Towards the prediction of molecular parameters from astronomical emission lines using Neural Networks

Molecular astronomy is a field that is blooming in the era of large observatories such as the Atacama Large Millimeter/Submillimeter Array (ALMA). With modern, sensitive, and high spectral resolution radio telescopes like ALMA and the Square Kilometer Array, the size of the data cubes is rapidly escalating, generating a need for powerful automatic analysis tools. This work introduces MolPred, a pilot study to perform predictions of molecular parameters such as excitation temperature (Tex) and column density (log(N)) from input spectra by the use of neural networks. We used as test cases the spectra of CO, HCO+, SiO and CH3CN between 80 and 400 GHz. Training spectra were generated with MADCUBA, a state-of-the-art spectral analysis tool. Our algorithm was designed to allow the generation of predictions for multiple molecules in parallel. Using neural networks, we can predict the column density and excitation temperature of these molecules with a mean absolute error of 8.5% for CO, 4.1% for HCO+, 1.5% for SiO and 1.6% for CH3CN. The prediction accuracy depends on the noise level, line saturation, and number of transitions. We performed predictions upon real ALMA data. The values predicted by our neural network for this real data differ by 13% from the MADCUBA values on average. Current limitations of our tool include not considering linewidth, source size, multiple velocity components, and line blending

The distribution and origin of C₂H in NGC 253 from ALCHEMI

Context. Observations of chemical species can provide insights into the physical conditions of the emitting gas however it is important to understand how their abundances and excitation vary within different heating environments. C2H is a molecule typically found in PDR regions of our own Galaxy but there is evidence to suggest it also traces other regions undergoing energetic processing in extragalactic environments. / Aims. As part of the ALCHEMI ALMA large program, we map the emission of C2H in the central molecular zone of the nearby starburst galaxy NGC 253 at 1.6″ (28 pc) resolution and characterize it to understand its chemical origins. / Methods. We used spectral modeling of the N = 1−0 through N = 4−3 rotational transitions of C2H to derive the C2H column densities towards the dense clouds in NGC 253. We then use chemical modeling, including photodissociation region (PDR), dense cloud, and shock models to investigate the chemical processes and physical conditions that are producing the molecular emission. / Results. We find high C2H column densities of ∼1015 cm−2 detected towards the dense regions of NGC 253. We further find that these column densities cannot be reproduced if it is assumed that the emission arises from the PDR regions at the edge of the clouds. Instead, we find that the C2H abundance remains high even in the high visual extinction interior of these clouds and that this is most likely caused by a high cosmic-ray ionization rate

Starburst Energy Feedback Seen through HCO+/HOC+ Emission in NGC 253 from ALCHEMI

Molecular abundances are sensitive to the UV photon flux and cosmic-ray ionization rate. In starburst environments, the effects of high-energy photons and particles are expected to be stronger. We examine these astrochemical signatures through multiple transitions of HCO+ and its metastable isomer HOC+ in the center of the starburst galaxy NGC 253 using data from the Atacama Large Millimeter/submillimeter Array large program ALMA Comprehensive High-resolution Extragalactic Molecular inventory. The distribution of the HOC+(1−0) integrated intensity shows its association with "superbubbles," cavities created either by supernovae or expanding H ii regions. The observed HCO+/HOC+ abundance ratios are ∼10–150, and the fractional abundance of HOC+ relative to H2 is ∼1.5 × 10−11–6 × 10−10, which implies that the HOC+ abundance in the center of NGC 253 is significantly higher than in quiescent spiral arm dark clouds in the Galaxy and the Galactic center clouds. Comparison with chemical models implies either an interstellar radiation field of G0 ≳ 103 if the maximum visual extinction is ≳5, or a cosmic-ray ionization rate of ζ ≳ 10−14 s−1 (3–4 orders of magnitude higher than that within clouds in the Galactic spiral arms) to reproduce the observed results. From the difference in formation routes of HOC+, we propose that a low-excitation line of HOC+ traces cosmic-ray dominated regions, while high-excitation lines trace photodissociation regions. Our results suggest that the interstellar medium in the center of NGC 253 is significantly affected by energy input from UV photons and cosmic rays, sources of energy feedback

Assessment of MISR Cloud Motion Vectors (CMVs) Relative to GOES and MODIS Atmospheric Motion Vectors (AMVs)

Cloud motion vector (CMV) winds retrieved from the Multiangle Imaging SpectroRadiometer (MISR) instrument on the polar-orbiting Terra satellite from 2003 to 2008 are compared with collocated atmospheric motion vectors (AMVs) retrieved from Geostationary Operational Environmental Satellite (GOES) imagery over the tropics and midlatitudes and from Moderate Resolution Imaging Spectroradiometer (MODIS) imagery near the poles. MISR imagery from multiple view angles is exploited to jointly retrieve stereoscopic cloud heights and motions, showing advantages over the AMV heights assigned by radiometric means, particularly at low heights (<3 km) that account for over 95% of MISR CMV sampling. MISR–GOES wind differences exhibit a standard deviation ranging with increasing height from 3.3 to 4.5 m s−1 for a high-quality [quality indicator (QI) ≥ 80] subset where height differences are <1.5 km. Much of the observed difference can be attributed to the less accurately retrieved component of CMV motion along the direction of satellite motion. MISR CMV retrieval is subject to correlation between error in retrieval of this along-track component and of height. This manifests as along-track bias varying with height to magnitudes as large as 2.5 m s−1. The cross-track component of MISR CMVs shows small (<0.5 m s−1) bias and standard deviation of differences (1.7 m s−1) relative to GOES AMVs. Larger differences relative to MODIS are attributed to the tracking of cloud features at heights lower than MODIS in multilayer cloud scenes

Reconstructing the shock history in the CMZ of NGC 253 with ALCHEMI

Context: HNCO and SiO are well-known shock tracers and have been observed in nearby galaxies, including the nearby (D = 3.5 Mpc) starburst galaxy NGC 253. The simultaneous detection of these two species in regions where the star-formation rate is high may be used to study the shock history of the gas. // Aims: We perform a multi-line molecular study of NGC 253 using the shock tracers SiO and HNCO and aim to characterize its gas properties. We also explore the possibility of reconstructing the shock history in the central molecular zone (CMZ) of the galaxy. // Methods: Six SiO transitions and eleven HNCO transitions were imaged at high resolution 1.″6 (28 pc) with the Atacama Large Millimeter/submillimeter Array (ALMA) as part of the ALCHEMI Large Programme. Both non local thermaldynamic equilibrium (non-LTE) radiative transfer analysis and chemical modeling were performed in order to characterize the gas properties and investigate the chemical origin of the emission. // Results: The nonLTE radiative transfer analysis coupled with Bayesian inference shows clear evidence that the gas traced by SiO has different densities and temperatures than that traced by HNCO, with an indication that shocks are needed to produce both species. Chemical modeling further confirms such a scenario and suggests that fast and slow shocks are responsible for SiO and HNCO production, respectively, in most GMCs. We are also able to infer the physical characteristics of the shocks traced by SiO and HNCO for each GMC. // Conclusions: Radiative transfer and chemical analysis of the SiO and HNCO in the CMZ of NGC 253 reveal a complex picture whereby most of the GMCs are subjected to shocks. We speculate on the possible shock scenarios responsible for the observed emission and provide potential history and timescales for each shock scenario. Observations of higher spatial resolution for these two species are required in order to quantitatively differentiate between the possible scenarios

Caveolin-1 protects B6129 mice against Helicobacter pylori gastritis.

Caveolin-1 (Cav1) is a scaffold protein and pathogen receptor in the mucosa of the gastrointestinal tract. Chronic infection of gastric epithelial cells by Helicobacter pylori (H. pylori) is a major risk factor for human gastric cancer (GC) where Cav1 is frequently down-regulated. However, the function of Cav1 in H. pylori infection and pathogenesis of GC remained unknown. We show here that Cav1-deficient mice, infected for 11 months with the CagA-delivery deficient H. pylori strain SS1, developed more severe gastritis and tissue damage, including loss of parietal cells and foveolar hyperplasia, and displayed lower colonisation of the gastric mucosa than wild-type B6129 littermates. Cav1-null mice showed enhanced infiltration of macrophages and B-cells and secretion of chemokines (RANTES) but had reduced levels of CD25+ regulatory T-cells. Cav1-deficient human GC cells (AGS), infected with the CagA-delivery proficient H. pylori strain G27, were more sensitive to CagA-related cytoskeletal stress morphologies ("humming bird") compared to AGS cells stably transfected with Cav1 (AGS/Cav1). Infection of AGS/Cav1 cells triggered the recruitment of p120 RhoGTPase-activating protein/deleted in liver cancer-1 (p120RhoGAP/DLC1) to Cav1 and counteracted CagA-induced cytoskeletal rearrangements. In human GC cell lines (MKN45, N87) and mouse stomach tissue, H. pylori down-regulated endogenous expression of Cav1 independently of CagA. Mechanistically, H. pylori activated sterol-responsive element-binding protein-1 (SREBP1) to repress transcription of the human Cav1 gene from sterol-responsive elements (SREs) in the proximal Cav1 promoter. These data suggested a protective role of Cav1 against H. pylori-induced inflammation and tissue damage. We propose that H. pylori exploits down-regulation of Cav1 to subvert the host's immune response and to promote signalling of its virulence factors in host cells

Pattern of mRNA expression of β-defensins in basal cell carcinoma

BACKGROUND: Although the human β-defensins hBDs today seem to have diverse functional activities in innate antimicrobial immunity, a few reports also indicated an altered expression of these antimicrobial peptides (AMPs) in tissues of cancers such as oral squamous cell carcinoma. The present work was aimed on the study of hBD gene expression in basal cell carcinoma (BCC) which is the most common cancer in humans. METHODS: Twenty-two non-ulcerated BCCs (12 nodular type, 10 superficial type) have been analysed for the presence of hBD (1–3) mRNA by quantitative real-time RT-PCR. As controls, non-lesional skin specimens of BCC patients as well as samples of healthy subjects were assessed by RT-PCR. RESULTS: hBD-1 levels in healthy controls and non-lesional skin of BCC patients were significantly (P < 0.05) higher than the levels observed in tumour tissue. Moreover, BCCs showed significantly (P < 0.05) increased mRNA expression of hBD-2 as compared to controls. There was no significant (P > 0.05) difference between lesional mRNA levels for hBD-3 and those levels observed in controls. The mRNA expression of hBDs (1–3) found in nodular and superficial BCCs did not significantly (P > 0.05) differ. CONCLUSION: The gene expression patterns of hBD-1 and hBD-2 are for the first time shown to be significantly altered in non-ulcerated BCCs as compared to intra-individual and inter-individual controls, respectively. The present findings may indicate that beside the antimicrobial activity of AMPs, hBDs may also play a role in the pathogenesis of BCC. However, functional and immunohistological studies investigating hBDs in patients with BCC are needed to confirm our data

Dynamic force microscopy for imaging of viruses under physiological conditions

Dynamic force microscopy (DFM) allows imaging of the structure and the assessment of the function of biological specimens in their physiological environment. In DFM, the cantilever is oscillated at a given frequency and touches the sample only at the end of its downward movement. Accordingly, the problem of lateral forces displacing or even destroying bio-molecules is virtually inexistent as the contact time and friction forces are reduced. Here, we describe the use of DFM in studies of human rhinovirus serotype 2 (HRV2) weakly adhering to mica surfaces. The capsid of HRV2 was reproducibly imaged without any displacement of the virus. Release of the genomic RNA from the virions was initiated by exposure to low pH buffer and snapshots of the extrusion process were obtained. In the following, the technical details of previous DFM investigations of HRV2 are summarized