Shoreland Buffer Module for GRANIT Data Mapper

The Complex Systems Research Center at the University of New Hampshire enhanced the GRANIT Data Mapper (http://mapper.granit.unh.edu) by incorporating data describing shoreline buffers in New Hampshire. The project supports an ongoing, comprehensive New Hampshire Estuaries Project (NHEP) outreach initiative that seeks to educate municipal decision-makers about the importance of stream buffers in preserving water quality in coastal New Hampshire. It complements these existing outreach efforts by allowing coastal managers, local land use boards, and the general public to readily visualize the spatial extent of current and/or proposed shoreline regulations in their community. The primary data source for the analysis was the high-resolution New Hampshire National Hydrography Dataset (NHHD). Using standard GIS tools, six concentric buffers incrementing in 50’ widths from 50’ to 300’ were generated around stream and shoreline features recorded in the NHHD. To provide the greatest flexibility to users, two data sets were generated at each buffer increment – one representing shorelines and streams classified as either perennial or intermittent, and the second comprising shorelines and only streams classified as perennial. The resulting buffers were merged with the GRANIT surface water data, and acreage by town and subwatershed was calculated for each buffer category. The shoreline buffer data sets were added to the water resources theme of the Data Mapper, thereby providing the public with the ability to view buffers of varying widths in the context of other data layers (including aerial imagery) available through the viewing tool. The associated acreage data tables were added to the water resources theme tool tab. Findings indicated that aggregated at the HUC-12 level, almost 24,000 acres within the Coastal Basin were covered by 50’ buffers when perennial and intermittent streams as well as shorelines were buffered, with over 133,000 acres covered by 300’ buffers. When only perennial streams and shorelines were considered eligible for buffering, the totals declined to just under 17,000 acres (50’ buffers) and over 96,000 acres (300’ buffers)

Impervious Surface Mapping in Coastal New Hampshire (2005)

Estimates of impervious surface acreage in 2005 were generated and compared to prior estimates for 1990 and 2000 for a 48-town region in coastal New Hampshire, including the 42 towns within Zones A and B of the New Hampshire Estuaries Project (NHEP) area. The estimates were based on applying both traditional and subpixel image classification techniques to 30-meter Landsat 5 Thematic Mapper (TM) satellite data, acquired 3 October 2005. The classifications indicated that impervious surface acreage increased from 4.3% (31,233 acres) in 1990, to 6.3% (45,445 acres) in 2000, to 7.4% (53,408 acres) in 2005. At the subwatershed level, the Portsmouth Harbor subwatershed recorded the highest percentage of impervious surface acreage in 1990 with 19.8% coverage (2,310 acres) and in 2000 with 25.5% coverage (2,975 acres), and this finding continued in 2005 with 28.9% (3,364 acres) of the watershed mapped as impervious. An accuracy assessment was applied to the regional data, and indicated an accuracy of 98.3% for the 2005 data, which compared favorably with the assessment of the 1990 effort (98.6% correct) as well as the 2000 data (93.1% correct). These figures reflect the overall presence/absence of impervious surfaces within the randomly selected pixels. The accuracy was further evaluated against April, 2003 Emerge 1-ft. resolution aerial photography to estimate the validity of the predicted range of imperviousness for a second set of randomly selected pixels. This assessment proved disappointing, as only 7% of the pixels sampled predicted the correct impervious percentage range. The data set representing impervious surface acreage in 2005 has been archived in the GRANIT GIS clearinghouse, thereby making it available to the coastal resource community as well as the general public. The data are appropriate for watershed and subwatershed level characterizations. Users are discouraged from accessing these data to support larger scale mapping and applications

Developing Impervious Surface Estimates for Coastal New Hampshire

Future population growth and the corresponding increase in development in the coastal zone of NH are widely recognized as major threats to the integrity of coastal systems and their watersheds. The potential impacts associated with the expansion of developed land, and specifically with increasing amounts of impervious surfaces – rooftops, sidewalks, roads, and parking lots - may include significant changes in water quantity, degradation in water quality, and habitat loss. Because asphalt, concrete, stone, and other impenetrable materials effectively seal the ground surface, water is repelled and is prevented from infiltrating soils. Instead, stormwater runoff flows directly into our surface waters, depositing metals, excess nutrients, organics, and other pollutants into the receiving bodies. In addition to these environmental impacts, increasing levels of imperviousness can dramatically alter our landscapes, as forested and other natural settings are converted to urban/suburban uses. Many of the impacts associated with impervious surfaces had been well documented by studies in other areas of the country. However, comprehensive studies in coastal New Hampshire had not been undertaken. The primary goals of this project were to provide an accurate, current description of the extent of impervious surface coverage in this region, as well as an estimate of change in the amount of “imperviousness” over a recent, ten-year period

Developing 1990, 2000, and 2005 Impervious Surface Estimates for Southern York County, Maine

Estimates of impervious surface acreage in 1990, 2000, and 2005 were generated for an 11-town region in York County, Maine, covered by the Piscataqua Region Estuaries Partnership (PREP). The project extended previous work done in New Hampshire, relying on comparable satellite-based data sources and image processing methodologies. As a result, standardized impervious surface estimates are now available for the entirety of the PREP region. The impervious surface estimates were derived by applying both traditional and subpixel classification techniques to 30-meter Landsat 5 Thematic Mapper (TM) and Landsat 7 Enhanced Thematic Mapper Plus (ETM+) satellite image data. The classifications indicated that 3.3% (9,098 acres) of the study area was impervious in 1990, with increases to 5.3 % (14,646 acres) in 2000 and 6.3% (17,394 acres) in 2005. At the subwatershed level, the Portsmouth Harbor subwatershed recorded the highest percentage of impervious surface acreage in 1990, 2000, and 2005 with 7.8% coverage (1,283 acres), 12.3% coverage (2,009 acres), and 14.5% coverage (2,380 acres) respectively. The regional accuracy assessment indicated an overall accuracy of 97.0% for the 1990 data, 93.0% for the 2000 data, and 92.0% for the 2005 data. These results reflect the overall presence/absence of impervious surfaces within the randomly selected assessment pixels. The three data sets have been archived in the GRANIT GIS clearinghouse, thereby making them available to the coastal resource community as well as the general public. The data are appropriate for watershed and subwatershed level characterizations. Users are discouraged from accessing them to support larger scale mapping and applications

Stream Buffer Characterization Study

The Complex Systems Research Center at the University of New Hampshire conducted a characterization of 2nd order and higher streams within the Piscataqua/Coastal Basin of New Hampshire. GIS and remote sensing data archived in the NH GRANIT database were used to map a suite of anthropogenic factors, including land use, impervious surface coverage, and transportation infrastructure, within standard buffers around each stream segment. These factors were then analyzed to produce a categorical indicator representing the status of each stream

Developing 2010 Impervious Surface Estimates for the Piscataque Region Estuaries Partnership Towns

Estimates of impervious surface acreage for 2010 were generated for the 59-town region covered by the Piscataqua Region Estuaries Partnership (PREP). The project extended previous work done in the region for the years 1990, 2000, and 2005 and relied on the same satellite-based data sources and image processing methodologies. As a result, standardized impervious surface estimates are now available for a 20-year time period in the PREP region. The current project mapped impervious surfaces (buildings, pavement, etc.) based on a Landsat 5 Thematic Mapper (TM) image acquired on April 24, 2010. Processing used both traditional and sub-pixel image classification techniques, as described in previous efforts (see Justice and Rubin, 2006 and Justice and Rubin 2003 for a complete processing description). The current study utilized comparable satellite imagery, and applied consistent techniques to map the PREP area for 2010. It should be noted that since the completion of the 2005 project, the U.S. Geological Survey (USGS) has modified its image offerings and now only serves TM data resampled using cubic convolution techniques. (Resampling algorithms are applied as part of the image registration processing, and describe the way output values are assigned to individual image pixels.) This is an important consideration because our previous sub-pixel classifications were conducted on data sets processed using nearest neighbor resampling (which is the recommended approach). While the classification process can be completed using data resampled using alternative techniques, the results may not be as reliable. Since the three previous data sets (1990, 2000, and 2005) were developed using images processed using the preferred nearest neighbor method, and because it is unlikely that features would revert from impervious to non-impervious status, we opted to use the 2005 impervious surface raster as the starting point for the current iteration. Accordingly, the 2005 impervious surface data was used to mask the 2010 TM image with any remaining, unmasked pixels classified using the techniques described in the documents referenced above. A second departure from previous processing streams is that the TM data is now delivered as a georeferenced, terrain-corrected file. This eliminated the requirement for GRANIT to perform these steps locally. The data set has been archived in the GRANIT GIS clearinghouse, thereby making it available to the coastal resource community as well as the general public. The data are appropriate for watershed and subwatershed level characterizations. Users are discouraged from accessing them to support larger scale mapping and applications

Global data for ecology and epidemiology: a novel algorithm for temporal Fourier processing MODIS data

Background. Remotely-sensed environmental data from earth-orbiting satellites are increasingly used to model the distribution and abundance of both plant and animal species, especially those of economic or conservation importance. Time series of data from the MODerate-resolution Imaging Spectroradiometer (MODIS) sensors on-board NASA's Terra and Aqua satellites offer the potential to capture environmental thermal and vegetation seasonality, through temporal Fourier analysis, more accurately than was previously possible using the NOAA Advanced Very High Resolution Radiometer (AVHRR) sensor data. MODIS data are composited over 8- or 16-day time intervals that pose unique problems for temporal Fourier analysis. Applying standard techniques to MODIS data can introduce errors of up to 30% in the estimation of the amplitudes and phases of the Fourier harmonics. Methodology/Principal Findings. We present a novel spline-based algorithm that overcomes the processing problems of composited MODIS data. The algorithm is tested on artificial data generated using randomly selected values of both amplitudes and phases, and provides an accurate estimate of the input variables under all conditions. The algorithm was then applied to produce layers that capture the seasonality in MODIS data for the period from 2001 to 2005. Conclusions/Significance. Global temporal Fourier processed images of 1 km MODIS data for Middle Infrared Reflectance, day- and night-time Land Surface Temperature (LST), Normalised Difference Vegetation Index (NDVI), and Enhanced Vegetation Index (EVI) are presented for ecological and epidemiological applications. The finer spatial and temporal resolution, combined with the greater geolocational and spectral accuracy of the MODIS instruments, compared with previous multi-temporal data sets, mean that these data may be used with greater confidence in species' distribution modelling

Development and validation of a 30-day mortality index based on pre-existing medical administrative data from 13,323 COVID-19 patients: The Veterans Health Administration COVID-19 (VACO) Index.

BACKGROUND: Available COVID-19 mortality indices are limited to acute inpatient data. Using nationwide medical administrative data available prior to SARS-CoV-2 infection from the US Veterans Health Administration (VA), we developed the VA COVID-19 (VACO) 30-day mortality index and validated the index in two independent, prospective samples. METHODS AND FINDINGS: We reviewed SARS-CoV-2 testing results within the VA between February 8 and August 18, 2020. The sample was split into a development cohort (test positive between March 2 and April 15, 2020), an early validation cohort (test positive between April 16 and May 18, 2020), and a late validation cohort (test positive between May 19 and July 19, 2020). Our logistic regression model in the development cohort considered demographics (age, sex, race/ethnicity), and pre-existing medical conditions and the Charlson Comorbidity Index (CCI) derived from ICD-10 diagnosis codes. Weights were fixed to create the VACO Index that was then validated by comparing area under receiver operating characteristic curves (AUC) in the early and late validation cohorts and among important validation cohort subgroups defined by sex, race/ethnicity, and geographic region. We also evaluated calibration curves and the range of predictions generated within age categories. 13,323 individuals tested positive for SARS-CoV-2 (median age: 63 years; 91% male; 42% non-Hispanic Black). We observed 480/3,681 (13%) deaths in development, 253/2,151 (12%) deaths in the early validation cohort, and 403/7,491 (5%) deaths in the late validation cohort. Age, multimorbidity described with CCI, and a history of myocardial infarction or peripheral vascular disease were independently associated with mortality-no other individual comorbid diagnosis provided additional information. The VACO Index discriminated mortality in development (AUC = 0.79, 95% CI: 0.77-0.81), and in early (AUC = 0.81 95% CI: 0.78-0.83) and late (AUC = 0.84, 95% CI: 0.78-0.86) validation. The VACO Index allows personalized estimates of 30-day mortality after COVID-19 infection. For example, among those aged 60-64 years, overall mortality was estimated at 9% (95% CI: 6-11%). The Index further discriminated risk in this age stratum from 4% (95% CI: 3-7%) to 21% (95% CI: 12-31%), depending on sex and comorbid disease. CONCLUSION: Prior to infection, demographics and comorbid conditions can discriminate COVID-19 mortality risk overall and within age strata. The VACO Index reproducibly identified individuals at substantial risk of COVID-19 mortality who might consider continuing social distancing, despite relaxed state and local guidelines

Components of SurA Required for Outer Membrane Biogenesis in Uropathogenic Escherichia coli

Background: SurA is a periplasmic peptidyl-prolyl isomerase (PPIase) and chaperone of Escherichia coli and other Gramnegative bacteria. In contrast to other PPIases, SurA appears to have a distinct role in chaperoning newly synthesized porins destined for insertion into the outer membrane. Previous studies have indicated that the chaperone activity of SurA rests in its ‘‘core module’ ’ (the N- plus C-terminal domains), based on in vivo envelope phenotypes and in vitro binding and protection of non-native substrates. Methodology/Principal Findings: In this study, we determined the components of SurA required for chaperone activity using in vivo phenotypes relevant to disease causation by uropathogenic E. coli (UPEC), namely membrane resistance to permeation by antimicrobials and maturation of the type 1 pilus usher FimD. FimD is a SurA-dependent, integral outer membrane protein through which heteropolymeric type 1 pili, which confer bladder epithelial binding and invasion capacity upon uropathogenic E. coli, are assembled and extruded. Consistent with prior results, the in vivo chaperone activity of SurA in UPEC rested primarily in the core module. However, the PPIase domains I and II were not expendable for wild-type resistance to novobiocin in broth culture. Steady-state levels of FimD were substantially restored in the UPEC surA mutant complemented with the SurA N- plus C-terminal domains. The addition of PPIase domain I augmented FimD maturation into the outer membrane, consistent with a model in which domain I enhances stability of and/or substrat