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"Chapman, John W."
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Tsunami-driven rafting
The 2011 East Japan earthquake generated a massive tsunami that launched an extraordinary transoceanic biological rafting event with no known historical precedent. We document 289 living Japanese coastal marine species from 16 phyla transported over 6 years on objects that traveled thousands of kilometers across the Pacific Ocean to the shores of North America and Hawai‘i. Most of this dispersal occurred on nonbiodegradable objects, resulting in the longest documented transoceanic survival and dispersal of coastal species by rafting. Expanding shoreline infrastructure has increased global sources of plastic materials available for biotic colonization and also interacts with climate change–induced storms of increasing severity to eject debris into the oceans. In turn, increased ocean rafting may intensify species invasions.
Journal Article
Robustness and reproducibility of an artificial intelligence‐assisted online segmentation and adaptive planning process for online adaptive radiation therapy
Clinical implementation of online adaptive radiation therapy requires initial and ongoing performance assessment of the underlying auto‐segmentation and adaptive planning algorithms, although a straightforward and efficient process for this in phantom is lacking. The purpose of this work was to investigate robustness and repeatability of the artificial intelligence‐assisted online segmentation and adaptive planning process on the Varian Ethos adaptive platform, and to develop an end‐to‐end test strategy for online adaptive radiation therapy. Five synthetic deformations were generated and applied to a computed tomography image of an anthropomorphic pelvis phantom, and reference treatment plans were generated from each of the resulting deformed images. The undeformed phantom was repeatedly imaged, and the online adaptive process was performed including auto‐segmentation, review and manual correction of contours, and adaptive plan creation. One adaptive fractions in five different deformation scenarios were performed. The manually corrected contours had a high degree of consistency (> 93% Dice similarity coefficient and < 1.0 mm mean surface distance) across repeated fractions, with no significant variation across the synthetic deformation instance except for bowel (p = 0.026, one‐way ANOVA). Adaptive treatment plans also resulted in highly consistent dose–volume values for targets and organs at risk. A straightforward and efficient process was developed and used to quantify a set of organ specific contouring and dosimetric action levels to help establish uncertainty bounds for an end‐to‐end test on the Varian Ethos system.
Journal Article
Spectral and Radiometric Calibration of the Next Generation Airborne Visible Infrared Spectrometer (AVIRIS-NG)
We describe advanced spectral and radiometric calibration techniques developed for NASA’s Next Generation Airborne Visible Infrared Imaging Spectrometer (AVIRIS-NG). By employing both statistically rigorous analysis and utilizing in situ data to inform calibration procedures and parameter estimation, we can dramatically reduce undesirable artifacts and minimize uncertainties of calibration parameters notoriously difficult to characterize in the laboratory. We describe a novel approach for destriping imaging spectrometer data through minimizing a Markov Random Field model. We then detail statistical methodology for bad pixel correction of the instrument, followed by the laboratory and field protocols involved in the corrections and evaluate their effectiveness on historical data. Finally, we review the geometric processing procedure used in production of the radiometrically calibrated image data.
Journal Article
A Spectacular Northeast Pacific Invasion by a Low Genetic Diversity Parasite, Orthione Griffenis
Invasive marine parasites can be established long before their introduction mechanisms are resolved, and factors contributing to their successes are often unknown. Understanding the ecology of these invasive parasites is urgently needed for economic and resource conservation efforts. In the eastern Pacific, the introduced Asian bopyid parasite, Orthione griffenis, extends at least from Sitka, Alaska, USA to San Quintín, Baja California, Mexico. In the new range, it infests at least two native hosts and one introduced host. We examined the genetic structure of O. griffenis from Morro Bay, California, to Ketchikan, Alaska, based on Double digest restriction‐site associated DNA (ddRAD) sequencing, and estimated its larval dispersal range from laboratory‐based survival tests. There was a lack of genetic diversity, structure, and isolation by distance across O. griffenis populations. There was also a lower‐than‐expected genetic polymorphism, consistent with previous hypotheses of its dispersal away from a single colonization event by a small number of initial propagules. Orthione griffenis larval survival appears sufficient for dispersal in coastal ocean currents over the observed northern invasion range and for transpacific dispersal via ballast water. The natural history and interaction of O. griffenis with its new and original hosts provide a unique system for understanding species adaptation in invaded ecosystems. This work demonstrates how genetically homogeneous invasive parasite populations can rapidly expand and potentially alter marine communities. Expanded efforts to understand the interactions of parasites and their vectors in their native and non‐indigenous habitats are critically needed for detecting, limiting, and mitigating their effects on endemic marine communities. This study examined the genetic structure of the invasive isopod parasite, Orthione griffenis, between Morro Bay, California, and Ketchikan, Alaska, using ddRAD sequencing and estimated its larval dispersal range from laboratory‐based survival tests. There was a lack of genetic diversity, structure, and isolation by distance across O. griffenis populations. This work highlights the potential for genetically homogeneous invasive parasite populations to rapidly expand and force fundamental alterations of marine communities.
Journal Article
Life History and Production of the Western Gray Whale’s Prey, Ampelisca eschrichtii Krøyer, 1842 (Amphipoda, Ampeliscidae)
Ampelisca eschrichtii are among the most important prey of the Western North Pacific gray whales, Eschrichtius robustus. The largest and densest known populations of this amphipod occur in the gray whale's Offshore feeding area on the Northeastern Sakhalin Island Shelf. The remote location, ice cover and stormy weather at the Offshore area have prevented winter sampling. The incomplete annual sampling has confounded efforts to resolve life history and production of A. eschrichtii. Expanded comparisons of population size structure and individual reproductive development between late spring and early fall over six sampling years between 2002 and 2013 however, reveal that A. eschrichtii are gonochoristic, iteroparous, mature at body lengths greater than 15 mm and have a two-year life span. The low frequencies of brooding females, the lack of early stage juveniles, the lack of individual or population growth or biomass increases over late spring and summer, all indicate that growth and reproduction occur primarily in winter, when sampling does not occur. Distinct juvenile and adult size cohorts additionally indicate growth and juvenile production occurs in winter through spring under ice cover. Winter growth thus requires that winter detritus or primary production are critical food sources for these ampeliscid populations and yet, the Offshore area and the Eastern Sakhalin Shelf ampeliscid communities may be the most abundant and productive amphipod population in the world. These A. eschrichtii populations are unlikely to be limited by western gray whale predation. Whether benthic community structure can limit access and foraging success of western gray whales is unclear.
Journal Article
First observations of ovary regeneration in an amphipod, Ampelisca eschrichtii Krøyer, 1842
Females of the gammaridean amphipod
with signs of regenerating, previously atrophied ovaries were recovered from the northeastern shelf of Sakhalin Island (Okhotsk Sea, Russia). Ovarian regeneration was previously unknown for any amphipod species.
have a predominantly 2-year life cycle (from embryo to adult death) and reproduce once between late winter or early spring at the age of 2 years. Occasionally, females survive to a third year. An adaptive value of extended survival among these females is likely to require that they are also reproductive.
Histological sections from a second-year female with ovarian atrophy, a female with normal ovaries, a third-year female with ovarian regeneration, as well as testes of an immature and a sexually mature male were compared to determine the sources of cells of the germinal and somatic lines necessary for ovarian regeneration.
Ovarian regeneration in the third-year female began with the formation of a new germinal zone from germ cells preserved in the atrophied ovaries and eosinophilic cells of the previously starving second-year female. Eosinophilic cells form the mesodermal component of the germinal zone. A mass of these cells appeared in the second-year female that had atrophied ovaries and in large numbers on the intestine wall of the third-year female with regenerating ovaries. These eosinophilic cells appear to migrate into the regenerating ovaries.
All germ cells of the second-year female are not lost during ovarian atrophy and can be involved in subsequent ovarian regeneration. Eosinophilic cells involved in ovarian regeneration are of mesodermal origin. The eosinophilic cell morphologies are similar to those of quiescence cells (cells in a reversible state that do not divide but retain the ability to re-enter cell division and participate in regeneration). These histological data thus indicate that eosinophilic and germ cells of third-year females can participate in the regeneration of the ovaries to reproduce a second brood. The precursors of these third-year females (a small number the second-year females with an asynchronous [summer] breeding period and ovaries that have atrophied due to seasonal starvation) appear to possess sources of somatic and germ cells that are sufficient for ovarian regeneration and that may be adaptations to starvation stress.
Journal Article
Richard Sorge, the GRU and the Pacific War
Sorge’s activities between 1930 and 1942 have tended to be lauded as those of a superlative human intelligence operator, and the Soviet Union’s GRU (Soviet military intelligence unit) as the optimum of spy-masters. Although it was unusual for a great deal of inside knowledge to be obtained from the Japanese side, most attention has always been paid on the German side to the roles played by representatives of the German Army in Japan. This book, supported by extensive notes and a bibliography, by contrast, highlights the friendly relations between Sorge and Paul Wenneker, German naval attaché in Japan from 1932 to 1937 and 1940-45. Wenneker, from extensive and expanding contacts inside the Japanese Navy (and also concealed contacts with the Japanese Army) supplied Sorge with key information on the depth of rivalry between the Japanese armed services.
eBook
Strong methane point sources contribute a disproportionate fraction of total emissions across multiple basins in the United States
Understanding, prioritizing, and mitigating methane (CH₄) emissions requires quantifying CH₄ budgets from facility scales to regional scales with the ability to differentiate between source sectors. We deployed a tiered observing system for multiple basins in the United States (San Joaquin Valley, Uinta, Denver-Julesburg, Permian, Marcellus). We quantify strong point source emissions (>10 kg CH₄ h−1) using airborne imaging spectrometers, attribute them to sectors, and assess their intermittency with multiple revisits. We compare these point source emissions to total basin CH₄ fluxes derived from inversion of Sentinel-5p satellite CH₄ observations. Across basins, point sources make up on average 40% of the regional flux. We sampled some basins several times across multiple months and years and find a distinct bimodal structure to emission timescales: the total point source budget is split nearly in half by short-lasting and longlasting emission events. With the increasing airborne and satellite observing capabilities planned for the near future, tiered observing systems will more fully quantify and attribute CH₄ emissions from facility to regional scales, which is needed to effectively and efficiently reduce methane emissions.
Journal Article
Is the Collapse of Mud Shrimp (Upogebia pugettensis) Populations Along the Pacific Coast of North America Caused by Outbreaks of a Previously Unknown Bopyrid Isopod Parasite (Orthione griffenis)?
A dramatic increase in prevalence of the recently discovered bopyrid isopod parasite, Orthione griffenis, likely introduced in the 1980s from Asia to the Pacific coast of North America, coincided with the 2002 collapse of a population of its burrowing mud shrimp host, Upogebia pugettensis, in Willapa Bay, Washington that had been stable since monitoring began in 1988. An examination of whether O. griffenis infections were sufficient to cause this decline and other recently noted U. pugettensis population collapses in Pacific Coast estuaries was conducted. O. griffenis prevalence was the highest in large reproductive-sized female shrimp and caused an estimated average 68% loss of U. pugettensis reproduction in Yaquina Bay, Oregon over a 5-year period. O. griffenis prevalence fluctuated from year to year, but trends were similar in all estuaries sampled. Uninfected shrimp transplanted back into locations from which they had disappeared acquired the parasite, suggesting that O. griffenis is extremely effective at finding its host even in estuaries with very low host density. Since both U. pugettensis and O. griffenis have pelagic larval stages, their population dynamics are also influenced by coastal nearshore oceanography and estuarine recruitment success. Coastwide lack of estuarine recruitment appears to coincide with declines in density of a co-occurring thalassinid shrimp, Neotrypaea californiensis, but cannot alone explain U. pugettensis population collapses. Although patterns observed to date could be explained by the presence of either a native or introduced parasitic castrator, assumptions of a resilient coevolved host-parasite relationship do not apply for introduced species, so continued efforts to follow the spatial extent and consequences of the O. griffenis-U. pugettensis host-parasite relationship are warranted.
Journal Article