Geomorphology of the Green River in Dinosaur National Monument

Longitudinal profile , channel cross-section geometry, and depositional patterns of the Green River in its course through the eastern Uinta Mountains are each strongly influenced by river-level geology and tributary sediment delivery processes. We surveyed channel cross sections at 1-km intervals, mapped surficial geology , and measured size and characteristics of bed material in order to evaluate the geomorphic organization of the 70- km study reach . Canyon reaches that are of high gradient and narrow channel geometry are associated with the most resistant lithologies exposed at river level and the most frequent occurrences of tributary debris fans. Meandering reaches that are characterized by low gradient and wide channel geometry are associated with river-level lithology that is of moderate to low resistance and very low debris fan frequency. The channel is in contact with bedrock or talus along only 42 percent of the bank length in canyon reaches and there is an alluvial fill of at least 12 m that separates the channe l bed from bedrock at three borehole sites. The influence of lithology primarily operates through the presence of resistant boulders in debris fans that are delivered by debris flows from steep tributaries. The depositional settings created by debris fans consist of (1) channel-margin deposits in the backwater above the debris fan, (2) eddy bars in the zone of recirculating flow below the constriction, and (3) expansion gravel bars in the expansion below the zone of recirculating flow. These fan-eddy complexes are the storage location of about 70 percent, by area, of all fine- and coarse-grained alluvium contained within the canyons above the low-water stage. Immediately adjacent meandering reaches contain an order of magnitude more alluvium by area but have no debris fan-created depositional settings. This study also describes the flood-plain and terrace stratigraphy of the Green River in the eastern Uinta Mountains and changes due to the operations of Aarning Gorge Dam, upstream from the study area. These landforms are vertically aggrading deposits that are longiuidinally correlative throughout the 65-km study reach. The suite of surfaces identified includes a terrace that is inundated by rare pre- or post-dam floods, an intermediate bench that is inundated by rare post-dam floods, and a post-dam flood plain that is inundated by the post-dam mean annual flood. Analysis of historical photographs in the study reach shows that both the intermediate bench and post-dam flood plain are landforms that were not present in any of the 6 years for which photographs were examined between 1871 and 1954. Photographic replications also show that gravel bars consisting of bare gravel in 1922 and earlier photographs are now covered by fine-grained alluvium and vegetation. Decreased gravel-bar mobility is indicated by estimates of critical and average boundary shear stress. Comprehensive surficial geologic mapping of the study area indicates that the bankfull channel has decreased in width by an average of about 20 percent

Twentieth Century Geomorphic Changes of the Lower Green River in Canyonlands National Park, Utah: An Investigation of Timing, Magnitude and Process

Since the early 20th century, the Green River, the longest tributary of the Colorado River, has narrowed, decreasing available riparian and aquatic habitat. Initially, the widespread establishment of non-native tamarisk was considered to be the primary driver of channel narrowing. An alternative hypothesis postulated that changes in hydrology drove narrowing. Reductions in total streamflow and changes to flow regime occurred due to wide-spread water development, decreased snowmelt flood magnitude, and the increased cyclicity of wet and dry years. The two hypotheses agree on channel narrowing, but each influences modern river management differently. A tamarisk-driven model of narrowing implies that modern flow management doesn’t substantially affect channel change. Conversely, channel narrowing driven by changes in hydrology implies that present flow management decisions matter and continued adjustments to flow regime may result in future channel change. To understand the roles of decreasing total annual flow, declining annual peak flood magnitude, and changing vegetation communities on 20th century channel narrowing, we investigated channel narrowing along the lower Green River within Canyonlands National Park (CNP). Previous studies agree that the channel has narrowed, however, the rate, timing and magnitude of documented narrowing are only partially understood. Multiple lines of evidence were used to reconstruct the history of channel narrowing in the lower Green River. This study focuses on channel narrowing, but additionally investigated possible changes to channel depth, identified process, timing and magnitude of floodplain formation. Floodplain formation was described in the field using stratigraphy, sedimentology, and dendrogeomorphology exposed in a floodplain trench. Channel and floodplain surveys were conducted to determine possible changes in bed elevation. Additionally, existing aerial imagery, hydrologic data, and sediment transport data were analyzed. These techniques were applied to determine magnitude, timing and processes of channel narrowing at multiple spatial and temporal scales. The floodplain investigation identified a new period of channel narrowing by vertical accretion after high peak flow years of 1983 and 1984. Narrowing was initiated by vertical accretion in the active channel, deposited by moderate floods exceeded more than 50% of the time. Vertical accretion continued in the early 1990s, converting the active channel into a periodically inundated floodplain surface. Suspended-sediment deposition dominated deposits, resulting in the formation of natural levees and floodplain troughs in both inset floodplains. Rates of deposition were highly variable, ranging from 0.03-0.50 m/yr. The lower Green River within Canyonlands National Park has narrowed substantially since the late 1800s, resulting in a narrower channel. Changes to flood magnitude, rate and timing since 1900, driven by increased water storage and diversion in the Green River basin and declines in annual precipitation, were responsible for inset floodplain formation. Floodplains of the contemporary lower Green River in CNP began forming in the late 1930s and continued to form and vertically aggrade in the 20th century by inset floodplain formation. During this time period, peak flow and total runoff declined due to climatic changes and water development. Analysis of aerial imagery covering 61 kilometers (km) of the Green River in CNP shows that changes to the floodplain identified in the trench are representative of the entire study area. The establishment of non-native tamarisk (Tamarix spp.) did not drive channel narrowing, though dense stands stabilized banks and likely promoted sediment deposition. The lower Green River narrowed 12% from 1940-2014, with the majority of narrowing (10% of all narrowing) occurring from the 1980s to the present. Inset floodplain formation reflects changes to flood magnitude and timing resulting from water development and decreases in natural runoff. Findings suggest that long-term management of the riverine corridor within Canyonlands National Park will require a greater focus on upstream flow contributions and how those flows are currently managed. Recovery of endangered endemic native fishes, the Colorado pikeminnow (Ptychocheilus lucius), and the razorback sucker (Xyrauchen texanus), plays a primary role in determining current flow allocations. Collaboration with upstream stakeholders and managers is necessary to maximize elements of the flow regime that preserve channel width and limit channel narrowing

Automated Riverbed Sediment Classification Using Low-Cost Sidescan Sonar

The use of low-cost, low-profile, and highly portable sidescan sonar is on the ascendancy for imaging shallow riverine benthic sediments. A new automated, spatially explicit, and physically-based method for calculating lengthscales of bed texture elements in sidescan echograms (a 2D plot of acoustic intensity as a function of slant range and distance) is suggested. It uses spectral analysis based on the wavelet transform of short sequences of echograms. The recursive application of the transform over small overlapping windows of the echogram provides a robust measure of lengthscales of alternating patterns of strong and weak echoes. This textural lengthscale is not a direct measure of grain size. Rather, it is a statistical representation that integrates over many attributes of bed texture, of which grain size is the most important. The technique is a physically-based means to identify regions of texture within a sidescan echogram, and could provide a basis for objective, automated riverbed sediment classification. Results are evaluated using data from two contrasting riverbed environments: those of the Colorado River in Grand Canyon, Arizona, and the West Branch of the Penobscot River, Maine

Riparian vegetation, Colorado River, and climate: Five decades of spatiotemporal dynamics in the Grand Canyon with river regulation

Documentation of the interacting effects of river regulation and climate on riparian vegetation has typically been limited to small segments of rivers or focused on individual plant species. We examine spatiotemporal variability in riparian vegetation for the Colorado River in Grand Canyon relative to river regulation and climate, over the five decades since completion of the upstream Glen Canyon Dam in 1963. Long-term changes along this highly modified, large segment of the river provide insights for management of similar riparian ecosystems around the world. We analyze vegetation extent based on maps and imagery from eight dates between 1965 and 2009, coupled with the instantaneous hydrograph for the entire period. Analysis confirms a net increase in vegetated area since completion of the dam. Magnitude and timing of such vegetation changes are river stage-dependent. Vegetation expansion is coincident with inundation frequency changes and is unlikely to occur for time periods when inundation frequency exceeds approximately 5%. Vegetation expansion at lower zones of the riparian area is greater during the periods with lower peak and higher base flows, while vegetation at higher zones couples with precipitation patterns and decreases during drought. Short pulses of high flow, such as the controlled floods of the Colorado River in 1996, 2004, and 2008, do not keep vegetation from expanding onto bare sand habitat. Management intended to promote resilience of riparian vegetation must contend with communities that are sensitive to the interacting effects of altered flood regimes and water availability from river and precipitation. å©2015. American Geophysical Union. All Rights Reserved

Linking morphodynamic response with sediment mass balance on the Colorado River in Marble Canyon: Issues of scale, geomorphic setting, and sampling design

Measurements of morphologic change are often used to infer sediment mass balance. Such measurements may, however, result in gross errors when morphologic changes over short reaches are extrapolated to predict changes in sediment mass balance for long river segments. This issue is investigated by examination of morphologic change and sediment influx and efflux for a 100 km segment of the Colorado River in Grand Canyon, Arizona. For each of four monitoring intervals within a 7 year study period, the direction of sand-storage response within short morphologic monitoring reaches was consistent with the flux-based sand mass balance. Both budgeting methods indicate that sand storage was stable or increased during the 7 year period. Extrapolation of the morphologic measurements outside the monitoring reaches does not, however, provide a reasonable estimate of the magnitude of sand-storage change for the 100 km study area. Extrapolation results in large errors, because there is large local variation in site behavior driven by interactions between the flow and local bed topography. During the same flow regime and reach-average sediment supply, some locations accumulate sand while others evacuate sand. The interaction of local hydraulics with local channel geometry exerts more control on local morphodynamic response than sand supply over an encompassing river segment. Changes in the upstream supply of sand modify bed responses but typically do not completely offset the effect of local hydraulics. Thus, accurate sediment budgets for long river segments inferred from reach-scale morphologic measurements must incorporate the effect of local hydraulics in a sampling design or avoid extrapolation altogether

Equilibrium Entrainment of Fine Sediment Over a Coarse Immobile Bed

The transported load in most fluvial systems, including gravel-bedded rivers, includes fine-grained sediment. Models for suspended sediment transport have focused on sand-covered beds, rendering incomplete the theoretical and empirical framework for predicting fine sediment transport and routing. We conducted laboratory experiments involving sand transport over large immobile grains. The experiments were scaled such that immobile particles were much larger than the mobile sediment, but less than 10% of flow depth, and that bed shear stresses, scaled by the size of the mobile sediment, were indicative of transport in suspension. The experiments were conducted in equilibrium transport and included measurements of near-bed sediment concentration and interstitial sand storage for a range of flow and transport rates. Partial filling of grain interstices occurred over a narrow range of flow and transport rates, indicating a sharp threshold between no interstitial sand storage and a sand-covered bed. Less sand coverage on the bed resulted in higher near-bed sand concentrations per unit area of sand than runs with greater sand coverage. As sand bed elevation decreased relative to the coarse grains, turbulent wakes shed by the large grains appeared to enhance grain entrainment more than the corresponding decrease in bed area covered by sand resulted in decreased entrainment. Elevated concentrations were maintained until the bed was depleted of fine sediment. These results are formalized in a proposed sand elevation correction function that scales the entrainment rate for a bed partially covered by sand to the entrainment rate that would be predicted for a sand-covered bed

Improving the prognosis of patients with severely decreased glomerular filtration rate (CKD G4+):Conclusions from a Kidney Disease: Improving Global Outcomes (KDIGO) Controversies Conference

Patients with severely decreased glomerular filtration rate (GFR) (i.e., chronic kidney disease [CKD] G4+) are at increased risk for kidney failure, cardiovascular disease (CVD) events (including heart failure), and death. However, little is known about the variability of outcomes and optimal therapeutic strategies, including initiation of kidney replacement therapy (KRT). Kidney Disease: Improving Global Outcomes (KDIGO) organized a Controversies Conference with an international expert group in December 2016 to address this gap in knowledge. In collaboration with the CKD Prognosis Consortium (CKD-PC) a global meta-analysis of cohort studies (n = 264,515 individuals with CKD G4+) was conducted to better understand the timing of clinical outcomes in patients with CKD G4+ and risk factors for different outcomes. The results confirmed the prognostic value of traditional CVD risk factors in individuals with severely decreased GFR, although the risk estimates vary for kidney and CVD outcomes. A 2- and 4-year model of the probability and timing of kidney failure requiring KRT was also developed. The implications of these findings for patient management were discussed in the context of published evidence under 4 key themes: management of CKD G4+, diagnostic and therapeutic challenges of heart failure, shared decision-making, and optimization of clinical trials in CKD G4+ patients. Participants concluded that variable prognosis of patients with advanced CKD mandates individualized, risk-based management, factoring in competing risks and patient preferences

Genome sequences of four cluster P mycobacteriophages

Four bacteriophages infecting Mycobacterium smegmatis mc2155 (three belonging to subcluster P1 and one belonging to subcluster P2) were isolated from soil and sequenced. All four phages are similar in the left arm of their genomes, but the P2 phage differs in the right arm. All four genomes contain features of temperate phages

Development of Risk Prediction Equations for Incident Chronic Kidney Disease

IMPORTANCE ‐ Early identification of individuals at elevated risk of developing chronic kidney disease  could improve clinical care through enhanced surveillance and better management of underlying health  conditions.  OBJECTIVE – To develop assessment tools to identify individuals at increased risk of chronic kidney  disease, defined by reduced estimated glomerular filtration rate (eGFR).  DESIGN, SETTING, AND PARTICIPANTS – Individual level data analysis of 34 multinational cohorts from  the CKD Prognosis Consortium including 5,222,711 individuals from 28 countries. Data were collected  from April, 1970 through January, 2017. A two‐stage analysis was performed, with each study first  analyzed individually and summarized overall using a weighted average. Since clinical variables were  often differentially available by diabetes status, models were developed separately within participants  with diabetes and without diabetes. Discrimination and calibration were also tested in 9 external  cohorts (N=2,253,540). EXPOSURE Demographic and clinical factors.  MAIN OUTCOMES AND MEASURES – Incident eGFR <60 ml/min/1.73 m2.  RESULTS – In 4,441,084 participants without diabetes (mean age, 54 years, 38% female), there were  660,856 incident cases of reduced eGFR during a mean follow‐up of 4.2 years. In 781,627 participants  with diabetes (mean age, 62 years, 13% female), there were 313,646 incident cases during a mean follow‐up of 3.9 years. Equations for the 5‐year risk of reduced eGFR included age, sex, ethnicity, eGFR, history of cardiovascular disease, ever smoker, hypertension, BMI, and albuminuria. For participants  with diabetes, the models also included diabetes medications, hemoglobin A1c, and the interaction  between the two. The risk equations had a median C statistic for the 5‐year predicted probability of  0.845 (25th – 75th percentile, 0.789‐0.890) in the cohorts without diabetes and 0.801 (25th – 75th percentile, 0.750‐0.819) in the cohorts with diabetes. Calibration analysis showed that 9 out of 13 (69%) study populations had a slope of observed to predicted risk between 0.80 and 1.25. Discrimination was  similar in 18 study populations in 9 external validation cohorts; calibration showed that 16 out of 18 (89%) had a slope of observed to predicted risk between 0.80 and 1.25. CONCLUSIONS AND RELEVANCE – Equations for predicting risk of incident chronic kidney disease developed in over 5 million people from 34 multinational cohorts demonstrated high discrimination and  variable calibration in diverse populations

Stromal Down-Regulation of Macrophage CD4/CCR5 Expression and NF-κB Activation Mediates HIV-1 Non-Permissiveness in Intestinal Macrophages

Tissue macrophages are derived exclusively from blood monocytes, which as monocyte-derived macrophages support HIV-1 replication. However, among human tissue macrophages only intestinal macrophages are non-permissive to HIV-1, suggesting that the unique microenvironment in human intestinal mucosa renders lamina propria macrophages non-permissive to HIV-1. We investigated this hypothesis using blood monocytes and intestinal extracellular matrix (stroma)-conditioned media (S-CM) to model the exposure of newly recruited monocytes and resident macrophages to lamina propria stroma, where the cells take up residence in the intestinal mucosa. Exposure of monocytes to S-CM blocked up-regulation of CD4 and CCR5 expression during monocyte differentiation into macrophages and inhibited productive HIV-1 infection in differentiated macrophages. Importantly, exposure of monocyte-derived macrophages simultaneously to S-CM and HIV-1 also inhibited viral replication, and sorted CD4+ intestinal macrophages, a proportion of which expressed CCR5+, did not support HIV-1 replication, indicating that the non-permissiveness to HIV-1 was not due to reduced receptor expression alone. Consistent with this conclusion, S-CM also potently inhibited replication of HIV-1 pseudotyped with vesicular stomatitis virus glycoprotein, which provides CD4/CCR5-independent entry. Neutralization of TGF-β in S-CM and recombinant TGF-β studies showed that stromal TGF-β inhibited macrophage nuclear translocation of NF-κB and HIV-1 replication. Thus, the profound inability of intestinal macrophages to support productive HIV-1 infection is likely the consequence of microenvironmental down-regulation of macrophage HIV-1 receptor/coreceptor expression and NF-κB activation