Investigation of heterotrophs reveals new insights in dinoflagellate evolution.

Dinoflagellates are diverse and ecologically important protists characterized by many morphological and molecular traits that set them apart from other eukaryotes. These features include, but are not limited to, massive genomes organized using bacterially-derived histone-like proteins (HLPs) and dinoflagellate viral nucleoproteins (DVNP) rather than histones, and a complex history of photobiology with many independent losses of photosynthesis, numerous cases of serial secondary and tertiary plastid gains, and the presence of horizontally acquired bacterial rhodopsins and type II RuBisCo. Elucidating how this all evolved depends on knowing the phylogenetic relationships between dinoflagellate lineages. Half of these species are heterotrophic, but existing molecular data is strongly biased toward the photosynthetic dinoflagellates due to their amenability to cultivation and prevalence in culture collections. These biases make it impossible to interpret the evolution of photosynthesis, but may also affect phylogenetic inferences that impact our understanding of character evolution. Here, we address this problem by isolating individual cells from the Salish Sea and using single cell, culture-free transcriptomics to expand molecular data for dinoflagellates to include 27 more heterotrophic taxa, resulting in a roughly balanced representation. Using these data, we performed a comprehensive search for proteins involved in chromatin packaging, plastid function, and photoactivity across all dinoflagellates. These searches reveal that 1) photosynthesis was lost at least 21 times, 2) two known types of HLP were horizontally acquired around the same time rather than sequentially as previously thought; 3) multiple rhodopsins are present across the dinoflagellates, acquired multiple times from different donors; 4) kleptoplastic species have nucleus-encoded genes for proteins targeted to their temporary plastids and they are derived from multiple lineages, and 5) warnowiids are the only heterotrophs that retain a whole photosystem, although some photosynthesis-related electron transport genes are widely retained in heterotrophs, likely as part of the iron-sulfur cluster pathway that persists in non-photosynthetic plastids.

Morphology, behavior, and phylogenomics of Oxytoxum lohmannii, Dinoflagellata.

Dinoflagellates are an abundant and diverse group of protists representing a wealth of unique biology and ecology. While many dinoflagellates are photosynthetic or mixotrophic, many taxa are heterotrophs, often with complex feeding strategies. Compared to their photosynthetic counterparts, heterotrophic dinoflagellates remain understudied, as they are difficult to culture. One exception, a long-cultured isolate originally classified as Amphidinium but recently reclassified as Oxytoxum, has been the subject of a number of feeding, growth, and chemosensory studies. This lineage was recently determined to be closely related to Prorocentrum using phylogenetics of ribosomal RNA gene sequences, but the exact nature of this relationship remains unresolved. Using transcriptomes sequenced from culture and three single cells from the environment, we produce a robust phylogeny of 242 genes, revealing Oxytoxum is likely sister to the Prorocentrum clade, rather than nested within it. Molecular investigations uncover evidence of a reduced, nonphotosynthetic plastid and proteorhodopsin, a photoactive proton pump acquired horizontally from bacteria. We describe the ultrastructure of O. lohmannii, including densely packed trichocysts, and a new type of mucocyst. We observe that O. lohmannii feeds preferentially on cryptophytes using myzocytosis, but can also feed on various phytoflagellates using conventional phagocytosis. O. lohmannii is amenable to culture, providing an opportunity to better study heterotrophic dinoflagellate biology and feeding ecology.

Publisher Correction: Genetic tool development in marine protists: emerging model organisms for experimental cell biology.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Genetic tool development in marine protists: emerging model organisms for experimental cell biology.

Diverse microbial ecosystems underpin life in the sea. Among these microbes are many unicellular eukaryotes that span the diversity of the eukaryotic tree of life. However, genetic tractability has been limited to a few species, which do not represent eukaryotic diversity or environmentally relevant taxa. Here, we report on the development of genetic tools in a range of protists primarily from marine environments. We present evidence for foreign DNA delivery and expression in 13 species never before transformed and for advancement of tools for eight other species, as well as potential reasons for why transformation of yet another 17 species tested was not achieved. Our resource in genetic manipulation will provide insights into the ancestral eukaryotic lifeforms, general eukaryote cell biology, protein diversification and the evolution of cellular pathways.

Phylogenomics shows that novel tapeworm-like traits of haplozoan parasites evolved from within the Peridiniales (Dinoflagellata).

Haplozoans are intestinal parasites of marine annelids with bizarre traits, including a differentiated and dynamic trophozoite stage that resembles the scolex and strobila of tapeworms. Described originally as "Mesozoa", comparative ultrastructural data and molecular phylogenetic analyses have shown that haplozoans are aberrant dinoflagellates; however, these data failed to resolve the phylogenetic position of haplozoans within this diverse group of protists. Several hypotheses for the phylogenetic position of haplozoans have been proposed: (1) within the Gymnodiniales based on tabulation patterns on the trophozoites, (2) within the Blastodiniales based on the parasitic life cycle, and (3) part of a new lineage of dinoflagellates that reflects the highly modified morphology. Here, we demonstrate the phylogenetic position of haplozoans by using three single-trophozoite transcriptomes representing two species: Haplozoon axiothellae and two isolates of H. pugnus collected from the Northwestern and Northeastern Pacific Ocean. Unexpectedly, our phylogenomic analysis of 241 genes showed that these parasites are unambiguously nested within the Peridiniales, a clade of single-celled flagellates that is well represented in marine phytoplankton communities around the world. Although the intestinal trophozoites of Haplozoon species do not show any peridinioid characteristics, we suspect that uncharacterized life cycle stages may reflect their evolutionary history within the Peridiniales.

Outcomes of Long-term Treatment of Chronic HBV Infection With Entecavir or Other Agents From a Randomized Trial in 24 Countries.

BACKGROUND & AIMS: Treatment of chronic hepatitis B virus (HBV) infection with entecavir suppresses virus replication and reduces disease progression, but could require life-long therapy. To investigate clinical outcome events and safety associated with long-term treatment with entecavir, we followed up patients treated with entecavir or another standard-of-care HBV nucleos(t)ide analogue for up to 10 years. We assessed long-term outcomes and relationships with virologic response. METHODS: Patients with chronic HBV infection at 299 centers in Asia, Europe, and North and South America were assigned randomly to groups that received entecavir (n = 6216) or an investigator-selected nonentecavir HBV nucleos(t)ide analogue (n = 6162). Study participants were followed up for up to 10 years in hospital-based or community clinics. Key end points were time to adjudicated clinical outcome events and serious adverse events. In a substudy, we examined relationships between these events and virologic response. RESULTS: There were no significant differences between groups in time to event assessments for primary end points including malignant neoplasms, liver-related HBV disease progression, and death. There were no differences between groups in the secondary end points of nonhepatocellular carcinoma malignant neoplasms and hepatocellular carcinoma. In a substudy of 5305 patients in China, virologic response, regardless of treatment group, was associated with a reduced risk of liver-related HBV disease progression (hazard ratio, 0.09; 95% CI, 0.038-0.221) and hepatocellular carcinoma (hazard ratio, 0.03; 95% CI, 0.009-0.113). Twelve patients given entecavir (0.2%) and 50 patients given nonentecavir drugs (0.8%) reported treatment-related serious adverse events. CONCLUSIONS: In a randomized controlled trial of patients with chronic HBV infection, we associated entecavir therapy with a low rate of adverse events over 10 years of follow-up evaluation. Patients receiving entecavir vs another nucleos(t)ide analogue had comparable rates of liver- and non-liver-related clinical outcome events. Participants in a China cohort who maintained a virologic response, regardless of treatment group, had a reduced risk of HBV-related outcome events including hepatocellular carcinoma. ClinicalTrials.gov identifier no: NCT00388674.

Contrasting effects of high-intensity photosynthetically active radiation on two bloom-forming dinoflagellates.

While light limitation can inhibit bloom formation in dinoflagellates, the potential for high-intensity photosynthetically active radiation (PAR) to inhibit blooms by causing stress or damage has not been well-studied. We measured the effects of high-intensity PAR on the bloom-forming dinoflagellates Alexandrium fundyense and Heterocapsa rotundata. Various physiological parameters (photosynthetic efficiency Fv /Fm , cell permeability, dimethylsulfoniopropionate [DMSP], cell volume, and chlorophyll-a content) were measured before and after exposure to high-intensity natural sunlight in short-term light stress experiments. In addition, photosynthesis-irradiance (P-E) responses were compared for cells grown at different light levels to assess the capacity for photophysiological acclimation in each species. Experiments revealed distinct species-specific responses to high PAR. While high light decreased Fv /Fm in both species, A. fundyense showed little additional evidence of light stress in short-term experiments, although increased membrane permeability and intracellular DMSP indicated a response to handling. P-E responses further indicated a high light-adapted species with Chl-a inversely proportional to growth irradiance and no evidence of photoinhibition; reduced maximum per-cell photosynthesis rates suggest a trade-off between photoprotection and C fixation in high light-acclimated cells. Heterocapsa rotundata cells, in contrast, swelled in response to high light and sometimes lysed in short-term experiments, releasing DMSP. P-E responses confirmed a low light-adapted species with high photosynthetic efficiencies associated with trade-offs in the form of substantial photoinhibition and a lack of plasticity in Chl-a content. These contrasting responses illustrate that high light constrains dinoflagellate community composition through species-specific stress effects, with consequences for bloom formation and ecological interactions within the plankton.

Discriminative Accuracy of Physician and Nurse Predictions for Survival and Functional Outcomes 6 Months After an ICU Admission.

IMPORTANCE: Predictions of long-term survival and functional outcomes influence decision making for critically ill patients, yet little is known regarding their accuracy. OBJECTIVE: To determine the discriminative accuracy of intensive care unit (ICU) physicians and nurses in predicting 6-month patient mortality and morbidity, including ambulation, toileting, and cognition. DESIGN, SETTING, AND PARTICIPANTS: Prospective cohort study conducted in 5 ICUs in 3 hospitals in Philadelphia, Pennsylvania, and enrolling patients who spent at least 3 days in the ICU from October 2013 until May 2014 and required mechanical ventilation, vasopressors, or both. These patients' attending physicians and bedside nurses were also enrolled. Follow-up was completed in December 2014. MAIN OUTCOMES AND MEASURES: ICU physicians' and nurses' binary predictions of in-hospital mortality and 6-month outcomes, including mortality, return to original residence, ability to toilet independently, ability to ambulate up 10 stairs independently, and ability to remember most things, think clearly, and solve day-to-day problems (ie, normal cognition). For each outcome, physicians and nurses provided a dichotomous prediction and rated their confidence in that prediction on a 5-point Likert scale. Outcomes were assessed via interviews with surviving patients or their surrogates at 6 months. Discriminative accuracy was measured using positive and negative likelihood ratios (LRs), C statistics, and other operating characteristics. RESULTS: Among 340 patients approached, 303 (89%) consented (median age, 62 years [interquartile range, 53-71]; 57% men; 32% African American); 6-month follow-up was completed for 299 (99%), of whom 169 (57%) were alive. Predictions were made by 47 physicians and 128 nurses. Physicians most accurately predicted 6-month mortality (positive LR, 5.91 [95% CI, 3.74-9.32]; negative LR, 0.41 [95% CI, 0.33-0.52]; C statistic, 0.76 [95% CI, 0.72-0.81]) and least accurately predicted cognition (positive LR, 2.36 [95% CI, 1.36-4.12]; negative LR, 0.75 [95% CI, 0.61-0.92]; C statistic, 0.61 [95% CI, 0.54-0.68]). Nurses most accurately predicted in-hospital mortality (positive LR, 4.71 [95% CI, 2.94-7.56]; negative LR, 0.61 [95% CI, 0.49-0.75]; C statistic, 0.68 [95% CI, 0.62-0.74]) and least accurately predicted cognition (positive LR, 1.50 [95% CI, 0.86-2.60]; negative LR, 0.88 [95% CI, 0.73-1.06]; C statistic, 0.55 [95% CI, 0.48-0.62]). Discriminative accuracy was higher when physicians and nurses were confident about their predictions (eg, for physicians' confident predictions of 6-month mortality: positive LR, 33.00 [95% CI, 8.34-130.63]; negative LR, 0.18 [95% CI, 0.09-0.35]; C statistic, 0.90 [95% CI, 0.84-0.96]). Compared with a predictive model including objective clinical variables, a model that also included physician and nurse predictions had significantly higher discriminative accuracy for in-hospital mortality, 6-month mortality, and return to original residence (P < .01 for all). CONCLUSIONS AND RELEVANCE: ICU physicians' and nurses' discriminative accuracy in predicting 6-month outcomes of critically ill patients varied depending on the outcome being predicted and confidence of the predictors. Further research is needed to better understand how clinicians derive prognostic estimates of long-term outcomes.

Peginterferon lambda for the treatment of HBeAg-positive chronic hepatitis B: A randomized phase 2b study (LIRA-B).

BACKGROUND & AIMS: Peginterferon lambda-1a (lambda) is a Type-III interferon, which, like alfa interferons, has antiviral activity in vitro against hepatitis B virus (HBV) and hepatitis C virus (HCV); however, lambda has a more limited extra-hepatic receptor distribution. This phase 2b study (LIRA-B) evaluated lambda in patients with chronic HBV infection. METHODS: Adult HBeAg+ interferon-naive patients were randomized (1:1) to weekly lambda (180 µg) or peginterferon alfa-2a (alfa) for 48 weeks. The primary efficacy endpoint was HBeAg seroconversion at week 24 post-treatment; lambda non-inferiority was demonstrated if the 80% confidence interval (80% CI) lower bound was >-15%. RESULTS: Baseline characteristics were balanced across groups (lambda N=80; alfa N=83). Early on-treatment declines in HBV-DNA and qHBsAg through week 24 were greater with lambda. HBeAg seroconversion rates were comparable for lambda and alfa at week 48 (17.5% vs. 16.9%, respectively); however lambda non-inferiority was not met at week 24 post-treatment (13.8% vs. 30.1%, respectively; lambda vs. alfa 80% CI lower bound -24%). Results for other key secondary endpoints (virologic, serologic, biochemical) and post hoc combined endpoints (HBV-DNA <2000 IU/ml plus HBeAg seroconversion or ALT normalization) mostly favored alfa. Overall adverse events (AE), serious AE, and AE-discontinuation rates were comparable between arms but AE-spectra differed (more cytopenias, flu-like, and musculoskeletal symptoms observed with alfa, more ALT flares and bilirubin elevations seen with lambda). Most on-treatment flares occurred early (weeks 4-12), associated with HBV-DNA decline; all post-treatment flares were preceded by HBV-DNA rise. CONCLUSIONS: On-treatment, lambda showed greater early effects on HBV-DNA and qHBsAg, and comparable serologic/virologic responses at end-of-treatment. However, post-treatment, alfa-associated HBeAg seroconversion rates were higher, and key secondary results mostly favored alfa. ClinicalTrials.gov number: NCT01204762.

A randomized trial of nighttime physician staffing in an intensive care unit.

BACKGROUND: Increasing numbers of intensive care units (ICUs) are adopting the practice of nighttime intensivist staffing despite the lack of experimental evidence of its effectiveness. METHODS: We conducted a 1-year randomized trial in an academic medical ICU of the effects of nighttime staffing with in-hospital intensivists (intervention) as compared with nighttime coverage by daytime intensivists who were available for consultation by telephone (control). We randomly assigned blocks of 7 consecutive nights to the intervention or the control strategy. The primary outcome was patients' length of stay in the ICU. Secondary outcomes were patients' length of stay in the hospital, ICU and in-hospital mortality, discharge disposition, and rates of readmission to the ICU. For length-of-stay outcomes, we performed time-to-event analyses, with data censored at the time of a patient's death or transfer to another ICU. RESULTS: A total of 1598 patients were included in the analyses. The median Acute Physiology and Chronic Health Evaluation (APACHE) III score (in which scores range from 0 to 299, with higher scores indicating more severe illness) was 67 (interquartile range, 47 to 91), the median length of stay in the ICU was 52.7 hours (interquartile range, 29.0 to 113.4), and mortality in the ICU was 18%. Patients who were admitted on intervention days were exposed to nighttime intensivists on more nights than were patients admitted on control days (median, 100% of nights [interquartile range, 67 to 100] vs. median, 0% [interquartile range, 0 to 33]; P<0.001). Nonetheless, intensivist staffing on the night of admission did not have a significant effect on the length of stay in the ICU (rate ratio for the time to ICU discharge, 0.98; 95% confidence interval [CI], 0.88 to 1.09; P=0.72), ICU mortality (relative risk, 1.07; 95% CI, 0.90 to 1.28), or any other end point. Analyses restricted to patients who were admitted at night showed similar results, as did sensitivity analyses that used different definitions of exposure and outcome. CONCLUSIONS: In an academic medical ICU in the United States, nighttime in-hospital intensivist staffing did not improve patient outcomes. (Funded by University of Pennsylvania Health System and others; ClinicalTrials.gov number, NCT01434823.).

Daclatasvir plus peginterferon and ribavirin is noninferior to peginterferon and ribavirin alone, and reduces the duration of treatment for HCV genotype 2 or 3 infection.

BACKGROUND & AIMS: Twenty-four weeks of treatment with peginterferon and ribavirin for chronic hepatitis C virus (HCV) genotype 2 or 3 infection produces a sustained virologic response (SVR) in 70%-80% of patients. We performed a randomized, double-blind, phase 2b study to assess whether adding daclatasvir, a nonstructural protein 5A (NS5A) inhibitor that is active against these genotypes, improves efficacy and shortens therapy. METHODS: Patients with HCV genotype 2 or 3 infection (n = 151), enrolled at research centers in North America, Europe, or Australia, were assigned randomly to groups given 12 or 16 weeks of daclatasvir (60 mg once daily), or 24 weeks of placebo, each combined with peginterferon alfa-2a and ribavirin. Treatment was extended to 24 weeks for recipients of daclatasvir who did not meet the criteria for early virologic response. The primary end point was SVR at 24 weeks after treatment (SVR24). RESULTS: Baseline characteristics were similar among patients within each HCV genotype group. However, the 80 patients with HCV genotype 3, compared with the 71 patients with HCV genotype 2, were younger (mean age, 45 vs 53 y, respectively), and a larger proportion had cirrhosis (23% vs 1%, respectively). Among patients with HCV genotype 2 infection, an SVR24 was achieved by 83%, 83%, and 63% of those in the daclatasvir 12-week group, the daclatasvir 16-week group, or the placebo group, respectively; among patients with HCV genotype 3 infection, an SVR24 was achieved by 69%, 67%, and 59% of patients in these groups, respectively. Differences between genotypes largely were attributable to the higher frequency of post-treatment relapse among patients infected with HCV genotype 3. In both daclatasvir arms for both HCV genotypes, the lower bound of the 80% confidence interval of the difference in SVR24 rates between the daclatasvir and placebo arms was above -20%, establishing noninferiority. Safety findings were similar among groups, and were typical of those expected from peginterferon alfa and ribavirin therapy. CONCLUSIONS: Twelve or 16 weeks of treatment with daclatasvir, in combination with peginterferon alfa-2a and ribavirin, is a well tolerated and effective therapy for patients with HCV genotype 2 or 3 infections. Daclatasvir-containing regimens could reduce the duration of therapy for these patients. Clinicaltrials.gov number: NCT01257204.

An Observational Study of Decision Making by Medical Intensivists.

OBJECTIVES: The ICU is a place of frequent, high-stakes decision making. However, the number and types of decisions made by intensivists have not been well characterized. We sought to describe intensivist decision making and determine how the number and types of decisions are affected by patient, provider, and systems factors. DESIGN: Direct observation of intensivist decision making during patient rounds. SETTING: Twenty-four-bed academic medical ICU. SUBJECTS: Medical intensivists leading patient care rounds. INTERVENTION: None. MEASUREMENTS AND MAIN RESULTS: During 920 observed patient rounds on 374 unique patients, intensivists made 8,174 critical care decisions (mean, 8.9 decisions per patient daily, 102.2 total decisions daily) over a mean of 3.7 hours. Patient factors associated with increased numbers of decisions included a shorter time since ICU admission and an earlier slot in rounding order (both p < 0.05). Intensivist identity explained the greatest proportion of variance in number of decisions per patient even when controlling for all other factors significant in bivariable regression. A given intensivist made more decisions per patient during days later in the 14-day rotation (p < 0.05). Female intensivists made significantly more decisions than male intensivists (p < 0.05). CONCLUSIONS: Intensivists made over 100 daily critical care decisions during rounds. The number of decisions was influenced by a variety of patient- and system-related factors and was highly variable among intensivists. Future work is needed to explore effects of the decision-making burden on providers' choices and on patient outcomes.

Outcomes and statistical power in adult critical care randomized trials.

RATIONALE: Intensive care unit (ICU)-based randomized clinical trials (RCTs) among adult critically ill patients commonly fail to detect treatment benefits. OBJECTIVES: Appraise the rates of success, outcomes used, statistical power, and design characteristics of published trials. METHODS: One hundred forty-six ICU-based RCTs of diagnostic, therapeutic, or process/systems interventions published from January 2007 to May 2013 in 16 high-impact general or critical care journals were studied. MEASUREMENT AND MAIN RESULTS: Of 146 RCTs, 54 (37%) were positive (i.e., the a priori hypothesis was found to be statistically significant). The most common primary outcomes were mortality (n = 40 trials), infection-related outcomes (n = 33), and ventilation-related outcomes (n = 30), with positive results found in 10, 58, and 43%, respectively. Statistical power was discussed in 135 RCTs (92%); 92 cited a rationale for their power parameters. Twenty trials failed to achieve at least 95% of their reported target sample size, including 11 that were stopped early due to insufficient accrual/logistical issues. Of 34 superiority RCTs comparing mortality between treatment arms, 13 (38%) accrued a sample size large enough to find an absolute mortality reduction of 10% or less. In 22 of these trials the observed control-arm mortality rate differed from the predicted rate by at least 7.5%. CONCLUSIONS: ICU-based RCTs are commonly negative and powered to identify what appear to be unrealistic treatment effects, particularly when using mortality as the primary outcome. Additional concerns include a lack of standardized methods for assessing common outcomes, unclear justifications for statistical power calculations, insufficient patient accrual, and incorrect predictions of baseline event rates.

Hidden syndinian and perkinsid infections in dinoflagellate hosts revealed by single-cell transcriptomics.

Free-living core dinoflagellates are commonly infected by members of two parasitic clades that are themselves closely related to dinoflagellates, the marine alveolates and perkinsids. These parasites are abundant and ecologically important, but most species have been difficult to observe directly or cultivate, so our knowledge of them is usually restricted to environmental 18S rRNA gene sequences, as genome-scale molecular data are not available for most species. Here, we report the finding of several of these parasites infecting free-living dinoflagellates. Of the 14 infected host cells collected, only five were identified as containing parasites via light microscopy at the time of collection. Single-cell transcriptome sequencing yielded relatively high transcriptomic coverage for parasites as well as their hosts. Host and parasite homologs were distinguished phylogenetically, allowing us to infer a robust phylogenomic tree based on 192 genes. The tree showed one parasite belongs to an undescribed lineage that is sister to perkinsids, whereas the remainder are members of the syndinian clade within the marine alveolates. Close relatives of all these parasites have been observed in 18S rRNA gene surveys, but until now none had been linked to a specific host. These findings illustrate the efficacy of single-cell isolation and transcriptome sequencing as strategies for gaining deeper insights into the evolutionary history and host relationships of hidden single-celled parasites.

Biosynthesis of chlorophyll c in a dinoflagellate and heterologous production in planta.

Chlorophyll c is a key photosynthetic pigment that has been used historically to classify eukaryotic algae. Despite its importance in global photosynthetic productivity, the pathway for its biosynthesis has remained elusive. Here we define the CHLOROPHYLL C SYNTHASE (CHLCS) discovered through investigation of a dinoflagellate mutant deficient in chlorophyll c. CHLCSs are proteins with chlorophyll a/b binding and 2-oxoglutarate-Fe(II) dioxygenase (2OGD) domains found in peridinin-containing dinoflagellates; other chlorophyll c-containing algae utilize enzymes with only the 2OGD domain or an unknown synthase to produce chlorophyll c. 2OGD-containing synthases across dinoflagellate, diatom, cryptophyte, and haptophyte lineages form a monophyletic group, 8 members of which were also shown to produce chlorophyll c. Chlorophyll c1 to c2 ratios in marine algae are dictated in part by chlorophyll c synthases. CHLCS heterologously expressed in planta results in the accumulation of chlorophyll c1 and c2, demonstrating a path to augment plant pigment composition with algal counterparts.

Do windows or natural views affect outcomes or costs among patients in ICUs?

OBJECTIVE: To determine whether potential exposure to natural light via windows or to more pleasing views through windows affects outcomes or costs among critically ill patients. DESIGN: Retrospective cohort study. SETTING: An academic hospital in Philadelphia, PA. PATIENTS: Six thousand one hundred thirty-eight patients admitted to a 24-bed medical ICU and 6,631 patients admitted to a 24-bed surgical ICU from July 1, 2006, to June 30, 2010. INTERVENTIONS: Assignment to medical ICU rooms with vs. without windows and to surgical ICU rooms with natural vs. industrial views based on bed availability. MEASUREMENTS AND MAIN RESULTS: In primary analyses adjusting for patient characteristics, medical ICU patients admitted to rooms with (n = 4,093) versus without (n = 2,243) windows did not differ in rates of ICU (p = 0.25) or in-hospital (p = 0.94) mortality, ICU readmissions (p = 0.37), or delirium (p = 0.56). Surgical ICU patients admitted to rooms with natural (n = 3,072) versus industrial (n = 3,588) views experienced slightly shorter ICU lengths of stay and slightly lower variable costs. Instrumental variable analyses based on initial bed assignment and exposure time did not show any differences in any outcomes in either the medical ICU or surgical ICU cohorts, and none of the differences noted in primary analyses remained statistically significant when adjusting for multiple comparisons. In a prespecified subgroup analysis among patients with ICU length of stay greater than 72 hours, MICU windows were associated with reduced ICU (p = 0.02) and hospital mortality (p = 0.04); these results did not meet criteria for significance after adjustment for multiple comparisons. CONCLUSIONS: ICU rooms with windows or natural views do not improve outcomes or reduce costs of in-hospital care for general populations of medical and surgical ICU patients. Future work is needed to determine whether targeting light from windows directly toward patients influences outcomes and to explore these effects in patients at high risk for adverse outcomes.

Photosystems in the eye-like organelles of heterotrophic warnowiid dinoflagellates.

Warnowiid dinoflagellates contain a highly complex camera-eye-like structure called the ocelloid that is composed of different organelles resembling parts of metazoan eyes, including a modified plastid that serves as the retinal body.1 The overall structure of the ocelloid has been investigated by microscopy; because warnowiids are not in culture and are rare in nature, we know little about their function.1,2 Here, we generate single-cell transcriptomes from 18 warnowiid cells collected directly from the marine environment representing all 4 known genera and 1 previously undescribed genus, as well as 8 cells from a related lineage, the polykrikoids. Phylogenomic analyses show that photosynthesis was independently lost twice in warnowiids. Interestingly, the non-photosynthetic taxa still express a variety of photosynthesis-related proteins. Nematodinium and Warnowia (known or suspected to be photosynthetic1,3) unsurprisingly express a full complement of photosynthetic pathway components. However, non-photosynthetic genera with ocelloids were also found to express light-harvesting complexes, photosystem I, photosynthetic electron transport (PET), cytochrome b6f, and, in Erythropsidinium, plastid ATPase, representing all major complexes except photosystem II and the Calvin cycle. This suggests that the non-photosynthetic retinal body has retained a reduced but still substantial photosynthetic apparatus that perhaps functions using cyclic electron flow (CEF). This may support ATP synthesis in a reduced capacity, but it is also possible that the photosystem has been co-opted to function as a light-driven proton pump at the heart of the sensory mechanism within the complex architecture of ocelloids.

Multiple parallel origins of parasitic Marine Alveolates.

Microbial eukaryotes are important components of marine ecosystems, and the Marine Alveolates (MALVs) are consistently both abundant and diverse in global environmental sequencing surveys. MALVs are dinoflagellates that are thought to be parasites of other protists and animals, but the lack of data beyond ribosomal RNA gene sequences from all but a few described species means much of their biology and evolution remain unknown. Using single-cell transcriptomes from several MALVs and their free-living relatives, we show that MALVs evolved independently from two distinct, free-living ancestors and that their parasitism evolved in parallel. Phylogenomics shows one subgroup (MALV-II and -IV, or Syndiniales) is related to a novel lineage of free-living, eukaryovorous predators, the eleftherids, while the other (MALV-I, or Ichthyodinida) is related to the free-living predator Oxyrrhis and retains proteins targeted to a non-photosynthetic plastid. Reconstructing the evolution of photosynthesis, plastids, and parasitism in early-diverging dinoflagellates shows a number of parallels with the evolution of their apicomplexan sisters. In both groups, similar forms of parasitism evolved multiple times and photosynthesis was lost many times. By contrast, complete loss of the plastid organelle is infrequent and, when this does happen, leaves no residual genes.

Efficacy and safety of entecavir versus adefovir in chronic hepatitis B patients with hepatic decompensation: a randomized, open-label study.

A randomized, open-label comparative study of entecavir versus adefovir therapy was performed in subjects with chronic hepatitis B who had hepatic decompensation (Child-Turcotte-Pugh score ≥7). Adult subjects were randomized and treated (n = 191) with entecavir 1.0 mg or adefovir 10 mg daily for up to 96 weeks from the date of last subject randomization. Subjects were positive or negative for hepatitis B e antigen and experienced or naive for treatment with nucleos(t)ide analogues. The primary efficacy endpoint was the mean reduction in serum hepatitis B virus (HBV) DNA, as determined by polymerase chain reaction, at week 24, adjusted for baseline HBV DNA and lamivudine resistance status by linear regression analysis. Entecavir demonstrated superiority to adefovir for this endpoint (treatment difference 1.74 log(10) copies/mL [95% confidence interval -2.30, -1.18]; P < 0.0001). The entecavir group showed a greater change from baseline in HBV DNA at all time points through week 48 and a higher proportion of subjects who achieved HBV DNA < 300 copies/mL at weeks 24 (entecavir 49%; adefovir 16%; P < 0.0001) and 48 (entecavir 57%; adefovir 20%; P < 0.0001). Approximately two-thirds of subjects in both groups showed improvement/stabilization in Child-Turcotte-Pugh status. Model for End-Stage Liver Disease score change at week 48 was -2.6 for entecavir and -1.7 for adefovir. Adverse event rates were comparable between groups. Cumulative hepatocellular carcinoma rates were 12% for entecavir and 20% for adefovir. Cumulative death rates were 23% for entecavir and 33% for adefovir. Week 24 mortality rates were 12% for both groups. conclusion: Entecavir demonstrated superior virologic efficacy to adefovir in a population of patients with chronic hepatitis B who had hepatic decompensation. Biochemical and clinical benefits were also demonstrated. Entecavir was well tolerated, and early mortality rates were consistent with rates observed in similar populations treated with lamivudine.