AtChem (version 1), an open-source box model for the Master Chemical Mechanism

AtChem is an open-source zero-dimensional box model for atmospheric chemistry. Any general set of chemical reactions can be used with AtChem, but the model was designed specifically for use with the Master Chemical Mechanism (MCM, http://mcm.york.ac.uk/, last access: 16 January 2020). AtChem was initially developed within the EUROCHAMP project as a web application (AtChem-online, https://atchem.leeds.ac.uk/webapp/, last access: 16 January 2020) for modelling environmental chamber experiments; it was recently upgraded and further developed into a stand-alone offline version (AtChem2), which allows the user to run complex and long simulations, such as those needed for modelling of intensive field campaigns, as well as to perform batch model runs for sensitivity studies. AtChem is installed, set up and configured using semi-automated scripts and simple text configuration files, making it easy to use even for inexperienced users. A key feature of AtChem is that it can easily be constrained to observational data which may have different timescales, thus retaining all the information contained in the observations. Implementation of a continuous integration workflow, coupled with a comprehensive suite of tests and version control software, makes the AtChem code base robust, reliable and traceable. The AtChem2 code and documentation are available at https://github.com/AtChem/ (last access: 16 January 2020) under the open-source MIT License

A photometric and astrometric investigation of the brown dwarfs in Blanco 1

We present the results of a photometric and astrometric study of the low mass stellar and substellar population of the young open cluster Blanco 1. We have exploited J band data, obtained recently with the Wide Field Camera (WFCAM) on the United Kingdom InfraRed Telescope (UKIRT), and 10 year old I and z band optical imaging from CFH12k and Canada France Hawaii Telescope (CFHT), to identify 44 candidate low mass stellar and substellar members, in an area of 2 sq. degrees, on the basis of their colours and proper motions. This sample includes five sources which are newly discovered. We also confirm the lowest mass candidate member of Blanco 1 unearthed so far (29MJup). We determine the cluster mass function to have a slope of alpha=+0.93, assuming it to have a power law form. This is high, but nearly consistent with previous studies of the cluster (to within the errors), and also that of its much better studied northern hemisphere analogue, the Pleiades.Comment: 8 Pages, 5 Figures, 2 Tables and 1 Appendix. Accepted for publication in MNRA

Trends and emissions of six perfluorocarbons in the Northern Hemisphere and Southern Hemisphere

Perfluorocarbons (PFCs) are potent greenhouse gases with global warming potentials up to several thousand times greater than CO2 on a 100-year time horizon. The lack of any significant sinks for PFCs means that they have long atmospheric lifetimes of the order of thousands of years. Anthropogenic production is thought to be the only source for most PFCs. Here we report an update on the global atmospheric abundances of the following PFCs, most of which have for the first time been analytically separated according to their isomers: c-octafluorobutane (c-C4F8), n-decafluorobutane (n-C4F10), n-dodecafluoropentane (n-C5F12), n-tetradecafluorohexane (n-C6F14), and n-hexadecafluoroheptane (n-C7F16). Additionally, we report the first data set on the atmospheric mixing ratios of perfluoro-2-methylpentane (i-C6F14). The existence and significance of PFC isomers have not been reported before, due to the analytical challenges of separating them. The time series spans a period from 1978 to the present. Several data sets are used to investigate temporal and spatial trends of these PFCs: time series of air samples collected at Cape Grim, Australia, from 1978 to the start of 2018; a time series of air samples collected between July 2015 and April 2017 at Tacolneston, UK; and intensive campaign-based sampling collections from Taiwan. Although the remote “background” Southern Hemispheric Cape Grim time series indicates that recent growth rates of most of these PFCs are lower than in the 1990s, we continue to see significantly increasing mixing ratios that are between 6 % and 27 % higher by the end of 2017 compared to abundances measured in 2010. Air samples from Tacolneston show a positive offset in PFC mixing ratios compared to the Southern Hemisphere baseline. The highest mixing ratios and variability are seen in air samples from Taiwan, which is therefore likely situated much closer to PFC sources, confirming predominantly Northern Hemispheric emissions for most PFCs. Even though these PFCs occur in the atmosphere at levels of parts per trillion molar or less, their total cumulative global emissions translate into 833 million metric tonnes of CO2 equivalent by the end of 2017, 23 % of which has been emitted since 2010. Almost two-thirds of the CO2 equivalent emissions within the last decade are attributable to c-C4F8, which currently also has the highest emission rates that continue to grow. Sources of all PFCs covered in this work remain poorly constrained and reported emissions in global databases do not account for the abundances found in the atmosphere

Salmonella effector SteE converts the mammalian serine/threonine kinase GSK3 into a tyrosine kinase to direct macrophage polarization.

Many Gram-negative bacterial pathogens antagonize anti-bacterial immunity through translocated effector proteins that inhibit pro-inflammatory signaling. In addition, the intracellular pathogen Salmonella enterica serovar Typhimurium initiates an anti-inflammatory transcriptional response in macrophages through its effector protein SteE. However, the target(s) and molecular mechanism of SteE remain unknown. Here, we demonstrate that SteE converts both the amino acid and substrate specificity of the host pleiotropic serine/threonine kinase GSK3. SteE itself is a substrate of GSK3, and phosphorylation of SteE is required for its activity. Remarkably, phosphorylated SteE then forces GSK3 to phosphorylate the non-canonical substrate signal transducer and activator of transcription 3 (STAT3) on tyrosine-705. This results in STAT3 activation, which along with GSK3 is required for SteE-mediated upregulation of the anti-inflammatory M2 macrophage marker interleukin-4Rα (IL-4Rα). Overall, the conversion of GSK3 to a tyrosine-directed kinase represents a tightly regulated event that enables a bacterial virulence protein to reprogram innate immune signaling and establish an anti-inflammatory environment

GJ 900: A new hierarchical system with low-mass components

Speckle interferometric observations made with the 6 m telescope of the Special Astrophysical Observatory of the Russian Academy of Sciences in 2000 revealed the triple nature of the nearby ($\pi_{Hip}=51.80\pm1.74$ mas) low-mass young ($\approx200$ Myr) star GJ 900. The configuration of the triple system allowed it to be dynamically unstable. Differential photometry performed from 2000 through 2004 yielded $I$- and $K$-band absolute magnitudes and spectral types for the components to be $I_{A}$=6.66$\pm$0.08, $I_{B}$=9.15$\pm$0.11, $I_{C}$=10.08$\pm$0.26, $K_{A}$=4.84$\pm$0.08, $K_{B}$=6.76$\pm$0.20, $K_{C}$=7.39$\pm$0.31, $Sp_{A}$$\approx$K5--K7, $Sp_{B}$$\approx$M3--M4, $Sp_{C}$$\approx$M5--M6. The ``mass--luminosity'' relation is used to estimate the individual masses of the components: $\mathcal{M}_{A}$$\approx0.64\mathcal{M}_{\odot}$, $\mathcal{M}_{B}$$\approx0.21\mathcal{M}_{\odot}$, $\mathcal{M}_{C}$$\approx0.13\mathcal{M}_{\odot}$. From the observations of the components relative motion in the period 2000--2006, we conclude that GJ 900 is a hierarchical triple star with the possible orbital periods P$_{A-BC}$$\approx$80 yrs and P$_{BC}$$\approx$20 yrs. An analysis of the 2MASS images of the region around GJ 900 leads us to suggest that the system can include other very-low-mass components.Comment: 7 pages, 5 figure

Time scales of Li evolution: a homogeneous analysis of open clusters from ZAMS to late-MS

We have performed a new and homogeneous analysis of all the Li data available in the literature for main sequence stars (spectral-types from late F to K) in open clusters. In the present paper we focus on a detailed investigation of MS Li depletion and its time scales for stars in the 6350-5500 K effective temperature range. For the first time, we were able to constrain the age at which non-standard mixing processes, driving MS Li depletion, appear. We have also shown that MS Li depletion is not a continuous process and cannot be simply described by a t^(-alpha) law. We confirm that depletion becomes ineffective beyond an age of 1-2 Gyr for the majority of the stars, leading to a Li plateau at old ages. We compared the empirical scenario of Li as a function of age with the predictions of three non-standard models. We found that models including only gravity waves as main mixing process are not able to fit the Li vs. age pattern and thus this kind of mixing can be excluded as the predominant mechanism responsible for Li depletion. On the other hand, models including slow mixing induced by rotation and angular momentum loss, and in particular those including also diffusive processes not related to rotation, can explain to some extent the empirical evidence. However, none of the currently proposed models can fit the plateau at old ages.Comment: 20 pages, 10 figures A&A accepte

Role of TNFα in pulmonary pathophysiology

Tumor necrosis factor alpha (TNFα) is the most widely studied pleiotropic cytokine of the TNF superfamily. In pathophysiological conditions, generation of TNFα at high levels leads to the development of inflammatory responses that are hallmarks of many diseases. Of the various pulmonary diseases, TNFα is implicated in asthma, chronic bronchitis (CB), chronic obstructive pulmonary disease (COPD), acute lung injury (ALI) and acute respiratory distress syndrome (ARDS). In addition to its underlying role in the inflammatory events, there is increasing evidence for involvement of TNFα in the cytotoxicity. Thus, pharmacological agents that can either suppress the production of TNFα or block its biological actions may have potential therapeutic value against a wide variety of diseases. Despite some immunological side effects, anti-TNFα therapeutic strategies represent an important breakthrough in the treatment of inflammatory diseases and may have a role in pulmonary diseases characterized by inflammation and cell death