New H2 collision-induced absorption and NH3 opacity and the spectra of the coolest brown dwarfs

We present new cloudy and cloudless model atmospheres for brown dwarfs using recent ab initio calculations of the line list of ammonia (NH3) and of the collision-induced absorption of molecular hydrogen (H2). We compare the new synthetic spectra with models based on an earlier description of the H2 and NH3 opacities. We find a significant improvement in fitting the nearly complete spectral energy distribution of the T7p dwarf Gliese 570D and in near infrared color-magnitude diagrams of field brown dwarfs. We apply these new models to the identification of NH3 absorption in the H band peak of very late T dwarfs and the new Y dwarfs and discuss the observed trend in the NH3-H spectral index. The new NH3 line list also allows a detailed study of the medium resolution spectrum of the T9/T10 dwarf UGPS J072227.51-054031.2 where we identify several specific features caused by NH3.Comment: 37 pages, 13 figures. Accepted for publication in the Astrophysical

A Search for z=7.3 Ly{\alpha} Emitters behind Gravitationally Lensing Clusters

We searched for z=7.3 Lya emitters (LAEs) behind two lensing clusters, Abell 2390 and CL 0024, with the Subaru Telescope Suprime-Cam and a narrowband NB1006 (FWHM ~ 21 nm centered at 1005 nm). We investigated if there exist objects consistent with the color of z=7.3 LAEs behind the clusters but could not detect any LAEs to the unlensed line limit F(Lya) ~ 6.9 x 10^{-18} erg/s/cm^2. Using several z=7 Lya luminosity functions (LFs) from the literature, we estimated and compared the expected detection numbers of z ~ 7 LAEs in lensing and blank field surveys in the case of using an 8m class ground based telescope. Given the steep bright-end slope of the LFs, when the detector field-of view (FOV) is comparable to the angular extent of a massive lensing cluster, imaging cluster(s) is more efficient in detecting z ~ 7 LAEs than imaging a blank field. However, the gain is expected to be modest, a factor of two at most and likely much less depending on the adopted LFs. The main advantage of lensing-cluster survey, therefore, remains to be the gain in depth and not necessarily in detection efficiency. For much larger detectors, the lensing effect becomes negligible and the efficiency of LAE detection is proportional to the instrumental FOV. We also inspected NB1006 images of three z ~ 7 z-dropouts previously detected in Abell 2390 and found that none of them are detected in NB1006. Two of them are consistent with predictions from the previous studies that they would be at lower redshifts. The other one has a photometric redshift of z ~ 7.3, and if it is at z=7.3, its unlensed Lya line flux would be very faint: F(Lya) < 4.4 x 10^{-18} erg/s/cm^2 (1 sigma upper limit) or rest frame equivalent width of W(Lya) < 26A. Its Lya emission might be attenuated by neutral hydrogen, as recent studies show that the fraction of Lyman break galaxies displaying strong Lya emission is lower at z ~ 7 than at z <~ 6.Comment: Abstract has been replaced; accepted for publication in Monthly Notices of the Royal Astronomical Society on April 11, 201

Masses, Radii, and Cloud Properties of the HR 8799 Planets

The near-infrared colors of the planets directly imaged around the A star HR 8799 are much redder than most field brown dwarfs of the same effective temperature. Previous theoretical studies of these objects have concluded that the atmospheres of planets b, c, and d are unusually cloudy or have unusual cloud properties. Some studies have also found that the inferred radii of some or all of the planets disagree with expectations of standard giant planet evolution models. Here we compare the available data to the predictions of our own set of atmospheric and evolution models that have been extensively tested against observations of field L and T dwarfs, including the reddest L dwarfs. Unlike some previous studies we require mutually consistent choices for effective temperature, gravity, cloud properties, and planetary radius. This procedure thus yields plausible values for the masses, effective temperatures, and cloud properties of all three planets. We find that the cloud properties of the HR 8799 planets are not unusual but rather follow previously recognized trends, including a gravity dependence on the temperature of the L to T spectral transition--some reasons for which we discuss. We find the inferred mass of planet b is highly sensitive to whether or not we include the H and K band spectrum in our analysis. Solutions for planets c and d are consistent with the generally accepted constraints on the age of the primary star and orbital dynamics. We also confirm that, like in L and T dwarfs and solar system giant planets, non-equilibrium chemistry driven by atmospheric mixing is also important for these objects. Given the preponderance of data suggesting that the L to T spectral type transition is gravity dependent, we present an exploratory evolution calculation that accounts for this effect. Finally we recompute the the bolometric luminosity of all three planets.Comment: 52 pages, 12 figures, Astrophysical Journal, in press. v2 features minor editorial updates and correction

Imaging of compartmentalised intracellular nitric oxide, induced during bacterial phagocytosis, using a metalloprotein–gold nanoparticle conjugate

Nitric oxide (NO) plays an essential role within the immune system since it is involved in the break-down of infectious agents such as viruses and bacteria. The ability to measure the presence of NO in the intracellular environment would provide a greater understanding of the pathophysiological mechanism of this important molecule. Here we report the detection of NO from the intracellular phagolysosome using a fluorescently tagged metalloprotein–gold nanoparticle conjugate. The metalloprotein cytochrome c, fluorescently tagged with an Alexa Fluor dye, was self-assembled onto gold nanoparticles to produce a NO specific nanobiosensor. Upon binding of NO, the cytochrome c protein changes conformation which induces an increase of fluorescence intensity of the tagged protein proportional to the NO concentration. The nanobiosensor was sensitive to NO in a reversible and selective manner, and exhibited a linear response at NO concentrations between 1 and 300 μM. In RAW264.7γ NO− macrophage cells, the nanobiosensor was used to detect the presence of NO that had been endogenously generated upon stimulation of the cells with interferon-γ and lipopolysaccharide, or spontaneously released following treatment of the cells with a NO donor. Significantly, the nanobiosensor was shown to be taken up by the macrophages within phagolysosomes, i.e., the precise location where the NO, together with other species, destroys bacterial infection. The nanobiosensor measured, for the first time, increasing concentrations of NO produced during combined stimulation and phagocytosis of Escherichia coli bacteria from within localised intracellular phagolysosomes, a key part of the immune system

Reduction and Emergence in Bose-Einstein Condensates

A closer look at some proposed Gedanken-experiments on BECs promises to shed light on several aspects of reduction and emergence in physics. These include the relations between classical descriptions and different quantum treatments of macroscopic systems, and the emergence of new properties and even new objects as a result of spontaneous symmetry breaking

SEPATH: benchmarking the search for pathogens in human tissue whole genome sequence data leads to template pipelines

Background : Human tissue is increasingly being whole genome sequenced as we transition into an era of genomic medicine. With this arises the potential to detect sequences originating from microorganisms, including pathogens amid the plethora of human sequencing reads. In cancer research, the tumorigenic ability of pathogens is being recognized, for example Helicobacter pylori and human papillomavirus in the cases of gastric non-cardia and cervical carcinomas respectively. As of yet, no benchmark has been carried out on the performance of computational approaches for bacterial and viral detection within host-dominated sequence data. Results : We present the results of benchmarking over 70 distinct combinations of tools and parameters on 100 simulated cancer datasets spiked with realistic proportions of bacteria. mOTUs2 and Kraken are the highest performing individual tools achieving median genus level F1-scores of 0.90 and 0.91 respectively. mOTUs2 demonstrates a high performance in estimating bacterial proportions. Employing Kraken on unassembled sequencing reads produces a good but variable performance depending on post-classification filtering parameters. These approaches are investigated on a selection of cervical and gastric cancer whole genome sequences where Alphapapillomavirus and Helicobacter are detected in addition to a variety of other interesting genera. Conclusions : We provide the top performing pipelines from this benchmark in a unifying tool called SEPATH, which is amenable to high throughput sequencing studies across a range of high-performance computing clusters. SEPATH provides a benchmarked and convenient approach to detect pathogens in tissue sequence data helping to determine the relationship between metagenomics and disease

Assessment of Dose to the Nursing Infant from Radionuclides in Breast Milk

A computer software package was developed to predict tissue doses to an infant due to intake of radionuclides in breast milk based on bioassay measurements and exposure data for the mother. The package is intended mainly to aid in decisions regarding the safety of breast feeding by a mother who has been acutely exposed to a radionuclide during lactation or pregnancy, but it may be applied to previous intakes during the mother s adult life. The package includes biokinetic and dosimetric information needed to address intake of Co-60, Sr-90, Cs-134, Cs-137, Ir-192, Pu-238, Pu-239, Am-241, or Cf-252 by the mother. It has been designed so that the library of biokinetic and dosimetric files can be expanded to address a more comprehensive set of radionuclides without modifying the basic computational module. The methods and models build on the approach used in Publication 95 of the International Commission on Radiological Protection (ICRP 2004), Doses to Infants from Ingestion of Radionuclides in Mothers Milk . The software package allows input of case-specific information or judgments such as chemical form or particle size of an inhaled aerosol. The package is expected to be more suitable than ICRP Publication 95 for dose assessment for real events or realistic planning scenarios in which measurements of the mother s excretion or body burden are available

Status of the Copenhagen Climate Change Negotiations

This report evaluates the Copenhagen climate talks, including the status of the negotiations on the key issues under the formal negotiating tracks and the provisions of the Copenhagen Accord, and draws implications for the implementation of actions in developing countries