Studies of a Next-Generation Silicon-Photomultiplier-Based Time-of-Flight PET/CT System.

This article presents system performance studies for the Discovery MI PET/CT system, a new time-of-flight system based on silicon photomultipliers. System performance and clinical imaging were compared between this next-generation system and other commercially available PET/CT and PET/MR systems, as well as between different reconstruction algorithms. Methods: Spatial resolution, sensitivity, noise-equivalent counting rate, scatter fraction, counting rate accuracy, and image quality were characterized with the National Electrical Manufacturers Association NU-2 2012 standards. Energy resolution and coincidence time resolution were measured. Tests were conducted independently on two Discovery MI scanners installed at Stanford University and Uppsala University, and the results were averaged. Back-to-back patient scans were also performed between the Discovery MI, Discovery 690 PET/CT, and SIGNA PET/MR systems. Clinical images were reconstructed using both ordered-subset expectation maximization and Q.Clear (block-sequential regularized expectation maximization with point-spread function modeling) and were examined qualitatively. Results: The averaged full widths at half maximum (FWHMs) of the radial/tangential/axial spatial resolution reconstructed with filtered backprojection at 1, 10, and 20 cm from the system center were, respectively, 4.10/4.19/4.48 mm, 5.47/4.49/6.01 mm, and 7.53/4.90/6.10 mm. The averaged sensitivity was 13.7 cps/kBq at the center of the field of view. The averaged peak noise-equivalent counting rate was 193.4 kcps at 21.9 kBq/mL, with a scatter fraction of 40.6%. The averaged contrast recovery coefficients for the image-quality phantom were 53.7, 64.0, 73.1, 82.7, 86.8, and 90.7 for the 10-, 13-, 17-, 22-, 28-, and 37-mm-diameter spheres, respectively. The average photopeak energy resolution was 9.40% FWHM, and the average coincidence time resolution was 375.4 ps FWHM. Clinical image comparisons between the PET/CT systems demonstrated the high quality of the Discovery MI. Comparisons between the Discovery MI and SIGNA showed a similar spatial resolution and overall imaging performance. Lastly, the results indicated significantly enhanced image quality and contrast-to-noise performance for Q.Clear, compared with ordered-subset expectation maximization. Conclusion: Excellent performance was achieved with the Discovery MI, including 375 ps FWHM coincidence time resolution and sensitivity of 14 cps/kBq. Comparisons between reconstruction algorithms and other multimodal silicon photomultiplier and non-silicon photomultiplier PET detector system designs indicated that performance can be substantially enhanced with this next-generation system.

The pelagic ecosystem in the Northern California Current off Oregon during the 2014-2016 warm anomalies within the context of the past 20 years.

A warm anomaly in the upper ocean, colloquially named "the Blob," appeared in the Gulf of Alaska during the calm winter of 2013-2014, spread across the northern North Pacific (NP) Ocean, and shifted eastward and onto the Oregon shelf. At least 14 species of copepods occurred which had never been observed in shelf/slope waters off Oregon, some of which are known to have NP Gyre affinities, indicating that the source waters of the coastal "Blob" were likely of both offshore (from the west) and subtropical/tropical origin. The anomalously warm conditions were reduced during strong upwelling in spring 2015 but returned when upwelling weakened in July 2015 and transitioned to downwelling in fall 2015. The extended period of warm conditions resulted in prolonged effects on the ecosystem off central Oregon, lasting at least through 2016. Impacts to the lower trophic levels were unprecedented and include a novel plankton community composition resulting from increased copepod, diatom, and dinoflagellate species richness and increased abundance of dinoflagellates. Additionally, the multiyear warm anomalies were associated with reduced biomass of copepods and euphausiids, high abundance of larvaceans and doliolids (indictors of oligotrophic ocean conditions), and a toxic diatom bloom (Pseudo-nitzschia) throughout the California Current in 2015, thereby changing the composition of the food web that is relied upon by many commercially and ecologically important species.

Experiments with Seasonal Forecasts of ocean conditions for the Northern region of the California Current upwelling system.

Resource managers at the state, federal, and tribal levels make decisions on a weekly to quarterly basis, and fishers operate on a similar timeframe. To determine the potential of a support tool for these efforts, a seasonal forecast system is experimented with here. JISAO's Seasonal Coastal Ocean Prediction of the Ecosystem (J-SCOPE) features dynamical downscaling of regional ocean conditions in Washington and Oregon waters using a combination of a high-resolution regional model with biogeochemistry and forecasts from NOAA's Climate Forecast System (CFS). Model performance and predictability were examined for sea surface temperature (SST), bottom temperature, bottom oxygen, pH, and aragonite saturation state through model hindcasts, reforecast, and forecast comparisons with observations. Results indicate J-SCOPE forecasts have measurable skill on seasonal timescales. Experiments suggest that seasonal forecasting of ocean conditions important for fisheries is possible with the right combination of components. Those components include regional predictability on seasonal timescales of the physical environment from a large-scale model, a high-resolution regional model with biogeochemistry that simulates seasonal conditions in hindcasts, a relationship with local stakeholders, and a real-time observational network. Multiple efforts and approaches in different regions would advance knowledge to provide additional tools to fishers and other stakeholders.

The impact of El Niño events on the pelagic food chain in the northern California Current.

The zooplankton of the northern California Current are typically characterized by an abundance of lipid-rich copepods that support rapid growth and survival of ecologically, commercially, and recreationally valued fish, birds, and mammals. Disruption of this food chain and reduced ecosystem productivity are often associated with climatic variability such as El Niño events. We examined the variability in timing, magnitude, and duration of positive temperature anomalies and changes in copepod species composition in the northern California Current in relation to 10 tropical El Niño events. Measurable impacts on mesozooplankton of the northern California Current were observed during seven of 10 of these events. The occurrence of anomalously warm water and the response of the copepod community was rapid (lag of zero to 2 months) following the initiation of canonical Eastern Pacific (EP) events, but delayed (lag of 2-8 months) following 'Modoki' Central Pacific (CP) events. The variable lags in the timing of a physical and biological response led to impacts in the northern California Current peaking in winter during EP events and in the spring during CP events. The magnitude and duration of the temperature and copepod anomalies were strongly and positively related to the magnitude and duration of El Niño events, but were also sensitive to the phase of the lower frequency Pacific Decadal Oscillation. When fisheries managers and biological oceanographers are faced with the prospect of a future El Niño event, prudent management and observation will require consideration of the background oceanographic conditions, the type of event, and both the magnitude and duration of the event when assessing the potential physical and biological impacts on the northern California Current.

Climate change. Six centuries of variability and extremes in a coupled marine-terrestrial ecosystem.

Reported trends in the mean and variability of coastal upwelling in eastern boundary currents have raised concerns about the future of these highly productive and biodiverse marine ecosystems. However, the instrumental records on which these estimates are based are insufficiently long to determine whether such trends exceed preindustrial limits. In the California Current, a 576-year reconstruction of climate variables associated with winter upwelling indicates that variability increased over the latter 20th century to levels equaled only twice during the past 600 years. This modern trend in variance may be unique, because it appears to be driven by an unprecedented succession of extreme, downwelling-favorable, winter climate conditions that profoundly reduce productivity for marine predators of commercial and conservation interest.

Assessing the relative importance of local and regional processes on the survival of a threatened salmon population.

Research on regulatory mechanisms in biological populations often focuses on environmental covariates. An integrated approach that combines environmental indices with organismal-level information can provide additional insight on regulatory mechanisms. Survival of spring/summer Snake River Chinook salmon (Oncorhynchus tshawytscha) is consistently low whereas some adjacent populations with similar life histories experience greater survival. It is not known if populations with differential survival respond similarly during early marine residence, a critical period in the life history. Ocean collections, genetic stock identification, and otolith analyses were combined to evaluate the growth-mortality and match-mismatch hypotheses during early marine residence of spring/summer Snake River Chinook salmon. Interannual variation in juvenile attributes, including size at marine entry and marine growth rate, was compared with estimates of survival and physical and biological metrics. Multiple linear regression and multi-model inference were used to evaluate the relative importance of biological and physical metrics in explaining interannual variation in survival. There was relatively weak support for the match-mismatch hypothesis and stronger evidence for the growth-mortality hypothesis. Marine growth and size at capture were strongly, positively related to survival, a finding similar to spring Chinook salmon from the Mid-Upper Columbia River. In hindcast models, basin-scale indices (Pacific Decadal Oscillation (PDO) and the North Pacific Gyre Oscillation (NPGO)) and biological indices (juvenile salmon catch-per-unit-effort (CPUE) and a copepod community index (CCI)) accounted for substantial and similar portions of variation in survival for juvenile emigration years 1998-2008 (R2>0.70). However, in forecast models for emigration years 2009-2011, there was an increasing discrepancy between predictions based on the PDO (50-448% of observed value) compared with those based on the NPGO (68-212%) or biological indices (CPUE and CCI: 83-172%). Overall, the PDO index was remarkably informative in earlier years but other basin-scale and biological indices provided more accurate indications of survival in recent years.

Multivariate models of adult Pacific salmon returns.

Most modeling and statistical approaches encourage simplicity, yet ecological processes are often complex, as they are influenced by numerous dynamic environmental and biological factors. Pacific salmon abundance has been highly variable over the last few decades and most forecasting models have proven inadequate, primarily because of a lack of understanding of the processes affecting variability in survival. Better methods and data for predicting the abundance of returning adults are therefore required to effectively manage the species. We combined 31 distinct indicators of the marine environment collected over an 11-year period into a multivariate analysis to summarize and predict adult spring Chinook salmon returns to the Columbia River in 2012. In addition to forecasts, this tool quantifies the strength of the relationship between various ecological indicators and salmon returns, allowing interpretation of ecosystem processes. The relative importance of indicators varied, but a few trends emerged. Adult returns of spring Chinook salmon were best described using indicators of bottom-up ecological processes such as composition and abundance of zooplankton and fish prey as well as measures of individual fish, such as growth and condition. Local indicators of temperature or coastal upwelling did not contribute as much as large-scale indicators of temperature variability, matching the spatial scale over which salmon spend the majority of their ocean residence. Results suggest that effective management of Pacific salmon requires multiple types of data and that no single indicator can represent the complex early-ocean ecology of salmon.

The mitochondrial genomes of Euphausia pacifica and Thysanoessa raschii sequenced using 454 next-generation sequencing, with a phylogenetic analysis of their position in the Malacostracan family tree.

Euphausiid krill play a critical role in coastal and oceanic food webs, linking primary producers to upper trophic levels. In addition, some species support commercial fisheries worldwide. Despite their ecological importance, the genetics of these important species remain poorly described. To improve our understanding of the genetics of these ecological links, we sequenced the mitochondrial genomes of two species of North Pacific krill, Euphausia pacifica and Thysanoessa raschii, using long-range PCR and 454 GS Junior next-generation sequencing technology. The E. pacifica mitogenome (14,692 + base pairs (bp)) encodes 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, and at least 22 transfer RNA (tRNA) genes. The T. raschii mitogenome (14,240 + bp) encodes 13 PCGs, two rRNA genes, and at least 19 tRNA genes. The gene order in both species is similar to that of E. superba. Comparisons between Bering Sea and Yellow Sea E. pacifica revealed a total of 644 variable sites. The most variable protein-coding gene were atp8 (7.55 %, 12 of 159 sites variable), nad4 (6.35 %, 85 variable sites) and nad6 (6.32 %, 33 variable sites). Phylogenetic analyses to assess the phylogenetic position of the Euphausiacea, using the concatenated nucleic acid sequences of E. pacifica and T. raschii along with 46 previously published malacostracan mitogenomes, support the monophyly of the order Decapoda and indicate that the Euphausiacea share a common ancestor with the Decapoda. Future research should utilize this sequence data to explore the population genetics and molecular ecology of these species.

Jet stream intraseasonal oscillations drive dominant ecosystem variations in Oregon's summertime coastal upwelling system.

Summertime wind stress along the coast of the northwestern United States typically exhibits intraseasonal oscillations (ISOs) with periods from approximately 15 to 40 days, as well as fluctuations on the 2- to 6-day "weather-band" and 1-day diurnal time scales. Coastal upwelling of cool, nutrient-rich water is driven by extended periods of equatorward alongshore winds, and we show that the approximately 20-day ISOs in alongshore wind stress dominated the upwelling process during summer 2001 off Oregon. These wind stress ISOs resulted from north-south positional ISOs of the atmospheric jet stream (JS). Upper-ocean temperature, phytoplankton, and zooplankton varied principally on the approximately 20-day time scale as well, and these correlated with the ISOs in alongshore wind stress and JS position, even though there also were weather-band stress fluctuations of comparable magnitude. Such wind stress ISOs are typical along Oregon in the summer upwelling season, occurring in 10 of 12 years examined, including 2001. We present a previously unreported direct connection from the atmospheric JS to oceanic primary and secondary production on the intraseasonal time scale and show the leading importance of ISOs in driving this coastal upwelling ecosystem during a typical summer.

The fine structure of the phoront of Gymnodinioides pacifica, a ciliated protozoan (Ciliophora, Apostomatida) from euphausiids of the Northeastern Pacific.

Phoretic stages of the exuviotrophic apostome Gymnodinioides pacifica were examined using transmission and scanning electron microscopy (TEM and SEM). TEM revealed that the mature cyst wall possesses 2 or 3 layers differing by the presence or absence of the third inner layer. This inner layer may represent a different form of the middle wall material. The inner cyst layer is approximately 0.15 microm thick and has striations with a periodicity of approximately 19 nm. The middle cyst layer has a variable thickness and the outer dense layer is approximately 0.1 microm thick. The 3 layered cyst wall had a thickness of 0.3-0.7 microm and averaged 0.5 microm. Advanced phoront stages were enclosed by fully formed cyst walls or by cyst walls thinned to approximately 0.1 microm, as the phoronts prepared to excyst prior to host ecdysis. Additionally, we report the fine structure of the rosette, trichocysts, nuclei, food plaquettes, oral fiber, and other cytoplasmic inclusions. SEM revealed an outer cyst wall layer connected to the secreted peduncle material, which was observed to extend over a wide (15 microm) area on the host setae. Cysts were usually attached at their posterior ends or, less frequently, along their side.

Gymnodinioides pacifica, n. sp., an exuviotrophic ciliated protozoan (Ciliophora, Apostomatida) from euphausiids of the Northeastern Pacific.

A new species of apostome ciliate, Gymnodinioides pacifica n. sp. from the euphausiid Euphausia pacifica is described. The ciliated protozoan encysts on the setae of the appendages, telson and antennae. It excysts and enters the exoskeleton of the host after moulting, where it feeds on exuvial fluid. The phoront and trophont stages of this ciliate are described. The ciliature of the trophont has the following characteristics that distinguish it from the other species of Gymnodinioides: (1) a short kinety 9a (ciliary row 9a or K9a), approximately half of the length of falciform field 8, that extends from the anterior end of the cell posteriorly to the level of K1, (2) a straight K5a, perpendicular to K5b, K6, and K7, and (3) two distinct bands of kineties, K9b-K5b and K4-K1. In addition to those on the host E. pacifica, phoront cysts of similar shape were observed on Thysanoessa spinifera, T. gregaria, T. inspinata, T. longipes, and Nematoscelis difficilis. High prevalence rates were recorded (83%) for these apostome cysts on E. pacifica and T. spinifera during summer collections from the Oregon and Washington coasts. Additionally, we report other apostome ciliate symbionts of euphausiids, including Phtorophrya sp., which preys on apostomes in the genus Gymnodinioides.

Discovery of a ciliate parasitoid of euphausiids off Oregon, USA: Collinia oregonensis n. sp. (Apostomatida: Colliniidae).

An apostome ciliate, Collinia oregonensis n. sp., is reported inhabiting the cephalothorax and abdomen of 3 euphausiid species from the Oregon-Washington coast: Euphausia pacifica Hansen, 1911, Thysanoessa spinifera Holmes, 1900, and Thysanoessa gregaria G.O. Sars, 1883. This ciliate is the 7th species described for the genus Collinia and the 2nd species known to infect euphausiids. Disease progression and ciliate morphology are described using (1) modified protargol stain, (2) hematoxylin counterstained with Fast Green, and (3) Scanning Electron Microscopy (SEM). All endoparasitic developmental stages (trophont, tomont, tomitogenesis, protomite, and tomite) of C. oregonensis are astomatous and possess between 14 and 22 kineties. C. oregonensis is smaller than C. beringensis Capriulo & Small, 1986, which infects the euphausiid Thysanoessa inermis Krøyer, 1846 in the Bering Sea and which possesses between 24 and 80 kineties. The ciliate is a parasitoid because it must kill the host to complete its life cycle. Infections and mortalities in multiple host species likely reflect the virulent nature of the ciliate. Adult euphausiids infected with this parasitoid possess a swollen and bright orange cephalothorax. C. oregonensis feeds and proliferates inside euphausiids, producing fulminating infections that rupture the cephalothorax and release large numbers of tomites into the surrounding water. After several hours in the free swimming stage under shipboard conditions in the present study, the tomites adhered to each other, forming filaments. Infection rates ranged between 3 and 20% within individual euphausiid aggregations, but infected aggregations were randomly and sparingly distributed. Infected euphausiids were found at 6.7% of 316 stations sampled during 3 summer cruises. No infected euphausiids were collected in winter. Because E. pacifica and T. spinifera account for about 90% of the euphausiid standing stock in the northern California Current System, this parasitoid ciliate may have a significant impact on euphausiid population abundance, distribution and secondary productivity.