The US Southern Ocean Global Ocean Ecosystems Dynamics Program

The article presents information on the U.S. Southern Ocean Global Ocean Ecosystem Dynamics program (US SO GLOBEC). It was aimed at understanding the environmental and biological factors that contribute to enhanced Antarctic krill growth, reproduction, recruitment and survivorship, as well as the interactions between Antarctic krill and its predators and competitors. The highlights of US SO GLOBEC research are also discussed

Exploring potential trade-offs in outdoor water use reductions and urban tree ecosystem services during an extreme drought in Southern California

In Southern California cities, urban trees play a vital role in alleviating heat waves through shade provision and evaporative cooling. Trees in arid to semi-arid regions may rely on irrigation, which is often the first municipal water use to be restricted during drought, causing further drought stress. Finding a balance between efficient water use and maintaining tree health will be crucial for long-term urban forestry and water resources management, as climate change will increase drought and extreme heat events. This study aimed to quantify how urban tree water and carbon fluxes are affected by irrigation reductions, and how that relationship changes with tree species and temperature. We used an ecohydrologic model that mechanistically simulates water, carbon, and energy cycling, parameterized for 5 common tree species in a semi-arid urban area. We simulated a range of irrigation reductions based on average outdoor water use data from the city for a recent extreme drought as well as with warmer temperatures. We then analyzed the response of model outcomes of plant carbon fluxes, leaf area index (LAI), and water use. Results show that reducing irrigation up to 25%, a comparable amount as the California state mandate in 2014, has minimal effects on tree primary productivity and water use efficiency. We found that transpiration was linearly related to irrigation input, which could lead to a short-term loss of evaporative cooling with irrigation reductions during drought. However, primary productivity and LAI had a nonlinear response to irrigation, indicating shade provision could be maintained throughout drought with partial irrigation reductions. Results varied across tree species, with some species showing greater sensitivity of productivity to both irrigation reductions and potentially warmer droughts. These results have implications for water resources management before and during drought, and for urban tree climate adaptation to future drought

Discovery and Validation of Kepler-452b: A 1.6-Re Super Earth Exoplanet in the Habitable Zone of a G2 Star

We report on the discovery and validation of Kepler-452b, a transiting planet identified by a search through the 4 years of data collected by NASA's Kepler Mission. This possibly rocky 1.63$^{+0.23}_{-0.20}$ R$_\oplus$ planet orbits its G2 host star every 384.843$^{+0.007}_{0.012}$ days, the longest orbital period for a small (R$_p$ < 2 R$_\oplus$) transiting exoplanet to date. The likelihood that this planet has a rocky composition lies between 49% and 62%. The star has an effective temperature of 5757$\pm$85 K and a log g of 4.32$\pm$0.09. At a mean orbital separation of 1.046$^{+0.019}_{-0.015}$ AU, this small planet is well within the optimistic habitable zone of its star (recent Venus/early Mars), experiencing only 10% more flux than Earth receives from the Sun today, and slightly outside the conservative habitable zone (runaway greenhouse/maximum greenhouse). The star is slightly larger and older than the Sun, with a present radius of 1.11$^{+0.15}_{-0.09}$ R$_\odot$ and an estimated age of 6 Gyr. Thus, Kepler-452b has likely always been in the habitable zone and should remain there for another 3 Gyr.Comment: 19 pages, 16 figure

The Architecture of the GW Ori Young Triple Star System and Its Disk: Dynamical Masses, Mutual Inclinations, and Recurrent Eclipses

We present spatially and spectrally resolved Atacama Large Millimeter/submillimeter Array (ALMA) observations of gas and dust orbiting the pre-main sequence hierarchical triple star system GW Ori. A forward-modeling of the ${}^{13}$CO and C${}^{18}$O $J$=2-1 transitions permits a measurement of the total stellar mass in this system, $5.29 \pm 0.09\,M_\odot$, and the circum-triple disk inclination, $137.6 \pm 2.0^\circ$. Optical spectra spanning a 35 year period were used to derive new radial velocities and, coupled with a spectroscopic disentangling technique, revealed that the A and B components of GW Ori form a double-lined spectroscopic binary with a $241.50\pm0.05$ day period; a tertiary companion orbits that inner pair with a $4218\pm50$ day period. Combining the results from the ALMA data and the optical spectra with three epochs of astrometry in the literature, we constrain the individual stellar masses in the system ($M_\mathrm{A} \approx 2.7\,M_\odot$, $M_\mathrm{B} \approx 1.7\,M_\odot$, $M_\mathrm{C} \approx 0.9\,M_\odot$) and find strong evidence that at least one (and likely both) stellar orbital planes are misaligned with the disk plane by as much as $45^\circ$. A $V$-band light curve spanning 30 years reveals several new $\sim$30 day eclipse events 0.1-0.7~mag in depth and a 0.2 mag sinusoidal oscillation that is clearly phased with the AB-C orbital period. Taken together, these features suggest that the A-B pair may be partially obscured by material in the inner disk as the pair approaches apoastron in the hierarchical orbit. Lastly, we conclude that stellar evolutionary models are consistent with our measurements of the masses and basic photospheric properties if the GW Ori system is $\sim$1 Myr old.Comment: 26 pages, 15 figures, accepted to Ap

recount3: summaries and queries for large-scale RNA-seq expression and splicing

We present recount3, a resource consisting of over 750,000 publicly available human and mouse RNA sequencing (RNA-seq) samples uniformly processed by our new Monorail analysis pipeline. To facilitate access to the data, we provide the recount3 and snapcount R/Bioconductor packages as well as complementary web resources. Using these tools, data can be downloaded as study-level summaries or queried for specific exon-exon junctions, genes, samples, or other features. Monorail can be used to process local and/or private data, allowing results to be directly compared to any study in recount3. Taken together, our tools help biologists maximize the utility of publicly available RNA-seq data, especially to improve their understanding of newly collected data. recount3 is available from http://rna.recount.bio

The Bathypelagic Biome of the Atlantic Ocean: Character and Ecological Discreteness of the Fish Fauna

Recent global synthetic analyses have revealed that marine taxonomic inventories are far from complete, nowhere more so than in the deep-pelagic ocean. At over a billion km3, it is the largest biome on Earth, yet only a tiny fraction of the biogeographic records include the bathypelagic fauna. This data gap served as the impetus for recent deepwater surveys, many of which have altered our perceptions of pelagic ecosystems. Here we examine data from four deep-pelagic (0-5000+ m) sampling programs in the Atlantic (60°N-25°S) in order to assess the character of bathypelagic fish communities with respect to faunal distinctiveness and ecological connectivity. Regions studied include the Gulf of Mexico, Sargasso 702 Sea, eastern North/South Atlantic, and mid-North Atlantic. Quantitative analyses give contrasting pictures with respect to faunal composition and ecosystem operation. The discreteness of the bathypelagic zone is exhibited faunistically by the suite of ―holobathypelagic‖ species found only below 1000 m, most of which are highly modified morphologically. Geometric abundance class analyses reveal that the character of relative species abundance distributions between the meso- and bathypelagic zones is fundamentally dissimilar; the former exhibit a much higher proportion of common species, while the latter exhibit a much higher percentage of rarer species. From a community energetics perspective, however, the bathy- and mesopelagic zones are highly interconnected. Approximately 70% of fish species collected below 1000 m are also found in the mesopelagic zone, and in the far North Atlantic, are also found in the epipelagial. These species comprised 66 to \u3e90% of individuals collected below 1000 m in the regions sampled. In the mid-North Atlantic, these species contribute to the unexpected water-column biomass maximum observed between 1500-2300 m. Thus, the ―transient‖ taxa (primarily mesopelagic migrators and spanner taxa) add considerably to the ichthyofaunal diversity of the world ocean below 1000 m, and appear to be the vectors that support the diverse array of holobathypelagic fishes whose taxonomic composition is dominated by piscivores. Data from the four regions studied suggests that classic pelagic biogeographic boundaries do not apply to bathypelagic realm, as shared species are the rule rather than the exception. Last, cumulative species curves suggest we are far from understanding the true complexity of the bathypelagic zone

The incidence of ventilator-associated pneumonia using the PneuX System with or without elective endotracheal tube exchange: A pilot study

<p>Abstract</p> <p>Background</p> <p>The PneuX System is a novel endotracheal tube and tracheal seal monitor, which has been designed to minimise the aspiration of oropharyngeal secretions. We aimed to determine the incidence of ventilator-associated pneumonia (VAP) in patients who were intubated with the PneuX System and to establish whether intermittent subglottic secretion drainage could be performed reliably and safely using the PneuX System.</p> <p>Findings</p> <p>In this retrospective observational study, data was collected from 53 sequential patients. Nine (17%) patients were initially intubated with the PneuX System and 44 (83%) patients underwent elective exchange to the PneuX System. There were no episodes of VAP while the PneuX System was <it>in situ</it>. On an intention to treat basis, the incidence VAP was 1.8%. There were no complications from, or failure of, subglottic secretion drainage during the study.</p> <p>Conclusions</p> <p>Our study demonstrates that a low incidence of VAP is possible using the PneuX System. Our study also demonstrates that elective exchange and intermittent subglottic secretion drainage can be performed reliably and safely using the PneuX System.</p

Prisoners Teaching ESL: A Learning Community among “Language Partners”

A program in which prisoners teach ESL classes, supported by volunteer teacher-trainers, is a learning community with immense and sometimes unforeseen value

L-Asparaginase II Produced by Salmonella Typhimurium Inhibits T Cell Responses and Mediates Virulence

SummarySalmonella enterica serovar Typhimurium avoids clearance by the host immune system by suppressing T cell responses; however, the mechanisms that mediate this immunosuppression remain unknown. We show that S. Typhimurium inhibit T cell responses by producing L-Asparaginase II, which catalyzes the hydrolysis of L-asparagine to aspartic acid and ammonia. L-Asparaginase II is necessary and sufficient to suppress T cell blastogenesis, cytokine production, and proliferation and to downmodulate expression of the T cell receptor. Furthermore, S. Typhimurium-induced inhibition of T cells in vitro is prevented upon addition of L-asparagine. S. Typhimurium lacking the L-Asparaginase II gene (STM3106) are unable to inhibit T cell responses and exhibit attenuated virulence in vivo. L-Asparaginases are used to treat acute lymphoblastic leukemia through mechanisms that likely involve amino acid starvation of leukemic cells, and these findings indicate that pathogens similarly use L-asparagine deprivation to limit T cell responses

Retreatment with brentuximab vedotin in patients with CD30-positive hematologic malignancies

BACKGROUND: Brentuximab vedotin is a CD30-directed antibody-drug conjugate. Retreatment with brentuximab vedotin monotherapy was investigated in patients with CD30-positive Hodgkin lymphoma (HL) or systemic anaplastic large cell lymphoma (ALCL) who relapsed after achieving complete or partial remission (CR or PR) with initial brentuximab vedotin therapy in a previous study (ClinicalTrials.gov NCT00947856). METHODS: Twenty-one patients with HL and 8 patients with systemic ALCL were retreated; 3 patients with systemic ALCL were retreated twice. Patients generally received brentuximab vedotin 1.8 mg/kg intravenously approximately every 3 weeks over 30 minutes as an outpatient infusion. The primary objectives of this study were to assess safety and to estimate antitumor activity of brentuximab vedotin retreatment. RESULTS: The objective response rate was 60% (30% CR) in HL patients and 88% (63% CR) in systemic ALCL patients. The estimated median duration of response for patients with an objective response was 9.5 months (range, 0.0+ to 28.0+ months) at the time of study closure. Of the 19 patients with objective response, 7 patients had not had an event of disease progression or death at the time of study closure; duration of response for these patients ranged from 3.5 to 28 months. Of the 11 patients with CR, 45% had response durations of over 1 year. Adverse events (AEs) occurring in ≥25% of patients during the retreatment period were generally similar in type and frequency to those observed in the pivotal trials of brentuximab vedotin monotherapy, with the exception of peripheral neuropathy, which is known to have a cumulative effect. Grade 3 or higher events were observed in 48% of patients; these were generally transient and managed by dose modifications or delays. Deaths due to AEs occurred in 3 HL patients; none were considered to be related to brentuximab vedotin retreatment. DISCUSSION: With the exception of a higher rate of peripheral motor neuropathy, retreatment with brentuximab vedotin was associated with similar side effects seen in the pivotal trials. CONCLUSIONS: Retreatment with brentuximab vedotin monotherapy is associated with response rates in 68% (39% CR) of patients with relapsed HL and systemic ALCL. TRIAL REGISTRATION: United States registry and results database ClinicalTrials.gov NCT00947856