The mysterious optical afterglow spectrum of GRB140506A at z=0.889

Context. Gamma-ray burst (GRBs) afterglows probe sightlines to star-forming regions in distant star-forming galaxies. Here we present a study of the peculiar afterglow spectrum of the z = 0.889 Swift GRB 140506A. Aims. Our aim is to understand the origin of the very unusual properties of the absorption along the line-of-sight. Methods. We analyse spectroscopic observations obtained with the X-shooter spectrograph mounted on the ESO/VLT at two epochs 8.8 h and 33 h after the burst as well as imaging from the GROND instrument. We also present imaging and spectroscopy of the host galaxy obtained with the Magellan telescope. Results. The underlying afterglow appears to be a typical afterglow of a long-duration GRB. However, the material along the line-of- sight has imprinted very unusual features on the spectrum. Firstly, there is a very broad and strong flux drop below 8000 AA (4000 AA in the rest frame), which seems to be variable between the two spectroscopic epochs. We can reproduce the flux-drops both as a giant 2175 AA extinction bump and as an effect of multiple scattering on dust grains in a dense environment. Secondly, we detect absorption lines from excited H i and He i. We also detect molecular absorption from CH+ . Conclusions. We interpret the unusual properties of these spectra as reflecting the presence of three distinct regions along the line-of-sight: the excited He i absorption originates from an H ii-region, whereas the Balmer absorption must originate from an associated photodissociation region. The strong metal line and molecular absorption and the dust extinction must originate from a third, cooler region along the line-of-sight. The presence of (at least) three separate regions is reflected in the fact that the different absorption components have different velocities relative to the systemic redshift of the host galaxy.Comment: 8 pages, 4 figures. Accepted for publications in A&

Identification and characterisation of novel SNP markers in Atlantic cod: Evidence for directional selection

<p>Abstract</p> <p>Background</p> <p>The Atlantic cod (<it>Gadus morhua</it>) is a groundfish of great economic value in fisheries and an emerging species in aquaculture. Genetic markers are needed to identify wild stocks in order to ensure sustainable management, and for marker-assisted selection and pedigree determination in aquaculture. Here, we report on the development and evaluation of a large number of Single Nucleotide Polymorphism (SNP) markers from the alignment of Expressed Sequence Tag (EST) sequences in Atlantic cod. We also present basic population parameters of the SNPs in samples of North-East Arctic cod and Norwegian coastal cod obtained from three different localities, and test for SNPs that may have been targeted by natural selection.</p> <p>Results</p> <p>A total of 17,056 EST sequences were used to find 724 putative SNPs, from which 318 segregating SNPs were isolated. The SNPs were tested on Atlantic cod from four different sites, comprising both North-East Arctic cod (NEAC) and Norwegian coastal cod (NCC). The average heterozygosity of the SNPs was 0.25 and the average minor allele frequency was 0.18. <it>F</it>_{<it>ST </it>}values were highly variable, with the majority of SNPs displaying very little differentiation while others had <it>F</it>_{<it>ST </it>}values as high as 0.83. The <it>F</it>_{<it>ST </it>}values of 29 SNPs were found to be larger than expected under a strictly neutral model, suggesting that these loci are, or have been, influenced by natural selection. For the majority of these outlier SNPs, allele frequencies in a northern sample of NCC were intermediate between allele frequencies in a southern sample of NCC and a sample of NEAC, indicating a cline in allele frequencies similar to that found at the Pantophysin I locus.</p> <p>Conclusion</p> <p>The SNP markers presented here are powerful tools for future genetics work related to management and aquaculture. In particular, some SNPs exhibiting high levels of population divergence have potential to significantly enhance studies on the population structure of Atlantic cod.</p

The SOFIA Pilot Trial:A cluster-randomized trial of coordinated, co-produced care to reduce mortality and improve quality of life in people with severe mental illness in the general practice setting

Abstract Background People with severe mental illness (SMI) have an increased risk of premature mortality, predominantly due to somatic health conditions. Evidence indicates that primary and tertiary prevention and improved treatment of somatic conditions in patients with SMI could reduce this excess mortality. This paper reports a protocol designed to evaluate the feasibility of a coordinated co-produced care program (SOFIA model, a Danish acronym for Severe Mental Illness and Physical Health in General Practice) in the general practice setting to reduce mortality and improve quality of life in patients with severe mental illness. Methods The SOFIA pilot trial is designed as a cluster randomized controlled trial targeting general practices in two regions in Denmark. We aim to include 12 practices, each of which is instructed to recruit up to 15 community-dwelling patients aged 18 and older with SMI. Practices will be randomized by a computer in a ratio of 2:1 to deliver a coordinated care program or usual care during a 6-month study period. A randomized algorithm is used to perform randomization. The coordinated care program includes educational training of general practitioners and their clinical staff educational training of general practitioners and their clinical staff, which covers clinical and diagnostic management and focus on patient-centered care of this patient group, after which general practitioners will provide a prolonged consultation focusing on individual needs and preferences of the patient with SMI and a follow-up plan if indicated. The outcomes will be parameters of the feasibility of the intervention and trial methods and will be assessed quantitatively and qualitatively. Assessments of the outcome parameters will be administered at baseline, throughout, and at end of the study period. Discussion If necessary the intervention will be revised based on results from this study. If delivery of the intervention, either in its current form or after revision, is considered feasible, a future, definitive trial to determine the effectiveness of the intervention in reducing mortality and improving quality of life in patients with SMI can take place. Successful implementation of the intervention would imply preliminary promise for addressing health inequities in patients with SMI. Trial registration The trial was registered in Clinical Trials as of November 5, 2020, with registration number NCT04618250 . Protocol version: January 22, 2021; original versio

B cells and monocytes from patients with active multiple sclerosis exhibit increased surface expression of both HERV-H Env and HERV-W Env, accompanied by increased seroreactivity

<p>Abstract</p> <p>Background</p> <p>The etiology of the neurogenerative disease multiple sclerosis (MS) is unknown. The leading hypotheses suggest that MS is the result of exposure of genetically susceptible individuals to certain environmental factor(s). Herpesviruses and human endogenous retroviruses (HERVs) represent potentially important factors in MS development. Herpesviruses can activate HERVs, and HERVs are activated in MS patients.</p> <p>Results</p> <p>Using flow cytometry, we have analyzed HERV-H Env and HERV-W Env epitope expression on the surface of PBMCs from MS patients with active and stable disease, and from control individuals. We have also analyzed serum antibody levels to the expressed HERV-H and HERV-W Env epitopes. We found a significantly higher expression of HERV-H and HERV-W Env epitopes on B cells and monocytes from patients with active MS compared with patients with stable MS or control individuals. Furthermore, patients with active disease had relatively higher numbers of B cells in the PBMC population, and higher antibody reactivities towards HERV-H Env and HERV-W Env epitopes. The higher antibody reactivities in sera from patients with active MS correlate with the higher levels of HERV-H Env and HERV-W Env expression on B cells and monocytes. We did not find such correlations for stable MS patients or for controls.</p> <p>Conclusion</p> <p>These findings indicate that both HERV-H Env and HERV-W Env are expressed in higher quantities on the surface of B cells and monocytes in patients with active MS, and that the expression of these proteins may be associated with exacerbation of the disease.</p

Optical and near-infrared observations of the GRB020405 afterglow

(Abridged) We report on observations of the optical and NIR afterglow of GRB020405. Ground-based optical observations started about 1 day after the GRB and spanned a period of ~10 days; archival HST data extended the coverage up to 70 days after the GRB. We report the first detection of the afterglow in NIR bands. The detection of emission lines in the optical spectrum indicates that the GRB is located at z = 0.691. Absorptions are also detected at z = 0.691 and at z = 0.472. The latter system is likely caused by clouds in a galaxy located 2 arcsec southwest of the GRB host. Hence, for the first time, the galaxy responsible for an intervening absorption system in the spectrum of a GRB afterglow is identified. Optical and NIR photometry indicates that the decay in all bands follows a single power law of index alpha = 1.54. The late-epoch VLT and HST points lie above the extrapolation of this power law, so that a plateau is apparent in the VRIJ light curves at 10-20 days after the GRB. The light curves at epochs later than day ~20 after the GRB are consistent with a power-law decay with index alphaprime = 1.85. We suggest that this deviation can be modeled with a SN having the same temporal profile as SN2002ap, but 1.3 mag brighter at peak, and located at the GRB redshift. Alternatively, a shock re-energization may be responsible for the rebrightening. A polarimetric R-band measurement shows that the afterglow is polarized, with P = 1.5 % and theta = 172 degrees. Optical-NIR spectral flux distributions show a change of slope across the J band which we interpret as due to the presence of nu_c. The analysis of the multiwavelength spectrum within the fireball model suggests that a population of relativistic electrons produces the optical-NIR emission via synchrotron in an adiabatically expanding blastwave, and the X-rays via IC.Comment: 17 pages, 10 figures, 4 tables, accepted for publication on A&A, main journa

Effectiveness of treatment with pegylated interferon and ribavirin in an unselected population of patients with chronic hepatitis C: A Danish nationwide cohort study

<p>Abstract</p> <p>Background</p> <p>The effect of peginterferon and ribavirin treatment on chronic hepatitis C virus (HCV) infection has been established in several controlled clinical studies. However, the effectiveness of treatment and predictors of treatment success in routine clinical practice remains to be established. Our aim was to estimate the effectiveness of peginterferon and ribavirin treatment in unselected HCV patients handled in routine clinical practice. The endpoint was sustained virological response (SVR), determined by the absence of HCV RNA 24 weeks after the end of treatment.</p> <p>Methods</p> <p>We determined the proportion of SVR in a nationwide, population-based cohort of 432 patients with chronic HCV infection who were starting treatment, and analyzed the impact of known covariates on SVR by using a logistic regression analysis.</p> <p>Results</p> <p>The majority of treated patients had genotype 1 (133 patients) and genotype 2/3 (285 patients) infections, with 44% and 72%, respectively, obtaining SVR. Other than genotype, the predictors of SVR were age ≤ 45 years at the start of treatment, completion of unmodified treatment, the absence of cirrhosis and non-European origin.</p> <p>Conclusions</p> <p>The effectiveness of peginterferon and ribavirin treatment for chronic hepatitis C in a routine clinical practice is comparable to that observed in controlled clinical trials, with a higher SVR rate in genotype 2 and 3 patients compared to genotype 1 patients. Our data further indicate that age at start of treatment is a strong predictor of SVR irrespective of HCV genotype, with patients 45 years or younger having a higher SVR rate.</p

Ocean current connectivity propelling the secondary spread of a marine invasive comb jelly across western Eurasia

Aim: Invasive species are of increasing global concern. Nevertheless, the mechanisms driving furtherdistribution after the initial establishment of non-native species remain largely unresolved, especiallyin marine systems. Ocean currents can be a major driver governing range occupancy, but this hasnot been accounted for in most invasion ecology studies so far. We investigate how well initialestablishment areas are interconnected to later occupancy regions to test for the potential role ofocean currents driving secondary spread dynamics in order to infer invasion corridors and thesource–sink dynamics of a non-native holoplanktonic biological probe species on a continental scale.Location: Western Eurasia.Time period: 1980s–2016.Major taxa studied: ‘Comb jelly’ Mnemiopsis leidyi.Methods: Based on 12,400 geo-referenced occurrence data, we reconstruct the invasion historyof M. leidyi in western Eurasia. We model ocean currents and calculate their stability to match thetemporal and spatial spread dynamics with large-scale connectivity patterns via ocean currents.Additionally, genetic markers are used to test the predicted connectivity between subpopulations.Results: Ocean currents can explain secondary spread dynamics, matching observed range expansionsand the timing of first occurrence of our holoplanktonic non-native biological probe species,leading to invasion corridors in western Eurasia. In northern Europe, regional extinctions after coldwinters were followed by rapid recolonizations at a speed of up to 2,000 km per season. SourceJASPERS ET AL. | 815areas hosting year-round populations in highly interconnected regions can re-seed genotypes overlarge distances after local extinctions.Main conclusions: Although the release of ballast water from container ships may contribute tothe dispersal of non-native species, our results highlight the importance of ocean currents drivingsecondary spread dynamics. Highly interconnected areas hosting invasive species are crucial forsecondary spread dynamics on a continental scale. Invasion risk assessments should considerlarge-scale connectivity patterns and the potential source regions of non-native marine species