flocculated and had similar size and settling velocity to the natural pond sediment it was intended to mimic. The tracer demonstrated that fine sediment was deposited across the entire pond, with the presence of reed beds and water depth being important factors for maximising sediment retention. The results of the sediment tracer experiment were in good agreement with those of a mathematical sediment transport model. Here, the deposited sediment tracer was sampled by collecting and analysing surface pond sediments for holmium. However, analysis and sampling of the three dimensional suspended tracer 'cloud' may provide more accurate information regarding internal pond sediment dynamics.

Use of principal components analysis (PCA) on estuarine sediment datasets: the effect of data pre-treatment.

Principal components analysis (PCA) is a multivariate statistical technique capable of discerning patterns in large environmental datasets. Although widely used, there is disparity in the literature with respect to data pre-treatment prior to PCA. This research examines the influence of commonly reported data pre-treatment methods on PCA outputs, and hence data interpretation, using a typical environmental dataset comprising sediment geochemical data from an estuary in SE England. This study demonstrated that applying the routinely used log (x + 1) transformation skewed the data and masked important trends. Removing outlying samples and correcting for the influence of grain size had the most significant effect on PCA outputs and data interpretation. Reducing the influence of grain size using granulometric normalisation meant that other factors affecting metal variability, including mineralogy, anthropogenic sources and distance along the salinity transect could be identified and interpreted more clearly.

Potential impacts of water injection dredging on water quality and ecotoxicity in Limehouse Basin, River Thames, SE England, UK.

The use of water injection dredging (WID) is increasing in the UK's inland waterways and marinas. Jets of water are injected under low pressure directly into bottom sediment creating a turbulent water-sediment mixture that flows under the influence of gravity. Many of these sediments are highly contaminated and little is known of the effects of contaminant release on water quality or the risk to biota living in both the sediment and the water column. Sediment cores were collected from Limehouse Basin, a proposed WID site in SE England and current sediment toxicity was assessed using a number of techniques. Comparison of metal data to US sediment quality guidelines indicated intermediate levels of toxicity while, calculation of acid volatile sulphide to simultaneously extracted metal ratios underestimated the potential toxicity to sediment dwelling organisms. In contrast, porewater ammonia concentrations were in excess of all published ecotoxicological guidelines and indicate serious risk to biota. Re-suspension experiments were used to mimic the effects of WID on overlying water quality and ecotoxicity tests were carried out on elutriates using Daphnia magna to examine the impacts on biota. Concentrations of a range of metals in the elutriates predict that adverse biological effects would be observed during WID, however only 10% of the elutriate samples caused an adverse effect on Daphnia. Limehouse Basin is a complex aquatic environment receiving predominantly fresh waters while the sediments have high porewater chloride concentrations reminiscent of previous tidal inputs to the basin, making the choice of test organism problematic.