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Concept: San Francisco


Amanita phalloides, colloquially known as the “death cap,” belongs to the Phalloideae section of the Amanita family of mushrooms and is responsible for most deaths following ingestion of foraged mushrooms worldwide (1). On November 28, 2016, members of the Bay Area Mycological Society notified personnel at the California Poison Control System (CPCS) of an unusually large A. phalloides bloom in the greater San Francisco Bay Area, coincident with the abundant rainfall and recent warm weather. Five days later, CPCS received notification of the first human A. phalloides poisoning of the season. Over the following 2 weeks, CPCS was notified of an additional 13 cases of hepatotoxicity resulting from A. phalloides ingestion. In the past few years before this outbreak, CPCS received reports of only a few mushroom poisoning cases per year. A summary of 14 reported cases is presented here. Data extracted from patient medical charts revealed a pattern of delayed gastrointestinal manifestations of intoxication leading to dehydration and hepatotoxicity. Three patients received liver transplants and all but one recovered completely. The morbidity and potential lethality associated with A. phalloides ingestion are serious public health concerns and warrant medical provider education and dissemination of information cautioning against consuming foraged wild mushrooms.

Concepts: San Francisco Bay, Amanita, San Francisco, Mushroom poisoning, California, Amanita phalloides, San Francisco Bay Area, Fungus


The current global projections of future sea level rise are the basis for developing inundation hazard maps. However, contributions from spatially variable coastal subsidence have generally not been considered in these projections. We use synthetic aperture radar interferometric measurements and global navigation satellite system data to show subsidence rates of less than 2 mm/year along most of the coastal areas along San Francisco Bay. However, rates exceed 10 mm/year in some areas underlain by compacting artificial landfill and Holocene mud deposits. The maps estimating 100-year inundation hazards solely based on the projection of sea level rise from various emission scenarios underestimate the area at risk of flooding by 3.7 to 90.9%, compared with revised maps that account for the contribution of local land subsidence. Given ongoing land subsidence, we project that an area of 125 to 429 km2will be vulnerable to inundation, as opposed to 51 to 413 km2considering sea level rise alone.

Concepts: San Francisco, Interferometry, Climate, San Francisco Bay, San Francisco Bay Area, Coast, Weather, Climate change


The El Niño-Southern Oscillation is the dominant mode of interannual climate variability across the Pacific Ocean basin, with influence on the global climate. The two end members of the cycle, El Niño and La Niña, force anomalous oceanographic conditions and coastal response along the Pacific margin, exposing many heavily populated regions to increased coastal flooding and erosion hazards. However, a quantitative record of coastal impacts is spatially limited and temporally restricted to only the most recent events. Here we report on the oceanographic forcing and coastal response of the 2015-2016 El Niño, one of the strongest of the last 145 years. We show that winter wave energy equalled or exceeded measured historical maxima across the US West Coast, corresponding to anomalously large beach erosion across the region. Shorelines in many areas retreated beyond previously measured landward extremes, particularly along the sediment-starved California coast.

Concepts: Alaska, San Diego, Weather, Marine debris, United States, San Francisco, Ocean, California


On March 28, 2016, two patients were evaluated at the Contra Costa Regional Medical Center emergency department (ED) in Contra Costa County, California, for nausea, vomiting, central nervous system depression, and respiratory depression, 30 minutes after ingesting what appeared to be Norco, a prescription opioid pain medication that contains acetaminophen and hydrocodone. The patients purchased the drug from a friend a few days earlier. The two cases of drug intoxication were reported to a Contra Costa County Health Department public health official who subsequently notified the California State Health Department.

Concepts: Hydrocodone, San Francisco Bay, United States, California, Opioid, Marin County, California, San Francisco, San Francisco Bay Area


The oversupply of postdoctoral scholars relative to available faculty positions has led to calls for better assessment of career outcomes. Here, we report the results of a study of postdoctoral outcomes at the University of California, San Francisco, and suggest that institutions have an obligation to determine where their postdoc alumni are employed and to share this information with current and future trainees. Further, we contend that local efforts will be more meaningful than a national survey, because of the great variability in training environment and the classification of postdoctoral scholars among institutions. We provide a framework and methodology that can be adopted by others, with the goal of developing a finely grained portrait of postdoctoral career outcomes across the United States.

Concepts: U.S. state, Research, Academia, San Francisco, Sociology, American football, California, United States


Eight whale sharks tagged with pop-up satellite archival tags off the Gulf of California, Mexico, were tracked for periods of 14-134 days. Five of these sharks were adults, with four females visually assessed to be pregnant. At least for the periods they were tracked, juveniles remained in the Gulf of California while adults moved offshore into the eastern Pacific Ocean. We propose that parturition occurs in these offshore waters. Excluding two juveniles that remained in the shallow tagging area for the duration of tracking, all sharks spent 65 ± 20.7% (SD) of their time near the surface, even over deep water, often in association with frontal zones characterized by cool-water upwelling. While these six sharks all made dives into the meso- or bathypelagic zones, with two sharks reaching the maximum depth recordable by the tags (1285.8 m), time spent at these depths represented a small proportion of the overall tracks. Most deep dives (72.7%) took place during the day, particularly during the early morning and late afternoon. Pronounced habitat differences by ontogenetic stage suggest that adult whale sharks are less likely to frequent coastal waters after the onset of maturity.

Concepts: Ocean, Indian Ocean, New Zealand, San Francisco, United States, California, Mexico, Pacific Ocean


The discovery of four new Xenoturbella species from deep waters of the eastern Pacific Ocean is reported here. The genus and two nominal species were described from the west coast of Sweden, but their taxonomic placement remains unstable. Limited evidence placed Xenoturbella with molluscs, but the tissues can be contaminated with prey. They were then considered deuterostomes. Further taxon sampling and analysis have grouped Xenoturbella with acoelomorphs (=Xenacoelomorpha) as sister to all other Bilateria (=Nephrozoa), or placed Xenacoelomorpha inside Deuterostomia with Ambulacraria (Hemichordata + Echinodermata). Here we describe four new species of Xenoturbella and reassess those hypotheses. A large species (>20 cm long) was found at cold-water hydrocarbon seeps at 2,890 m depth in Monterey Canyon and at 1,722 m in the Gulf of California (Mexico). A second large species (~10 cm long) also occurred at 1,722 m in the Gulf of California. The third large species (~15 cm long) was found at ~3,700 m depth near a newly discovered carbonate-hosted hydrothermal vent in the Gulf of California. Finally, a small species (~2.5 cm long), found near a whale carcass at 631 m depth in Monterey Submarine Canyon (California), resembles the two nominal species from Sweden. Analysis of whole mitochondrial genomes places the three larger species as a sister clade to the smaller Atlantic and Pacific species. Phylogenomic analyses of transcriptomic sequences support placement of Xenacoelomorpha as sister to Nephrozoa or Protostomia.

Concepts: San Francisco, Indian Ocean, Atlantic Ocean, Deuterostome, California, United States, Pacific Ocean, Mexico


Exosphaeromaamplicauda (Stimpson, 1857) from the west coast of North America is reviewed and redescribed and revealed to be a group of closely related species. A neotype is designated and the species redescribed based on the neotype and topotypic specimens. Exosphaeromaamplicauda is known only from the coast of California, at Marin, Sonoma and San Mateo Counties. Exosphaeromaaphrodita (Boone, 1923), type locality La Jolla, California and previously considered nomen dubium is taken out of synonymy and re-validated. A further three species: Exosphaeromapaydenae sp. n., Exosphaeromarussellhansoni sp. n., and Exosphaeromapentcheffi sp. n. are described herein. Sphaeromaoctonctum Richardson, 1899 is placed into junior synonymy with Exosphaeromaamplicauda. A key to the Pacific West Coast Exosphaeroma is provided.

Concepts: Nomen dubium, North America, San Francisco, Los Angeles, San Diego, Zoological nomenclature, United States, California


Habitat heterogeneity influences pathogen ecology by affecting vector abundance and the reservoir host communities. We investigated spatial patterns of disease risk for two human pathogens in the Borrelia genus-B. burgdorferi and B. miyamotoi-that are transmitted by the western black-legged tick, Ixodes pacificus. We collected ticks (349 nymphs, 273 adults) at 20 sites in the San Francisco Bay Area, California, USA. Tick abundance, pathogen prevalence and density of infected nymphs varied widely across sites and habitat type, though nymphal western black-legged ticks were more frequently found, and were more abundant in coast live oak forest and desert/semi-desert scrub (dominated by California sagebrush) habitats. We observed Borrelia infections in ticks at all sites where we able to collect >10 ticks. The recently recognized human pathogen, B. miyamotoi, was observed at a higher prevalence (13/349 nymphs = 3.7%, 95% CI = 2.0-6.3; 5/273 adults = 1.8%, 95% CI = 0.6-4.2) than recent studies from nearby locations (Alameda County, east of the San Francisco Bay), demonstrating that tick-borne disease risk and ecology can vary substantially at small geographic scales, with consequences for public health and disease diagnosis.

Concepts: Disease, Ixodes scapularis, Infection, California, San Francisco, San Francisco Bay, San Francisco Bay Area, Lyme disease


Mortality from collisions with vessels is one of the main human causes of death for large whales. Ship strikes are rarely witnessed and the distribution of strike risk and estimates of mortality remain uncertain at best. We estimated ship strike mortality for blue humpback and fin whales in U.S. West Coast waters using a novel application of a naval encounter model. Mortality estimates from the model were far higher than current minimum estimates derived from stranding records and are closer to extrapolations adjusted for detection probabilities of dead whales. Our most conservative model estimated mortality to be 7.8x, 2.0x and 2.7x the U.S. recommended limit for blue, humpback and fin whales, respectively, suggesting that death from vessel collisions may be a significant impediment to population growth and recovery. Comparing across the study area, the majority of strike mortality occurs in waters off California, from Bodega Bay south and tends to be concentrated in a band approximately 24 Nm (44.5 km) offshore and in designated shipping lanes leading to and from major ports. While some mortality risk exists across nearly all West Coast waters, 74%, 82% and 65% of blue, humpback and fin whale mortality, respectively, occurs in just 10% of the study area, suggesting conservation efforts can be very effective if focused in these waters. Risk is highest in the shipping lanes off San Francisco and Long Beach, but only a fraction of total estimated mortality occurs in these proportionally small areas, making any conservation efforts exclusively within these areas insufficient to address overall strike mortality. We recommend combining shipping lane modifications and re-locations, ship speed reductions and creation of ‘Areas to be Avoided’ by vessels in ecologically important locations to address this significant source of whale mortality.

Concepts: Demography, San Francisco, United States, Whale, Fin whale, Humpback whale