Analyzing the Role of Model Uncertainty for Electronic Health Records

In medicine, both ethical and monetary costs of incorrect predictions can be significant, and the complexity of the problems often necessitates increasingly complex models. Recent work has shown that changing just the random seed is enough for otherwise well-tuned deep neural networks to vary in their individual predicted probabilities. In light of this, we investigate the role of model uncertainty methods in the medical domain. Using RNN ensembles and various Bayesian RNNs, we show that population-level metrics, such as AUC-PR, AUC-ROC, log-likelihood, and calibration error, do not capture model uncertainty. Meanwhile, the presence of significant variability in patient-specific predictions and optimal decisions motivates the need for capturing model uncertainty. Understanding the uncertainty for individual patients is an area with clear clinical impact, such as determining when a model decision is likely to be brittle. We further show that RNNs with only Bayesian embeddings can be a more efficient way to capture model uncertainty compared to ensembles, and we analyze how model uncertainty is impacted across individual input features and patient subgroups.Comment: Published in the ACM Conference on Health, Inference, and Learning (CHIL) 2020. Code available at https://github.com/Google-Health/records-researc

Host–symbiont combinations dictate the photo-physiological response of reef-building corals to thermal stress

High sea surface temperatures often lead to coral bleaching wherein reef-building corals lose significant numbers of their endosymbiotic dinoflagellates (Symbiodiniaceae). These increasingly frequent bleaching events often result in large scale coral mortality, thereby devasting reef systems throughout the world. The reef habitats surrounding Palau are ideal for investigating coral responses to climate perturbation, where many inshore bays are subject to higher water temperature as compared with offshore barrier reefs. We examined fourteen physiological traits in response to high temperature across various symbiotic dinoflagellates in four common Pacific coral species, Acropora muricata, Coelastrea aspera, Cyphastrea chalcidicum and Pachyseris rugosa found in both offshore and inshore habitats. Inshore corals were dominated by a single homogenous population of the stress tolerant symbiont Durusdinium trenchii, yet symbiont thermal response and physiology differed significantly across coral species. In contrast, offshore corals harbored specific species of Cladocopium spp. (ITS2 rDNA type-C) yet all experienced similar patterns of photoinactivation and symbiont loss when heated. Additionally, cell volume and light absorption properties increased in heated Cladocopium spp., leading to a greater loss in photo-regulation. While inshore coral temperature response was consistently muted relative to their offshore counterparts, high physiological variability in D. trenchii across inshore corals suggests that bleaching resilience among even the most stress tolerant symbionts is still heavily influenced by their host environment

A Connection between Colony Biomass and Death in Caribbean Reef-Building Corals

Increased sea-surface temperatures linked to warming climate threaten coral reef ecosystems globally. To better understand how corals and their endosymbiotic dinoflagellates (Symbiodinium spp.) respond to environmental change, tissue biomass and Symbiodinium density of seven coral species were measured on various reefs approximately every four months for up to thirteen years in the Upper Florida Keys, United States (1994–2007), eleven years in the Exuma Cays, Bahamas (1995–2006), and four years in Puerto Morelos, Mexico (2003–2007). For six out of seven coral species, tissue biomass correlated with Symbiodinium density. Within a particular coral species, tissue biomasses and Symbiodinium densities varied regionally according to the following trends: Mexico≥Florida Keys≥Bahamas. Average tissue biomasses and symbiont cell densities were generally higher in shallow habitats (1–4 m) compared to deeper-dwelling conspecifics (12–15 m). Most colonies that were sampled displayed seasonal fluctuations in biomass and endosymbiont density related to annual temperature variations. During the bleaching episodes of 1998 and 2005, five out of seven species that were exposed to unusually high temperatures exhibited significant decreases in symbiotic algae that, in certain cases, preceded further decreases in tissue biomass. Following bleaching, Montastraea spp. colonies with low relative biomass levels died, whereas colonies with higher biomass levels survived. Bleaching- or disease-associated mortality was also observed in Acropora cervicornis colonies; compared to A. palmata, all A. cervicornis colonies experienced low biomass values. Such patterns suggest that Montastraea spp. and possibly other coral species with relatively low biomass experience increased susceptibility to death following bleaching or other stressors than do conspecifics with higher tissue biomass levels

Building consensus around the assessment and interpretation of Symbiodiniaceae diversity

Within microeukaryotes, genetic variation and functional variation sometimes accumulate more quickly than morphological differences. To understand the evolutionary history and ecology of such lineages, it is key to examine diversity at multiple levels of organization. In the dinoflagellate family Symbiodiniaceae, which can form endosymbioses with cnidarians (e.g., corals, octocorals, sea anemones, jellyfish), other marine invertebrates (e.g., sponges, molluscs, flatworms), and protists (e.g., foraminifera), molecular data have been used extensively over the past three decades to describe phenotypes and to make evolutionary and ecological inferences. Despite advances in Symbiodiniaceae genomics, a lack of consensus among researchers with respect to interpreting genetic data has slowed progress in the field and acted as a barrier to reconciling observations. Here, we identify key challenges regarding the assessment and interpretation of Symbiodiniaceae genetic diversity across three levels: species, populations, and communities. We summarize areas of agreement and highlight techniques and approaches that are broadly accepted. In areas where debate remains, we identify unresolved issues and discuss technologies and approaches that can help to fill knowledge gaps related to genetic and phenotypic diversity. We also discuss ways to stimulate progress, in particular by fostering a more inclusive and collaborative research community. We hope that this perspective will inspire and accelerate coral reef science by serving as a resource to those designing experiments, publishing research, and applying for funding related to Symbiodiniaceae and their symbiotic partnerships.journal articl

Building consensus around the assessment and interpretation of Symbiodiniaceae diversity

Within microeukaryotes, genetic variation and functional variation sometimes accumulate more quickly than morphological differences. To understand the evolutionary history and ecology of such lineages, it is key to examine diversity at multiple levels of organization. In the dinoflagellate family Symbiodiniaceae, which can form endosymbioses with cnidarians (e.g., corals, octocorals, sea anemones, jellyfish), other marine invertebrates (e.g., sponges, molluscs, flatworms), and protists (e.g., foraminifera), molecular data have been used extensively over the past three decades to describe phenotypes and to make evolutionary and ecological inferences. Despite advances in Symbiodiniaceae genomics, a lack of consensus among researchers with respect to interpreting genetic data has slowed progress in the field and acted as a barrier to reconciling observations. Here, we identify key challenges regarding the assessment and interpretation of Symbiodiniaceae genetic diversity across three levels: species, populations, and communities. We summarize areas of agreement and highlight techniques and approaches that are broadly accepted. In areas where debate remains, we identify unresolved issues and discuss technologies and approaches that can help to fill knowledge gaps related to genetic and phenotypic diversity. We also discuss ways to stimulate progress, in particular by fostering a more inclusive and collaborative research community. We hope that this perspective will inspire and accelerate coral reef science by serving as a resource to those designing experiments, publishing research, and applying for funding related to Symbiodiniaceae and their symbiotic partnerships

Wave Your Flag: A Narrative Criticism of Cultural Appeals, Unification, and National Pride in Coca-Cola\u27s Wavin\u27 Flag Campaign

This study examined the unification appeals, cultural artifacts, and other musical rhetoric strategies contained in K’naan and Coca-Cola’s “Wavin’ Flag” campaign. This was accomplished by analyzing the Spanish, Greek, and Thai remixes of K’naan’s song, “Wavin’ Flag.” The three versions studied are 3-4 minute long advertisements in the form of music videos. The study employed a methodology of narrative criticism to rhetorically analyze the instrumentation, lyrics, and video of each of the three versions. The findings were synthesized, and the study identified the principal methods by which the versions imparted the campaign’s core messages in each individual culture it targeted, as well as overall. It was found that the values most emphasized in the campaign’s overarching narrative included spontaneity, national pride, vibrancy, and confidence. By highlighting the methods used in Coca-Cola’s extremely successful campaign, the study contributed to the scholarship in the field of musical rhetoric. The findings of the study can help not only with musical advertising in the same vein as the “Wavin’ Flag” campaign, but with musical education, protest rallies, and other fields that make use of musical rhetoric

Host Hybridization Alters Specificity of Cnidarian-Dinoflagellate Associations

Scleractinian coral evolution is often characterized by alternating patterns of lineage diversification and fusion, thus leading to reticulate evolution. Although this pattern is hypothesized in many coral lineages, including the Montastraea annularis species complex, it is not known what effects cladogenesis and hybridization have on the symbioses between corals and their endosymbiotic dinoflagellates (genus Symbiodinium). To explore this, the genetic diversity of M. faveolata and M. annularis in the Upper Florida Keys, USA, and Exuma Cays, The Bahamas, was examined using a mtDNA intergenic region. The host genotypic data were then analyzed in relation to the diversity of the corals’ Symbiodinium communities as determined by internal transcribed spacer region 2 (ITS2) and 3 microsatellite markers specific to Symbiodinium Clade B. M. faveolata and M. annularis in the Upper Florida Keys were genetically distinct from one another while these coral species in the Exuma Cays shared mtDNA haplotypes. These findings suggest possible regional differences in the degree of intergressive hybridization between M. faveolata and M. annularis. When Symbiodinium diversity was examined, Montastraea spp. from both regions shared Symbiodinium ITS2 genotypes; however, host–symbiont specificity was observed using higher resolution microsatellite markers. Specifically, M. faveolata and M. annularis from the Upper Florida Keys all harbored genetically distinct multilocus Clade B genotypes, whereas these 2 coral species in the Exuma Cays shared Clade B genotypes. Consequently, the degree of fine-scale specificity between Symbiodinium Clade B geno- types and Montastraea spp. appears to be governed by the degree of genetic distinction, and possibly hybridization, between these host ‘species’

Different Physiology in the Jellyfish Cassiopea xamachana and C. frondosa in Florida Bay

The jellyfish Cassiopea xamachana and C. frondosa co-occur within some habitats in the Florida Keys, but the frequency with which this occurs is low. It is hypothesized that the symbiosis with different dinoflagellates in the Symbiodiniaceae is the reason: the medusae of C. xamachana contain heat-resistant Symbiodinium microadriaticum (ITS-type A1), whereas C. frondosa has heat-sensitive Breviolum sp. (ITS-type B19). Cohabitation occurs at depths of about 3–4 m in Florida Bay, where the water is on average 0.36 °C cooler, or up to 1.1 °C cooler per day. C. frondosa tends not to be found in the warmer and shallower (<2 m) depths of Florida Bay. While the density of symbionts is about equal in the small jellyfish of the two species, large C. frondosa medusae have a greater density of symbionts and appear darker in color compared to large C. xamachana. However, the number of symbionts per amebocyte are about the same, which implies that the large C. frondosa has more amebocytes than the large C. xamachana. The photosynthetic rate is similar in small medusae, but a greater reduction in photosynthesis is observed in the larger medusae of C. xamachana compared to those of C. frondosa. Medusae of C. xamachana have greater pulse rates than medusae of C. frondosa, suggestive of a greater metabolic demand. The differences in life history traits of the two species were also investigated to understand the factors that contribute to observed differences in habitat selection. The larvae of C. xamachana require lower concentrations of inducer to settle/metamorphose, and they readily settle on mangrove leaves, submerged rock, and sand compared to the larvae of C. frondosa. The asexual buds of C. xamachana are of a uniform and similar shape as compared to the variably sized and shaped buds of C. frondosa. The larger polyps of C. frondosa can have more than one attachment site compared to the single holdfast of C. xamachana. This appears to be an example of niche diversification that is likely influenced by the symbiont, with the ecological generalist and heat-resistant S. microadriaticum thriving in C. xamachana in a wider range of habitats as compared to the heat-sensitive symbiont Breviolum sp., which is only found in C. frondosa in the cooler and deeper waters

Correspondence between Cold Tolerance and Temperate Biogeography in a Western Atlantic Symbiodinium (Dinophyta) Lineage1

Many corals form obligate symbioses with photosynthetic dinoflagellates of the genus Symbiodinium Freudenthal (1962). These symbionts vary genotypically, with their geographical distribution and abundance dependent upon host specificity and tolerance to temperature and light variation. Despite the importance of these mutualistic relationships, the physiology and ecology of Symbiodinium spp. remain poorly characterized. Here, we report that rDNA internal transcribed spacer region 2 (ITS2) defined Symbiodinium type B2 associates with the cnidarian hosts Astrangia poculata and Oculina arbuscula from northerly habitats of the western Atlantic. Using pulse-amplitude-modulated (PAM) fluorometry, we compared maximum photochemical efficiency of PSII of type B2 to that of common tropical Symbiodinium lineages (types A3, B1, and C2) under cold-stress conditions. Symbiont cultures were gradually cooled from 26°C to 10°C to simulate seasonal temperature declines. Cold stress decreased the maximum photochemical efficiency of PSII and likely the photosynthetic potential for all Symbiodinium clades tested. Cultures were then maintained at 10°C for a 2-week period and gradually returned to initial conditions. Subsequent to low temperature stress, only type B2 displayed rapid and full recovery of PSII photochemical efficiency, whereas other symbiont phylotypes remained nonfunctional. These findings indicate that the distribution and abundance of Symbiodinium spp., and by extension their cnidarian hosts, in temperate climates correspond significantly with the photosynthetic cold tolerance of these symbiotic algae