331 research outputs found

    Conflicting and ambiguous names of overlapping ORFs in the SARS-CoV-2 genome: A homology-based resolution.

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    At least six small alternative-frame open reading frames (ORFs) overlapping well-characterized SARS-CoV-2 genes have been hypothesized to encode accessory proteins. Researchers have used different names for the same ORF or the same name for different ORFs, resulting in erroneous homological and functional inferences. We propose standard names for these ORFs and their shorter isoforms, developed in consultation with the Coronaviridae Study Group of the International Committee on Taxonomy of Viruses. We recommend calling the 39 codon Spike-overlapping ORF ORF2b; the 41, 57, and 22 codon ORF3a-overlapping ORFs ORF3c, ORF3d, and ORF3b; the 33 codon ORF3d isoform ORF3d-2; and the 97 and 73 codon Nucleocapsid-overlapping ORFs ORF9b and ORF9c. Finally, we document conflicting usage of the name ORF3b in 32 studies, and consequent erroneous inferences, stressing the importance of reserving identical names for homologs. We recommend that authors referring to these ORFs provide lengths and coordinates to minimize ambiguity caused by prior usage of alternative names

    Attentional demand influences strategies for encoding into visual working memory

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    Visual selective attention and visual working memory (WM) share the same capacity-limited resources. We investigated whether and how participants can cope with a task in which these 2 mechanisms interfere. The task required participants to scan an array of 9 objects in order to select the target locations and to encode the items presented at these locations into WM (1 to 5 shapes). Determination of the target locations required either few attentional resources (“popout condition”) or an attention-demanding serial search (“non pop-out condition”). Participants were able to achieve high memory performance in all stimulation conditions but, in the non popout conditions, this came at the cost of additional processing time. Both empirical evidence and subjective reports suggest that participants invested the additional time in memorizing the locations of all target objects prior to the encoding of their shapes into WM. Thus, they seemed to be unable to interleave the steps of search with those of encoding. We propose that the memory for target locations substitutes for perceptual pop-out and thus may be the key component that allows for flexible coping with the common processing limitations of visual WM and attention. The findings have implications for understanding how we cope with real-life situations in which the demands on visual attention and WM occur simultaneously

    Low Temperature Opacities

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    Previous computations of low temperature Rosseland and Planck mean opacities from Alexander & Ferguson (1994) are updated and expanded. The new computations include a more complete equation of state with more grain species and updated optical constants. Grains are now explicitly included in thermal equilibrium in the equation of state calculation, which allows for a much wider range of grain compositions to be accurately included than was previously the case. The inclusion of high temperature condensates such as Al2_2O3_3 and CaTiO3_3 significantly affects the total opacity over a narrow range of temperatures before the appearance of the first silicate grains. The new opacity tables are tabulated for temperatures ranging from 30000 K to 500 K with gas densities from 10−4^{-4} g cm−3^{-3} to 10−19^{-19} g cm−3^{-3}. Comparisons with previous Rosseland mean opacity calculations are discussed. At high temperatures, the agreement with OPAL and Opacity Project is quite good. Comparisons at lower temperatures are more divergent as a result of differences in molecular and grain physics included in different calculations. The computation of Planck mean opacities performed with the opacity sampling method are shown to require a very large number of opacity sampling wavelength points; previously published results obtained with fewer wavelength points are shown to be significantly in error. Methods for requesting or obtaining the new tables are provided.Comment: 39 pages with 12 figures. To be published in ApJ, April 200

    Land Use Dynamics of the Fast-Growing Shanghai Metropolis, China (1979–2008) and its Implications for Land Use and Urban Planning Policy

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    Through the integrated approach of remote sensing and geographic information system (GIS) techniques, four Landsat TM/ETM+ imagery acquired during 1979 and 2008 were used to quantitatively characterize the patterns of land use and land cover change (LULC) and urban sprawl in the fast-growing Shanghai Metropolis, China. Results showed that, the urban/built-up area grew on average by 4,242.06 ha yr−1. Bare land grew by 1,594.66 ha yr−1 on average. In contrast, cropland decreased by 3,286.26 ha yr−1 on average, followed by forest and shrub, water, and tidal land, which decreased by 1,331.33 ha yr−1, 903.43 ha yr−1, and 315.72 ha yr−1 on average, respectively. As a result, during 1979 and 2008 approximately 83.83% of the newly urban/built-up land was converted from cropland (67.35%), forest and shrub (9.12%), water (4.80%), and tidal land (2.19%). Another significant change was the continuous increase in regular residents, which played a very important role in contributing to local population growth and increase in urban/built-up land. This can be explained with this city’s huge demand for investment and qualified labor since the latest industrial transformation. Moreover, with a decrease in cropland, the proportion of population engaged in farming decreased 13.84%. Therefore, significant socio-economic transformation occurred, and this would lead to new demand for land resources. However, due to very scarce land resources and overload of population in Shanghai, the drive to achieve economic goals at the loss of cropland, water, and the other lands is not sustainable. Future urban planning policy aiming at ensuring a win-win balance between sustainable land use and economic growth is urgently needed

    The Role of Hydrogeography and Climate in the Landscape Epidemiology of West Nile Virus in New York State from 2000 to 2010

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    The epidemiology and ecology of West Nile virus (WNV) have not yet been completely described. In particular, the specific roles of climate and water in the landscape in the occurrence of human WNV cases remain unknown. This study used Poisson regression to describe the relationships between WNV cases and temperature, precipitation, and the hydrogeography of the landscape in New York State from 2000 to 2010. Fully adjusted models showed that hydrogeographic area was significantly inversely associated with WNV cases (incidence rate ratio (IRR) = 0.99; 95% C.I. = 0.98–0.997, p = 0.04), such that each one square kilometer increase in hydrogeographic area was associated with a 1% decrease in WNV incidence. This association was independent of both temperature, which was also associated with WNV incidence (IRR = 2.06; 95% C.I. = 1.84–2.31, p<0.001), and precipitation, which was not (IRR = 1.0; 95% C.I. = 0.99–1.01, p = 0.16). While the results are only suggestive due to the county-level aggregated data, these findings do identify a potentially important surveillance signal in the landscape epidemiology of WNV infection

    On the abundance of non-cometary HCN on Jupiter

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    Using one-dimensional thermochemical/photochemical kinetics and transport models, we examine the chemistry of nitrogen-bearing species in the Jovian troposphere in an attempt to explain the low observational upper limit for HCN. We track the dominant mechanisms for interconversion of N2-NH3 and HCN-NH3 in the deep, hightemperature troposphere and predict the rate-limiting step for the quenching of HCN at cooler tropospheric altitudes. Consistent with other investigations that were based solely on time-scale arguments, our models suggest that transport-induced quenching of thermochemically derived HCN leads to very small predicted mole fractions of hydrogen cyanide in Jupiter's upper troposphere. By the same token, photochemical production of HCN is ineffective in Jupiter's troposphere: CH4-NH3 coupling is inhibited by the physical separation of the CH4 photolysis region in the upper stratosphere from the NH3 photolysis and condensation region in the troposphere, and C2H2-NH3 coupling is inhibited by the low tropospheric abundance of C2H2. The upper limits from infrared and submillimeter observations can be used to place constraints on the production of HCN and other species from lightning and thundershock sources.Comment: 56 pages, 0 tables, 6 figures. Submitted to Faraday Discussions [in press

    ‘Look this way’:using gaze maintenance to facilitate the detection of children's false reports

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    In two experiments, we investigated whether imposing a secondary task is an effective technique for detecting child deceit. Firstly, 85 children aged 8 to 11 years old provided either a true or false report of a recent school event. At interview, some children were asked to gaze towards either the interviewer’s face (IF) or a teddy bear’s face (TF), whereas some children were given no gaze instruction. In both the IF and TF conditions, lie-tellers provided significantly fewer details than truth-tellers. 192 adult evaluators then judged the credibility of ten children’s reports from one of the three ‘gaze’ conditions with and without guidance on level of detail. Evaluators discriminated truths from lies successfully when judging children instructed to look at IF, but not when children were asked to gaze towards TF. Evaluators who received guidance demonstrated better discrimination between true and false reports than evaluators who received no such information

    The Limiting Effects of Dust in Brown Dwarf Model Atmospheres

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    We present opacity sampling model atmospheres, synthetic spectra and colors for brown dwarfs and very low mass stars in two limiting case of dust grain formation: 1) inefficient gravitational settling i.e. the dust is distributed according to the chemical equilibrium predictions, 2) efficient gravitational settling i.e. the dust forms and depletes refractory elements from the gas, but their opacity does not affect the thermal structure. The models include the formation of over 600 gas phase species, and 1000 liquids and crystals, and the opacities of 30 different types of grains including corundum (Al2_2O3_3), the magnesium aluminum spinel MgAl2_2O4_4, iron, enstatite (MgSiO3_3), forsterite (Mg2_2SiO4_4), amorphous carbon, SiC, and a number of calcium silicates. The models extend from the beginning of the grain formation regime well into the condensation regime of water ice (\teff= 3000 - 100 K) and encompasses the range of log⁥g=2.5−6.0\log g= 2.5 - 6.0 at solar metallicity. We find that silicate dust grains can form abundantly in the outer atmospheric layers of red and brown dwarfs with spectral type later than M8. The greenhouse effects of dust opacities provide a natural explanation for the peculiarly red spectroscopic distribution of the latest M dwarfs and young brown dwarfs. The grainless (Cond) models on the other hand, correspond closely to methane brown dwarfs such as Gliese 229B. We also recover that the λ\lambda5891,5897\AA Na I D and λ\lambda7687,7701\AA K I resonance doublets plays a critical role in T dwarfs where their red wing define the pseudo-continuum from the II to the ZZ bandpass.Comment: 49 pages, ApJ, in press. 22 figures (included). Corrected nasty typos. Also available at http:/phoenix.physast.uga.ed
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