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Digital data used to relate nutrient inputs to water quality in the Chesapeake Bay watershed, version 3.0

Chesapeake Bay restoration efforts are focused on improving water quality, living resources, and ecological habitats by 2010. One aspect of the water-quality restoration is the refinement of strategies designed to implement nutrient-reduction practices within the Bay watershed. These strategies are being refined and implemented by resource managers of the Chesapeake Bay Program (CBP), a partnership comprised of various Federal, State, and local agencies that includes jurisdictions within Delaware, Maryland, New York, Pennsylvania, Virginia, West Virginia, and the District of Columbia. The U.S. Geological Survey (USGS), an active member of the CBP, provides necessary water-quality information for these Chesapeake Bay nutrient-reduction strategy revisions and evaluations. The formulation and revision of effective nutrient-reduction strategies requires detailed scientific information and an analytical understanding of the sources, transport, and delivery of nutrients to the Chesapeake Bay. The USGS is supporting these strategies by providing scientific information to resource managers that can help them evaluate and understand these processes. One statistical model available to resource managers is a collection of SPAtially Referenced Regressions On Watershed (SPARROW) attributes, which uses a nonlinear regression approach to spatially relate nutrient sources and watershed characteristics to nutrient loads of streams throughout the Chesapeake Bay watershed. Developed by the USGS, information generated by SPARROW can help resource managers determine the geographical distribution and relative contribution of nutrient sources and the factors that affect their transport to the Bay. Nutrient source information representing the late 1990s time period was obtained from several agencies and used to create and compile digital spatial datasets of total nitrogen and total phosphorus contributions that served as input sources to the SPARROW models. These data represent atmospheric deposition, point-source locations, land-use, land-cover, and agricultural sources such as commercial fertilizer and manure applications. Watershed-characteristics datasets representing factors that affect the transport of nutrients also were compiled from previous applications of the SPARROW models in the Chesapeake Bay watershed. Datasets include average-annual precipitation and temperature, slope, soil permeability, and hydrogeomorphic regions. Nutrient-input and watershed-characteristics datasets representing conditions during the late 1990s were merged with a connected network of stream reaches and watersheds to provide the spatial detail required by SPARROW. Stream-nutrient load estimates for 125 sampling sites (87 for total nitrogen and 103 for total phosphorus) served as the dependent variables for the regressions, and were used to calibrate models of total nitrogen and total phosphorus depicting late 1990s conditions in the Chesapeake Bay watershed. Spatial data generated for the models can be used to identify the location of nutrient sources, while the models' nutrient estimates can be used to evaluate stream-nutrient load contributed locally by each source evaluated, the amount of local load generated that is transported to the Bay, and the factors that affect the nutrient transport. Applying the SPARROW methodology to late 1990s information completes three time periods (late 1980s, early 1990s, and late 1990s) of viable data that resource managers can use to evaluate the water-quality conditions within the Bay watershed in order to refine restoration goals and nutrient-reduction strategies.

Chesapeake Bay watershed

Velocity, water-quality, and bathymetric surveys of the Grays Landing and Maxwell Navigation Pools, and Selected Tributaries to the Monongahela River, Pennsylvania, 2010–11

The U.S. Geological Survey (USGS) conducted velocity, water-quality, and bathymetric surveys from spring 2010 to summer 2011 in the Grays Landing and Maxwell navigation pools of the Monongahela River, Pennsylvania, and selected tributaries in response to elevated levels of total dissolved solids (TDS) recorded in early September 2009. Velocity data were collected using an Acoustic Doppler Current Profiler. Water-quality surveys included the in-situ collection of specific-conductance, water-temperature, and turbidity data using a water-quality sonde. Additionally, discrete water samples were collected and analyzed for TDS, chloride, and sulfate. Bathymetric data were collected using an echo sounder, and the shoreline was delineated using a laser range finder and electronic compass. The data were geo-referenced using a differential global positioning system and navigational software. Horizontal (x, y) coordinates were referenced to the North American Datum of 1983. Depth (z) elevations were referenced to the North American Vertical Datum of 1988. The data are provided in electronic format (appendix 1) and may be downloaded and can be used in a geographic information system for cartographic display and data analysis.

Pennsylvania

Very high-temperature impact melt products as evidence for cosmic airbursts and impacts 12,900 years ago

It has been proposed that fragments of an asteroid or comet impacted Earth, deposited silica-and iron-rich microspherules and other proxies across several continents, and triggered the Younger Dryas cooling episode 12,900 years ago. Although many independent groups have confirmed the impact evidence, the hypothesis remains controversial because some groups have failed to do so. We examined sediment sequences from 18 dated Younger Dryas boundary (YDB) sites across three continents (North America, Europe, and Asia), spanning 12,000 km around nearly one-third of the planet. All sites display abundant microspherules in the YDB with none or few above and below. In addition, three sites (Abu Hureyra, Syria; Melrose, Pennsylvania; and Blackville, South Carolina) display vesicular, high-temperature, siliceous scoria-like objects, or SLOs, that match the spherules geochemically. We compared YDB objects with melt products from a known cosmic impact (Meteor Crater, Arizona) and from the 1945 Trinity nuclear airburst in Socorro, New Mexico, and found that all of these high-energy events produced material that is geochemically and morphologically comparable, including: (i) high-temperature, rapidly quenched microspherules and SLOs; (ii) corundum, mullite, and suessite (Fe 3,/sup>Si), a rare meteoritic mineral that forms under high temperatures; (iii) melted SiO 2 glass, or lechatelierite, with flow textures (or schlieren) that form at > 2,200 °C; and (iv) particles with features indicative of high-energy interparticle collisions. These results are inconsistent with anthropogenic, volcanic, authigenic, and cosmic materials, yet consistent with cosmic ejecta, supporting the hypothesis of extraterrestrial airbursts/impacts 12,900 years ago. The wide geographic distribution of SLOs is consistent with multiple impactors.

Proceedings of the National Academy of Sciences of

National water summary 1987: Hydrologic events and water supply and use

Water use in the United States, as measured by freshwater withdrawals in 1985, averaged 338,000 Mgal/d (million gallons per day), which is enough water to cover the 48 conterminous States to a depth of about 2.4 inches. Only 92,300 Mgal/d, or 27.3 percent of the water withdrawn, was consumptive use and thus lost to immediate further use; the remainder of the withdrawals (72.7 percent) was return flow available for reuse a number of times as the water flowed to the sea. The 1985 freshwater withdrawals were much less than the average 30 inches of precipitation that falls on the conterminous States each year; consumptive use accounted for only 7 percent of the estimated annual runoff of 1,230,000 Mgal/d. Nonetheless, as the State summaries on water supply and use clearly show, water is not always available when and where it is needed. Balancing water demands with available water supplies constitutes one of the major resource allocation issues that will face the United States in the coming decade. Of the 1985 freshwater withdrawals, 78.3 percent (265,000 Mgal/d) came from surface-water sources (streams and lakes), and 21.7 percent (73,300 Mgal/d) came from ground water. Surface water provided drinking water for about 47 percent of the Nation's total population. It was the source of 59.9 percent of the Nation's public-supply systems. For self-supplied withdrawals, surface water accounted for 1.6 percent of the domestic and commercial uses; 64.0 percent of the industrial and mining use; 99.4 percent of the thermoelectric generation withdrawals, mainly for cooling water; and 65.6 percent of the agricultural withdrawals. Eight States accounted for 43 percent of the surface-water use; California, Colorado, and Idaho used surface water primarily for irrigation, and Dlinois, Michigan, Ohio, Pennsylvania, and Texas used surface-water primarily for cooling condensers or reactors in thermoelectric plants. Ground water provided drinking water for 53 percent of the Nation's total population and nearly all the rural population. It was the source of 40.1 percent of the public-supply systems withdrawals. For self-supplied withdrawals, ground water accounted for 11.3 percent of the domestic and commercial use, 17.3 percent of the industrial and mining withdrawals, less than 1 percent of the thermoelectric generation withdrawals, and 34.4 percent of the agricultural withdrawals (irrigation and livestock). Eight States Arizona, Arkansas, California, Florida, Idaho, Kansas, Nebraska, and Texas accounted for 66 percent of the ground water used. In each of those States, as in many other States, irrigation was the major use of ground water. Each offstream-use category described in the State summaries public supply, domestic and commercial, industrial and mining, thermoelectric power, and agriculture (irrigation and livestock) followed its own geographic pattern as described below. Consumptive use of water effectively removes the water from immediate further use downstream of the withdrawal point. Of the total amount of consumptive water use in 1985, agricultural use accounted for about 82.5 percent. More than one-half (53 percent) of irrigation water is consumptively used by evapotranspiration or is incorporated into the crop. This is a good indication of the effect that irrigated agriculture can have in a river basin where irrigation is a major activity. The availability of return flows for reuse depends largely on where the water reenters the system. If the return flows are discharged to a stream, they usually can be reused; if they are discharged to a saltwater estuary, they are effectively lost to further use because of water-quality degradation just as if the water had been consumptively used. Similarly, water that recharges a highly transmissive aquifer can be available for reuse either through pumpage from a well or as discharge to a local stream. Thus, much of the water withdrawn for different uses can and does become available for further use although the quality might degrade with each additional use. The allocation and the management of water resources are the responsibilities of the individual States and water institutions within the States. These institutions are evolving in response to the challenges of water management problems. As the individual State summaries indicate, recent State legislation deals with facilitating water transfers within the States as a means of reducing imbalances between water supplies and use, with emphasizing water conservation in times of drought and at places where groundwater depletion is a problem of long standing, and with reducing threats to public health and the environment from water pollution. Most of the State summaries indicate the expectation that water use will continue to increase in the future and that water contamination will continue to be a major water concern. Both issues will require increasingly intensive water management in the future. Whether the water resources under management are considered to be fully appropriated or over appropriated, as in some Western States, or whether the resource could support additional development, as is the situation in most States, improved water-use information will play a key role in future water management efforts.

Water Supply Paper

Large-scale assessment of genetic structure to assess risk of populations of a large herbivore to disease

Chronic wasting disease (CWD) can spread among cervids by direct and indirect transmission, the former being more likely in emerging areas. Identifying subpopulations allows the delineation of focal areas to target for intervention. We aimed to assess the population structure of white-tailed deer ( Odocoileus virginianus ) in the northeastern United States at a regional scale to inform managers regarding gene flow throughout the region. We genotyped 10 microsatellites in 5701 wild deer samples from Maryland, New York, Ohio, Pennsylvania, and Virginia. We evaluated the distribution of genetic variability through spatial principal component analysis and inferred genetic structure using non-spatial and spatial Bayesian clustering algorithms (BCAs). We simulated populations representing each inferred wild cluster, wild deer in each state and each physiographic province, total wild population, and a captive population. We conducted genetic assignment tests using these potential sources, calculating the probability of samples being correctly assigned to their origin. Non-spatial BCA identified two clusters across the region, while spatial BCA suggested a maximum of nine clusters. Assignment tests correctly placed deer into captive or wild origin in most cases (94%), as previously reported, but performance varied when assigning wild deer to more specific origins. Assignments to clusters inferred via non-spatial BCA performed well, but efficiency was greatly reduced when assigning samples to clusters inferred via spatial BCA. Differences between spatial BCA clusters are not strong enough to make assignment tests a reliable method for inferring the geographic origin of deer using 10 microsatellites. However, the genetic distinction between clusters may indicate natural and anthropogenic barriers of interest for management.

Maryland, New York, Ohio, Pennsylvania, West Virgi

Moose habitat in Massachusetts: Assessing use at the southern edge of the range

Moose (Alces alces) have recently re-occupied a portion of their range in the temperate deciduous forest of the northeastern United States after a more than 200 year absence. In southern New England, moose are exposed to a variety of forest types, increasing development, and higher ambient temperatures as compared to other parts of their geographic range. Additionally, large-scale disturbances that shape forest structure and expansive naturally occurring shrub-willow communities used commonly elsewhere are lacking. We used utilization distributions to determine third order habitat selection (selection within the home range) of GPS-collared moose. In central Massachusetts, forests regenerating from logging were the most heavily used cover type in all seasons (48 - 63% of core area use). Habitat use of moose in western Massachusetts varied more seasonally, with regenerating forests used most heavily in summer and fall (57 and 46%, respectively), conifer and mixed forests in winter (47 - 65%), and deciduous forests in spring (41%). This difference in habitat selection reflected the transition from northern forest types to more southern forest types across the state. The intensive use of patches of regenerating forest emphasizes the importance of sustainable forest harvesting to moose. This study provides the first assessment of habitat requirements in this southern portion of moose range and provides insights into re-establishment of moose in unoccupied portions of its historic range in New York and Pennsylvania.

Massachusetts, New Hampshire, Vermont

On the fossil faunas of the Upper Devonian: The Genesee section, New York

I have the honor to transmit herewith for publication as a bulletin a second contribution to the study of Devonian paleontology, Bulletin No. 3, "On the Fossil Faunas of the Upper Devonian," having been designed as the first of a series of papers on the comparative paleontology of the Devonian and Carboniferous. In that paper I gave the results of a study of the section along the meridian of Ithaca and Cayuga Lake, running southward, which may be called the Cayuga section. In 1883 examination was made south along the meridian running through Genesee County, New York, into McKean County, Pennsylvania, where the Alton coal beds were reached. The general results of this survey were communicated to the Director of the United States Geological Survey and an abstract of my communication was published in Science, Vol. II, pp. 836, 837, December 28, 1883. The present paper is a detailed report of the study of the materials of this Genesee section. Since the field work was done several additional sections have been examined: in 1884, sections through Western New York (and adjoining Pennsylvania) from Chautauqua County westward and into Ohio as far as the meridian of Cleveland; and in 1885 the region between the Cayuga section and those of Delaware and Otsego Counties, as far as Oneonta, were examined. The materials are under investigation and will be reported upon as soon as their study is completed. The sections are made along meridians, in order to make them more readily and simply comparable. Each long meridional section runs through the same stratigraphical series of deposits and is made up of a series of small local sections, such as the individual outcrop of the rocks renders possible. It is not supposed that in any case these sections are exhaustive, but it is intended that so far as they go the relative position of the faunas in the sections shall be precise and the association of species in each horizon shall be given as it is, so that the faunas can be identified, and thus, while they will leave much to be added, these studies, it is hoped, will give an outline of the geographical distribution and geological range of faunas and their species which will make a comparative study of the faunas possible. Respectfully yours, HENRY S. WILLIAMS.

New York

Thermal maturity patterns (conodont color alteration index and vitrinite reflectance) in Upper Ordovician and Devonian rocks of the Appalachian basin: A major revision of USGS Map I-917-E using new subsurface collections

Introduction The conodont color alteration index (CAI) introduced by Epstein and others (1977) and Harris and others (1978) is an important criterion for estimating the thermal maturity of Ordovician to Mississippian rocks in the Appalachian basin. Consequently, the CAI isograd maps of Harris and others (1978) are commonly used by geologists to characterize the thermal and burial history of the Appalachian basin and to better understand the origin and distribution of oil and gas resources in the basin. The main objectives of this report are to present revised CAI isograd maps for Ordovician and Devonian rocks in the Appalachian basin and to interpret the geologic and petroleum resource implications of these maps. The CAI isograd maps presented herein complement, and in some areas replace, the CAI-based isograd maps of Harris and others (1978) for the Appalachian basin. The CAI data presented in this report were derived almost entirely from subsurface samples, whereas the CAI data used by Harris and others (1978) were derived almost entirely from outcrop samples. Because of the different sampling methods, there is little geographic overlap of the two data sets. The new data set is mostly from the Allegheny Plateau structural province and most of the data set of Harris and others (1978) is from the Valley and Ridge structural province, east of the Allegheny structural front (fig. 1). Vitrinite reflectance, based on dispersed vitrinite in Devonian black shale, is another important parameter for estimating the thermal maturity in pre-Pennsylvanian-age rocks of the Appalachian basin (Streib, 1981; Cole and others, 1987; Gerlach and Cercone, 1993; Rimmer and others, 1993; Curtis and Faure, 1997). This chapter also presents a revised percent vitrinite reflectance (%R 0 ) isograd map based on dispersed vitrinite recovered from selected Devonian black shales. The Devonian black shales used for the vitrinite studies reported herein also were analyzed by RockEval pyrolysis and total organic carbon (TOC) content in weight percent. Although the RockEval and TOC data are included in this chapter (table 1), they are not shown on the maps. The revised CAI isograd and percent vitrinite reflectance isograd maps cover all or parts of Kentucky, New York, Ohio, Pennsylvania, Virginia, and West Virginia (fig. 1), and the following three stratigraphic intervals: Upper Ordovician carbonate rocks, Lower and Middle Devonian carbonate rocks, and Middle and Upper Devonian black shales. These stratigraphic intervals were chosen for the following reasons: (1) they represent target reservoirs for much of the oil and gas exploration in the Appalachian basin; (2) they are stratigraphically near probable source rocks for most of the oil and gas; (3) they include geologic formations that are nearly continuous across the basin; (4) they contain abundant carbonate grainstone-packstone intervals, which give a reasonable to good probability of recovery of conodont elements from small samples of drill cuttings; and (5) the Middle and Upper Devonian black shale contains large amounts of organic matter for RockEval, TOC, and dispersed vitrinite analyses. Thermal maturity patterns of the Upper Ordovician Trenton Limestone are of particular interest here, because they closely approximate the thermal maturity patterns in the overlying Upper Ordovician Utica Shale, which is the probable source rock for oil and gas in the Upper Cambrian Rose Run Sandstone (sandstone), Upper Cambrian and Lower Ordovician Knox Group (Dolomite), Lower and Middle Ordovician Beekmantown Group (dolomite or Dolomite), Upper Ordovician Trenton and Black River Limestones, and Lower Silurian Clinton/Medina sandstone (Cole and others, 1987; Jenden and others, 1993; Laughrey and Baldassare, 1998; Ryder and others, 1998; Ryder and Zagorski, 2003). The thermal maturity patterns of the Lower Devonian Helderberg Limestone (Group), Middle Devonian Onondaga Limestone, and Middle Devonian Marcellus Shale-Upper Devonian Rhine street Shale Member-Upper Devonian Ohio Shale are of interest, because they closely approximate the thermal maturity patterns in the Marcellus Shale, Upper Devonian Rhinestreet Shale Member, and Upper Devonian Huron Member of the Ohio Shale, which are the most important source rocks for oil and gas in the Appalachian basin (de Witt and Milici, 1989; Klemme and Ulmishek, 1991). The Marcellus, Rhinestreet, and Huron units are black-shale source rocks for oil and (or) gas in the Lower Devonian Oriskany Sandstone, the Upper Devonian sandstones, the Middle and Upper Devonian black shales, and the Upper Devonian-Lower Mississippian(?) Berea Sandstone (Patchen and others, 1992; Roen and Kepferle, 1993; Laughrey and Baldassare, 1998).

Appalachian basin

Occurrence of fecal-indicator bacteria and protocols for identification of fecal-contamination sources in selected reaches of the West Branch Brandywine Creek, Chester County, Pennsylvania

The presence of fecal-indicator bacteria indicates the potential presence of pathogens originating from the fecal matter of warm-blooded animals. These pathogens are responsible for numerous human diseases ranging from common diarrhea to meningitis and polio. The detection of fecal-indicator bacteria and interpretation of the resultant data are, therefore, of great importance to water-resource managers. Current (2005) techniques used to assess fecal contamination within the fluvial environment primarily assess samples collected from the water column, either as grab samples or as depth- and (or) width-integrated samples. However, current research indicates approximately 99 percent of all bacteria within nature exist as attached, or sessile, bacteria. Because of this condition, most current techniques for the detection of fecal contamination, which utilize bacteria, assess only about 1 percent of the total bacteria within the fluvial system and are, therefore, problematic. Evaluation of the environmental factors affecting the occurrence and distribution of bacteria within the fluvial system, as well as the evaluation and modification of alternative approaches that effectively quantify the larger population of sessile bacteria within fluvial sediments, will present water-resource managers with more effective tools to assess, prevent, and (or) eliminate sources of fecal contamination within pristine and impaired watersheds. Two stream reaches on the West Branch Brandywine Creek in the Coatesville, Pa., region were studied between September 2002 and August 2003. The effects of sediment particle size, climatic conditions, aquatic growth, environmental chemistry, impervious surfaces, sediment and soil filtration, and dams on observed bacteria concentrations were evaluated. Alternative approaches were assessed to better detect geographic sources of fecal contamination including the use of turbidity as a surrogate for bacteria, the modification and implementation of sandbag bacteria samplers, and the use of optical brighteners. For the purposes of this report, sources of bacteria were defined as geographic locations where elevated concentrations of bacteria are observed within, or expected to enter, the main branch of the West Branch Brandywine Creek. Biologic sources (for example, waterfowl) were noted where applicable; however, no specific study of biologic sources (such as bacterial source tracking) was conducted. Data indicated that specific bacterial populations within fluvial sediments could be related to specific particle-size ranges. This relation is likely the result of the reduced porosity and permeability associated with finer sediments and the ability of specific bacteria to tolerate particular environments. Escherichia coli (E. coli) showed a higher median concentration (2,160 colonies per gram of saturated sediment) in the 0.125 to 0.5-millimeter size range of natural sediments than in other ranges, and enterococcus bacteria showed a higher median concentration (61,830 colonies per gram of saturated sediment) in the 0.062 to 0.25-millimeter size range of natural sediments than in other ranges. There were insufficient data to assess the particle-size relation to fecal coliform bacteria and (or) fecal streptococcus bacteria. Climatic conditions were shown to affect bacteria concentrations in both the water column and fluvial sediments. Drought conditions in 2002 resulted in lower overall bacteria concentrations than the more typically wet year of 2003. E. coli concentrations in fluvial sediment along the Coatesville study reach in 2002 had a median concentration of 92 colonies per gram of saturated sediment; in 2003, the median concentration had risen to 4,752 colonies per gram of saturated sediment. Symbiotic relations between bacteria and aquatic growth were likely responsible for increased bacteria concentrations observed within an impoundment area on the Coatesville study reach. This reach showed evidence of elevated aquatic growth and sharp increases in E. coli concentrations from upstream to downstream through the impoundment area in both 2002 and 2003. In 2003, E. coli concentrations within the waters column increased from 940 colonies per 100 milliliters upstream to 6,000 colonies per 100 milliliters at the dam crest. Given that these bacteria likely resulted from natural bacterial regrowth, the use of E. coli as an indicator of fecal contamination was severely impaired. Variable environmental conditions along the West Branch Brandywine Creek made the common field-chemical parameters of specific conductance, temperature, pH, and dissolved oxygen ineffective and (or) impossible to use for the determination of inputs of fecal contamination. Extreme variations in chemical gradients commonly were related to the urban/industrial signature of the watershed. For example, during base-flow sampling in 2002, specific-conductance values exceeding 1,000 microsiemens per centimeter observed in effluent from a local steel mill. This effluent raised the specific conductance within the West Branch Brandywine from just above 200 microsiemens per centimeter upstream from the outfall to just below 500 microsiemens per centimeter downstream from the outfall. These chemical gradients also, likely, had an effect on the initial colonization of bacteria, the formation of biofilms, and the persistence of certain types of bacteria along the study reach. Data collected in 2003 indicated that nutrients increased during both base-flow and stormflow conditions along the Coatesville study reach. For example, during base-flow sampling in 2003, 20 pounds of phosphorus was shown to enter the West Branch Brandywine Creek along the Coatesville study reach. The largest contributors to this base-flow nutrient load were likely two wastewater-treatment facilities adjacent to the study reach. During stormflow sampling in 2003, 480 pounds of phosphorus was shown to enter the West Branch Brandywine Creek along the Coatesville study reach. Data, along with other research, indicated the largest contributor to this stormflow nutrient load was likely remobilized sediment originating from a large dam impoundment. These elevated nutrient concentrations were considered sufficient to promote accelerated aquatic growth along the reach. Data collected in 2003 showed that wastewater constituents entered the West Branch Brandywine Creek largely from urban storm-sewer systems. Samples from the primary storm sewer for the city of Coatesville had detections for 20 of 69 wastewater constituents. These constituents included both strong and weak indicators of fecal contamination and generally indicated the storm-sewer system along the Coatesville study reach was a likely source of fecal-indicator bacteria and fecal contamination under base-flow conditions. By comparison, 5 constituents were detected in samples from the upstream end of the reach, and 10 constituents were detected in samples from the downstream end of the reach. During stormflow, numbers of detections were similar along the entire length of the study reach-five in samples from the upstream end, eight in samples from the center of the reach, and seven in samples from the downstream end of the reach. These data indicate that point sources (such as culverts and pipes, septic systems, and wastewater-treatment facilities) are not likely the origin of bacteria contamination during stormflow. The bacteria concentrations observed during stormflow events probably result from remobilized sessile bacteria stored within fluvial sediments. In this case, these bacteria should not be considered indicators of current fecal contamination. Impervious surfaces were found to increase bacteria concentrations along the West Branch Brandywine Creek because contaminated runoff from impervious areas generally flows into, and is concentrated within, the confines of the local storm-sewer system. During 2002, storm-sewer outfalls draining impervious areas were associated with all major locations of elevated bacterial concentrations (greater than 1,200 colonies per gram of saturated sediment) in fluvial sediments. During 2003, wetter conditions and overall bacteria concentrations higher than in 2002 resulted in point sources of bacterial contamination becoming less pronounced; however, the storm-sewer system, draining adjacent impervious areas, was still observed to be the primary source of bacteria along the reach. Where stormwater and (or) other runoff from these areas was allowed to infiltrate and (or) flow through wetland and riparian buffers, bacteria concentrations were not observed to be elevated above background levels commonly observed throughout similar areas of the same reach. Two run-of-the-river dams along the Coatesville study reach were evaluated for their effects on observed bacterial concentrations. These dams were shown to have greater or lesser effects on bacterial concentrations depending on the size of the structure and the capacity of the structure to impede flows. The smaller upstream dam had an approximate height of 3 feet and showed little observed effect on measured turbidity values; these data indicated that the dam did not effectively impede the flow of water or sediment within the West Branch Brandywine Creek. Consequently, this small dam did not show any observed effect on bacterial concentrations either upstream or downstream of the structure. The larger dam, near the middle of the reach, had an approximate height of 20 feet and showed greater effects on both turbidity and bacteria concentrations. The capacity of the larger dam to impede flows, combined with nutrients entering the reach, resulted in increased biologic activity throughout the impoundment area. Within this larger impoundment, enterococcus bacteria populations were observed to decrease sharply and E. coli bacteria populations were observed to increase sharply as flow approached the dam crest. All bacteria levels were then observed to drop to background levels, in both the water column and fluvial sediment, immediately downstream from the dam crest. Additional study is required to determine the cause for this rapid die off. Turbidity was assessed as a potential surrogate for E. coli bacteria. Regression analysis indicated higher turbidity levels usually can indicate higher concentrations of bacteria (R2 = 0.67), but the relation was too sporadic on the West Branch Brandywine Creek to use turbidity as a surrogate for estimated bacteria concentrations. Evaluation of data from individual base-flow and stormflow events resulted in variable and generally poor statistical relations between E. coli bacteria and turbidity (R2 values ranged from 0.02 to 0.94). Sandbag samplers were used in 2003 to determine their suitability for the assessment of fecal contamination. Sandbag samplers rely on the ability of bacteria to attach to surfaces and use the larger sessile bacteria populations instead of the more commonly used planktonic bacteria populations. E. coli bacteria concentrations observed in the sandbag samplers, after 1 week in place, were similar to those found within natural sediments collected concurrently. Enterococcus bacteria concentrations within the same sandbag samplers were not similar, and were generally lower, than those observed within the natural sediments. This discrepancy was likely because sand within the samplers was sieved to a size that was likely too coarse for enterococcus bacteria to persist. Optical-brightener samplers were installed along with each sandbag sampler. Optical brighteners are additives used in common household detergents; therefore, detection of optical brighteners, along with elevated fecal-indicator bacteria concentrations, strongly indicates a link to humans. Positive results for optical brighteners were detected only at the outfalls of two sewage-treatment facilities; because of treatment of the effluent from these facilities, these samples did not have elevated bacteria concentrations. The lack of additional positive results was largely because this method is not sensitive to low concentrations of optical brighteners.

Pennsylvania

Digital data in support of studies and assessments of coal and petroleum resources in the Appalachian basin

The Appalachian basin is a mature basin containing abundant oil, gas, and coal resources. Its fossil-fuel-bearing strata range in age from Cambrian to Permian and extend over the States of New York, Pennsylvania, Maryland, Ohio, West Virginia, Virginia, Kentucky, Tennessee, Georgia, and Alabama. The basin has provided abundant fossil fuels to support the Nation’s economic growth for at least 150 years and U.S. Geological Survey (USGS) assessments suggest that substantial untapped resources remain. A merger of new and old geologic data and ideas is required to locate and extract those remaining resources. This chapter brings together abundant existing datasets in a common and integrated spatial format to advance our understanding of the distribution, geologic framework, burial history, and geochemical character of the basin’s oil, gas, and coal resources. These datasets support the information and findings in chapters B through G of this volume, which include (1) geologic cross sections, seismic profiles, and burial history models that document the depositional and structural framework of the basin; (2) assessments of Carboniferous coal-bed gas and Devonian shale gas; (3) studies about the distribution of oil, gas, and coal fields and the geochemistry of natural gas and oil; and (4) a history of fossil-fuel production in the basin. The data that supported these studies were refined and made more accessible using geographic information system (GIS) tools. The following types of data are included: (1) the bedrock geology of States included within the boundary of the Appalachian basin, (2) the locations of oil and gas wells and fields, (3) data produced for the National Oil and Gas Assessment, and (4) the stratigraphy, geochemistry, and production of coal. Data layers are available in shapefile and Zipped Keyhole Markup Language (KMZ) formats, which can be viewed using ArcGIS, Google Earth, or any software package that supports these data formats. Metadata for these datasets are available in HTML and XML formats. Metadata files contain information about the sources of data used to create the dataset, the creation process steps, the data quality, the geographic coordinate system and horizontal datum used for the dataset, the values of attributes used in the dataset table, information about the publication and the publishing organization, and other information that may be useful to the reader. All links in the metadata were valid at the time of compilation. Some of these links may no longer be valid. No attempt has been made to determine the new online location (if one exists) for the data.

Appalachian basin

Metadata for ReVA logistic regression dataset

The U.S. Geological Survey in cooperation with the U.S. Environmental Protection Agency's Regional Vulnerability Assessment Program, has developed a set of statistical tools to support regional-scale, ground-water quality and vulnerability assessments. The Regional Vulnerability Assessment Program goals are to develop and demonstrate approaches to comprehensive, regional-scale assessments that effectively inform water-resources managers and decision-makers as to the magnitude, extent, distribution, and uncertainty of current and anticipated environmental risks. The U.S. Geological Survey is developing and exploring the use of statistical probability models to characterize the relation between ground-water quality and geographic factors in the Mid-Atlantic Region. Available water-quality data obtained from U.S. Geological Survey National Water-Quality Assessment Program studies conducted in the Mid-Atlantic Region were used in association with geographic data (land cover, geology, soils, and others) to develop logistic-regression equations that use explanatory variables to predict the presence of a selected water-quality parameter exceeding specified management concentration thresholds. The resulting logistic-regression equations were transformed to determine the probability, P(X), of a water-quality parameter exceeding a specified management threshold. Additional statistical procedures modified by the U.S. Geological Survey were used to compare the observed values to model-predicted values at each sample point. In addition, procedures to evaluate the confidence of the model predictions and estimate the uncertainty of the probability value were developed and applied. The resulting logistic-regression models were applied to the Mid-Atlantic Region to predict the spatial probability of nitrate concentrations exceeding specified management thresholds. These thresholds are usually set or established by regulators or managers at national or local levels. At management thresholds of 1 milligram per liter, and 3 milligrams per liter, the probability of nitrate concentrations exceeding these levels is greater than 50 percent (.50) throughout much of the Mid-Atlantic Region. This includes extensive areas throughout central Maryland, southeastern Pennsylvania, northwestern Pennsylvania and the Delmarva Peninsula. In addition, extensive areas in North Carolina and Virginia also have high probabilities of nitrate concentrations in ground water exceeding management thresholds of 1 milligram per liter and 3 milligrams per liter. The mapped areas showing a high predicted probability of nitrate concentrations in ground water exceeding 1 milligram per liter and 3 milligrams per liter correspond to areas that are mapped as cultivated land cover overlying carbonate rocks. At a management threshold of 10 milligrams per liter (corresponding to the U.S. Environmental Protection Agency standard for nitrate in drinking water of 10 milligrams per liter), the predicted probability of nitrate concentrations in ground water exceeding this level are low for most of the Mid-Atlantic Region except for the Delmarva Peninsula, southeastern Pennsylvania, and areas mapped as carbonate rocks in Virginia, Maryland, and Pennsylvania.

Open-File Report

Ground-water vulnerability to nitrate contamination at multiple thresholds in the mid-Atlantic region using spatial probability models

The U.S. Geological Survey, in cooperation with the U.S. Environmental Protection Agency?s Regional Vulnerability Assessment Program, has developed a set of statistical tools to support regional-scale, ground-water quality and vulnerability assessments. The Regional Vulnerability Assessment Program?s goals are to develop and demonstrate approaches to comprehensive, regional-scale assessments that effectively inform managers and decision-makers as to the magnitude, extent, distribution, and uncertainty of current and anticipated environmental risks. The U.S. Geological Survey is developing and exploring the use of statistical probability models to characterize the relation between ground-water quality and geographic factors in the Mid-Atlantic Region. Available water-quality data obtained from U.S. Geological Survey National Water-Quality Assessment Program studies conducted in the Mid-Atlantic Region were used in association with geographic data (land cover, geology, soils, and others) to develop logistic-regression equations that use explanatory variables to predict the presence of a selected water-quality parameter exceeding a specified management concentration threshold. The resulting logistic-regression equations were transformed to determine the probability, P(X), of a water-quality parameter exceeding a specified management threshold. Additional statistical procedures modified by the U.S. Geological Survey were used to compare the observed values to model-predicted values at each sample point. In addition, procedures to evaluate the confidence of the model predictions and estimate the uncertainty of the probability value were developed and applied. The resulting logistic-regression models were applied to the Mid-Atlantic Region to predict the spatial probability of nitrate concentrations exceeding specified management thresholds. These thresholds are usually set or established by regulators or managers at National or local levels. At management thresholds of 1 milligram per liter and 3 milligrams per liter as nitrogen, the probability of nitrate concentrations exceeding these levels is greater than 50 percent (0.50) throughout much of the Mid-Atlantic Region. This includes extensive areas throughout central Maryland, southeastern Pennsylvania, northwestern Pennsylvania, and the Delmarva Peninsula. In addition, extensive areas in North Carolina and Virginia also have high probabilities of nitrate concentrations in ground water exceeding management thresholds of 1 milligram per liter and 3 milligrams per liter. The mapped areas showing a high predicted probability of nitrate concentrations in ground water exceeding 1 milligram per liter and 3 milligrams per liter correspond to areas that are mapped as cultivated land cover and/or overlying carbonate rocks. At a management threshold of 10 milligrams per liter (corresponding to the U.S. Environmental Protection Agency standard for nitrate in drinking water of 10 milligrams per liter), the predicted probability of nitrate concentrations in ground water exceeding this level is low for most of the Mid-Atlantic Region, except for the Delmarva Peninsula, southeastern Pennsylvania, and areas mapped as carbonate rocks in Virginia, Maryland, and Pennsylvania.

Scientific Investigations Report

Comparing risk of chronic wasting disease occurrence using Bayesian hierarchical spatial models and different surveillance types

Spatial modeling of wildlife diseases can be used to describe patterns of disease risk, understand biological mechanisms of disease occurrence, and for spatial prediction. Risk of wildlife disease occurrence in relation to environmental variables is often modeled and predicted using Markov chain Monte Carlo (MCMC) methods, which are unsuitable for large datasets and those covering large spatial extents. Integrated nested Laplace approximation (INLA) and INLA using the stochastic partial differential equation (INLA-SPDE) approach have become popular alternatives to MCMC for Bayesian inference because of their fast computational time and ability to process large datasets. Studies investigating risk of disease occurrence in wildlife, to our knowledge, have not yet compared Bayesian hierarchical spatial models over large spatial extents using real world data. Using chronic wasting disease (CWD) surveillance data from white-tailed deer ( Odocoileus virginianus ) collected in Pennsylvania, United States, as a case study, we first demonstrate how parameter estimates compare among MCMC, INLA, and INLA-SPDE modeling frameworks. We then model CWD (detected/non-detected) using INLA-SPDE over a much larger spatial extent than has been conducted previously for this disease to determine how surveillance type (e.g., hunter harvest, roadkill, or all surveillance) influences model parameters and predicted risk of CWD occurrence at locations not sampled. Fixed effects considered in the models included deer age and sex, elevation, slope, distance to streams, percent clay, and proportion of two habitat classes (forest and open) known to influence deer movements. We found INLA to produce comparable estimates to MCMC and permit modeling large datasets covering expansive spatial extents much faster and more efficiently than MCMC. We identified potential biases in surveillance types, indicating the value of including all surveillance in models rather than only a single type. Comparing modeling tools available for mapping diseases of wildlife in relation to ecological variables at large spatial extents will guide future modeling efforts for CWD and other wildlife diseases. Understanding spatial patterns of CWD using different surveillance types can help improve understanding of CWD disease outbreaks, assist with control of CWD through geographical targeting, and inform future CWD surveillance efforts.

Ecological Modeling

Seismicity map of the state of Pennsylvania

This map is one of a series of seismicity maps produced by the U. S. Geological Survey that show earthquake data of individual states or groups of states at the scale of 1:1,000,000. This map shows only those earthquakes with epicenters located within the boundaries of Pennsylvania, even though earthquakes in nearby states may have been felt or may have caused damage in Pennsylvania. The data in table 1 were used to compile the seismicity map; these data are a corrected, expanded, and updated (through 1983) version of the data used by Algermissen (1969) for a study of seismic risk in the United States. The locations and intensities of some earthquakes were revised and intensities were assigned where none had been before. Many earthquakes were added to the original list from new data sources as well as from some old data sources that had not been previously used. The data in table 1 represent best estimates of the location of the epicenter, magnitude, and intensity of each earthquake on the basis of historical and current information. Some of the aftershocks from large earthquakes are listed, but not all, especially for earthquakes that occurred before seismic instruments were universally used. The latitude and longitude coordinates of each epicenter were rounded to the nearest tenth of a degree and sorted so that all identical locations were grouped and counted. These locations are represented on the map by a triangle. The number of earthquakes at each location is shown on the map by the arabic number to the right of the triangle. A Roman numeral to the left of a triangle is the maximum Modified Mercalli intensity (Wood and Neumann, 1931) of a11 earthquakes at that geographic location. The absence of an intensity value indicates that no intensities have been assigned to earthquakes at that location. The year shown below each triangle is the latest year for which the maximum intensity was recorded.

Pennsylvania

Flood-inundation maps for the West Branch Susquehanna River near the Boroughs of Lewisburg and Milton, Pennsylvania

Digital flood-inundation maps for an approximate 8-mile reach of the West Branch Susquehanna River from approximately 2 miles downstream from the Borough of Lewisburg, extending upstream to approximately 1 mile upstream from the Borough of Milton, Pennsylvania, were created by the U.S. Geological Survey (USGS) in cooperation with the Susquehanna River Basin Commission (SRBC). The inundation maps, which can be accessed through the USGS Flood Inundation Mapping Science Web site at http://water.usgs.gov/osw/flood_inundation/ , depict the estimated areal extent and depth of flooding corresponding to selected water levels (stages) at the USGS streamgage 01553500, West Branch Susquehanna River at Lewisburg, Pa. In addition, the information has been provided to the Susquehanna River Basin Commission (SRBC) for incorporation into their Susquehanna Inundation Map Viewer (SIMV) flood warning system ( http://maps.srbc.net/simv/ ). The National Weather Service (NWS) forecasted peak-stage information ( http://water.weather.gov/ahps ) for USGS streamgage 01553500, West Branch Susquehanna River at Lewisburg, Pa., may be used in conjunction with the maps developed in this study to show predicted areas of flood inundation. In this study, flood profiles were computed for the stream reach by means of a one-dimensional step-backwater model. Calibration of the model was achieved using the most current stage-discharge relations (rating number 11.1) at USGS streamgage 01553500, West Branch Susquehanna River at Lewisburg, Pa., a documented water-surface profile from the December 2, 2010, flood, and recorded peak stage data. The hydraulic model was then used to determine 26 water-surface profiles for flood stages at 1-foot intervals referenced to the streamgage datum ranging from 14 feet (ft) to 39 ft. Modeled flood stages, as defined by NWS, include Action Stage, 14 ft; Flood Stage, 18 ft; Moderate Flood Stage, 23 ft; and Major Flood Stage, 28 ft. Geographic information system (GIS) technology was then used to combine the simulated water-surface profiles with a digital elevation model (DEM) derived from light detection and ranging (lidar) data to delineate the area flooded at each water level. The availability of these maps, along with World Wide Web information regarding current stage from USGS streamgages and forecasted stream stages from the NWS, provide emergency management personnel and residents with information that is critical for flood response activities, such as evacuations and road closures, as well as for post-flood recovery efforts.

Pennsylvania

Flood-inundation maps for the Mississinewa River at Marion, Indiana, 2013

Digital flood-inundation maps for a 9-mile (mi) reach of the Mississinewa River from 0.75 mi upstream from the Pennsylvania Street bridge in Marion, Indiana, to 0.2 mi downstream from State Route 15 were created by the U.S. Geological Survey (USGS) in cooperation with the Indiana Office of Community and Rural Affairs. The flood inundation maps, which can be accessed through the USGS Flood Inundation Mapping Science Web site at http://water.usgs.gov/osw/flood_inundation, depict estimates of the areal extent and depth of flooding corresponding to selected water levels (stages) at the USGS streamgage on the Mississinewa River at Marion (station number 03326500). Near-real-time stages at this streamgage may be obtained on the Internet from the USGS National Water Information System at http://waterdata.usgs.gov/ or the National Weather Service (NWS) Advanced Hydrologic Prediction Service at http://water.weather.gov/ahps/, which also forecasts flood hydrographs at this site. Flood profiles were computed for the stream reach by means of a one-dimensional step-backwater model. The model was calibrated by using the current stage-discharge relation at the Mississinewa River streamgage, in combination with water-surface profiles from historic floods and from the current (2002) flood-insurance study for Grant County, Indiana. The hydraulic model was then used to compute seven water-surface profiles for flood stages at 1-fo (ft) intervals referenced to the streamgage datum and ranging from 10 ft, which is near bankfull, to 16 ft, which is between the water levels associated with the estimated 10- and 2-percent annual exceedance probability floods (floods with recurrence interval between 10 and 50 years) and equals the “major flood stage” as defined by the NWS. The simulated water-surface profiles were then combined with a Geographic Information System digital elevation model (derived from light detection and ranging (lidar) data having a 0.98 ft vertical accuracy and 4.9 ft horizontal resolution) to delineate the area flooded at each water level. The availability of these maps, along with Internet information regarding current stage from the USGS streamgage and forecasted high-flow stages from the NWS, will provide emergency management personnel and residents with information that is critical for flood response activities such as evacuations and road closures, as well as for post-flood recovery efforts.

Indiana

Preliminary geologic framework developed for a proposed environmental monitoring study of a deep, unconventional Marcellus Shale drill site, Washington County, Pennsylvania

Background In the fall of 2011, the U.S. Geological Survey (USGS) was afforded an opportunity to participate in an environmental monitoring study of the potential impacts of a deep, unconventional Marcellus Shale hydraulic fracturing site. The drill site of the prospective case study is the “Range Resources MCC Partners L.P. Units 1-5H” location (also referred to as the “RR–MCC” drill site), located in Washington County, southwestern Pennsylvania. Specifically, the USGS was approached to provide a geologic framework that would (1) provide geologic parameters for the proposed area of a localized groundwater circulation model, and (2) provide potential information for the siting of both shallow and deep groundwater monitoring wells located near the drill pad and the deviated drill legs. The lead organization of the prospective case study of the RR–MCC drill site was the Groundwater and Ecosystems Restoration Division (GWERD) of the U.S. Environmental Protection Agency. Aside from the USGS, additional partners/participants were to include the Department of Energy, the Pennsylvania Geological Survey, the Pennsylvania Department of Environmental Protection, and the developer Range Resources LLC. During the initial cooperative phase, GWERD, with input from the participating agencies, drafted a Quality Assurance Project Plan (QAPP) that proposed much of the objectives, tasks, sampling and analytical procedures, and documentation of results. Later in 2012, the proposed cooperative agreement between the aforementioned partners and the associated land owners for a monitoring program at the drill site was not executed. Therefore, the prospective case study of the RR–MCC site was terminated and no installation of groundwater monitoring wells nor the collection of nearby soil, stream sediment, and surface-water samples were made. Prior to the completion of the QAPP and termination of the perspective case study the geologic framework was rapidly conducted and nearly completed. This was done for three principal reasons. First, there was an immediate need to know the distribution of the relatively undisturbed surface to near-surface bedrock geology and unconsolidated materials for the collection of baseline surface data prior to drill site development (drill pad access road, drill pad leveling) and later during monitoring associated with well drilling, well development, and well production. Second, it was necessary to know the bedrock geology to support the siting of: (1) multiple shallow groundwater monitoring wells (possibly as many as four) surrounding and located immediately adjacent to the drill pad, and (2) deep groundwater monitoring wells (possibly two) located at distance from the drill pad with one possibly being sited along one of the deviated production drill legs. Lastly, the framework geology would provide the lateral extent, thickness, lithology, and expected discontinuities of geologic units (to be parsed or grouped as hydrostratigraphic units) and regional structure trends as inputs into the groundwater model. This report provides the methodology of geologic data accumulation and aggregation, and its integration into a geographic information system (GIS) based program. The GIS program will allow multiple data to be exported in various formats (shapefiles [.shp], database files [.dbf], and Keyhole Markup Language files [.KML]) for use in surface and subsurface geologic site characterization, for sampling strategies, and for inputs for groundwater modeling.

Pennsylvania

Executive summary

Fossil fuels from the Appalachian basin region have been major contributors to the Nation’s energy needs over much of the last three centuries. Early records indicate that Appalachian coal was first mined in the middle 1700s (Virginia and Pennsylvania) and was used sparingly to fuel colonial settlements and, later, a fledgling industrial-based economy along the eastern seaboard of the United States (de Witt and Milici, 1989). In 2011, central Appalachian basin coal production accounted for approximately 77 percent of all U.S. metallurgical (or coking) coal and 29 percent of total U.S. production (U.S. Energy Information Administration, 2013). Following initial discoveries and commercial use in western New York (1821) and Ohio and West Virginia (mid-1830s), the Appalachian petroleum (oil and gas) industry began in earnest in 1859 with the discovery of oil at the Drake well in northwestern Pennsylvania. Between 1860 and 1989, the Appalachian basin produced more than 2.5 billion barrels of oil (BBO) and more than 30 trillion cubic feet of gas (TCFG) from more than 500,000 wells (de Witt and Milici, 1989). Although both oil and gas continue to be produced in the Appalachian basin, most new wells in the region are drilled in shale reservoirs to produce natural gas. Appalachian coal and petroleum resources are still available in sufficient quantities to contribute significantly to the Nation’s energy needs. For example, the U.S. Energy Information Administration (2010) estimated that there are 6,484 million short tons of recoverable coal reserves in the Appalachian basin. Similarly, about 14.7 billion barrels of oil equivalent (BBOE) (1.2 BBO+81 TCFG [or 13.5 BBOE]) of recoverable Appalachian basin oil and gas remain available of an estimated ultimate endowment of approximately 25.5 billion BBOE (cumulative production + reserves + estimated recoverable undiscovered resources) (this volume, chap. C.1). U.S. Geological Survey (USGS) Professional Paper 1708 is a modern, indepth collection of reports, cross sections, and maps that describe the geology of the Appalachian basin and its fossil fuel resources. Several of the chapters have been published in outside journals or as other USGS publications. Although this volume is not a comprehensive regional treatment of all notable geologic and fossil fuel localities in the Appalachian basin, the selected study areas and topics presented in the chapters cover large segments of the basin and a wide range of stratigraphic intervals. As the title implies, this volume addresses topics that refer to the locations of coal and petroleum accumulations, the stratigraphic and structural framework, and the geochemical characteristics of the coal beds and petroleum in the basin, as well as the results and documentation of recent USGS assessments of coal, oil, and gas resources in the basin. Many of the maps and accompanying data supporting the reports in this volume are available as downloadable geographic information system (GIS) data files (such as selected coal beds, selected oil and gas fields, locations of oil and gas wells, coal production, coal chemistry, total petroleum system (TPS) boundaries, and bedrock geology). Log ASCII Standard (LAS) files for geophysical (gamma ray) wireline well logs also are included. This publication supplements and updates older USGS regional studies of Appalachian basin coal and petroleum resources such as those by Arndt and others (1968) and the numerous contributors to USGS Miscellaneous Map Series I−917 (for example, Harris and others, 1978), respectively. USGS Professional Paper 1708 is intended primarily for geoscientists in academia, industry, and government who are interested in Appalachian basin geology and its coal and petroleum resources. Other users, however, may find the wide variety of topics, papers, and digital images of value for landuse and policy planning issues. Among the anticipated benefits of the report are improvements in (1) resource assessment estimates and methodology, (2) exploration strategies, (3) basin models, and (4) energy use policies.

Appalachian Basin