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A bibliography of literature pertaining to plague ( Yersinia pestis )

Plague is an acute and often fatal zoonotic disease caused by the bacterium Yersinia pestis . Y. pestis mainly cycles between small mammals and their fleas; however, it has the potential to infect humans and frequently causes fatalities if left untreated. It is often considered a disease of the past; however, since the late 1800s, plagueis geographic range has expanded greatly, posing new threats in previously unaffected regions of the world, including the Western United States. A literature search was conducted using Internet resources and databases. The keywords chosen for the searches included plague, Yersinia pestis , management, control, wildlife, prairie dogs, fleas, North America, and mammals. Keywords were used alone or in combination with the other terms. Although this search pertains mostly to North America, citations were included from the international research community, as well. Databases and search engines used included Google ( http://www.google.com ), Google Scholar ( http://scholar.google.com ), SciVerse Scopus ( http://www.scopus.com ), ISI Web of Knowledge ( http://apps.isiknowledge.com ), and the USGS Library's Digital Desktop ( http://library.usgs.gov ). The literature-cited sections of manuscripts obtained from keyword searches were cross-referenced to identify additional citations or gray literature that was missed by the Internet search engines. This Open-File Report, published as an Internet-accessible bibliography, is intended to be periodically updated with new citations or older references that may have been missed during this compilation. Hence, the authors would be grateful to receive notice of any new or old papers that the audience (users) think need to be included.

Open-File Report

Ecosystem history of South Florida; Biscayne Bay sediment core descriptions

The 'Ecosystem History of Biscayne Bay and the southeast Coast' project of the U.S. Geological Survey is part of a multi-disciplinary effort that includes Florida Bay and the Everglades to provide paleoecologic reconstructions for the south Florida region. Reconstructions of past salinity, nutrients, substrate, and water quality are needed to determine ecosystem variability due to both natural and human-induced causes. Our understanding of the relations between the south Florida ecosystem and introduced forces will allow managers to make informed decisions regarding the south Florida ecosystem restoration and monitoring. The record of past ecosystem conditions can be found in shallow sediment cores. This U.S. Geological Survey Open-File Report describes six shallow sediment cores collected from Biscayne Bay. The cores described herein are being processed for a variety of analytical procedures, and this provides the descriptive framework for future analyses of the included cores. This report is preliminary and has not been reviewed for conformity with U.S. Geological Survey editorial standards or with the North American Stratigraphic Code. Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government.

Open-File Report

Ages of rocks in southwestern Washington and northwestern Oregon as indicated by paleontological and isotopic dates

This report presents a compilation of 1,019 paleontologic dates and 301 isotopic dates of rocks in southwestern Washington and northwestern Oregon. The study area extends from Portland, Oregon (latitude 45°30' N.) to Bellevue, Washington (latitude 47°35' N.) and from the east flank of the Cascade Range (longitude 121°20' W.) to the coastline (longitude approximately 124°00' W.). The data are presented in two tables and come from previous summaries of isotopic ages, open-file reports, published papers and maps, and theses. Parke D. Snavely, Jr. of the U.S. Geological Survey and Weldon W. Rau of the Washington Division of Geology and Earth Resources (WDGER) generously allowed us access to files and records of more than 40 years of micropaleontological research in western Washington and Oregon. We also present unpublished data from our research since 1971 in northwestern Oregon. This compilation was undertaken for the southwestern Washington and northwestern Oregon project of the U.S. Geological Survey Evolution of Sedimentary Basins Program.

Oregon, Washington

Summary of West Virginia Water-Resource Data through September 2008

The West Virginia Water Science Center of the U.S. Geological Survey, in cooperation with State and Federal agencies, obtains a large amount of data pertaining to the water resources of West Virginia each water year. A water year is the 12-month period beginning October 1 and ending September 30. These data, accumulated during many years, constitute a valuable database for developing an improved understanding of the water resources of the State. These data are maintained in the National Water Information System (NWIS) and are available through its World-Wide Web interface, NWISWeb, at http://waterdata.usgs.gov/wv/nwis. Data can be retrieved in a variety of common formats, and a tutorial is available at http://nwis.waterdata.usgs.gov/tutorial. Location information for all continuous-record gaging stations operated in West Virginia through September 2008 is provided in this report, as well as statistical summaries of the available daily records. This report can serve as an index to the daily records data available on the World-Wide Web. Hydrologic data for nearly all of the gaging stations identified in this report are also available in the annual publication series titled Water-Resources Data - West Virginia. This series of annual reports for West Virginia began with the 1961 water year with a report that contained only data relating to quantities of surface water. For the 1964 water year, a similar report was introduced that contained only data relating to water quality. Beginning with the 1975 water year, the report format was changed to include data on quantities of surface water, quality of surface water and groundwater, and groundwater levels. Prior to the introduction of the Water-Resources Data - West Virginia series and for several water years concurrent with it, water-resources data for West Virginia were published in U.S. Geological Survey Water-Supply Papers. Data on stream discharge and stage and on lake or reservoir contents and stage through September 1960 were published annually under the title Surface-Water Supply of the United States, Parts 6A and 6B. For the 1961 through 1970 water years, the data were published in two 5-year reports. Data on chemical quality, temperature, and suspended sediment for the 1941 through 1970 water years were published annually under the title Quality of Surface Water of the United States, and water levels for the 1935 through 1974 water years were published under the title Ground-Water Levels in the United States. Many of the above mentioned Water-Supply Papers are available at the USGS Publications Warehouse (http://pubs.er.usgs.gov), and most of the others may be found in the collections of large libraries or may be purchased from the U.S. Geological Survey, Books and Open-File Reports, Federal Center, Box 25425, Denver, Colorado 80225. Annual reports on hydrologic data are published by the Geological Survey for all states, and each has an identification number consisting of the two-letter state abbreviation, the last two digits of the water year, and the volume number. For example, the 2005 water year report for West Virginia is identified as U.S. Geological Survey Water-Data Report WV-05-01. Water-Data Reports for West Virginia for 2001-2005 are available online at http://pubs.usgs.gov/wdr/#WV. Water-Data Reports for water years prior to 2006 are for sale in paper copy or microfiche by the National Technical Information Service, U.S. Department of Commerce, Springfield, Virginia 22161. Since the 2006 water year, the report is published online only and is available at http://wdr.water.usgs.gov/. When substantial errors in published records are discovered, the records are revised. Such revisions are routine and are made to records regardless of the age of the original records. Revisions have been made for many stations for which data are published in this report. The USGS National Water Information System always contains the most recent data revisions. For critical a

Open-File Report

Focus areas for data acquisition for potential domestic sources of critical minerals—Rare earth elements

Rare earth elements (REEs) are critical mineral commodities for the United States. In response to a need for information on potential domestic sources of REEs in mineral deposits, the U.S. Geological Survey (USGS) identified broad focus areas throughout the conterminous United States and Alaska as a guide for selecting new geoscience research areas. This study was done to support the USGS Earth Mapping Resources Initiative (Earth MRI). Focus areas are identified in four regions of the United States (Alaska, West, Central, and East) by mineral deposit type. The areas are described in a companion USGS data release that consists of a map in a geographic information system and accompanying tables that document the rationale for each focus area (C.L. Dicken and others, 2019, https://doi.org/10.5066/P95CHIL0 ). This open-file report describes the methodology that was used to identify focus areas and determine new data acquisition needs. Deposit types that are likely to be of interest for future exploration and development of domestic nonfuel REE resources include deposits associated with carbonatites and peralkaline rocks, iron oxide-apatite deposits, monazite-bearing placers, and REE-enriched phosphorites.

Open-File Report

Hydrogeology and water quality of the Galena-Platteville aquifer at the Parson's Casket Hardware Superfund site, Belvidere, Illinois, 1991-92

The purpose of this letter is to describe the results of the final phase (phase 3) of the U.S. Geological Survey's (USGS) ground-water investigation at the Parson's Casket Hardware site, Belvidere, Ill. (figs. 1 and 2), for the U.S. Environmental Protection Agency (USEPA). Included in this letter are brief descriptions of (1) study methods employed in the phase 3 investigation that have not been previously described in earlier reports, and (2) results of the phase 3 investigation as they relate to the results of the previous phases of the investigation. The data from the phase 3 investigation that are presented and described herein were collected during November 1991-January 1992. The Galena-Platteville aquifer is the uppermost bedrock aquifer beneath the site. The Glenwood Formation of Ordovician age, a potential confining unit, separates the Galena-Platteville aquifer from the underlying St. Peter Sandstone aquifer (fig. 3). The St. Peter Sandstone aquifer is an important source of ground water to Belvidere and other cities in the region. The phase 3 investigation was done (1) to determine the lithology of the Glenwood Formation; (2) to determine the vertical distribution of horizontal hydraulic conductivity (K) and concentrations of volatile organic compounds (VOC's) in the upper 150 ft (feet) of the Galena-Platteville aquifer at an existing monitoring location, borehole G127GP (figs. 2 and 3) ; and (3) to confirm the presence or absence of VOC's in the St. Peter Sandstone aquifer at a new monitoring location, well G127SP (figs. 2 and 3). Additional components of the site investigation described in this letter include determination of vertical hydraulic gradients between the Galena-Platteville and St. Peter Sandstone aquifers and in situ measurement of selected water-quality characteristics (pH, temperature, specific conductance, Eh, and dissolved oxygen) in borehole G127GP. The results of the first and second phases of the USGS investigation at the Parson's Casket Hardware site are presented in two previous USGS Open-File Reports prepared for the USEPA (Mills, 1993a, 1993b) . These reports describe the hydrogeology of the study site, principally the Galena-Platteville aquifer, and the distribution of VOC concentrations in the Galena-Platteville aquifer. (The stratigraphic nomenclature used in this report is that of the Illinois State Geological Survey (Willman and others, 1975, p. 47-87) and does not necessarily follow the usage of the USGS. The aquifer nomenclature is that generally used by the Illinois State Geological Survey and the U.S. Environmental Protection Agency.) The previous two reports also describe most of the study methods employed in the phase 3 investigation.

Open-File Report

Geologic constraints on the upper limits of reserve growth

For many oil and gas fields, estimates of ultimate recovery (the sum of cumulative production plus estimated reserves) tend to increase from one year to the next, and the gain is called reserve growth. Forecasts of reserve growth by the U.S. Geological Survey rely on statistical analyses of historical records of oil and gas production and estimated reserves. The preproposal in this Open-File Report suggests that this traditional petroleum–engineering approach to reserve growth might be supplemented, or at least better understood, by using geological data from individual oil and gas fields, 3–D modeling software, and standard volumetric techniques to estimate in–place volumes of oil and gas. Such estimates, in turn, can be used to constrain the upper limits of reserve growth and ultimate recovery from those fields.

California

Digital data for volcano hazards of the Three Sisters region, Oregon

Three Sisters is one of three active volcanic centers that lie close to rapidly growing communities and resort areas in Central Oregon. The major composite volcanoes of this area are clustered near the center of the region and include South Sister, Middle Sister, and Broken Top. Additionally, hundreds of mafic volcanoes are scattered throughout the Three Sisters area. These range from small cinder cones to large shield volcanoes like North Sister and Belknap Crater. Hazardous events include landslides from the steep flanks of large volcanoes and floods, which need not be triggered by eruptions, as well as eruption-triggered events such as fallout of tephra (volcanic ash) and lava flows. A proximal hazard zone roughly 20 kilometers (12 miles) in diameter surrounding the Three Sisters and Broken Top could be affected within minutes of the onset of an eruption or large landslide. Distal hazard zones that follow river valleys downstream from the Three Sisters and Broken Top could be inundated by lahars (rapid flows of water-laden rock and mud) generated either by melting of snow and ice during eruptions or by large landslides. Slow-moving lava flows could issue from new mafic volcanoes almost anywhere within the region. Fallout of tephra from eruption clouds can affect areas hundreds of kilometers (miles) downwind, so eruptions at volcanoes elsewhere in the Cascade Range also contribute to volcano hazards in Central Oregon. Scientists at the Cascades Volcano Observatory created a geographic information system (GIS) data set which depicts proximal and distal lahar hazard zones as well as a regional lava flow hazard zone for Three Sisters (USGS Open-File Report 99-437, Scott and others, 1999). The various distal lahar zones were constructed from LaharZ software using 20, 100, and 500 million cubic meter input flow volumes. Additionally, scientists used the depositional history of past events in the Three Sisters Region as well as experience and judgment derived from the study of volcanoes to help construct the regional hazard zone.

Open-File Report

United States Geological Survey uranium and thorium resource assessment and exploration research program, fiscal year 1977

The U.S. Geological Survey Uranium and Thorium Resource Assessment and Exploration Research Program began in July 1974 (FY 1975). The first year was spent chiefly in redirecting an on-going effort and in staffing for the nearly fourfold increase in funding. A summary of the Fiscal Year 1976 program, including objectives, program model, and project descriptions, is published as Open-File Report 75-575. The overall objectives and program model remain essentially the same as in FY 1976. It should be noted that the beginning of the fiscal year was changed from July 1 to October 1 during the 1976 calendar year and that a transitional quarter was used to make this change. Some program changes were made during the transitional quarter, but these details are not recorded in the present summary.

Open-File Report

Southwest Exotic Mapping Program 2007: Occurrence summary and maps of select invasive, non-native plants in Arizona

An important aspect of management of invasive, non-native plants (invasive plants) is information on the type, location, and magnitude of infestations. Regional development of this information requires an integrated program of data collection, management, and delivery. The Southwest Exotic Plant Mapping Program (SWEMP), coordinated through the U.S. Geological Survey’s Southwest Biological Science Center, annually compiles occurrence records for infestations of invasive plants. Operating since 1998, the SWEMP team has accepted occurrence records contributed voluntarily by federal, tribal, state, and private collaborators and has compiled these contributions accumulatively with previous versions of SWEMP. The SWEMP 2007 regional database update, SWEMP07, contains 62,000 records for 221 plant species with records dating as far back as 1911 and up to December, 2006. Records include invasive plants in Arizona, eastern California, Colorado, New Mexico, and Utah. SWEMP07 is available through the Southwest Exotic Plant Information Clearinghouse ( http://sbsc.wr.usgs.gov/research/projects/swepic/swepic.asp , click SWEMP). Not all invasive plants are non-native and not all invasive plants are even invasive. The Arizona Invasive Species Advisory Council (2006) defined an invasive species as “a species that is (1) non-native to the ecosystem under consideration and, (2) whose introduction causes or is likely to cause economic or environmental harm, or harm to human health”. SWEMP uses the U.S. Department of Agriculture PLANTS database ( http://plants.usda.gov/ ) to determine if a plant is native or not to Arizona. As SWEMP does not independently assess the current or potential impact of invasive plants, we include most non-native plant records contributed. We have not included agricultural crops that are non-native, for example apples, oranges, etc. In this open-file-report, we use the SWEMP07 update to summarize the occurrence of invasive plants in Arizona and present distribution maps for a select invasive plants in Arizona. We use the word occurrence purposefully instead of the word distribution. The SWEMP07 database only provides an estimate of the actual distribution of invasive plants in Arizona. The information provided is a first approximation of the state-wide extent of invasive plant distribution.

Open-File Report

Exploratory analysis of environmental interactions in central California

As part of its global change research program, the United States Geological Survey (USGS) has produced raster data that describe the land cover of the United States using a consistent format. The data consist of elevations, satellite measurements, computed vegetation indices, land cover classes, and ancillary political, topographic and hydrographic information. This open-file report uses some of these data to explore the environment of a (256-km)? region of central California. We present various visualizations of the data, multiscale correlations between topography and vegetation, a path analysis of more complex statistical interactions, and a map that portrays the influence of agriculture on the region's vegetation. An appendix contains C and Mathematica code used to generate the graphics and some of the analysis.

Open-File Report

Digital geologic map of the Spokane 1:100,000 quadrangle, Washington and Idaho: A digital database for the 1990 N.L. Joseph map

Geologic data from the geologic map of the Spokane 1:100,000-scale quadrangle compiled by Joseph (1990) were entered into a geographic information system (GIS) as part of a larger effort to create regional digital geology for the Pacific Northwest. The map area is located in eastern Washington and extends across the state border into western Idaho (Fig. 1). This open-file report describes the methods used to convert the geologic map data into a digital format, documents the file structures, and explains how to download the digital files from the U.S. Geological Survey public access World Wide Web site on the Internet.

Idaho, Washington

National Geochemical Database, U.S. Geological Survey RASS (Rock Analysis Storage System) geochemical data for Alaska

This dataset contains geochemical data for Alaska produced by the analytical laboratories of the Geologic Division of the U.S. Geological Survey (USGS). These data represent analyses of stream-sediment, heavy-mineral-concentrate (derived from stream sediment), soil, and organic material samples. Most of the data comes from mineral resource investigations conducted in the Alaska Mineral Resource Assessment Program (AMRAP). However, some of the data were produced in support of other USGS programs. The data were originally entered into the in-house Rock Analysis Storage System (RASS) database. The RASS database, which contains over 580,000 data records, was used by the Geologic Division from the early 1970's through the late 1980's to archive geochemical data. Much of the data have been previously published in paper copy USGS Open-File Reports by the submitter or the analyst but some of the data have never been published. Over the years, USGS scientists recognized several problems with the database. The two primary issues were location coordinates (either incorrect or lacking) and sample media (not precisely identified). This dataset represents a re-processing of the original RASS data to make the data accessible in digital format and more user friendly. This re-processing consisted of checking the information on sample media and location against the original sample submittal forms, the original analytical reports, and published reports. As necessary, fields were added to the original data to more fully describe the sample preparation methods used and sample medium analyzed. The actual analytical data were not checked in great detail, but obvious errors were corrected.

Alaska

Digital geologic map of the Coeur d'Alene 1:100,000 quadrangle, Idaho and Montana

Between 1961 and 1969, Alan Griggs and others conducted fieldwork to prepare a geologic map of the Spokane 1:250,000 map (Griggs, 1973). Their field observations were posted on paper copies of 15-minute quadrangle maps. In 1999, the USGS contracted with the Idaho Geological Survey to prepare a digital version of the Coeur d’Alene 1:100,000 quadrangle. To facilitate this work, the USGS obtained the field maps prepared by Griggs and others from the USGS Field Records Library in Denver, Colorado. The Idaho Geological Survey (IGS) digitized these maps and used them in their mapping program. The mapping focused on field checks to resolve problems in poorly known areas and in areas of disagreement between adjoining maps. The IGS is currently in the process of preparing a final digital spatial database for the Coeur d’Alene 1:100,000 quadrangle. However, there was immediate need for a digital version of the geologic map of the Coeur d’Alene 1:100,000 quadrangle and the data from the field sheets along with several other sources were assembled to produce this interim product. This interim product is the digital geologic map of the Coeur d’Alene 1:100,000 quadrangle, Idaho and Montana. It was compiled from the preliminary digital files prepared by the Idaho Geological, and supplemented by data from Griggs (1973) and from digital databases by Bookstrom and others (1999) and Derkey and others (1996). The resulting digital geologic map (GIS) database can be queried in many ways to produce a variety of geologic maps. Digital base map data files (topography, roads, towns, rivers and lakes, etc.) are not included: they may be obtained from a variety of commercial and government sources. This database is not meant to be used or displayed at any scale larger than 1:100,000 (e.g., 1:62,500 or 1:24,000). The digital geologic map graphics (of00-135_map.pdf) that are provided are representations of the digital database. The map area is located in north Idaho. This open-file report describes the geologic map units, the methods used to convert the geologic map data into a digital format, the ArcInfo GIS file structures and relationships, and explains how to download the digital files from the U.S. Geological Survey public access World Wide Web site on the Internet.

Idaho, Montana

Digital Data for Volcano Hazards from Mount Rainier, Washington, Revised 1998

Mount Rainier at 4393 meters (14,410 feet) is the highest peak in the Cascade Range; a dormant volcano having glacier ice that exceeds that of any other mountain in the conterminous United States. This tremendous mass of rock and ice, in combination with great topographic relief, poses a variety of geologic hazards, both during inevitable future eruptions and during the intervening periods of repose. The volcano's past behavior is the best guide to possible future hazards. The written history (about A.D. 1820) of Mount Rainier includes one or two small eruptions, several small debris avalanches, and many small lahars (debris flows originating on a volcano). In addition, prehistoric deposits record the types, magnitudes, and frequencies of other events, and areas that were affected. Mount Rainier deposits produced since the latest ice age (approximately during the past 10,000 years) are well preserved. Studies of these deposits indicate we should anticipate potential hazards in the future. Some phenomena only occur during eruptions such as tephra falls, pyroclastic flows and surges, ballistic projectiles, and lava flows while others may occur without eruptive activity such as debris avalanches, lahars, and floods. The five geographic information system (GIS) volcano hazard data layers used to produce the Mount Rainier volcano hazard map in USGS Open-File Report 98-428 (Hoblitt and others, 1998) are included in this data set. Case 1, case 2, and case 3 layers were delineated by scientists at the Cascades Volcano Observatory and depict various lahar innundation zones around the mountain. Two additional layers delineate areas that may be affected by post-lahar sedimentation (postlahar layer) and pyroclastic flows (pyroclastic layer).

Open-File Report

Trace element and Nd, Sr, Pb isotope geochemistry of Kilauea Volcano, Hawai'i, near-vent eruptive products: 1983-2001

This open-file report serves as a repository for geochemical data referred to in U.S. Geological Survey Professional Paper 1676 (Heliker, Swanson, and Takahashi, eds., 2003), which includes multidisciplinary research papers pertaining to the first twenty years of Puu Oo Kupaianaha eruption activity. Details of eruption characteristics and nomenclature are provided in the introductory chapter of that volume (Heliker and Mattox, 2003). Geochemical relations of this data are depicted and interpreted by Thornber (2003), Thornber and others (2003a) and Thornber (2001). This report supplements Thornber and others (2003b) in which whole-rock and glass major-element data on ~1000 near-vent lava samples collected during the 1983 to 2001 eruptive interval of Kilauea Volcano, Hawai'i, are presented. Herein, we present whole-rock trace element compositions of 85 representative samples collected from January 1983 to May 2001; glass trace-element compositions of 39 Pele’s Tear (tephra) samples collected from September 1995 to September 1996, and whole-rock Nd, Sr and Pb isotopic analyses of 10 representative samples collected from September 1983 to September 1993. Thornber and others (2003b) provide a specific record of sample characteristics, location, etc., for each of the samples reported here. Spreadsheets of both reports may be integrated and sorted based upon time of formation or sample numbers. General information pertaining to the selectivity and petrologic significance of this sample suite is presented by Thornber and others (2003b). As justified in that report, this select suite of time-constrained geochemical data is suitable for constructing petrologic models of pre-eruptive magmatic processes associated with prolonged rift zone eruption of Hawaiian shield volcanoes.

Hawai'i

Preliminary geologic map of early Miocene felsic eruptive centers in the Aquarius Mountains, west-central Arizona

The first author, Gary S. Fuis, conducted this mapping in the summer of 1967 in partial fulfillment of the entry requirements into the Ph.D program of the Division of Geological and Planetary Sciences of the California Institute of Technology, Pasadena, Calif. The area mapped lies wholly within the Fort Rock Ranch, a private ranch spanning ~50 square miles in Mohave and Yavapai Counties, Arizona. Access to the ranch is limited, and it is uncertain whether a detailed geologic map of the Aquarius Mountains can be recreated today. Therefore, we are making this map available to the public in this Open-File Report. The original mapping was compiled on an enlarged single aerial photograph at an approximate scale of 1:15,600. The second author, J. Luke Blair, photogrammetrically rectified the original map and added modern topography, which was not available at the time the original map was completed. Modern roads and drainages were also added, including I–40, built after the original map was completed. Both authors reformatted the original map using current USGS geologic map standards.

Arizona