Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Insights into Centennial-Scale Salt Marsh Morphodynamics from the Oregon Coast

Quantification and comparison of morphological changes over the last ~300 y in Oregon salt marshes provide valuable insights into the tectonic, hydroclimatic, and anthropogenic processes shaping this important intertidal zone. Understanding of the rates and drivers of salt marsh change contextualizes intertidal habitats within the sediment routing system (i.e., source to sink); informs models of local and global biogeochemical cycles, important for global climate predictions; and guides ecosystem service protection and restoration efforts. The estimation of rates and drivers of sediment accumulation is made possible by analysis of sediment archives, and though complex, comparison of histories of sediment accumulation between systems with spatiotemporally variable drivers reveals relationships, feedbacks, and thresholds. In particular, the Oregon margin provides an opportunity to compare a number of important drivers of centennial salt marsh morphologic change, including relative sea level rise, suspended sediment supply, basin area, bay morphology, and coseismic subsidence related to Cascadia Subduction Zone (CSZ) earthquakes, all of which will be discussed in this dissertation. To quantify sediment and carbon accumulation rates within Oregon intertidal areas (mudflat, low marsh, high marsh, and scrub-shrub wetland) and to assess the relative importance of elevation, relative sea level rise, and fluvial suspended sediment supply on vertical accretion, excess 210Pb derived accretion rates were measured within seven Oregon estuaries (Youngs, Nehalem, Tillamook, Netarts, Salmon, Alsea, & Coquille). Accretion rates combined with downcore measurements of dry bulk density and organic carbon content produce rates of carbon burial, therefore further highlighting the importance of determining the factors controlling sediment accretion. In a subset of estuaries (Nehalem, Netarts, Salmon, Alsea, & Coquille), excess 210Pb profiles were reanalyzed to estimate time-varying rates of accumulation and lateral growth rates were assessed by comparing georeferenced and digitized aerial salt marsh imagery over the last ~80 y at roughly decadal resolution. Further, to establish the impact of coseismic subsidence during CSZ earthquakes on the evolution of Oregon intertidal areas, an age-depth method of combining excess 210Pb and high-resolution 14C dates with Bayesian modeling was tested as proof of concept in Netarts Bay stratigraphy following the 1700 CE earthquake. Taken together, results of these investigations provide both much needed data on and insights into drivers of salt marsh morphodynamic change. For instance, two (Salmon & Alsea) of the seven estuaries exhibit mean rates of accretion less than relative sea level rise over the last century and thus are drowning, possibly linked to comparatively high rates of relative sea level rise, though mean annual sediment is not apparently limited. Further assessment of the temporal changes in rates of vertical accretion reveals that only Alsea is accreting at a pace significantly lower than the rate of relative sea level rise (the uncertainty range associated with the rate of accretion in Salmon overlaps with the uncertainty range for relative sea level rise). As Alsea experiences one of the fastest sea level rise rates along the coast (2.8 ± 0.8 mm y-1), it is possible that inundation stress and resulting loss of marsh plants could be the cause of drowning through decreased sediment retention, and therefore the threshold rate of drowning is relatively low. Further, high marshes that experience neutral or negative rates of sea level rise (Youngs & Coquille, respectively) have been accreting over the last century, even though the conceptual morphodynamic model requires the creation of accommodation space (volume of space created by long-term relative sea level rise) for growth. Unexpectedly high rates of accretion in systems with low or negative rates of sea level rise (Young, Nehalem, & Coquille) could be linked to large sediment fluxes, but time varying rates of accretion are not significantly higher during a period of elevated sediment loads (1944 to 1977), as a result of timber harvest and the wet phase of the Pacific Decadal Oscillation (PDO), indicating another cause. Comparison of storm hydrographs between Alsea and Nehalem reveals that Nehalem’s larger basin area results in longer flood durations and likely increased inundation by turbid-water. This relationship between large basins, long storm hydrographs, and increased inundation when sediment concentrations are likely high appears to explain the observed patterns of sediment accretion. Systems inundated with sediment-rich water will accrete (perhaps the case in Nehalem), systems inundated without sediment-rich water will not accrete (perhaps the case in Alsea as sea level rise is fast), and systems with sediment-rich water that does not inundate the platform will not accrete (perhaps the case in Coquille as sea level is falling). Further, vertical accretion appears linked to lateral expansion, as only salt marshes accreting at the same pace or greater as sea level rise expanded over the last century. However, comparisons between a period of enhanced fluvial sediment discharge (1944 to 1977) to more recent decades reveal that Oregon salt marshes expanded under elevated sediment fluxes, though the amount was limited in areas without available lateral accommodation space (Salmon & Coquille) or without filled vertical accommodation spaces (Alsea). The earthquake deformation cycle is additionally important in controlling marsh growth. Indeed, high resolution (~decadal) age-depth modeling of the last 300 y assessed with downcore facies indicators (e.g., dry bulk density) indicates that Netarts Bay has not yet reestablished the pre-1700 CE CSZ earthquake elevation and scrub-shrub habitat, despite having experienced comparatively moderate coseismic subsidence (~0.5 m). The filling of Netarts salt marsh accommodation space may be limited by a lack of suspended sediment, but comparison with the timing of accommodation space filling in other Oregon salt marshes and along elevation transects is required to better elucidate the mechanisms of filling. Clearly, in addition to shedding light on important rates and drivers of salt marsh growth, the results of this dissertation highlight multiple questions that warrant further investigation.

Spatiotemporal variation in Oregon salt marsh expansion and contraction (GIS data)

The dataset is a layer file created in ArcGIS Pro 2.2. The dataset includes digitized outlines of the seaward edges of five Oregon salt marshes (Nehalem, Netarts, Salmon, Alsea, and Coquille). These are roughly decadal from 1939 to 2018 and were hand-digitized using historical aerial photography (1939 to the late 1990s) scanned at the University of Oregon’s Map & Aerial Photography Library and aerial imagery downloaded from the Oregon Statewide Imagery Program (https://www.oregon.gov/geo/Pages/imagery_data.aspx). Historical aerial imagery were georeferenced using ≥ 10 control points that were placed at stable locations including road and channel intersections, and using a second order polynomial transformation. Salt marsh areas were determined using a stable upslope edge (Pacific Marine & Estuarine Fish Habitat Partnership current extent map https://www.pacificfishhabitat.org/data/). The dataset also includes rates of salt marsh seaward edge change which was calculated using the USGS Digital Shoreline Analysis System (DSAS; https://www.usgs.gov/centers/whcmsc/science/digital-shoreline-analysis-system-dsas?qt-science_center_objects=0#qt-science_center_objects) in ArcMap 10.7.1 over roughly decadal periods from 1939 to 2018 and integrated over the period of record. DSAS automatically placed transects at 5 m intervals perpendicular to digitized marsh edges. When calculating the rate of edge change integrated over all digitized edges, regressions were fit for any transect that passed through ≥ 6 edges. Error estimates associated with the regressions were calculated with 95% confidence intervals. These rates and uncertainties can be found in the attribute tables of each shapefile.Research context: These data were collected to assess potential drivers of marsh lateral rates of expansion/contraction over the last ~80 y in five Oregon estuaries: Nehalem Bay, Netarts Bay, Salmon River Estuary, Alsea Bay, and Coquille River Estuary (focusing on marshes relatively unimpacted by dikes). These systems vary in terms of bay morphology, mean annual fluvial sediment supply, and relative sea level changes. These forcings were assessed by comparing net lateral rates of edge change within and across estuaries. Further, to assess the importance of changing land use and hydroclimate on marsh morphodynamics, roughly decadal rates of marsh expansion/contraction were compared for each estuary. These rates were binned into four distinct periods to assess the relative importance of the PDO and history of timber harvest in uplands on marsh expansion/contraction (1939 to 1944, 1944 to 1977, 1977 to 2000, and 2000 to 2018). Results will elucidated both spatiotemporal patterns of marsh lateral change and provided an idea of future trajectories under changing climate and land use scenarios

Controls on sediment accretion and blue carbon burial in tidal saline wetlands : insights from the Oregon Coast, USA

Oregon estuaries provide important opportunities to assess controls on tidal saline wetland carbon burial and sediment accretion as both rates of relative sea level rise (RSLR; −1.4 ± 0.9 to 2.8 ± 0.8 mm yr⁻¹) and fluvial suspended sediment load relative to estuary area (0.23 to 17 × 10³ t km⁻² yr⁻¹) vary along the coast. We hypothesized that vertical accretion, measured using excess ²¹⁰Pb in least‐disturbed wetlands within seven Oregon estuaries, would vary with either RSLR or sediment load relative to estuary area, and carbon burial would correlate strongly to sediment accretion. Mean rates of high marsh accretion (0.8 ± 0.2 to 4.1 ± 0.2 mm yr⁻¹) indicate that Oregon tidal wetlands have mainly kept pace with twentieth‐century RSLR with the exception that the accretionary balance in the central coast is negative, suggesting drowning. Experiencing the fastest rates of RSLR, central‐coast estuaries may foreshadow the fates of other Oregon estuaries under future accelerated sea level rise. Comparison of mass accumulation rates with sediment loads, however, indicates low trapping efficiency and therefore no fluvial sediment limitation. Thus, nonlinear feedback between RSLR and sediment accretion may enhance wetland resistance to drowning. Among wetlands keeping pace with or exceeding RSLR, sediment accretion displays no significant relationship with elevation but rather appears controlled by both the rate of RSLR and relative sediment load, highlighting the importance of incorporating both factors into future studies of tidal saline wetlands. Carbon burial rates, controlled by sediment accretion, will likely increase with future accelerated sea level rise

Influence of relict milldams on riparian sediment biogeochemistry

Purpose: Riparian zones are important modifiers of nutrient flux between terrestrial and aquatic ecosystems. However, dams alter riparian zones—trapping fine-grained, organic matter-rich sediment and creating poorly mixed, low oxygen conditions—thereby affecting sediment biogeochemistry in poorly understood ways. Methods: We characterized the impact of two relict US mid-Atlantic milldams (one from a primarily agricultural watershed and one from a mixed land use/urban watershed) on spatial patterns of bioavailable element concentrations (Mehlich-3 extractable P, K, Ca, Mg, Mn, Zn, Cu, Fe, B, S, and Na) in sediments upstream and downstream of milldams, with depth, and along transects running parallel and perpendicular to the stream. Results: Element concentrations were not clearly correlated with grain size or organic matter content and, although generally higher, were not significantly more concentrated in upstream riparian sediments when similar (shallow, variably saturated) depths were compared. Pronounced differences were observed: upstream of milldams, sediment concentrations of Ca and Mg were highest in variably saturated shallow sediments, while Fe and Mn were highest in deeper, continuously saturated, low-oxygen sediments. Additionally, data was significantly different by milldam site, a result of differences in land-use histories (e.g., road salt and fertilizer application/runoff) and dominant bedrock geology. Conclusion: Overall, results highlight the combined importance of milldams (and associated influences on groundwater hydrology and sediment redox conditions) and external drivers (other land-use legacies and bedrock geology) in influencing spatial patterns of bioavailable elements in riparian sediments

35 Designing Implicit Interfaces for Physiological Computing: Guidelines and Lessons Learned Using fNIRS

A growing body of recent work has shown the feasibility of brain and body sensors as input to interactive systems. However, the interaction techniques and design decisions for their effective use are not well defined. We present a conceptual framework for considering implicit input from the brain, along with design principles and patterns we have developed from our work. We also describe a series of controlled, offline studies that lay the foundation for our work with functional near-infrared spectroscopy (fNIRS) neuroimaging, as well as our real-time platform that serves as a testbed for exploring brain-based adaptive interaction techniques. Finally, we present case studies illustrating the principles and patterns for effective use of brain data in human-computer interaction. We focus on signals coming from the brain, but these principles apply broadly to other sensor data and in domains such as aviation, education, medicine, driving, and anything involving multitasking or varying cognitive workload

Nitrogen Sinks or Sources? Denitrification and Nitrogen Removal Potential in Riparian Legacy Sediment Terraces Affected by Milldams

Riparian zones are key ecotones that buffer aquatic ecosystems through removal of nitrogen (N) via processes such as denitrification. However, how dams alter riparian N cycling and buffering capacity is poorly understood. Here, we hypothesized that elevated groundwater and anoxia due to the backup of stream water above milldams may enhance denitrification. We assessed denitrification rates (using denitrification enzyme assays) and potential controlling factors in riparian sediments at various depths upstream and downstream of two relict U.S. mid-Atlantic milldams. Denitrification was not significantly different between upstream and downstream, although was greater per river km upstream considering deeper and wider geometries. Further, denitrification typically occurred in hydrologically variable shallow sediments where nitrate-N and organic matter were most concentrated. At depths below 1 m, both denitrification and nitrate-N decreased while ammonium-N concentrations substantially increased, indicating suppression of ammonium consumption or dissimilatory nitrate reduction to ammonium. These results suggest that denitrification occurs where dynamic groundwater levels result in higher rates of nitrification and mineralization, while another N process that produces ammonium-N competes with denitrification for limited nitrate-N at deeper, more stagnant/poorly mixed depths. Ultimately, while it is unclear whether relict milldams are sources of N, limited denitrification rates indicate that they are not always effective sinks; thus, milldam removal—especially accompanied by removal of ammonium-N rich legacy sediments—may improve riparian N buffering

Backed-Up, Saturated, and Stagnant: Effect of Milldams on Upstream Riparian Groundwater Hydrologic and Mixing Regimes

How milldams alter riparian hydrologic and groundwater mixing regimes is not well understood. Understanding the effects of milldams and their legacies on riparian hydrology is key to assessing riparian pollution buffering potential and for making appropriate watershed management decisions. We examined the spatiotemporal effects of milldams on groundwater gradients, flow directions, and mixing regime for two dammed sites on Chiques Creek, Pennsylvania (2.4 m tall milldam), and Christina River, Delaware (4 m tall dam), USA. Riparian groundwater levels were recorded every 30 min for multiple wells and transects. Groundwater mixing regime was characterized using 30-min specific conductance data and selected chemical tracers measured monthly for about 2 years. Three distinct regimes were identified for riparian groundwaters—wet, dry, and storm. Riparian groundwater gradients above the dam were low but were typically from the riparian zone to the stream. These flow directions were reversed (stream to riparian) during dry periods due to riparian evapotranspiration losses and during peak stream flows. Longitudinal (parallel to the stream) riparian flow gradients and directions also varied across the hydrologic regimes. Groundwater mixing varied spatially and temporally between storms and seasons. Near-stream groundwater was poorly flushed or mixed during storms whereas that in the adjacent swales revealed greater mixing. This differential groundwater behavior was attributed to milldam legacies that include: berm and swale topography that influenced the routing of surface waters, varying riparian legacy sediment depths and hydraulic conductivities, evapotranspiration losses from riparian vegetation, and runoff input from adjoining roads

Infant sex differences in human milk intake and composition from 1- to 3-month post-delivery in a healthy United States cohort

Background Macronutrient composition of human milk differs by infant sex, but few studies have examined sex differences in other milk components, or their potential modification by maternal body mass index (BMI). Aim We compared milk intake and human milk hormone and cytokine concentrations at 1- and 3-month post-delivery and tested infant sex by maternal BMI (OW/OB vs. NW) interactions. Subjects and method Data were analysed for 346 mother–infant dyads in the Mothers and Infants Linked for Healthy Growth (MILk) Study at 1- and 3-month post-delivery. Infant milk intake was estimated by the change in infant weight after test feedings. Concentrations of glucose, insulin, leptin, adiponectin, interleukin-6 (IL-6), and C-reactive protein (CRP) were measured using ELISA. Multivariable linear regression and linear mixed models were used to estimate sex main effects and their interaction with maternal BMI. Results Mean glucose concentration at 1 month was 2.62 mg/dl higher for male infants, but no difference at 3 months was observed. Milk intake and concentrations for the other milk components were similar for males and females at both time points. Associations with infant sex did not differ significantly by maternal BMI. Conclusions Among healthy United States mother–infant dyads, appetite, and growth-regulating factors in human milk did not differ significantly by infant sex