In order to produce useful hydrologic and aquatic habitat data from the Landsat system, the U.S. Geological Survey has developed the “Dynamic Surface Water Extent” (DSWE) Landsat Science Product. ...DSWE will provide long-term, high-temporal resolution data on variations in inundation extent. The model used to generate DSWE is composed of five decision-rule based tests that do not require scene-based training. To allow its general application, required inputs are limited to the Landsat at-surface reflectance product and a digital elevation model. Unlike other Landsat-based water products, DSWE includes pixels that are only partially covered by water to increase inundation dynamics information content. Previously published DSWE model development included one wetland-focused test developed through visual inspection of field-collected Everglades spectra. A comparison of that test’s output against Everglades Depth Estimation Network (EDEN) in situ data confirmed the expectation that omission errors were a prime source of inaccuracy in vegetated environments. Further evaluation exposed a tendency toward commission error in coniferous forests. Improvements to the subpixel level “partial surface water” (PSW) component of DSWE was the focus of this research. Spectral mixture models were created from a variety of laboratory and image-derived endmembers. Based on the mixture modeling, a more “aggressive” PSW rule improved accuracy in herbaceous wetlands and reduced errors of commission elsewhere, while a second “conservative” test provides an alternative when commission errors must be minimized. Replication of the EDEN-based experiments using the revised PSW tests yielded a statistically significant increase in mean overall agreement (4%, p = 0.01, n = 50) and a statistically significant decrease (11%, p = 0.009, n = 50) in mean errors of omission. Because the developed spectral mixture models included image-derived vegetation endmembers and laboratory spectra for soil groups found across the US, simulations suggest where the revised DSWE PSW tests perform as they do in the Everglades and where they may prove problematic. Visual comparison of DSWE outputs with an unusual variety of coincidently collected images for locations spread throughout the US support conclusions drawn from Everglades quantitative analyses and highlight DSWE PSW component strengths and weaknesses.
Synthetic aperture radar (SAR) sensors represent an indispensable data source for flood disaster planners and responders, given their ability to image the Earth's surface nearly independently of ...weather conditions and time of day. The decision by the European Space Agency (ESA) Copernicus program to open data from its Sentinel-1 SAR satellites to the public marks the first time global, operational SAR data have been made freely available. Combined with the emergence of cloud computing platforms like the Google Earth Engine (GEE), this development presents a tremendous opportunity to the disaster response community, for whom rapid access to analysis-ready data is needed to inform effective flood disaster response interventions and management plans. Here, we present an algorithm that exploits all available Sentinel-1 SAR images in combination with historical Landsat and other auxiliary data sources hosted on the GEE to rapidly map surface inundation during flood events. Our algorithm relies on multi-temporal SAR statistics to identify unexpected floods in near real-time. Additionally, historical Landsat-based surface water class probabilities are used to distinguish unexpected floods from permanent or seasonally occurring surface water. We assessed our algorithm over three recent flood events using coincident very high- spatial resolution imagery and operational flood maps. Using very high resolution optical imagery, we estimated an area-normalized accuracy of 89.8 ± 2.8% (95% c.i.) over Houston, Texas following Hurricane Harvey in late August 2017, representing an improvement of between 1.6% and 9.8% over flood maps derived from a simple backscatter threshold. Additionally, comparison of our results with SAR-derived Copernicus Emergency Management Service (EMS) maps following devastating floods in Thessaly, Greece and Eastern Madagascar in January and March 2018, respectively, yielded overall agreement rates of 98.5% in both cases. Importantly, our algorithm was able to ingest hundreds of SAR and optical images served on the GEE to produce flood maps over affected areas within minutes, circumventing the need for time-consuming data download and pre-processing steps. The flexibility of our algorithm will allow for the rapid processing of future open-access SAR data, including data from future Sentinel-1 missions.
•A new flood detection and monitoring algorithm based on dense Sentinel-1 SAR data is presented.•Temporal backscatter anomalies correct for bias arising from difference in sensor configuration and view angles.•Temporal Z-scores provide an objective measure of change due to flooding.•Integrating Sentinel-1 and Landsat data allow for distinction between seasonal water regimes and new flooding.•Google Earth Engine allows for rapid deployment of algorithm during flood events.
The U.S. Geological Survey is developing new Landsat science products. One, named Dynamic Surface Water Extent (DSWE), is focused on the representation of ground surface inundation as detected in ...cloud-/shadow-/snow-free pixels for scenes collected over the U.S. and its territories. Characterization of DSWE uncertainty to facilitate its appropriate use in science and resource management is a primary objective. A unique evaluation dataset developed from data made publicly available through the Everglades Depth Estimation Network (EDEN) was used to evaluate one candidate DSWE algorithm that is relatively simple, requires no scene-based calibration data, and is intended to detect inundation in the presence of marshland vegetation. A conceptual model of expected algorithm performance in vegetated wetland environments was postulated, tested and revised. Agreement scores were calculated at the level of scenes and vegetation communities, vegetation index classes, water depths, and individual EDEN gage sites for a variety of temporal aggregations. Landsat Archive cloud cover attribution errors were documented. Cloud cover had some effect on model performance. Error rates increased with vegetation cover. Relatively low error rates for locations of little/no vegetation were unexpectedly dominated by omission errors due to variable substrates and mixed pixel effects. Examined discrepancies between satellite and in situ modeled inundation demonstrated the utility of such comparisons for EDEN database improvement. Importantly, there seems no trend or bias in candidate algorithm performance as a function of time or general hydrologic conditions, an important finding for long-term monitoring. The developed database and knowledge gained from this analysis will be used for improved evaluation of candidate DSWE algorithms as well as other measurements made on Everglades surface inundation, surface water heights and vegetation using radar, lidar and hyperspectral instruments. Although no other sites have such an extensive in situ network or long-term records, the broader applicability of this and other candidate DSWE algorithms is being evaluated in other wetlands using this work as a guide. Continued interaction among DSWE producers and potential users will help determine whether the measured accuracies are adequate for practical utility in resource management.
The assembly of DNA barcode libraries is particularly relevant within species-rich natural communities for which accurate species identifications will enable detailed ecological forensic studies. In ...addition, well-resolved molecular phylogenies derived from these DNA barcode sequences have the potential to improve investigations of the mechanisms underlying community assembly and functional trait evolution. To date, no studies have effectively applied DNA barcodes sensu strictu in this manner. In this report, we demonstrate that a three-locus DNA barcode when applied to 296 species of woody trees, shrubs, and palms found within the 50-ha Forest Dynamics Plot on Barro Colorado Island (BCI), Panama, resulted in >98% correct identifications. These DNA barcode sequences are also used to reconstruct a robust community phylogeny employing a supermatrix method for 281 of the 296 plant species in the plot. The three-locus barcode data were sufficient to reliably reconstruct evolutionary relationships among the plant taxa in the plot that are congruent with the broadly accepted phylogeny of flowering plants (APG II). Earlier work on the phylogenetic structure of the BCI forest dynamics plot employing less resolved phylogenies reveals significant differences in evolutionary and ecological inferences compared with our data and suggests that unresolved community phylogenies may have increased type I and type II errors. These results illustrate how highly resolved phylogenies based on DNA barcode sequence data will enhance research focused on the interface between community ecology and evolution.
We present new measurements of the parallax of seven long-period (≥10 days) Milky Way (MW) Cepheid variables (SS CMa, XY Car, VY Car, VX Per, WZ Sgr, X Pup, and S Vul) using one-dimensional ...astrometric measurements from spatial scanning of Wide-Field Camera 3 on the Hubble Space Telescope (HST). The observations were obtained at ∼6 month intervals over 4 years. The distances are 1.7-3.6 kpc, with a mean precision of 45 as (signal-to-noise ratio (S/N) 10) and a best precision of 29 as (S/N = 14). The accuracy of the parallaxes is demonstrated through independent analyses of >100 reference stars. This raises to 10 the number of long-period Cepheids with significant parallax measurements, 8 obtained from this program. We also present high-precision mean F555W, F814W, and F160W magnitudes of these Cepheids, allowing a direct, zeropoint-independent comparison to >1800 extragalactic Cepheids in the hosts of 19 SNe Ia. This sample addresses two outstanding systematic uncertainties affecting prior comparisons of MW and extragalactic Cepheids used to calibrate the Hubble constant (H0): their dissimilarity of periods and photometric systems. Comparing the new parallaxes to their predicted values derived from reversing the distance ladder gives a ratio (or independent scale for H0) of 1.037 0.036, consistent with no change and inconsistent at the 3.5 level with a ratio of 0.91 needed to match the value predicted by Planck cosmic microwave background data in concert with ΛCDM. Using these data instead to augment the Riess et al. measurement of H0 improves the precision to 2.3%, yielding 73.48 1.66 km s−1 Mpc−1, and the tension with Planck + ΛCDM increases to 3.7 . The future combination of Gaia parallaxes and HST spatial scanning photometry of 50 MW Cepheids can support a <1% calibration of H0.
Accurately quantifying surface water extent in wetlands is critical to understanding their role in ecosystem processes. However, current regional- to global-scale surface water products lack the ...spatial or temporal resolution necessary to characterize heterogeneous or variable wetlands. Here, we proposed a fully automatic classification tree approach to classify surface water extent using Sentinel-1 synthetic aperture radar (SAR) data and training datasets derived from prior class masks. Prior classes of water and non-water were generated from the Shuttle Radar Topography Mission (SRTM) water body dataset (SWBD) or composited dynamic surface water extent (cDSWE) class probabilities. Classification maps of water and non-water were derived over two distinct wetlandscapes: the Delmarva Peninsula and the Prairie Pothole Region. Overall classification accuracy ranged from 79% to 93% when compared to high-resolution images in the Prairie Pothole Region site. Using cDSWE class probabilities reduced omission errors among water bodies by 10% and commission errors among non-water class by 4% when compared with results generated by using the SWBD water mask. These findings indicate that including prior water masks that reflect the dynamics in surface water extent (i.e., cDSWE) is important for the accurate mapping of water bodies using SAR data.
How plants recognize pathogens and activate defense is still mysterious. Direct interaction between pathogen avirulence (Avr) proteins and plant disease resistance proteins is the exception rather ...than the rule. During infection, Cladosporium fulvum secretes Avr2 protein into the apoplast of tomato leaves and, in the presence of the extracellular leucine-rich repeat receptor-like Cf-2 protein, triggers a hypersensitive response (HR) that also requires the extracellular tomato cysteine protease Rcr3. We show here that Avr2 binds and inhibits Rcr3 and propose that the Rcr3-Avr2 complex enables the Cf-2 protein to activate an HR.
HIV-specific CD8+ T-cell responses limit viral replication in untreated infection. After the initiation of antiretroviral therapy (ART), these responses decay and the infected cell population that ...remains is commonly considered to be invisible to T-cells. We hypothesized that HIV antigen recognition may persist in ART-treated individuals due to low-level or episodic protein expression. We posited that if persistent recognition were occurring it would be preferentially directed against the early HIV gene products Nef, Tat, and Rev as compared to late gene products, such as Gag, Pol, and Env, which have higher barriers to expression. Using a primary cell model of latency, we observed that a Nef-specific CD8+ T-cell clone exhibited low-level recognition of infected cells prior to reactivation and robust recognition shortly thereafter. A Gag-specific CD8+ T-cell clone failed to recognized infected cells under these conditions, corresponding with a lack of detectable Gag expression. We measured HIV-specific T-cell responses in 96 individuals who had been suppressed on ART for a median of 7 years, and observed a significant, direct correlation between cell-associated HIV DNA levels and magnitudes of IFN-γ-producing Nef/Tat/Rev-specific T-cell responses. This correlation was confirmed in an independent cohort (n = 18). Correlations were not detected between measures of HIV persistence and T-cell responses to other HIV antigens. The correlation with Nef/Tat/Rev-specific T-cells was attributable to Nef-specific responses, the breadth of which also correlated with HIV DNA levels. These results suggest that ongoing Nef expression in ART-treated individuals drives preferential maintenance and/or expansion of T-cells reactive to this protein, implying sensing of infected cells by the immune system. The direct correlation, however, suggests that recognition does not result in efficient elimination of infected cells. These results raise the possibility that enhancing the cytolytic activity of Nef-specific T-cells may lead to reductions in infected cell frequencies, even in the absence of therapeutic latency reversal.
Objectives The aim of this study was to compare Friedewald-estimated and directly measured low-density lipoprotein cholesterol (LDL-C) values. Background LDL-C is routinely estimated by the ...Friedewald equation to guide treatment; however, compatibility with direct measurement has received relatively little scrutiny, especially at levels <70 mg/dl now targeted in high-risk patients. Methods We examined 1,340,614 U.S. adults who underwent lipid profiling by vertical spin density gradient ultracentrifugation (Atherotech, Birmingham, Alabama) from 2009 to 2011. Following standard practice, Friedewald LDL-C was not estimated if triglyceride levels were ≥400 mg/dl (n = 30,174), yielding 1,310,440 total patients and 191,333 patients with Friedewald LDL-C <70 mg/dl. Results Patients were 59 ± 15 years of age and 52% were women. Lipid distributions closely matched those in the National Health and Nutrition Examination Survey. A greater difference in the Friedewald-estimated versus directly measured LDL-C occurred at lower LDL-C and higher triglyceride levels. If the Friedewald-estimated LDL-C was <70 mg/dl, the median directly measured LDL-C was 9.0 mg/dl higher (5th to 95th percentiles, 1.8 to 15.4 mg/dl) when triglyceride levels were 150 to 199 mg/dl and 18.4 mg/dl higher (5th to 95th percentiles, 6.6 to 36.0 mg/dl) when triglyceride levels were 200 to 399 mg/dl. Of patients with a Friedewald-estimated LDL-C <70 mg/dl, 23% had a directly measured LDL-C ≥70 mg/dl (39% if triglyceride levels were concurrently 150 to 199 mg/dl; 59% if triglyceride levels were concurrently 200 to 399 mg/dl). Conclusions The Friedewald equation tends to underestimate LDL-C most when accuracy is most crucial. Especially if triglyceride levels are ≥150 mg/dl, Friedewald estimation commonly classifies LDL-C as <70 mg/dl despite directly measured levels ≥70 mg/dl, and therefore additional evaluation is warranted in high-risk patients.
The mammalian cortex is a laminar structure containing many areas and cell types that are densely interconnected in complex ways, and for which generalizable principles of organization remain mostly ...unknown. Here we describe a major expansion of the Allen Mouse Brain Connectivity Atlas resource
, involving around a thousand new tracer experiments in the cortex and its main satellite structure, the thalamus. We used Cre driver lines (mice expressing Cre recombinase) to comprehensively and selectively label brain-wide connections by layer and class of projection neuron. Through observations of axon termination patterns, we have derived a set of generalized anatomical rules to describe corticocortical, thalamocortical and corticothalamic projections. We have built a model to assign connection patterns between areas as either feedforward or feedback, and generated testable predictions of hierarchical positions for individual cortical and thalamic areas and for cortical network modules. Our results show that cell-class-specific connections are organized in a shallow hierarchy within the mouse corticothalamic network.
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