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Sediment regimes, i.e., the processes that recruit, transport, and store sediment, create the physical habitats that underpin river‐floodplain ecosystems. Natural and human‐induced disturbances that alter sediment regimes can have cascading effects on river and floodplain morphology, ecosystems, and a river's ability to provide ecosystem services, yet prediction of the response of sediment dynamics to disturbance is challenging. We developed the Sediment Routing and Floodplain Exchange (SeRFE) model, which is a network‐based, spatially explicit framework for modeling sediment recruitment to and subsequent transport through drainage networks. SeRFE additionally tracks the spatially and temporally variable balance between sediment supply and transport capacity. Simulations using SeRFE can account for various types of watershed disturbance and for channel‐floodplain sediment exchange. SeRFE is simple, adaptable, and can be run with widely available geospatial data and limited field data. The model is driven by real or user‐generated hydrographs, allowing the user to assess the combined effects of disturbance, channel‐floodplain interactions and particular flow scenarios on the propagation of disturbances throughout a drainage network, and the resulting impacts to reaches of interest. We tested the model in the Santa Clara River basin, Southern California, in subbasins affected by large dams and wildfire. Model results highlight the importance of hydrologic conditions on postwildfire sediment yield and illustrate the spatial extent of dam‐induced sediment deficit during a flood. SeRFE can provide contextual information on reach‐scale sediment balance conditions, sensitivity to altered sediment regimes, and potential for morphologic change for managers and practitioners working in disturbed watersheds. Plain Language Summary Understanding how sediment moves through watersheds is important for not only landscape evolution but also natural‐resource management. Natural and human‐caused disturbances like dams or wildfires can alter sediment connectivity in watersheds, which in turn can alter habitat and ecosystem services. Modeling approaches to simulate sediment movement through watersheds and how sediment dynamics respond to disturbance are important for managers. Here we present a new model, the Sediment Routing and Floodplain Exchange (SeRFE) model. SeRFE allows users to assess how a river reach may respond to different flow and disturbance scenarios. We tested the model in a Southern California watershed, where outputs highlighted how a wildfire changed sediment output and dams caused sediment deficit. Key Points Riverine practitioners need tools to understand sediment regimes in rivers and how disturbance alters them SeRFE is spatially explicit and simulates sediment recruitment, transport, and storage at the reach‐scale, applied across drainage basins Simulations suggest wildfire‐induced sediment yield depends on hydrologic conditions and illustrate the extent of dam impacts on sediment

Values representing grain size distributions of stream reaches are essential for estimating sediment transport at the reach scale. Various modeling frameworks exist that attempt to simulate reach-scale sediment transport across entire drainage basins to characterize sediment dynamics at a watershed scale. Such frameworks require estimates of grain size at each reach. Because obtaining direct measurements at this scale is impractical and logistically difficult, methods to estimate or extrapolate grain size measurements are needed, however, few currently exist. Here I present an extrapolation algorithm that uses one or more pebble counts to extrapolate full grain size distributions to each reach of a drainage network. In addition to the pebble count measurements, the tool requires a stream network geospatial feature class, attributed with values for reach-averaged slope and some consistent measure of relative flow magnitude (or a proxy for flow). I tested the tool in a set of sub-watersheds in the Bitterroot River basin of western Montana, US, with varying valley morphologies, and compared predictions to measurements at 16 sites. When using multiple measurements for calibration, mean absolute percent error averaged 5.8 % of the measured grain sizes in the phi scale. When using a single measurement for calibration, error averaged 8.4 %.

Environmental stressors associated with human land and water-use activities have degraded many riparian ecosystems across the western United States. These stressors include (i) the widespread expansion of invasive plant species that displace native vegetation and exacerbate streamflow and sediment regime alteration; (ii) agricultural and urban development in valley bottoms that decouple streams and rivers from their floodplains and reduce instream wood recruitment and retention; and (iii) flow modification that reduces water quantity and quality, degrading aquatic habitats. Here we apply a novel drainage network model to assess the impacts of multiple stressors on reach-scale riparian condition across two large U.S. regions. In this application, we performed a riparian condition assessment evaluating three dominant stressors: (1) riparian vegetation departure from historical condition; (2) land-use intensity within valley bottoms; and (3) floodplain fragmentation caused by infrastructure within valley bottoms, combining these stressors in a fuzzy inference system. We used freely available, geospatial data to estimate reach-scale (500 m) riparian condition for 52,800 km of perennial streams and rivers, 25,600 km in Utah, and 27,200 km in 12 watersheds of the interior Columbia River Basin (CRB). Model outputs showed that riparian condition has been at least moderately impaired across ≈70% of the streams and rivers in Utah and ≈49% in the CRB. We found 84% agreement (Cohen’s ĸ = 0.79) between modeled reaches and field plots, indicating that modeled riparian condition reasonably approximates on-the-ground conditions. Our approach to assessing riparian condition can be used to prioritize watershed-scale floodplain conservation and restoration by providing network-scale data on the extent and severity of riparian degradation. The approach that we applied here is flexible and can be expanded to run with additional riparian stressor data and/or finer resolution input data.

Eurasian beaver (Castor fiber) populations are expanding across Europe. Depending on location, beaver dams bring multiple benefits and/or require management. Using nationally available data, we developed: a Beaver Forage Index (BFI), identifying beaver foraging habitat, and a Beaver Dam Capacity (BDC) model, classifying suitability of river reaches for dam construction, to estimate location and number of dams at catchment scales. Models were executed across three catchments, in Great Britain (GB), containing beaver. An area of 6747 km2 was analysed for BFI and 16,739 km of stream for BDC. Field surveys identified 258 km of channel containing beaver activity and 89 dams, providing data to test predictions. Models were evaluated using a categorical binomial Bayesian framework to calculate probability of foraging and dam construction. BFI and BDC models successfully categorised the use of reaches for foraging and damming, with higher scoring reaches being preferred. Highest scoring categories were ca. 31 and 79 times more likely to be used than the lowest for foraging and damming respectively. Zero-inflated negative binomial regression showed that modelled dam capacity was significantly related (p = 0.01) to observed damming and was used to predict numbers of dams that may occur. Estimated densities of dams, averaged across each catchment, ranged from 0.4 to 1.6 dams/km, though local densities may be up to 30 dams/km. These models provide fundamental information describing the distribution of beaver foraging habitat, where dams may be constructed and how many may occur. This supports the development of policy and management concerning the reintroduction and recolonisation of beaver.

For centuries, streams and rivers have been altered and degraded such that the conveyance of water downstream is unnaturally efficient, often to the detriment of other biophysical processes that maintain healthy riverscapes. Structural elements, such as beaver dams, can impact hydraulics and alter downstream water conveyance. While the hydraulic, hydrologic, geomorphic, and ecological effects of beaver dams have been quantified at individual study sites, study methods are often cost-prohibitive and complicated, making them less practical for monitoring at large spatial scales and in diverse settings. We mapped inundation extent and type (free flowing, ponded, and overflowing) in beaver dam complexes in diverse hydrogeomorphic settings as a simple method to monitor beaver-influenced riverscapes based on delineating inundation patterns. Our mapping of over 75 inundation events at 37 sites suggests that, on average, under undammed conditions valley bottom inundation ranged from 2.7% - 17.4% (mean 6.8%) whereas under dammed conditions the same sites had valley bottom inundation that ranged from 9.5% - 47.5% (mean 23.2%). We observed that, when beaver dams are present, roughly half of surface water inundation is converted from a free-flowing type to ponded and overflow types. This research also reveals that the focus of most previous beaver dam studies on low gradients and low stream orders is unnecessarily restrictive. We report similar magnitudes of influence in steeper gradient riverscapes as well as in beaver-modified floodplains and anabranches of higher-order rivers that are typically considered to be too large for beaver dams. While the quantification of inundated area and type presented here is valuable as a simple metric, we postulate that delineation of inundation type and extent can be used as a practical proxy for physical processes and indicators of riverscape health such as longer and more varied water residence times (i.e., hydrologic inefficiency).

We use nationally representative household-level panel survey data in two neighboring countries in Southern Africa—Zambia and Malawi—to characterize the current status of rural land rental market participation by smallholder farmers, and their subsequent welfare impacts. Rural rental market participation is much higher in densely-populated Malawi than in lower-density Zambia, reflecting the role of land scarcity in driving rental market development. Consistent with previous literature, we find evidence that rental markets contribute to efficiency gains within the smallholder sector by facilitating the transfer of land from less-able to more-able producers, on average, in both countries. Furthermore, we find that rental markets serve to re-allocate land from relatively land-rich to landpoor households. We examine the impacts of participation on a number of welfare outcomes and find evidence for generally positive returns to renting in land in both countries, on average. However, our analysis also indicates that the returns to renting in land vary strongly with scale of production: tenants who produce more have larger returns to renting in, and many of the smaller producers who rent in do so at an economic loss. The impacts of renting out (i.e., participating in markets as landlords) are decidedly more mixed, with overall negative returns to landlords in Malawi and negligible returns to landlords in Zambia. The findings in this article highlight the need for researchers and policymakers in sub-Saharan Africa to stay attuned to how land rental market participation and its impacts evolve in the near future.

Background. In Thailand, phase 1/2 trials of monovalent subtype B and bivalent subtype B/E (CRF01_AE) recombinant glycoprotein 120 human immunodeficiency virus type 1 (HIV‐1) vaccines were successfully conducted from 1995 to 1998, prompting the first HIV‐1 vaccine efficacy trial in Asia. Methods. This randomized, double‐blind, placebo‐controlled efficacy trial of AIDSVAX B/E (VaxGen), which included 36‐months of follow‐up, was conducted among injection drug users (IDUs) in Bangkok, Thailand. The primary end point was HIV‐1 infection; secondary end points included plasma HIV‐1 load, CD4 cell count, onset of acquired immunodeficiency syndrome–defining conditions, and initiation of antiretroviral therapy. Results. A total of 2546 IDUs were enrolled between March 1999 and August 2000; the median age was 26 years, and 93.4% were men. The overall HIV‐1 incidence was 3.4 infections/100 person‐years (95% confidence interval [CI], 3.0–3.9 infections/100 person‐years), and the cumulative incidence was 8.4%. There were no differences between the vaccine and placebo arms. HIV‐1 subtype E (83 vaccine and 81 placebo recipients) accounted for 77% of infections. Vaccine efficacy was estimated at 0.1% (95% CI, −30.8% to 23.8%; P=.99, log‐rank test). No statistically significant effects of the vaccine on secondary end points were observed. Conclusion. Despite the successful completion of this efficacy trial, the vaccine did not prevent HIV‐1 infection or delay HIV‐1 disease progression.

DNA replication occurs through an intricately regulated series of molecular events and is fundamental for genome stability 1 , 2 . At present, it is unknown how the locations of replication origins are determined in the human genome. Here we dissect the role of topologically associating domains (TADs) 3 – 6 , subTADs 7 and loops 8 in the positioning of replication initiation zones (IZs). We stratify TADs and subTADs by the presence of corner-dots indicative of loops and the orientation of CTCF motifs. We find that high-efficiency, early replicating IZs localize to boundaries between adjacent corner-dot TADs anchored by high-density arrays of divergently and convergently oriented CTCF motifs. By contrast, low-efficiency IZs localize to weaker dotless boundaries. Following ablation of cohesin-mediated loop extrusion during G1, high-efficiency IZs become diffuse and delocalized at boundaries with complex CTCF motif orientations. Moreover, G1 knockdown of the cohesin unloading factor WAPL results in gained long-range loops and narrowed localization of IZs at the same boundaries. Finally, targeted deletion or insertion of specific boundaries causes local replication timing shifts consistent with IZ loss or gain, respectively. Our data support a model in which cohesin-mediated loop extrusion and stalling at a subset of genetically encoded TAD and subTAD boundaries is an essential determinant of the locations of replication origins in human S phase. A study shows that the three-dimensional conformation of the human genome influences the positioning of DNA replication initiation zones, highlighting cohesin-mediated loop anchors as essential determinants of their precise location.

We use three waves of nationally representative panel data from Tanzania to estimate the extent to which land rental markets provide a pathway for youth to enter into agriculture. We also investigate how transaction costs may impede youth access to renting-in land. Results suggest that rental markets are important mechanisms through which young farmers access land, but younger farmers face higher transaction costs when renting land than do older farmers. We also find evidence that younger farmers pay higher prices for rented land and are somewhat less likely to belong to village savings groups than are their older counterparts.

Hemostasis encompasses an ensemble of interactions among platelets, coagulation factors, blood cells, endothelium, and hemodynamic forces, but current assays assess only isolated aspects of this complex process. Accordingly, here we develop a comprehensive in vitro mechanical injury bleeding model comprising an “endothelialized” microfluidic system coupled with a microengineered pneumatic valve that induces a vascular “injury”. With perfusion of whole blood, hemostatic plug formation is visualized and “in vitro bleeding time” is measured. We investigate the interaction of different components of hemostasis, gaining insight into several unresolved hematologic issues. Specifically, we visualize and quantitatively demonstrate: the effect of anti-platelet agent on clot contraction and hemostatic plug formation, that von Willebrand factor is essential for hemostasis at high shear, that hemophilia A blood confers unstable hemostatic plug formation and altered fibrin architecture, and the importance of endothelial phosphatidylserine in hemostasis. These results establish the versatility and clinical utility of our microfluidic bleeding model. Hemostasis is a complex ensemble of events, but current bleeding assays only analyze single components like coagulation or platelet function. Here the authors present a comprehensive vascularized microfluidic mechanical injury bleeding model that addresses different aspects of the hemostatic process.