Origin of hydrogen fluoride emission in the Orion Bar An excellent tracer for CO-dark H-2 gas clouds

Context. The hydrogen fluoride (HF) molecule is seen in absorption in the interstellar medium (ISM) along many lines of sight. Surprisingly, it is observed in emission toward the Orion Bar, which is an interface between the ionized region around the Orion Trapezium stars and the Orion molecular cloud.Aims. We aim to understand the origin of HF emission in the Orion Bar by comparing its spatial distribution with other tracers. We examine three mechanisms to explain the HF emission: thermal excitation, radiative dust pumping, and chemical pumping.Methods. We used a Herschel/HIFI strip map of the HF J = 1 -&gt; 0 line, covering 0.5' by 1.5' that is oriented perpendicular to the Orion Bar. We used the RADEX non-local thermodynamic equilibrium (non-LTE) code to construct the HF column density map. We use the Meudon PDR code to explain the morphology of HF.Results. The bulk of the HF emission at 10 km s(-1) emerges from the CO-dark molecular gas that separates the ionization front from the molecular gas that is deeper in the Orion Bar. The excitation of HF is caused mainly by collisions with H-2 at a density of 10(5) cm(-3) together with a small contribution of electrons in the interclump gas of the Orion Bar. Infrared pumping and chemical pumping are not important.Conclusions. We conclude that the HF J = 1 -&gt; 0 line traces CO-dark molecular gas. Similarly, bright photodissociation regions associated with massive star formation may be responsible for the HF emission observed toward active galactic nuclei.</p

Protostellar Feedback in Massive Star Forming Regions

We examine mechanical feedback mechanisms during the protostellar phase through jets and outflows. To do so, we make use of velocity-resolved CII observations at 158 $\mu$m taken with the SOFIA observatory. We identify CII emitting cavities at velocities ranging from 1-2 km s$^{-1}$ to 15 km s$^{-1}$ relative to the Veil shell ($v_\mathrm{LSR}$ = 13 km s$^{-1}$). The momentum and dynamical timescales of these cavities imply that the cavities in Orion were formed by fossil and active outflows from stars with luminosities ranging from 10$^3$ to 10$^5$ L$_\odot$. The momentum deposited during protostellar feedback is $\sim$1/6 of the momentum of the Veil shell deposited through winds from $\theta^1$ Ori C. By creating cavities, the fossil outflows may already have broken the Veil shell, and outflows from less massive stars may have made the Veil shell porous

Search for radio jets from massive young stellar objects. Association of radio jets with H₂O and CH₃OH masers

Context. Recent theoretical and observational studies debate the similarities of the formation process of high- (>8 M⊙) and low-mass stars. The formation of low-mass stars is directly associated with the presence of disks and jets. Theoretical models predict that stars with masses up to 140 M⊙ can be formed through disk-mediated accretion in disk-jet systems. According to this scenario, radio jets are expected to be common in high-mass star-forming regions. Aims. We aim to increase the number of known radio jets in high-mass star-forming regions by searching for radio-jet candidates at radio continuum wavelengths. Methods. We used the Karl G. Jansky Very Large Array (VLA) to observe 18 high-mass star-forming regions in the C band (6 cm, ≈1′′.0 resolution) and K band (1.3 cm, ≈0′′.3 resolution). We searched for radio-jet candidates by studying the association of radio continuum sources with shock activity signs (e.g., molecular outflows, extended green objects, and maser emission). Our VLA observations also targeted the 22 GHz H2O and 6.7 GHz CH3OH maser lines. Results. We have identified 146 radio continuum sources, 40 of which are located within the field of view of both images (C and K band maps). We derived the spectral index, which is consistent with thermal emission (between − 0.1 and + 2.0) for 73% of these sources. Based on the association with shock-activity signs, we identified 28 radio-jet candidates. Out of these, we identified 7 as the most probable radio jets. The radio luminosity of the radio-jet candidates is correlated with the bolometric luminosity and the outflow momentum rate. About 7–36% of the radio-jet candidates are associated with nonthermal emission. The radio-jet candidates associated with 6.7 GHz CH3OH maser emission are preferentially thermal winds and jets, while a considerable fraction of radio-jet candidates associated with H2O masers show nonthermal emission that is likely due to strong shocks. Conclusions. About 60% of the radio continuum sources detected within the field of view of our VLA images are potential radio jets. The remaining sources could be compact H I

Probing ISM Structure in Trumpler 14 & Carina I Using The Stratospheric Terahertz Observatory 2

We present observations of the Trumpler 14/Carina I region carried out using the Stratospheric Terahertz Observatory 2 (STO2). The Trumpler 14/Carina I region is in the west part of the Carina Nebula Complex, which is one of the most extreme star-forming regions in the Milky Way. We observed Trumpler 14/Carina I in the 158 $\mu$m transition of [C\,{\sc ii}] with a spatial resolution of 48$''$ and a velocity resolution of 0.17 km s$^{-1}$. The observations cover a 0.25$^\circ$ by 0.28$^\circ$ area with central position {\it l} = 297.34$^\circ$, {\it b} = -0.60$^\circ$. The kinematics show that bright [C\,{\sc ii}] structures are spatially and spectrally correlated with the surfaces of CO clouds, tracing the photodissociation region and ionization front of each molecular cloud. Along 7 lines of sight that traverse Tr 14 into the dark ridge to the southwest, we find that the [C\,{\sc ii}] luminosity from the HII region is 3.7 times that from the PDR. In same los we find in the PDRs an average ratio of 1:4.1:5.6 for the mass in atomic gas:dark-CO gas: molecular gas traced by CO. Comparing multiple gas tracers including HI 21cm, [C\,{\sc ii}], CO, and radio recombination lines, we find that the HII regions of the Carina Nebula Complex are well-described as HII regions with one-side freely expanding towards us, consistent with the champagne model of ionized gas evolution. The dispersal of the GMC in this region is dominated by EUV photoevaporation; the dispersal timescale is 20-30 Myr.Comment: ApJ accepte

Discovery and genotyping of novel sequence insertions in many sequenced individuals

Motivation: Despite recent advances in algorithms design to characterize structural variation using high-throughput short read sequencing (HTS) data, characterization of novel sequence insertions longer than the average read length remains a challenging task. This is mainly due to both computational difficulties and the complexities imposed by genomic repeats in generating reliable assemblies to accurately detect both the sequence content and the exact location of such insertions. Additionally, de novo genome assembly algorithms typically require a very high depth of coverage, which may be a limiting factor for most genome studies. Therefore, characterization of novel sequence insertions is not a routine part of most sequencing projects. There are only a handful of algorithms that are specifically developed for novel sequence insertion discovery that can bypass the need for the whole genome de novo assembly. Still, most such algorithms rely on high depth of coverage, and to our knowledge there is only one method (PopIns) that can use multi-sample data to "collectively" obtain a very high coverage dataset to accurately find insertions common in a given population. Result: Here, we present Pamir, a new algorithm to efficiently and accurately discover and genotype novel sequence insertions using either single or multiple genome sequencing datasets. Pamir is able to detect breakpoint locations of the insertions and calculate their zygosity (i.e. heterozygous versus homozygous) by analyzing multiple sequence signatures, matching one-end-anchored sequences to small-scale de novo assemblies of unmapped reads, and conducting strand-aware local assembly. We test the efficacy of Pamir on both simulated and real data, and demonstrate its potential use in accurate and routine identification of novel sequence insertions in genome projects. © 2017 The Author. Published by Oxford University Press. All rights reserved

Robustness of massively parallel sequencing platforms

The improvements in high throughput sequencing technologies (HTS) made clinical sequencing projects such as ClinSeq and Genomics England feasible. Although there are significant improvements in accuracy and reproducibility of HTS based analyses, the usability of these types of data for diagnostic and prognostic applications necessitates a near perfect data generation. To assess the usability of a widely used HTS platform for accurate and reproducible clinical applications in terms of robustness, we generated whole genome shotgun (WGS) sequence data from the genomes of two human individuals in two different genome sequencing centers. After analyzing the data to characterize SNPs and indels using the same tools (BWA, SAMtools, and GATK), we observed significant number of discrepancies in the call sets. As expected, the most of the disagreements between the call sets were found within genomic regions containing common repeats and segmental duplications, albeit only a small fraction of the discordant variants were within the exons and other functionally relevant regions such as promoters. We conclude that although HTS platforms are sufficiently powerful for providing data for first-pass clinical tests, the variant predictions still need to be confirmed using orthogonal methods before using in clinical applications. © 2015 Kavak et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Activating mutations of STAT5B and STAT3 in lymphomas derived from γδ-T or NK cells

Lymphomas arising from NK or γδ-T cells are very aggressive diseases and little is known regarding their pathogenesis. Here we report frequent activating mutations of STAT3 and STAT5B in NK/T-cell lymphomas (n=51), γδ-T-cell lymphomas (n=43) and their cell lines (n=9) through next generation and/or Sanger sequencing. STAT5B N642H is particularly frequent in all forms of γδ-T-cell lymphomas. STAT3 and STAT5B mutations are associated with increased phosphorylated protein and a growth advantage to transduced cell lines or normal NK cells. Growth-promoting activity of the mutants can be partially inhibited by a JAK1/2 inhibitor. Molecular modelling and surface plasmon resonance measurements of the N642H mutant indicate a marked increase in binding affinity of the phosphotyrosine-Y699 with the mutant histidine. This is associated with the prolonged persistence of the mutant phosphoSTAT5B and marked increase of binding to target sites. Our findings suggest that JAK-STAT pathway inhibition may represent a therapeutic strategy. © 2015 Macmillan Publishers Limited. All rights reserved

Bias associated with delayed verification in test accuracy studies: accuracy of tests for endometrial hyperplasia may be much higher than we think!

BACKGROUND: To empirically evaluate bias in estimation of accuracy associated with delay in verification of diagnosis among studies evaluating tests for predicting endometrial hyperplasia. METHODS: Systematic reviews of all published research on accuracy of miniature endometrial biopsy and endometr ial ultrasonography for diagnosing endometrial hyperplasia identified 27 test accuracy studies (2,982 subjects). Of these, 16 had immediate histological verification of diagnosis while 11 had verification delayed > 24 hrs after testing. The effect of delay in verification of diagnosis on estimates of accuracy was evaluated using meta-regression with diagnostic odds ratio (dOR) as the accuracy measure. This analysis was adjusted for study quality and type of test (miniature endometrial biopsy or endometrial ultrasound). RESULTS: Compared to studies with immediate verification of diagnosis (dOR 67.2, 95% CI 21.7–208.8), those with delayed verification (dOR 16.2, 95% CI 8.6–30.5) underestimated the diagnostic accuracy by 74% (95% CI 7%–99%; P value = 0.048). CONCLUSION: Among studies of miniature endometrial biopsy and endometrial ultrasound, diagnostic accuracy is considerably underestimated if there is a delay in histological verification of diagnosis