Constraining turbulence in protoplanetary discs using the gap contrast: an application to the DSHARP sample

Constraining the strength of gas turbulence in protoplanetary discs is an open problem that has relevant implications for the physics of gas accretion and planet formation. In this work, we gauge the amount of turbulence in 6 of the discs observed in the DSHARP programme by indirectly measuring the vertical distribution of their dust component. We employ the differences in the gap contrasts observed along the major and the minor axes due to projection effects, and build a radiative transfer model to reproduce these features for different values of the dust scale heights. We find that (a) the scale heights that yield a better agreement with data are generally low ($\lesssim 4$ AU at a radial distance of $100$ AU), and in almost all cases we are only able to place upper limits on their exact values; these conclusions imply (assuming an average Stokes number of $\approx10^{-2}$) low turbulence levels of $\alpha_{\rm SS}\lesssim10^{-3}-10^{-4}$; (b) for the 9 other systems we considered out of the DSHARP sample, our method yields no significant constraints on the disc vertical structure; we conclude that this is because these discs have either a low inclination or gaps that are not deep enough. Based on our analysis we provide an empirical criterion to assess whether a given disc is suitable to measure the vertical scale height.Comment: Accepted for publication in MNRAS. 13 pages + appendix, 12 figure

Temperature Switch PCR (TSP): Robust assay design for reliable amplification and genotyping of SNPs

Background Many research and diagnostic applications rely upon the assay of individual single nucleotide polymorphisms (SNPs). Thus, methods to improve the speed and efficiency for single-marker SNP genotyping are highly desirable. Here, we describe the method of temperature-switch PCR (TSP), a biphasic four-primer PCR system with a universal primer design that permits amplification of the target locus in the first phase of thermal cycling before switching to the detection of the alleles. TSP can simplify assay design for a range of commonly used single-marker SNP genotyping methods, and reduce the requirement for individual assay optimization and operator expertise in the deployment of SNP assays. Results We demonstrate the utility of TSP for the rapid construction of robust and convenient endpoint SNP genotyping assays based on allele-specific PCR and high resolution melt analysis by generating a total of 11,232 data points. The TSP assays were performed under standardised reaction conditions, requiring minimal optimization of individual assays. High genotyping accuracy was verified by 100% concordance of TSP genotypes in a blinded study with an independent genotyping method. Conclusion Theoretically, TSP can be directly incorporated into the design of assays for most current single-marker SNP genotyping methods. TSP provides several technological advances for single-marker SNP genotyping including simplified assay design and development, increased assay specificity and genotyping accuracy, and opportunities for assay automation. By reducing the requirement for operator expertise, TSP provides opportunities to deploy a wider range of single-marker SNP genotyping methods in the laboratory. TSP has broad applications and can be deployed in any animal and plant species.Tania Tabone, Diane E Mather and Matthew J Hayde

RNA-seq transcriptome analysis reveals long terminal repeat retrotransposon modulation in human peripheral blood mononuclear cells after in vivo lipopolysaccharide injection

Human endogenous retroviruses (HERVs) and mammalian apparent long terminal repeat (LTR) retrotransposons (MaLRs) are retroviral sequences that integrated into germ line cells millions of years ago. Transcripts of these LTR retrotransposons are present in several tissues, and their expression is modulated in pathological conditions, although their function remains often far from being understood. Here, we focused on the HERV/MaLR expression and modulation in a scenario of immune system activation. We used a public data set of human peripheral blood mononuclear cells (PBMCs) RNA-Seq from 15 healthy participants to a clinical trial before and after exposure to lipopolysaccharide (LPS), for which we established an RNA-Seq workflow for the identification of expressed and modulated cellular genes and LTR retrotransposon elements. IMPORTANCE We described the HERV and MaLR transcriptome in PBMCs, finding that about 8.4% of the LTR retrotransposon loci were expressed and identifying the betaretrovirus-like HERVs as those with the highest percentage of expressed loci. We found 4,607 HERV and MaLR loci that were modulated as a result of in vivo stimulation with LPS. The HERV-H group showed the highest number of differentially expressed most intact proviruses. We characterized the HERV and MaLR loci as differentially expressed, checking their genomic context of insertion and observing a general colocalization with genes that are involved and modulated in the immune response, as a consequence of LPS stimulation. The analyses of HERV and MaLR expression and modulation show that these LTR retrotransposons are expressed in PBMCs and regulated in inflammatory settings. The similar regulation of HERVs/MaLRs and genes after LPS stimulation suggests possible interactions of LTR retrotransposons and the immune host response

Directly tracing the vertical stratification of molecules in protoplanetary disks

We aim to directly trace the vertical location of the emitting surface of multiple molecular tracers in protoplanetary disks. Our sample of disks includes Elias 2-27, WaOph 6 and the sources targeted by the MAPS ALMA Large Program. The set of molecules studied include CO isotopologues in various transitions, HCN, CN, H2CO, HCO+, C2H and c-C3H2. The vertical emitting region is determined directly from the channel maps, implementing accurate masking of the channel emission to recover the vertical location of the emission surface even at large radial distances from the star and for low-SNR lines. The vertical location of the emitting layer is obtained for 4-10 lines in each disk. IM Lup, HD163296 and MWC 480 12CO and 13CO show vertical modulations, which are coincident with dust gaps and kinematical perturbations. We also present estimates of the gas pressure scale height in the disks from the MAPS sample. Compared to physical-chemical models we find good agreement with the vertical location of CO isotopologues. In HD 163296 CN and HCN trace a similar intermediate layer, for the other disks, the UV flux tracers and the vertical profiles of HCN and C2H are lower than predicted in theoretical models. HCN and H2CO show a highly structured vertical profile, possibly indicative of different formation pathways. It is possible to trace the vertical locations of multiple molecular species that trace a wide variety of physical and chemical disk properties. The distribution of CO isotopologues are found at a wide range of vertical heights $z/r =$ 0.5-0.05. Other molecular lines are mostly found at $z/r \leq$0.15. The vertical layering of molecules is in agreement with theory in some systems, but not in all, therefore dedicated chemical-physical models are needed to further study and understand the emission surfaces.Comment: Accepted for publication in A&A. 29 pages, 28 figure

Evidence for ubiquitous carbon grain destruction in hot protostellar envelopes

Earth is deficient in carbon and nitrogen by up to ${\sim}4$ orders of magnitude compared with the Sun. Destruction of (carbon- and nitrogen-rich) refractory organics in the high-temperature planet forming regions could explain this deficiency. Assuming a refractory cometary composition for these grains, their destruction enhances nitrogen-containing oxygen-poor molecules in the hot gas ($\gtrsim 300$K) after the initial formation and sublimation of these molecules from oxygen-rich ices in the warm gas (${\sim}150$K). Using observations of $37$ high-mass protostars with ALMA, we find that oxygen-containing molecules (CH$_3$OH and HNCO) systematically show no enhancement in their hot component. In contrast, nitrogen-containing, oxygen-poor molecules (CH$_3$CN and C$_2$H$_3$CN) systematically show an enhancement of a factor ${\sim} 5$ in their hot component, pointing to additional production of these molecules in the hot gas. Assuming only thermal excitation conditions, we interpret these results as a signature of destruction of refractory organics, consistent with the cometary composition. This destruction implies a higher C/O and N/O in the hot gas than the warm gas, while, the exact values of these ratios depend on the fraction of grains that are effectively destroyed. This fraction can be found by future chemical models that constrain C/O and N/O from the abundances of minor carbon, nitrogen and oxygen carriers presented here.Comment: Accepted for publication in ApJ Letter

Bariatric Surgery Outcomes in Appalachia Influenced by Surgery Type, Diabetes, and Depression

Background Most effective treatment for morbid obesity and its comorbidities is bariatric surgery. However, research is limited on weight loss and associated outcomes among patients in Appalachia. The objective of this study was to examine demographic and comorbidity influence on surgical outcomes of this population including age, sex, race, state of residence, education, marital status, body mass index (BMI kg/m2), excess body weight (EBW), percent excess weight loss (%EWL), blood pressure, diagnosed depression, diagnosed type 2 diabetes (T2D), Beck Depression Inventory-II (BDI-II), and laboratory values (i.e., hemoglobin A1c). Methods A retrospective electronic medical record (EMR) data extraction was performed on N = 582 patients receiving bariatric surgery (laparoscopic Roux-en-Y gastric bypass [RYGB] and laparoscopic sleeve gastrectomy [SG]) between 10/2013 and 2/2017. Results Patient population was 92.5% Caucasian, 79.3% female, 62.8% married, 45 ± 11.1 years, 75.8% received RYGB, and 24.2% received SG. Average %EWL from baseline to 1-year follow-up was 68.5 ± 18.4% (n = 224). In final descriptive models, surgery type, diagnosed T2D, HbA1c, and depressive symptoms were significant covariates associated with lower %EWL. Conclusions Findings suggest patients completing surgery within an Appalachian region have successful surgical outcomes at 1-year post-surgery, as indicated by significant reductions of \u3e 50% EWL, regardless of other covariates. Results suggest that bariatric programs should consider paying special consideration to patients with T2D or depressive symptoms to improve outcomes. Results have potential to inform future prospective studies and aid in guiding specific interventions tailored to address needs of this unique population

A major asymmetric ice trap in a planet-forming disk IV. Nitric oxide gas and a lack of CN tracing sublimating ices and a C/O ratio <1< 1

[Abridged] Most well-resolved disks observed with ALMA show signs of dust traps. These dust traps set the chemical composition of the planet forming material in these disks, as the dust grains with their icy mantles are trapped at specific radii and could deplete the gas and dust of volatiles at smaller radii. In this work we analyse the first detection of nitric oxide (NO) in a protoplanetary disk. We aim to constrain the nitrogen chemistry and the gas-phase C/O ratio in the highly asymmetric dust trap in the Oph-IRS 48 disk. We use ALMA observations of NO, CN, C$_2$H, and related molecules and model the effect of the dust trap on the physical and chemical structure using the thermochemical code DALI. Furthermore, we explore how ice sublimation contributes to the observed emission lines. NO is only observed at the location of the dust trap but CN and C$_2$H are not detected in the Oph-IRS 48 disk. This results in an CN/NO column density ratio of $< 0.05$ and thus a low C/O ratio at the location of the dust trap. The main gas-phase formation pathways to NO through OH and NH in the fiducial model predict NO emission that is an order of magnitude lower than is observed. The gaseous NO column density can be increased by factors ranging from 2.8 to 10 when the H$_2$O and NH$_3$ gas abundances are significantly boosted by ice sublimation. However, these models are inconsistent with the upper limits on the H$_2$O and OH column densities derived from observations. We propose that the NO emission in the Oph-IRS 48 disk is closely related to the nitrogen containing ices sublimating in the dust trap. The non-detection of CN constrains the C/O ratio both inside and outside the dust trap to be $< 1$ if all nitrogen initially starts as N$_2$ and $\leq 0.6$, consistent with the Solar value, if (part of) the nitrogen initially starts as N or NH$_3$.Comment: Accepted for publication in Astronomy and Astrophysic