Hydraulic validation of two-dimensional simulations of braided river flow with spatially continuous aDcp data

Gravel‐bed braided rivers are characterized by shallow, branching flow across low relief, complex, and mobile bed topography. These conditions present a major challenge for the application of higher dimensional hydraulic models, the predictions of which are nevertheless vital to inform flood risk and ecosystem management. This paper demonstrates how high‐resolution topographic survey and hydraulic monitoring at a density commensurate with model discretization can be used to advance hydrodynamic simulations in braided rivers. Specifically, we detail applications of the shallow water model, Delft3d, to the Rees River, New Zealand, at two nested scales: a 300 m braid bar unit and a 2.5 km reach. In each case, terrestrial laser scanning was used to parameterize the topographic boundary condition at hitherto unprecedented resolution and accuracy. Dense observations of depth and velocity acquired from a mobile acoustic Doppler current profiler (aDcp), along with low‐altitude aerial photography, were then used to create a data‐rich framework for model calibration and testing at a range of discharges. Calibration focused on the estimation of spatially uniform roughness and horizontal eddy viscosity, νH, through comparison of predictions with distributed hydraulic data. Results revealed strong sensitivity to νH, which influenced cross‐channel velocity and localization of high shear zones. The high‐resolution bed topography partially accounts for form resistance, and the recovered roughness was found to scale by 1.2–1.4 D84 grain diameter. Model performance was good for a range of flows, with minimal bias and tight error distributions, suggesting that acceptable predictions can be achieved with spatially uniform roughness and νH.Field campaigns were primarily funded by NERC Grant NE/G005427/1 and NERC Geophysical Equipment Facility Loan 892 as well as NSERC and CFI (Canada) grants to Colin Rennie. Damia Vericat was supported by a Ramon y Cajal Fellowship (RYC‐2010‐06264) funded by the Spanish Ministry of Science and Innovation during the preparation of this manuscript. Numerical simulations were undertaken during a visit by Richard Williams to NIWA. This visit was funded by the British Hydrology Society and an Aberystwyth University Postgraduate Studentship. Murray Hicks and Richard Measures were funded by NIWA core funding under the Sustainable Water Allocation Programme

Modelling Braided River Morphodynamics Using a Particle Travel Length Framework

Numerical models that predict channel evolution are an essential tool for investigating processes that occur over timescales which render field observation intractable. The current generation of morphodynamic models, however, either oversimplify the relevant physical processes or, in the case of more physically complete codes based on computational fluid dynamics (CFD), have computational overheads that severely restrict the space–time scope of their application. Here we present a new, open-source, hybrid approach that seeks to reconcile these modelling philosophies. This framework combines steady-state, two-dimensional CFD hydraulics with a rule-based sediment transport algorithm to predict particle mobility and transport paths which are used to route sediment and evolve the bed topography. Data from two contrasting natural braided rivers (Rees, New Zealand, and Feshie, United Kingdom) were used for model verification, incorporating reach-scale quantitative morphological change budgets and volumetric assessment of different braiding mechanisms. The model was able to simulate 8 of the 10 empirically observed braiding mechanisms from the parameterized bed erosion, sediment transport, and deposition. Representation of bank erosion and bar edge trimming necessitated the inclusion of a lateral channel migration algorithm. Comparisons between simulations based on steady effective discharge versus event hydrographs discretized into a series of model runs were found to only marginally increase the predicted volumetric change, with greater deposition offsetting erosion. A decadal-scale simulation indicates that accurate prediction of event-scale scour depth and subsequent deposition present a methodological challenge because the predicted pattern of deposition may never “catch up” to erosion if a simple path-length distribution is employed, thus resulting in channel over-scouring. It may thus be necessary to augment path-length distributions to preferentially deposit material in certain geomorphic units. We anticipate that the model presented here will be used as a modular framework to explore the effect of different process representations, and as a learning tool designed to reveal the relative importance of geomorphic transport processes in rivers at multiple timescales

Complementary and Alternative Medicine Use in African Americans With Rheumatoid Arthritis: Prevalence of CAM in an African American Cohort

Racial/ethnic differences with regard to complementary and alternative medicine (CAM) use have been reported in the US. However, specific details of CAM use by African Americans with rheumatoid arthritis (RA) are lacking

Most Common SNPs Associated with Rheumatoid Arthritis in Subjects of European Ancestry Confer Risk of Rheumatoid Arthritis in African-Americans

Large-scale genetic association studies have identified over 20 rheumatoid arthritis (RA) risk alleles among individuals of European ancestry. The influence of these risk alleles has not been comprehensively studied in African-Americans. We therefore sought to examine whether these validated RA risk alleles are associated with RA in an African-American population

Association of IL4R single-nucleotide polymorphisms with rheumatoid nodules in African Americans with rheumatoid arthritis

Abstract Introduction To determine whether IL4R single-nucleotide polymorphisms (SNPs) rs1805010 (I50V) and rs1801275 (Q551R), which have been associated with disease severity in rheumatoid arthritis (RA) patients of European ancestry, relate to the presence of rheumatoid nodules and radiographic erosions in African Americans. Methods Two IL4R SNPs, rs1805010 and rs1801275, were genotyped in 749 patients from the Consortium for Longitudinal Evaluation of African-Americans with Early Rheumatoid Arthritis (CLEAR) registries. End points were rheumatoid nodules defined as present either by physical examination or by chest radiography and radiographic erosions (radiographs of hands/wrists and feet were scored using the modified Sharp/van der Heijde system). Statistical analyses were performed by using logistic regression modeling adjusted for confounding factors. Results Of the 749 patients with RA, 156 (20.8%) had rheumatoid nodules, with a mean age of 47.0 years, 84.6% female gender, and median disease duration of 1.9 years. Of the 461 patients with available radiographic data, 185 (40.1%) had erosions (score >0); their mean age was 46.7 years; 83.3% were women; and median disease duration was 1.5 years. Patients positive for HLA-DRB1 shared epitope (SE) and autoantibodies (rheumatoid factor (RF) or anti-cyclic citrullinated peptide (CCP)) had a higher risk of developing rheumatoid nodules in the presence of the AA and AG alleles of rs1801275 (odds ratio (OR)adj = 8.08 (95% confidence interval (CI): 1.60-40.89), P = 0.01 and ORadj = 2.97 (95% CI, 1.08 to 8.17), P = 0.04, respectively). Likewise, patients positive for the HLA-DRB1 SE and RF alone had a higher risk of developing rheumatoid nodules in presence of the AA and AG alleles of rs1801275 (ORadj = 8.45 (95% CI, 1.57 to 45.44), P = 0.01, and ORadj = 3.57 (95% CI, 1.18 to 10.76), P = 0.02, respectively) and in the presence of AA allele of rs1805010 (ORadj = 4.52 (95% CI, 1.20 to 17.03), P = 0.03). No significant association was found between IL4R and radiographic erosions or disease susceptibility, although our statistical power was limited by relatively small numbers of cases and controls. Conclusions We found that IL4R SNPs, rs1801275 and rs1805010, are associated with rheumatoid nodules in autoantibody-positive African-American RA patients with at least one HLA-DRB1 allele encoding the SE. These findings highlight the need for analysis of genetic factors associated with clinical RA phenotypes in different racial/ethnic populations

An African Ancestry-Specific Allele of CTLA4 Confers Protection against Rheumatoid Arthritis in African Americans

Cytotoxic T-lymphocyte associated protein 4 (CTLA4) is a negative regulator of T-cell proliferation. Polymorphisms in CTLA4 have been inconsistently associated with susceptibility to rheumatoid arthritis (RA) in populations of European ancestry but have not been examined in African Americans. The prevalence of RA in most populations of European and Asian ancestry is ∼1.0%; RA is purportedly less common in black Africans, with little known about its prevalence in African Americans. We sought to determine if CTLA4 polymorphisms are associated with RA in African Americans. We performed a 2-stage analysis of 12 haplotype tagging single nucleotide polymorphisms (SNPs) across CTLA4 in a total of 505 African American RA patients and 712 African American controls using Illumina and TaqMan platforms. The minor allele (G) of the rs231778 SNP was 0.054 in RA patients, compared to 0.209 in controls (4.462×10−26, Fisher's exact). The presence of the G allele was associated with a substantially reduced odds ratio (OR) of having RA (AG+GG genotypes vs. AA genotype, OR 0.19, 95% CI: 0.13–0.26, p = 2.4×10−28, Fisher's exact), suggesting a protective effect. This SNP is polymorphic in the African population (minor allele frequency [MAF] 0.09 in the Yoruba population), but is very rare in other groups (MAF = 0.002 in 530 Caucasians genotyped for this study). Markers associated with RA in populations of European ancestry (rs3087243 [+60C/T] and rs231775 [+49A/G]) were not replicated in African Americans. We found no confounding of association for rs231778 after stratifying for the HLA-DRB1 shared epitope, presence of anti-cyclic citrullinated peptide antibody, or degree of admixture from the European population. An African ancestry-specific genetic variant of CTLA4 appears to be associated with protection from RA in African Americans. This finding may explain, in part, the relatively low prevalence of RA in black African populations

Variable responses of individual species to tropical forest degradation

The functional stability of ecosystems depends greatly on interspecific differences in responses to environmental perturbation. However, responses to perturbation are not necessarily invariant among populations of the same species, so intraspecific variation in responses might also contribute. Such inter-population response diversity has recently been shown to occur spatially across species ranges, but we lack estimates of the extent to which individual populations across an entire community might have perturbation responses that vary through time. We assess this using 524 taxa that have been repeatedly surveyed for the effects of tropical forest logging at a focal landscape in Sabah, Malaysia. Just 39 % of taxa – all with non-significant responses to forest degradation – had invariant responses. All other taxa (61 %) showed significantly different responses to the same forest degradation gradient across surveys, with 6 % of taxa responding to forest degradation in opposite directions across multiple surveys. Individual surveys had low power (< 80 %) to determine the correct direction of response to forest degradation for one-fifth of all taxa. Recurrent rounds of logging disturbance increased the prevalence of intra-population response diversity, while uncontrollable environmental variation and/or turnover of intraspecific phenotypes generated variable responses in at least 44 % of taxa. Our results show that the responses of individual species to local environmental perturbations are remarkably flexible, likely providing an unrealised boost to the stability of disturbed habitats such as logged tropical forests

Thresholds for adding degraded tropical forest to the conservation estate

Logged and disturbed forests are often viewed as degraded and depauperate environments compared with primary forest. However, they are dynamic ecosystems1 that provide refugia for large amounts of biodiversity2,3, so we cannot afford to underestimate their conservation value4. Here we present empirically defined thresholds for categorizing the conservation value of logged forests, using one of the most comprehensive assessments of taxon responses to habitat degradation in any tropical forest environment. We analysed the impact of logging intensity on the individual occurrence patterns of 1,681 taxa belonging to 86 taxonomic orders and 126 functional groups in Sabah, Malaysia. Our results demonstrate the existence of two conservation-relevant thresholds. First, lightly logged forests (68%) of their biomass removed, and these are likely to require more expensive measures to recover their biodiversity value. Overall, our data confirm that primary forests are irreplaceable5, but they also reinforce the message that logged forests retain considerable conservation value that should not be overlooked

A brief history of informed consent in the United States

Poster for the 57th Historia Medica lecture.https://digitalcommons.wustl.edu/historyofmedicine_historia_medica_posters/1028/thumbnail.jp