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Divide and conquer: Separating the two probabilities in seismic phase picking

There are two fundamental probabilities in the seismic phase picking process – the probability of the existence of a seismic phase (detection probability) and the probability of correctly identifying the phase arrival time (timing probability). The nearly ubiquitous approach in developing deep learning phase picking models is to use a kernel, such as a truncated Gaussian, to mask the labeled phase arrival time, and train a segmentation model. Once a model is trained, the times of the peaks in the output are taken as phase arrival times (picks) and the height of the peaks are taken as “probability” of the picks. Here, we show that this “probability” represents neither the detection nor the timing probabilty because this approach forces the output to follow the shape of the kernel. We introduce an approach using two models to estimate these two distinct probabilities. We use a binary classifier with a calibrated confidence to address the detection probability and a multi-class classifier to obtain a probability mass function to address the timing probability. This new approach makes the deep learning-based phase picking process more interpretable and gives us options to logically control seismic monitoring workflows.

Geophysical Journal International

Causal interpretations can be based on mechanistic knowledge

There exists a long-standing disconnect between statistical and mechanistic approaches to the development of causal understanding. Statistical approaches, which have dominated the literature, have focused on the need to obtain perfectly unbiased estimates of causal effects often using either experimental, quasi-experimental or other methods. Mechanistic approaches have instead focused on investigating how systems work by elucidating the structures and processes whereby variations in one system property can propagate to other system properties. Explicit references to ‘causal effects’ have tended to require adherence to statistical methods and standards, inadvertently downplaying the suitability of mechanistic knowledge for that purpose. It has been recently demonstrated that both mechanistic and statistical approaches can contribute to the long-term goal of developing causal knowledge and understanding. Proponents of statistical causal inference have seldom recommended that mechanistic evidence be relied upon to support causal interpretations. This paper provides a clear and thorough example where a causal interpretation can be supported based on mechanistic knowledge. Arguing for a causal interpretation based on knowledge of mechanisms has typically been an informal process and one that has thus far infrequently led to explicit declarations of causal knowledge by scientists. To overcome this problem, we illustrate a recently described procedure referred to as ‘causal knowledge analysis’ to summarize explicit support for causal interpretations. In this paper, we first clarify the basis of the long-standing disagreement by describing the crux of the problem as viewed from a statistical perspective and by describing how it can be overcome when there is sufficient mechanistic knowledge. We then offer a proof-of-concept example based on robust documentation and description of the mechanisms whereby plants causally regulate the responses of coastal marsh elevation to changes in sea level. Synthesis —The evidential requirements for declaring a relationship to be causal have been obscured until very recently, leading to a long neglect of this issue by scientists. Meanwhile, subject matter experts have accumulated a vast body of undeclared causal knowledge that we now need to recognize in order to position scientists as essential players in defending causal interpretations.

Journal of Ecology

Effect of sulfate and carbonate minerals on particle-size distributions in arid soils

Arid soils pose unique problems during measurement and interpretation of particle-size distributions (PSDs) because they often contain high concentrations of water-soluble salts. This study investigates the effects of sulfate and carbonate minerals on grain-size analysis by comparing analyses in water, in which the minerals dissolve, and isopropanol (IPA), in which they do not. The presence of gypsum, in particular, substantially affects particle-size analysis once the concentration of gypsum in the sample exceeds the mineral’s solubility threshold. For smaller concentrations particle-size results are unaffected. This is because at concentrations above the solubility threshold fine particles cement together or bind to coarser particles or aggregates already present in the sample, or soluble mineral coatings enlarge grains. Formation of discrete crystallites exacerbates the problem. When soluble minerals are dissolved the original, insoluble grains will become partly or entirely liberated. Thus, removing soluble minerals will result in an increase in measured fine particles. Distortion of particle-size analysis is larger for sulfate minerals than for carbonate minerals because of the much higher solubility in water of the former. When possible, arid soils should be analyzed using a liquid in which the mineral grains do not dissolve, such as IPA, because the results will more accurately reflect the PSD under most arid soil field conditions. This is especially important when interpreting soil and environmental processes affected by particle size.

Soil Science Society of America Journal

Driving- stress waveform and the determination of rock internal friction by the stress-strain curve method.

Harmonic distortion in the stress-time function applied to rock specimens affects the measurement of rock internal friction in the seismic wave periods by the stress-strain hysteresis loop method. If neglected, the harmonic distortion can cause measurements of rock internal friction to be in error by 3O% in the linear range. The stress-time function therefore must be recorded and Fourier analysed for correct interpretation of the experimental data. Such a procedure would also yield a value for internal friction at the higher harmonic frequencies.-Author

Geophysical Journal of the Royal Astronomical Soci

Sedimentary petrology of a declining reef ecosystem, Florida reef tract (U.S.A.)

Petrologic evaluation of biogenic sediments collected shelf-wide along the Florida reef tract in 1989 revealed three principal components: coral, the calcareous green alga Halimeda, and mollusc. The dominant grain was dependent in part upon local morphology that controlled composition and vitality of the biota. Either Halimeda or mollusc grains prevailed in sands off the upper Keys. In the middle and lower Keys, Halimeda grains prevailed nearshore and coral grains offshore. Comparison with similar analyses of samples collected in 1952 and 1963 indicates that, over 37 years, the relative abundance of molluscan grains more than doubled in the upper Keys and that of particulate coral tripled in the middle Keys. These changes can be interpreted in the context of physical and biological events that affected Florida Keys reefs over that period of time. In the 1970s, outbreaks of extremely cold water killed even representatives of the hardiest coral species. In the 1980s, black-band and white-band diseases decimated the major reef-building acroporid corals, and the pivotal herbivore, Diadema antillarum, disappeared. Although Diadema is a major coral bioeroder, the sea urchin is also essential to healthy reef growth. The increase in coral debris in the middle Keys may be related to Hurricane Donna in 1960, but it is also consistent with the prediction of accelerated bioerosion by boring organisms in response to increased plankton productivity. Plankton productivity is stimulated by nutrients from Florida Bay and by well-documented eutrophication of nearshore environments. In the upper Keys, where reefs are somewhat removed from bay and nearshore influence, a relative decrease in coral debris over the 37 years may reflect proliferation of algae and algae-grazing molluscs as well as suppressed rates of bioerosion in the absence of Diadema. Human activities have substantially increased the natural flux of fixed nitrogen to coastal systems worldwide. Waters in the Florida Keys are no exception. Spatial and temporal trends in sediment constituents are compared to a previously published model that predicts the response of benthic biota to changes in nutrient supply. As adapted to interpret changes observed in reef-tract sediments, the model provides insights into the natural nutrient gradient along the Florida reef tract.

Journal of Coastal Research

Studies of hydroxyaluminum complexes in aqueous solution

The coagulating ability of partly neutralized AlCl 3 solutions used in water treatment depends on their basicity, expressed here as the ratio NaOH/AlC 3 . This work presents an identification of the aluminum species active in the coagulation process. The results give rise to an interpretative model which is consistent with those models proposed for high ionic strength by other investigators.

Journal of Research of the U.S. Geological Survey

Compositions of modern dust and surface sediments in the Desert Southwest, United States

Modern dusts across southwestern United States deserts are compositionally similar to dust-rich Av soil horizons (depths of 0-0.5 cm and 1-4 cm at 35 sites) for common crustal elements but distinctly different for some trace elements. Chemical compositions and magnetic properties of the soil samples are similar among sites relative to dust sources, geographic areas, and lithologic substrates. Exceptions are Li, U, and W, enriched in Owens Valley, California, and Mg and Sr, enriched in soils formed on calcareous fan gravel in southeast Nevada. The Av horizons are dominated by dust and reflect limited mixing with substrate sediments. Modern dust samples are also similar across the region, except that Owens Valley dusts are higher in Mg, Ba, and Li and dusts both there and at sites to the north on volcanic substrates are higher in Sb and W. Thus, dust and Av horizons consist of contributions from many different sources that are well mixed before deposition. Modern dusts contain significantly greater amounts of As, Cd, Cr, Cu, Ni, Pb, and Sb than do Av horizons, which record dust additions over hundreds to thousands of years. These results suggest that modern dust compositions are influenced by anthropogenic sources and emissions from Owens (dry) Lake after its artificial desiccation in 1926. Both modern dusts and Av horizons are enriched in As, Ba, Cu, Li, Sb, Th, U, and W relative to average crustal composition, which we interpret to indicate that the geologic sources of dust in the southwestern United States are geochemically distinctive.

Journal of Geophysical Research F: Earth Surface

Rhyolitic calderas of the Yukon-Tanana Terrane, east central Alaska: volcanic remnants of a mid-Cretaceous magmatic arc

Four large but poorly exposed rhyolitic calderas are present in the Yukon-Tanana terrane (YTT) in east central Alaska. At least two are mid-Cretaceous in age (~93 Ma). Similar volcanic rocks, the South Fork Volcanics, occur northeast of the Tintina fault in Yukon Territory. Evidence for the calderas consists of thick deposits of devitrified crystal- and lithic-rich densely welded tuff, interpreted as caldera fill, associated with lava domes or shallow intrusive rocks. Coeval outflow sheets have been largely stripped by erosion. The calderas are preserved within a northeast trending depression extending across the axis of the elongate mid-Cretaceous plutonic province. Trace element abundances in andesites and rhyolites associated with the caldera structures are similar to those of volcanic and plutonic rocks of subduction-related magmatic arcs developed on continental crust and thus are suggestive of formation in such an environment. Late Cretaceous and early Tertiary igneous rocks in the YTT near the calderas are interpreted to have been emplaced in a more extensional setting when the subduction-related magmatic front was farther oceanward.

Alaska

Structural properties of the Southern San Andreas fault zone in northern Coachella Valley from magnetotelluric imaging

The Southern San Andreas fault (SSAF) poses one of the largest seismic risks in California. Yet, there is much ambiguity regarding its deeper structural properties around Coachella Valley, in large part due to the relative paucity of everyday seismicity. Here, we image a multistranded section of the SSAF using a non-seismic method, namely magnetotelluric (MT) soundings, to help inform depth-dependent fault zone geometry, fluid content and porosity. The acquired MT data and resultant inversion models highlight a conductive column encompassing the SSAF zone that includes a 2–3 km wide vertical to steeply northeast dipping conductor down to ∼4 km depth (maximum of ∼1 Ω·m at 2 km depth) and another prominent conductor in the ductile crust (∼1 Ω·m at 12 km depth and slightly southwest of the surface SSAF). We estimate porosities of 18–44 per cent for the conductive uppermost 500 m, a 10–15 per cent porosity at 2 km depth and that small amounts (0.1–3 per cent) of interconnected hypersaline fluids produce the deeper conductor. Located northeast of this conductive region is mostly resistive crust indicating dry crystalline rock that extends down to ∼20 km in places. Most of the local seismicity is associated with this resistive region. Located farther northeast still is a conductive region at >13 km depth and separate from the one to the southwest. The imaged anomalies permit two interpretations. The SSAF zone is vertical to steeply northeast dipping in the upper crust and (1) is near vertical at greater depth creating mostly an impermeable barrier for northeast fluid migration or (2) continues to dip northeast but is relatively dry and resistive up to ∼13 km depth where it manifests as a secondary deep ductile crustal conductor. Taken together with existing knowledge, the first interpretation is more likely but more MT investigations are required.

California

Marsh sediment in translation: A review of sediment transport across a natural tidal salt marsh in northern San Francisco Bay

Deposition of inorganic sediment is essential for the sustainability of tidal salt marshes. Understanding variability in sediment sources and the processes of sediment delivery to salt marshes are high priorities for decision-makers responsible for managing sediment and conserving and restoring marshes. Research on sediment transport to marshes is published in technical journals, but these scientific findings must be translated and communicated to inform critical decisions related to managing sediment in estuaries. We convened a diverse group of collaborators—including natural-resource managers, regulators, scientists, and restoration planners and practitioners—to review and interpret the results of previously published field investigations on and around the salt marsh at China Camp State Park in Marin County, California. We discussed and translated key results of those studies using new graphics and more accessible language. Here, we present a general introduction to the topic of sediment delivery to salt marshes, background descriptions of the China Camp marsh and the physical processes that we characterized there, key scientific conclusions, and proposed management implications. Key conclusions include (1) bay shallows are an important but variable source of marsh sediment, (2) flood tides and waves move sediment across the bay–marsh edge, (3) tidal creeks may not always import sediment to the marsh platform, and (4) protective effects of marsh vegetation depend on species and season. China Camp marsh is one of the last remaining pre-colonial salt marshes in the San Francisco Estuary and is unique in being relatively unmodified by humans and in retaining an unimpeded transition into natural uplands. Additional studies in a variety of marshes with different attributes and sediment regimes will broaden understanding of how best to conserve, manage, and restore tidal marshes that provide numerous ecosystem services to for humans and wildlife.

California

Normalized rare earth elements in water, sediments, and wine: identifying sources and environmental redox conditions

The concentrations of the rare earth elements (REE) in surface waters and sediments, when normalized on an element-by-element basis to one of several rock standards and plotted versus atomic number, yield curves that reveal their partitioning between different sediment fractions and the sources of those fractions, for example, between terrestrial-derived lithogenous debris and seawater-derived biogenous detritus and hydrogenous metal oxides. The REE of ancient sediments support their partitioning into these same fractions and further contribute to the identification of the redox geochemistry of the sea water in which the sediments accumulated. The normalized curves of the REE that have been examined in several South American wine varietals can be interpreted to reflect the lithology of the bedrock on which the vines may have been grown, suggesting limited fractionation during soil development.

American Journal of Analytical Chemistry

Demographic and temporal variations in immunity and condition of polar bears (Ursus maritimus) from the southern Beaufort Sea

Assessing the health and condition of animals in their natural environment can be problematic. Many physiological metrics, including immunity, are highly influenced by specific context and recent events to which researchers may be unaware. Thus, using a multifaceted physiological approach and a context-specific analysis encompassing multiple time scales can be highly informative. Ecoimmunological tools in particular can provide important indications to the health of animals in the wild. We collected blood and hair samples from free-ranging polar bears (Ursus maritimus) in the southern Beaufort Sea and examined the influence of sex, age, and reproductive status on metrics of immunity, stress, and body condition during 2013–2015. We examined metrics of innate immunity (bactericidal ability and lysis) and stress (hair cortisol, reactive oxygen species, and oxidative barrier), in relation to indices of body condition considered to be short term (urea to creatinine ratio; UC ratio) and long term (storage energy and body mass index). We found the factors of sex, age, and reproductive status of the bear were critical for interpreting different physiological metrics. Additionally, the metrics of body condition were important predictors for stress indicators. Finally, many of these metrics differed between years, illustrating the need to examine populations on a longer time scale. Taken together, this study demonstrates the complex relationship between multiple facets of physiology and how interpretation requires us to examine individuals within a specific context.

Alaska

Characterization of DOC in riparian wetland pore water and its interference in stable water isotope analysis of δ2H and δ18O

Wetlands play an important role in carbon retention, which is greatly dependent on hydrological conditions. Therefore, the interest in wetland hydrology has increased over recent decades. In wetland hydrology, stable water isotopes ( δ 2 H, δ 18 O) have found increasing use, as laser-based instruments have become readily available and allow for faster analysis and lower costs. However, the use of laser-based determinations of stable hydrogen and oxygen isotopes in wetland pore waters might be challenging because of dissolved organic carbon (DOC), especially as wetland pore waters often contain elevated DOC concentrations. To study the potential interference of DOC on laser-based stable water isotopes determination, we determined concentration, fluorescence and absorbance characteristics of DOC in pore waters collected from six restored and six near-natural riparian wetlands. The water samples’ δ 2 H and δ 18 O values were determined by two laser absorption spectrometers (LAS) and, for reference, in parallel by dual-inlet isotope-ratio mass spectrometry (DI-IRMS). The two LAS methods showed significant deviations from the DI-IRMS-determinations. Variations in the specific UV absorbance index (SUVA 254 , the quotient of the absorbance at 254 nm and the DOC concentration), which indicates the aromaticity of the DOC, partially accounted for interference for δ 2 H measurements. Elevated SUVA 254 index values were especially linked to restored wetlands. Studies that investigate pore waters with high DOC aromaticity but where the DOC is not characterized, and which require a high accuracy of the δ 2 H-values for interpretation of the hydrological system, may be severely affected by DOC interference.

Journal of Hydrology

In-situ analysis of solid bitumen in coal: Examples from the Bowen Basin and the Illinois Basin

Solid bitumen and associated vitrinite from selected coals from the Bowen Basin and the Illinois Basin were studied using electron microprobe and micro-FTIR techniques. The coal studied covers a range of vitrinite reflectance from 0.59% to 1.33%. Carbon content in the bitumen is generally lower than in vitrinite in coals with vitrinite reflectance below 0.67%. In coals with reflectance above 0.67%, carbon content of bitumen is higher than in vitrinite, reflecting higher aromaticity due to hydrocarbon generation. Sulfur and iron content are comparable between vitrinite and bitumen. Functional group distribution suggests the presence of two types of bitumen in the Illinois Basin coals. The more aliphatic variety occurring in veins and cleats is interpreted as pre-gas generation bitumen, and the more aromatic variety filling cells and voids in inertinite as post-gas generation bitumen. (C) 2000 Elsevier Science B.V. All rights reserved.Solid bitumen and associated vitrinite from selected coals from the Bowen Basin and the Illinois Basin were studied using electron microprobe and micro-FTIR techniques. The coal studied covers a range of vitrinite reflectance from 0.59% to 1.33%. Carbon content in the bitumen is generally lower than in vitrinite in coals with vitrinite reflectance below 0.67%. In coals with reflectance above 0.67%, carbon content of bitumen is higher than in vitrinite, reflecting higher aromaticity due to hydrocarbon generation. Sulfur and iron content are comparable between vitrinite and bitumen. Functional group distribution suggests the presence of two types of bitumen in the Illinois Basin coals. The more aliphatic variety occurring in veins and cleats is interpreted as pre-gas generation bitumen, and the more aromatic variety filling cells and voids in inertinite as post-gas generation bitumen.

International Journal of Coal Geology

Hydrothermal circulation at the Cleft-Vance overlapping spreading center: Results of a magnetometric resistivity survey

We report on a magnetometric resistivity sounding carried out in the overlapping spreading center between the Cleft and Vance segments of the Juan de Fuca Ridge. The data collected reveal a strong three dimensionality in the crustal electrical resistivity structure on wavelengths of a few kilometers. Areas of reduced crustal electrical resistivities, with values approaching that of seawater, are seen beneath the neovolcanic zones of both active spreading centers. We interpret these reduced resistivities as evidence of active hydrothermal circulation within the uppermost 1 km of hot, young oceanic crust.

Journal of Geophysical Research B: Solid Earth

Using climate, energy, and spatial-based hypotheses to interpret macroecological patterns of North America chelonians

Our study investigates how factors, such as latitude, productivity, and several environmental variables, influence contemporary patterns of the species richness in North American turtles. In particular, we test several hypotheses explaining broad-scale species richness patterns on several species richness data sets: ( i ) total turtles, ( ii ) freshwater turtles only, ( iii ) aquatic turtles, ( iv ) terrestrial turtles only, ( v ) Emydidae, and ( vi ) Kinosternidae. In addition to spatial data, we used a combination of 25 abiotic variables in spatial regression models to predict species richness patterns. Our results provide support for multiple hypotheses related to broad-scale patterns of species richness, and in particular, hypotheses related to climate, productivity, water availability, topography, and latitude. In general, species richness patterns were positively associated with temperature, precipitation, diversity of streams, coefficient of variation of elevation, and net primary productivity. We also found that North America turtles follow the general latitudinal diversity gradient pattern (i.e., increasing species richness towards equator) by exhibiting a negative association with latitude. Because of the incongruent results among our six data sets, our study highlights the importance of considering phylogenetic constraints and guilds when interpreting species richness patterns, especially for taxonomic groups that occupy a myriad of habitats.

Canadian Journal of Zoology

Rate of disappearance of gas bubble trauma signs in juvenile salmonids

To assess the rate of disappearance of gas bubble trauma (GBT) signs in juvenile salmonids, we exposed spring chinook salmon Oncorhynchus tshawytscha and steelhead O. mykiss to water containing high levels of dissolved gas supersaturation (DGS) for a time period sufficient to induce signs of GBT, reduced the DGS to minimal levels, and then sampled fish through time to document changes in severity of GBT. Because of the tendency of GBT signs to dissipate at different rates, we conducted trials focusing on emboli (bubbles) in the gill filaments and lateral line and separate trials that focused on bubbles in the external surfaces (fins, eyes, and opercula). Bubbles in gill filaments dissipated almost completely within 2 h after transfer of fish to water of nearly normal DGS (104%), whereas bubbles in the lateral line dissipated to negligible levels within 5 h. Bubbles on external surfaces were more persistent through time than they were in gill filaments and the lateral line. Although typically dissipating to low levels within 48 h, external bubbles sometimes remained for 4 d. Assuming a direct relation exists between easily observable signs and direct mortality, our results suggest that fish can recover quickly from the potentially lethal effects of DGS once they move from water with high DGS to water of almost normal gas saturation. These results should be of fundamental importance to fishery managers interpreting the results of monitoring for the severity and prevalence of GBT in juvenile salmonids in the Columbia River system and perhaps elsewhere.

Journal of Aquatic Animal Health

Joint 3-D tomographic imaging of Vp, Vs and Vp/Vs and hypocenter relocation at Sinabung volcano, Indonesia from November to December 2013

We conducted travel time tomography using P- and S-wave arrival times of volcanic-tectonic (VT) events that occurred between November and December 2013 to determine the three-dimensional (3D) seismic velocity structure (Vp, Vs, and Vp/Vs) beneath Sinabung volcano, Indonesia in order to delineate geological subsurface structure and to enhance our understanding of the volcanism itself. This was a time period when phreatic explosions became phreatomagmatic and then magma migrated to the surface forming a summit lava dome. We used 4846 VT events with 16,138 P- and 16,138 S-wave arrival time phases recorded by 6 stations for the tomographic inversion. The relocated VTs collapse into three clusters at depths from the surface to sea level, from 2 to 4 km below sea level, and from 5 to 8.5 km below sea level. The tomographic inversion results show three prominent regions of high Vp/Vs (~ 1.8) beneath Sinabung volcano at depths consistent with the relocated earthquake clusters. We interpret these anomalies as intrusives associated with previous eruptions and possibly surrounding the magma conduit, which we cannot resolve with this study. One anomalous region might contain partial melt, at sea level and below the eventual eruption site at the summit. Our results are important for the interpretation of a conceptual model of the “plumbing system” of this hazardous volcano.

Sinabung Volcano