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Observing systems, modeling, and forecasting

Predicting harmful algal blooms (HABs) requires integrating physical, chemical, and biological data collected from observing networks and then assimilating these data into models, which are used to generate forecasts. In 2005, the Harmful Algal Research and Response: A National Environmental Science Strategy 2005-2015 (HARRNESS, 2005) made recommendations on how to improve HAB modeling and forecasting over the next decade. Key HARRNESS recommendations related to sensing, networking, and modeling HABs included: ● Support the development and validation of new and improved technologies for remote cell and toxin detection, and for modeling and forecasting, ● Improve coordination of monitoring/ and modeling efforts, both at national and regional levels, ● Improve the use of networking technologies for monitoring and modeling efforts, ● Conduct sustained time series measurements of the biotic, chemical, and physical environments impacted by HABs, ● Develop food web models on the ecosystem fate and effects of toxins, ● Develop and improve species-specific models that link to physical-biological models. Here we review HAB observing, modeling, and forecasting advances and technologies and recommend research and management priorities for the next decade and beyond. Our report encompasses sensing technologies, sensor networking and data management, models and forecasts, and the paths to operationalize forecasts. Continued improvements of deployable sensors are foundational to improving early warning indicators, models, and forecasts, which are only as good as the underlying data. Sensing technology has advanced considerably in the last decade; for example, more capable fluorometric pigment sensors can track changes in bloom biomass in real-time. Additionally, automated imaging/classifying systems to identify and quantify key harmful algal (HA) taxa are being routinely deployed. However, deployable toxin sensors are available for only some HAB toxins and continue to be identified as a critical need by researchers and managers. As more and improved sensors and technologies become available, the data quality associated with each sensor needs to be assessed. Data quality encompasses the reliability, accuracy, and uncertainty associated with sensor-generated data. These data need to be of known quality so that researchers, managers, and end-users can reliably determine if the information is appropriate for their intended applications. Many of the data quality recommendations from HARRNESS (2005) are still relevant and have been reiterated within the management community. Understanding and documenting data quality, and when applicable, standardizing best practices for sensor use, continue to be recommended.

Report

Introduction to the digitization of seismic data: A user’s guide

Modern seismic data are collected, distributed, and analyzed using digital formats, and this has become a standard for the field. Although most modern seismometers still make use of analog electronic circuits, their data are converted from an analog voltage output to time‐tagged counts by way of digitization. Although much of the digitization process is not complicated to conceptualize, there is a fair bit of jargon in digitizer specifications, and a few pitfalls that can arise in the processes of recording and analyzing ground‐motion data. In this article, we review some of the fundamental physical properties of data acquisition systems and the basic steps in digitizing data from an analog instrument (specifically a seismometer). We then briefly discuss the digitization process and some of the key properties needed to make these data useful for seismological applications. Finally, we discuss some of the filtering processes that naturally arise from digitization and how it can affect the processing workflow. The end goal is to provide a user guide that will enable seismologists to have a working knowledge of the digitization process. We focus on aspects central to seismological applications and have tried to avoid getting bogged down in signal processing formalism.

Seismological Research Letters

10,000 m under the sea: An overview of the HADES expedition to Kermadec Trench

The hadal zone of the world oceans (6000– 11,000 m) occupies <1% of the marine realm and is found almost exclusively in trenches but represents ~40% of the total ocean depth range. Jamison et al. (2010 & Jamison, 2015) have reviewed the current state of knowledge about the hydrology, physical characteristics, food supply, ecology and biodiversity of life in hadal trenches. This review concluded that, there appears to be a high level of endemism based on the few specimens collected from historical sampling efforts in the 1950s (Danish Galathea and Soviet Vitjaz expeditions), but because trenches are still largely unexplored there is a lot we do not know about the ecological structure and functioning of hadal environments. However, relatively recent advances in technology using remotely operated vehicles (ROV) and landers can help us explore hadal trenches in greater detail.

Conference Paper

35 - Strength and energetics of active fault zones

The strength of active fault zones, i.e., the shear stress level required to cause fault slip, is fundamental to understanding the physics of earthquakes and to assessing earthquake hazard. Although many researchers have concluded that fault zones are weak (shear stresses 10 MPa or less averaged between 0 and ˜20 km depth), others maintain that faults are strong (˜100 MPa average of an approximate linear increase with depth). Thus, despite 30 y of dedicated research, relevant data remain inconclusive and fault strength remains uncertain by an order of magnitude. In part, this is because the main source of energy release in earthquakes is at depths greater than 5 km, inaccessible to direct instrumental observation. Very large earthquakes rupture to the Earth's surface where direct observation of the shallow rupture process is possible. However, the rupture characteristics at shallow depth may differ from those at seismogenic depths. To date no great ( M ≥ 7.75) earthquakes have occurred within a network of modern strong-motion instruments, but the large, well-recorded 1999 earthquakes in Turkey and Taiwan, both M = 7.6, show that this data gap is rapidly being filled. Furthermore, shear stress changes at the earthquake source (and the resulting seismic waves) are nearly linear perturbations of the absolute stress field. Thus, an unknown absolute background stress does not greatly affect the basic characteristics of the observed low frequency seismic waves and the observed geodetic deformation. Other, less-direct data must then be used to infer the physical state and ambient stress levels on active faults. This chapter discusses available evidence and current ideas about fault zone strength and energetics. In our review we begin by outlining the general physical conditions prevailing in the Earth around active faults and summarize the generally agreed upon observational features of faulting and earthquake occurrence ( Section 2 ). In doing so we make as few assumptions as possible, because making uncertain assumptions may lead to logical inconsistencies and apparent paradoxes. For example, the absence of a measurable, frictionally generated heat flow anomaly near active faults, the so-called stress-heat flow paradox, rests upon assumptions that must somehow be incorrect. We wish to avoid such inconsistencies and to begin we introduce the observations and briefly state what they imply about fault zones. Subsequently, in Sections 3–8 , we place these observations in an interpretative context and show how they have been used to infer various measures of fault shear stress. Section 9 summarizes our assessment of the average shear stress state near faults, argues for the general importance of stress heterogeneity in faulting processes, and discusses its implications.

International Geophysics

Identifying key stressors driving biological impairment in freshwater streams in the Chesapeake Bay watershed, USA

Biological communities in freshwater streams are often impaired by multiple stressors (e.g., flow or water quality) originating from anthropogenic activities such as urbanization, agriculture, or energy extraction. Restoration efforts in the Chesapeake Bay watershed, USA seek to improve biological conditions in 10% of freshwater tributaries and to protect the biological integrity of existing healthy watersheds. To achieve these goals, resource managers need to better understand which stressors are most likely driving biological impairment. Our study addressed this knowledge gap through two approaches: 1) reviewing and synthesizing published multi-stressor studies, and 2) examining 303(d) listed impairments linked to biological impairment as identified by jurisdiction regulatory agencies (the states within the watershed and the District of Columbia). Results identified geomorphology (i.e., physical habitat), salinity, and toxic contaminants as important for explaining variability in benthic community metrics in the literature review. Geomorphology (i.e., physical habitat and sediment), salinity, and nutrients were the most reported stressors in the jurisdictional impairment analysis. Salinity is likely a major stressor in urban and mining settings, whereas geomorphology was commonly reported in agricultural settings. Toxic contaminants, such as pesticides, were rarely measured; more research is needed to quantify the extent of their effects in the region. Flow alteration was also highlighted as an important urban stressor in the literature review but was rarely measured in the literature or reported by jurisdictions as a cause of impairment. These results can be used to prioritize stressor monitoring by managers, and to improve stressor identification methods for identifying causes of biological impairment.

Chesapeake Bay Watershed

A conceptual framework for the identification and characterization of lacustrine spawning habitats for native lake charr Salvelinus namaycush

Lake charr Salvelinus namaycush are endemic to the formerly glaciated regions of North America and spawn primarily in lakes, unlike most other Salmoninae. Spawning habitats for lake charr are thought to be characterized by relatively large substrate particle sizes which provide sufficient interstitial spaces for egg incubation, but little is known about the physical processes that create or maintain suitable habitats. We review the literature on lake charr spawning habitat and present a conceptual framework that examines the roles of physical variables in creating the appropriate conditions for egg incubation. A critical underlying assumption of this framework is that lake charr will select spawning habitats that provide suitable hypolentic flows for egg incubation. We suggest that the characterization of lakebed surface roughness, current patterns, substrate particle size, and groundwater flows at multiple spatial scales may yield significant insight into the physical mechanisms supporting lacustrine spawning habitats for lake charr and will be useful in creating predictive models of these habitats. This framework may also apply to other lake-spawning lithophilic fish species.

Environmental Biology of Fishes

Is Carbon dioxide an ore-forming fluid under shallow-earth conditions?

A review of some of the physical-chemical properties of CO 2 and of the system CO 2 --H 2 O indicates that under some shallow-earth conditions CO 2 can exist as a separate phase with a density approximately that of water. The effect of dissolved neutral or acid salts on the solubility of CO 2 in H 2 O is not large. Carbonates, oxides, and silicates, through reactions with a CO 2 -saturated water phase, will eventually cause the disappearance of a CO 2 phase. The prevalence of CO 2 in the earth's crust is attested by its abundance in natural gases and fluid inclusions in minerals. Some of the characteristics of uranium ores of the Colorado Plateau are not incompatible with the assumption that deposition was from a fluid CO 2 phase.

Economic Geology

Magnitude and Frequency of Rural Floods in the Southeastern United States, through 2006: Volume 2, North Carolina

Reliable estimates of the magnitude and frequency of floods are required for the economical and safe design of transportation and water-conveyance structures. A multistate approach was used to update methods for estimating the magnitude and frequency of floods in rural, ungaged basins in North Carolina, South Carolina, and Georgia that are not substantially affected by regulation, tidal fluctuations, or urban development. In North Carolina, annual peak-flow data available through September 2006 were available for 584 sites; 402 of these sites had a total of 10 or more years of systematic record that is required for at-site, flood-frequency analysis. Following data reviews and the computation of 20 physical and climatic basin characteristics for each station as well as at-site flood-frequency statistics, annual peak-flow data were identified for 363 sites in North Carolina suitable for use in this analysis. Among these 363 sites, 19 sites had records that could be divided into unregulated and regulated/ channelized annual peak discharges, which means peak-flow records were identified for a total of 382 cases in North Carolina. Considering the 382 cases, at-site flood-frequency statistics are provided for 333 unregulated cases (also used for the regression database) and 49 regulated/channelized cases. The flood-frequency statistics for the 333 unregulated sites were combined with data for sites from South Carolina, Georgia, and adjacent parts of Alabama, Florida, Tennessee, and Virginia to create a database of 943 sites considered for use in the regional regression analysis. Flood-frequency statistics were computed by fitting logarithms (base 10) of the annual peak flows to a log-Pearson Type III distribution. As part of the computation process, a new generalized skew coefficient was developed by using a Bayesian generalized least-squares regression model. Exploratory regression analyses using ordinary least-squares regression completed on the initial database of 943 sites resulted in defining five hydrologic regions for North Carolina, South Carolina, and Georgia. Stations with drainage areas less than 1 square mile were removed from the database, and a procedure to examine for basin redundancy (based on drainage area and periods of record) also resulted in the removal of some stations from the regression database. Flood-frequency estimates and basin characteristics for 828 gaged stations were combined to form the final database that was used in the regional regression analysis. Regional regression analysis, using generalized least-squares regression, was used to develop a set of predictive equations that can be used for estimating the 50-, 20-, 10-, 4-, 2-, 1-, 0.5-, and 0.2-percent chance exceedance flows for rural ungaged, basins in North Carolina, South Carolina, and Georgia. The final predictive equations are all functions of drainage area and the percentage of drainage basin within each of the five hydrologic regions. Average errors of prediction for these regression equations range from 34.0 to 47.7 percent. Discharge estimates determined from the systematic records for the current study are, on average, larger in magnitude than those from a previous study for the highest percent chance exceedances (50 and 20 percent) and tend to be smaller than those from the previous study for the lower percent chance exceedances when all sites are considered as a group. For example, mean differences for sites in the Piedmont hydrologic region range from positive 0.5 percent for the 50-percent chance exceedance flow to negative 4.6 percent for the 0.2-percent chance exceedance flow when stations are grouped by hydrologic region. Similarly for the same hydrologic region, median differences range from positive 0.9 percent for the 50-percent chance exceedance flow to negative 7.1 percent for the 0.2-percent chance exceedance flow. However, mean and median percentage differences between the estimates from the previous and curre

North Carolina

Coincident seismic reflection/refraction studies of the continental lithosphere: A global review

Vertical-incidence reflection profiling has identified several characteristic features of the continental lithosphere including a generally transparent upper crust, a reflective lower crust, reflections from the crust-mantle boundary, and a commonly transparent upper mantle. The underlying physical causes of these characteristic features remain poorly understood. This review summarizes additional information brought to bear on the physical properties of these characteristic crustal structures through the use of coincident wide-angle refraction profiling.

Geophysical Journal International

Crust and lithospheric structure – Global crustal structure

The Earth’s crust has played an important role in all aspects of this planet’s evolution. This chapter presents a review of our current understanding of the physical properties of the crust on a global basis. This understanding comes from extensive seismic measurements using many techniques, as well as nonseismic geophysics, including gravity, magnetic, geoelectric, and heat flow measurements. Seismic measurements include those that employ active (man-made) sources and those that use passive (naturally occurring) sources. Deep seismic reflection profiles provide a seismic image of the crust in twodimensions with a high (50–100m) resolution. Local earthquake tomography can provide three-dimensional (3-D) seismic images at moderate (500–1000m) resolution and higher, depending on the number and spacing of seismographs. Nonseismic methods provide estimates of crustal density, magnetic properties, conductivity and geotherms (temperature vs depth). The crust in deep ocean basins is 6–7km thick and has a relatively uniform seismic velocity structure, but there are numerous oceanic regions with anomalous crustal structure, including mid-ocean ridges, trenches, volcanic islands, and oceanic plateaux. Ocean–continent passive margins are also highly variable in structure, and may be classified as volcanic versus nonvolcanic margins. Continental crust ranges in thickness from 16 to 80km, and has a highly variable seismic velocity and density structure. The proportions of continental crust, by area, are 69% shield and platform (cratons), 15% old and young orogens, 9% extended (stretched) crust, 6 % magmatic arc, and 1% rifts. The weighted mean continental crustal thickness and average crustal velocity are 41km (SD 6.2km) and 6.45kms−1 (SD 0.21kms−1), respectively. A global geographic distribution of seismic data has made it possible to create global crustal models with cell sizes as small as 2°×2°. These models provide a complete description of seismic velocities and density within the crust and uppermost mantle, including, where present, ice, water, and sedimentary layers and the crystalline crust (parameterized in three layers, upper, middle and lower crust), and sub-Moho properties. The crust is the most intensely studied region of the Earth’s interior and consequently is the best understood in terms of its structure, composition, and evolution. © 2007 Elsevier B.V. All rights reserved.

Book chapter

Puget Sound shorelines and the impacts of armoring: Proceedings of a state of the science workshop, May 2009

The widespread extent and continued construction of seawalls and bulkheads on Puget Sound's beaches has emerged as a significant issue in shoreline management and coastal restoration in the region. Concerns about the impacts of shoreline armoring and managing the potential risks to coastal property are in many ways similar to those in other places, but Puget Sound also poses unique challenges related to its sheltered setting, glacially formed geology, rich estuarine ecology, and historical development pattern. The effects of armoring on shorelines are complex, involving both physical and biological science and requiring consideration of the cumulative impacts of small-scale activities over large scales of space and time. In addition, the issue is controversial, as it often places strongly held private interests in protecting shoreline property against broad public mandates to preserve shorelines for public uses and to protect environmental resources. Communities making difficult decisions about regulating shoreline activities and prioritizing restoration projects need to be informed by the best science available. To address these issues, a scientific workshop was convened in May 2009, specifically to bring local and national experts together to review the state of the science regarding the physical and biological impacts of armoring on sheltered shorelines such as those of Puget Sound.

Washington

Atomic weights of the elements. Review 2000 (IUPAC Technical Report)

A consistent set of internationally accepted atomic weights has long been an essential aim of the scientific community because of the relevance of these values to science and technology, as well as to trade and commerce subject to ethical, legal, and international standards. The standard atomic weights of the elements are regularly evaluated, recommended, and published in updated tables by the Commission on Atomic Weights and Isotopic Abundances (CAWIA) of the International Union of Pure and Applied Chemistry (IUPAC). These values are invariably associated with carefully evaluated uncertainties. Atomic weights were originally determined by mass ratio measurements coupled with an understanding of chemical stoichiometry, but are now based almost exclusively on knowledge of the isotopic composition (derived from isotope-abundance ratio measurements) and the atomic masses of the isotopes of the elements. Atomic weights and atomic masses are now scaled to a numerical value of exactly 12 for the mass of the carbon isotope of mass number 12. Technological advances in mass spectrometry and nuclear-reaction energies have enabled atomic masses to be determined with a relative uncertainty of better than 1 ×10−7 . Isotope abundances for an increasing number of elements can be measured to better than 1 ×10−3 . The excellent precision of such measurements led to the discovery that many elements, in different specimens, display significant variations in their isotope-abundance ratios, caused by a variety of natural and industrial physicochemical processes. While such variations increasingly place a constraint on the uncertainties with which some standard atomic weights can be stated, they provide numerous opportunities for investigating a range of important phenomena in physical, chemical, cosmological, biological, and industrial processes. This review reflects the current and increasing interest of science in the measured differences between source-specific and even sample-specific atomic weights. These relative comparisons can often be made with a smaller uncertainty than is achieved in the best calibrated “absolute ” (=SI-traceable) atomic-weight determinations. Accurate determinations of the atomic weights of certain elements also influence the values of fundamental constants such as the Avogadro, Faraday, and universal gas constants. This review is in two parts: the first summarizes the development of the science of atomic-weight determinations during the 20th century; the second summarizes the changes and variations that have been recognized in the values and uncertainties of atomic weights, on an element-by-element basis, in the latter part of the 20th century.

Pure and Applied Chemistry

Physical oceanography of continental shelves

Knowledge of the physical oceanography of continental shelves has increased tremendously in recent years, primarily as a result of new current and hydrographic measurements made in locations where no comparable measurements existed previously. In general, observations from geographically distinct continental shelves have shown that the nature of the flow may vary considerably from region to region. Although some characteristics, such as the response of currents to wind forcing, are common to many shelves, the relative importance of various physical processes in influencing the shelf flow field frequently is different. In the last several years, the scientific literature on shelf studies has expanded rapidly, with that for separate regions, to some extent, developing independently because of the variable role played by different physical effects.

Reviews of Geophysics and Space Physics

Anticipating environmental and environmental-health implications of extreme storms: ARkStorm scenario

The ARkStorm Scenario predicts that a prolonged winter storm event across California would cause extreme precipitation, flooding, winds, physical damages, and economic impacts. This study uses a literature review and geographic information system-based analysis of national and state databases to infer how and where ARkStorm could cause environmental damages, release contamination from diverse natural and anthropogenic sources, affect ecosystem and human health, and cause economic impacts from environmental-remediation, liability, and health-care costs. Examples of plausible ARkStorm environmental and health concerns include complex mixtures of contaminants such as petroleum, mercury, asbestos, persistent organic pollutants, molds, and pathogens; adverse physical and contamination impacts on riverine and coastal marine ecosystems; and increased incidences of mold-related health concerns, some vector-borne diseases, and valley fever. Coastal cities, the San Francisco Bay area, the Sacramento-San Joaquin River Delta, parts of the Central Valley, and some mountainous areas would likely be most affected. This type of screening analysis, coupled with follow-up local assessments, can help stakeholders in California and disaster-prone areas elsewhere better plan for, mitigate, and respond to future environmental disasters.

Natural Hazards Review

Progress and challenges in coupled hydrodynamic-ecological estuarine modeling

Numerical modeling has emerged over the last several decades as a widely accepted tool for investigations in environmental sciences. In estuarine research, hydrodynamic and ecological models have moved along parallel tracks with regard to complexity, refinement, computational power, and incorporation of uncertainty. Coupled hydrodynamic-ecological models have been used to assess ecosystem processes and interactions, simulate future scenarios, and evaluate remedial actions in response to eutrophication, habitat loss, and freshwater diversion. The need to couple hydrodynamic and ecological models to address research and management questions is clear because dynamic feedbacks between biotic and physical processes are critical interactions within ecosystems. In this review, we present historical and modern perspectives on estuarine hydrodynamic and ecological modeling, consider model limitations, and address aspects of model linkage, skill assessment, and complexity. We discuss the balance between spatial and temporal resolution and present examples using different spatiotemporal scales. Finally, we recommend future lines of inquiry, approaches to balance complexity and uncertainty, and model transparency and utility. It is idealistic to think we can pursue a “theory of everything” for estuarine models, but recent advances suggest that models for both scientific investigations and management applications will continue to improve in terms of realism, precision, and accuracy.

Estuaries and Coasts

Primer for identifying cold-water refuges to protect and restore thermal diversity in riverine landscapes

In 2003, EPA issued Region 10 guidance for Pacific Northwest state and tribal temperature water quality standards. This document was the culmination of a multi-agency, multi-disciplinary effort to develop a temperature standard for the protection of salmon, steelhead, bull trout, and redband and Lahontan cutthroat trout (collectively termed coldwater salmonids). Since its release, the Oregon and Washington have adopted the temperature standard for their waters designated for protection of coldwater salmonids. One of the unique aspects of the temperature standard, which strived to integrate the physical nature of rivers and streams and the biological requirements of coldwater salmonids, is the requirement to protect and restore cold-water refuges. This requirement is incorporated into the temperature criterion for the protection of migration corridors in the Willamette, Columbia, and Snake rivers. The intent of this provision is the recognition that some coldwater salmonids migrate through waters during thermally stressful months of summer and most likely are able to do so by using features in the rivers that provide cold water spatially or temporally. The challenge is to ensure that these features are identified, protected, and restored in order for these waters to meet the temperature standard. This primer is intended to assist Region 10 states, tribes, and local watershed groups in meeting this goal and thereby further the protection and restoration of coldwater salmonids. It provides an up-to-date summary with easily referenced information and illustrations on the scientific advances and management applications of research on cold-water refuges and can be used as a "roadmap" for identifying cold-water refuges and learning more about processes that create thermal diversity in riverine landscapes. The specific objectives are to 1. define cold-water refuge in scientific and management contexts. 2. outline an approach for identifying cold-water refuges to address water quality standards. 3. classify and characterize the types and physical processes that create cold-water refuges. 4. review methods and tools for identifying cold-water refuges in small streams to large rivers. 5. describe ecological perspectives and on-the-ground approaches for protecting and restoring thermal diversity in rivers.

Oregon