Global atmospheric budget of acetaldehyde: 3-D model analysis and constraints from in-situ and satellite observations

We construct a global atmospheric budget for acetaldehyde using a 3-D model of atmospheric chemistry (GEOS-Chem), and use an ensemble of observations to evaluate present understanding of its sources and sinks. Hydrocarbon oxidation provides the largest acetaldehyde source in the model (128 Tg a<sup>−1</sup>, a factor of 4 greater than the previous estimate), with alkanes, alkenes, and ethanol the main precursors. There is also a minor source from isoprene oxidation. We use an updated chemical mechanism for GEOS-Chem, and photochemical acetaldehyde yields are consistent with the Master Chemical Mechanism. We present a new approach to quantifying the acetaldehyde air-sea flux based on the global distribution of light absorption due to colored dissolved organic matter (CDOM) derived from satellite ocean color observations. The resulting net ocean emission is 57 Tg a<sup>−1</sup>, the second largest global source of acetaldehyde. A key uncertainty is the acetaldehyde turnover time in the ocean mixed layer, with quantitative model evaluation over the ocean complicated by known measurement artifacts in clean air. Simulated concentrations in surface air over the ocean generally agree well with aircraft measurements, though the model tends to overestimate the vertical gradient. PAN:NO<sub>x</sub> ratios are well-simulated in the marine boundary layer, providing some support for the modeled ocean source. We introduce the Model of Emissions of Gases and Aerosols from Nature (MEGANv2.1) for acetaldehyde and ethanol and use it to quantify their net flux from living terrestrial plants. Including emissions from decaying plants the total direct acetaldehyde source from the land biosphere is 23 Tg a<sup>−1</sup>. Other terrestrial acetaldehyde sources include biomass burning (3 Tg a<sup>−1</sup>) and anthropogenic emissions (2 Tg a<sup>−1</sup>). Simulated concentrations in the continental boundary layer are generally unbiased and capture the spatial gradients seen in observations over North America, Europe, and tropical South America. However, the model underestimates acetaldehyde levels in urban outflow, suggesting a missing source in polluted air. Ubiquitous high measured concentrations in the free troposphere are not captured by the model, and based on present understanding are not consistent with concurrent measurements of PAN and NO<sub>x</sub>: we find no compelling evidence for a widespread missing acetaldehyde source in the free troposphere. We estimate the current US source of ethanol and acetaldehyde (primary + secondary) at 1.3 Tg a<sup>−1</sup> and 7.8 Tg a<sup>−1</sup>, approximately 60{%} and 480% of the corresponding increases expected for a national transition from gasoline to ethanol fuel

Analysis of inositol phosphate metabolism by capillary electrophoresis electrospray ionization mass spectrometry

The analysis of myo-inositol phosphates (InsPs) and myo-inositol pyrophosphates (PP-InsPs) is a daunting challenge due to the large number of possible isomers, the absence of a chromophore, the high charge density, the low abundance, and the instability of the esters and anhydrides. Given their importance in biology, an analytical approach to follow and understand this complex signaling hub is desirable. Here, capillary electrophoresis (CE) coupled to electrospray ionization mass spectrometry (ESI-MS) is implemented to analyze complex mixtures of InsPs and PP-InsPs with high sensitivity. Stable isotope labeled (SIL) internal standards allow for matrix-independent quantitative assignment. The method is validated in wild-type and knockout mammalian cell lines and in model organisms. SIL-CE-ESI-MS enables the accurate monitoring of InsPs and PP-InsPs arising from compartmentalized cellular synthesis pathways, by feeding cells with either [13C6]-myo-inositol or [13C6]-D-glucose. In doing so, we provide evidence for the existence of unknown inositol synthesis pathways in mammals, highlighting the potential of this method to dissect inositol phosphate metabolism and signalling

Sterile neutrino production via active-sterile oscillations: the quantum Zeno effect

We study several aspects of the kinetic approach to sterile neutrino production via active-sterile mixing. We obtain the neutrino propagator in the medium including self-energy corrections up to $\mathcal{O}(G^2_F)$, from which we extract the dispersion relations and damping rates of the propagating modes. The dispersion relations are the usual ones in terms of the index of refraction in the medium, and the damping rates are $\Gamma_1(k) = \Gamma_{aa}(k) \cos^2\theta_m(k); \Gamma_2(k) = \Gamma_{aa}(k) \sin^2\theta_m(k)$ where $\Gamma_{aa}(k)\propto G^2_F k T^4$ is the active neutrino scattering rate and $\theta_m(k)$ is the mixing angle in the medium. We provide a generalization of the transition probability in the \emph{medium from expectation values in the density matrix}: $P_{a\to s}(t) = \frac{\sin^22\theta_m}{4}[e^{-\Gamma_1t} + e^{-\Gamma_2 t}-2e^{-{1/2}(\Gamma_1+\Gamma_2)t} \cos\big(\Delta E t\big)]$ and study the conditions for its quantum Zeno suppression directly in real time. We find the general conditions for quantum Zeno suppression, which for $m_s\sim \textrm{keV}$ sterile neutrinos with $\sin2\theta \lesssim 10^{-3}$ \emph{may only be} fulfilled near an MSW resonance. We discuss the implications for sterile neutrino production and argue that in the early Universe the wide separation of relaxation scales far away from MSW resonances suggests the breakdown of the current kinetic approach.Comment: version to appear in JHE

Managing toxicities associated with immune checkpoint inhibitors: consensus recommendations from the Society for Immunotherapy of Cancer (SITC) Toxicity Management Working Group.

Cancer immunotherapy has transformed the treatment of cancer. However, increasing use of immune-based therapies, including the widely used class of agents known as immune checkpoint inhibitors, has exposed a discrete group of immune-related adverse events (irAEs). Many of these are driven by the same immunologic mechanisms responsible for the drugs\u27 therapeutic effects, namely blockade of inhibitory mechanisms that suppress the immune system and protect body tissues from an unconstrained acute or chronic immune response. Skin, gut, endocrine, lung and musculoskeletal irAEs are relatively common, whereas cardiovascular, hematologic, renal, neurologic and ophthalmologic irAEs occur much less frequently. The majority of irAEs are mild to moderate in severity; however, serious and occasionally life-threatening irAEs are reported in the literature, and treatment-related deaths occur in up to 2% of patients, varying by ICI. Immunotherapy-related irAEs typically have a delayed onset and prolonged duration compared to adverse events from chemotherapy, and effective management depends on early recognition and prompt intervention with immune suppression and/or immunomodulatory strategies. There is an urgent need for multidisciplinary guidance reflecting broad-based perspectives on how to recognize, report and manage organ-specific toxicities until evidence-based data are available to inform clinical decision-making. The Society for Immunotherapy of Cancer (SITC) established a multidisciplinary Toxicity Management Working Group, which met for a full-day workshop to develop recommendations to standardize management of irAEs. Here we present their consensus recommendations on managing toxicities associated with immune checkpoint inhibitor therapy

Measuring neutrino masses with a future galaxy survey

We perform a detailed forecast on how well a Euclid-like photometric galaxy and cosmic shear survey will be able to constrain the absolute neutrino mass scale. Adopting conservative assumptions about the survey specifications and assuming complete ignorance of the galaxy bias, we estimate that the minimum mass sum of sum m_nu ~ 0.06 eV in the normal hierarchy can be detected at 1.5 sigma to 2.5 sigma significance, depending on the model complexity, using a combination of galaxy and cosmic shear power spectrum measurements in conjunction with CMB temperature and polarisation observations from Planck. With better knowledge of the galaxy bias, the significance of the detection could potentially reach 5.4 sigma. Interestingly, neither Planck+shear nor Planck+galaxy alone can achieve this level of sensitivity; it is the combined effect of galaxy and cosmic shear power spectrum measurements that breaks the persistent degeneracies between the neutrino mass, the physical matter density, and the Hubble parameter. Notwithstanding this remarkable sensitivity to sum m_nu, Euclid-like shear and galaxy data will not be sensitive to the exact mass spectrum of the neutrino sector; no significant bias (< 1 sigma) in the parameter estimation is induced by fitting inaccurate models of the neutrino mass splittings to the mock data, nor does the goodness-of-fit of these models suffer any significant degradation relative to the true one (Delta chi_eff ^2< 1).Comment: v1: 29 pages, 10 figures. v2: 33 pages, 12 figures; added sections on shape evolution and constraints in more complex models, accepted for publication in JCA

Reactive Nitrogen, Ozone and Ozone Production in the Arctic Troposphere and the Impact of Stratosphere-Troposphere Exchange

We analyze the aircraft observations obtained during the Arctic Research of the Composition of the Troposphere from Aircraft and Satellite (ARCTAS) mission together with the GEOS-5 CO simulation to examine O3 and NOy in the Arctic and sub-Arctic region and their source attribution. Using a number of marker tracers and their probability density distributions, we distinguish various air masses from the background troposphere and examine their contribution to NOx, O3, and O3 production in the Arctic troposphere. The background Arctic troposphere has mean O3 of approximately 60 ppbv and NOx of approximately 25 pptv throughout spring and summer with CO decreases from approximately 145 ppbv in spring to approximately 100 ppbv in summer. These observed CO, NOx and O3 mixing ratios are not notably different from the values measured during the 1988 ABLE-3A and the 2002 TOPSE field campaigns despite the significant changes in the past two decades in processes that could have changed the Arctic tropospheric composition. Air masses associated with stratosphere-troposphere exchange are present throughout the mid and upper troposphere during spring and summer. These air masses with mean O3 concentration of 140-160 ppbv are the most important direct sources of O3 in the Arctic troposphere. In addition, air of stratospheric origin is the only notable driver of net O3 formation in the Arctic due to its sustainable high NOx (75 pptv in spring and 110 pptv in summer) and NOy (approximately 800 pptv in spring and approximately 1100 pptv in summer) levels. The ARCTAS measurements present observational evidence suggesting significant conversion of nitrogen from HNO3 to NOx and then to PAN (a net formation of approximately 120 pptv PAN) in summer when air of stratospheric origin is mixed with tropospheric background during stratosphere-to-troposphere transport. These findings imply that an adequate representation of stratospheric O3 and NOy input are essential in accurately simulating O3 and NOx photochemistry as well as the atmospheric budget of PAN in tropospheric chemistry transport models of the Arctic. Anthropogenic and biomass burning pollution plumes observed during ARCTAS show highly elevated hydrocarbons and NOy (mostly in the form of NOx and PAN), but do not contribute significantly to O3 in the Arctic troposphere except in some of the aged biomass burning plumes sampled during spring. Convection and/or lightning influences are negligible sources of O3 in the Arctic troposphere but can have significant impacts in the upper troposphere in the continental sub-Arctic during summer

MIMOX: a web tool for phage display based epitope mapping

BACKGROUND: Phage display is widely used in basic research such as the exploration of protein-protein interaction sites and networks, and applied research such as the development of new drugs, vaccines, and diagnostics. It has also become a promising method for epitope mapping. Research on new algorithms that assist and automate phage display based epitope mapping has attracted many groups. Most of the existing tools have not been implemented as an online service until now however, making it less convenient for the community to access, utilize, and evaluate them. RESULTS: We present MIMOX, a free web tool that helps to map the native epitope of an antibody based on one or more user supplied mimotopes and the antigen structure. MIMOX was coded in Perl using modules from the Bioperl project. It has two sections. In the first section, MIMOX provides a simple interface for ClustalW to align a set of mimotopes. It also provides a simple statistical method to derive the consensus sequence and embeds JalView as a Java applet to view and manage the alignment. In the second section, MIMOX can map a single mimotope or a consensus sequence of a set of mimotopes, on to the corresponding antigen structure and search for all of the clusters of residues that could represent the native epitope. NACCESS is used to evaluate the surface accessibility of the candidate clusters; and Jmol is embedded to view them interactively in their 3D context. Initial case studies show that MIMOX can reproduce mappings from existing tools such as FINDMAP and 3DEX, as well as providing novel, rational results. CONCLUSION: A web-based tool called MIMOX has been developed for phage display based epitope mapping. As a publicly available online service in this area, it is convenient for the community to access, utilize, and evaluate, complementing other existing programs. MIMOX is freely available at

Constraining Sterile Neutrino Warm Dark Matter with Chandra Observations of the Andromeda Galaxy

We use the Chandra unresolved X-ray emission spectrum from a 12'-28' (2.8-6.4 kpc) annular region of the Andromeda galaxy to constrain the radiative decay of sterile neutrino warm dark matter. By excising the most baryon-dominated, central 2.8 kpc of the galaxy, we reduce the uncertainties in our estimate of the dark matter mass within the field of view and improve the signal-to-noise ratio of prospective sterile neutrino decay signatures relative to hot gas and unresolved stellar emission. Our findings impose the most stringent limit on the sterile neutrino mass to date in the context of the Dodelson-Widrow model, m_s < 2.2 keV (95% C.L.). Our results also constrain alternative sterile neutrino production scenarios at very small active-sterile neutrino mixing angles.Comment: minor revisions, key results unchanged, accepted for publication in JCA