The Cosmic Linear Anisotropy Solving System (CLASS) IV: Efficient implementation of non-cold relics

We present a new flexible, fast and accurate way to implement massive neutrinos, warm dark matter and any other non-cold dark matter relics in Boltzmann codes. For whatever analytical or numerical form of the phase-space distribution function, the optimal sampling in momentum space compatible with a given level of accuracy is automatically found by comparing quadrature methods. The perturbation integration is made even faster by switching to an approximate viscous fluid description inside the Hubble radius, which differs from previous approximations discussed in the literature. When adding one massive neutrino to the minimal cosmological model, CLASS becomes just 1.5 times slower, instead of about 5 times in other codes (for fixed accuracy requirements). We illustrate the flexibility of our approach by considering a few examples of standard or non-standard neutrinos, as well as warm dark matter models.Comment: 23 pages, 8 figures, 3 tables. Matches published version. Code available at http://class-code.ne

Sommerfeld Enhancement of DM Annihilation: Resonance Structure, Freeze-Out and CMB Spectral Bound

In the last few years there has been some interest in WIMP Dark Matter models featuring a velocity dependent cross section through the Sommerfeld enhancement mechanism, which is a nonrelativistic effect due to massive bosons in the dark sector. In the first part of this article, we find analytic expressions for the boost factor for three different model potentials, the Coulomb potential, the spherical well and the spherical cone well and compare with the numerical solution of the Yukawa potential. We find that the resonance pattern of all the potentials can be cast into the same universal form. In the second part of the article we perform a detailed computation of the Dark Matter relic density for models having Sommerfeld enhancement by solving the Boltzmann equation numerically. We calculate the expected distortions of the CMB blackbody spectrum from WIMP annihilations and compare these to the bounds set by FIRAS. We conclude that only a small part of the parameter space can be ruled out by the FIRAS observations.Comment: 15 pages, 15 figures, version accepted by JCA

Systematic overviews of partnership principles and strategies identified from health research about spinal cord injury and related health conditions:A scoping review

Study design: Scoping review.Objective: To identify and provide systematic overviews of partnership principles and strategies identified from health research about spinal cord injury (SCI) and related health conditions.Methods: Four health electronic databases (Medline, Embase, CINAHL, PsycINFO) were searched from inception to March 2019. We included articles that described, reflected, and/or evaluated one or more collaborative research activities in health research about SCI, stroke, multiple sclerosis, Parkinson's disease, amputation, cerebral palsy, spina bifida, amyotrophic lateral sclerosis, acquired brain injury, or wheelchair-users. Partnership principles (i.e. norms or values) and strategies (i.e. observable actions) were extracted and analyzed using directed qualitative content analysis.Results: We included 39 articles about SCI (n = 13), stroke (n = 15), multiple sclerosis (n = 5), amputation (n = 2), cerebral palsy (n = 2), Parkinson's disease (n = 1), and wheelchair users (n = 1). We extracted 110 principles and synthesized them into 13 overarching principles. Principles related to building and maintaining relationships between researchers and research users were most frequently reported. We identified 32 strategies that could be applied at various phases of the research process and 26 strategies that were specific to a research phase (planning, conduct, or dissemination).Conclusion: We provided systematic overviews of principles and strategies for research partnerships. These could be used by researchers and research users who want to work in partnership to plan, conduct and/or disseminate their SCI research. The findings informed the development of the new SCI Integrated Knowledge Translation Guiding Principles (www.iktprinciples.com) and will support the implementation of these Principles within the SCI research system.</p

Far-infrared Polarization of the Supernova Remnant Cassiopeia A with SOFIA HAWC+

We present polarization observations of the young supernova remnant (SNR) Cas A using the High-resolution Airborne Wideband Camera-Plus (HAWC+) instrument onboard the Stratospheric Observatory for Infrared Astronomy (SOFIA). The polarization map at 154 microns reveals dust grains with strong polarization fractions (5 - 30 percent), supporting previous measurements made over a smaller region of the remnant at 850 microns. The 154 microns emission and the polarization signal is coincident with a region of cold dust observed in the southeastern shell and in the unshocked central ejecta. The highly polarized far-IR emission implies the grains are large (greater than 0.14 microns) and silicate-dominated. The polarization level varies across the SNR, with an inverse correlation between the polarization degree and the intensity and smaller polarization angle dispersion for brighter SNR emission. Stronger polarization is detected between the bright structures. This may result from a higher collision rate between the gas and dust producing a lower grain alignment efficiency where the gas density is higher. We use the dust emission to provide an estimate of the magnetic field strength in Cas A using the Davis-Chandrasekhar-Fermi method. The high polarization level is direct evidence that grains are highly elongated and strongly aligned with the magnetic field of the SNR. The dust mass from the polarized region is 0.14+-0.04 Msun, a lower limit of the amount of dust present within the ejecta of Cas A. This result strengthens the hypothesis that core-collapse SNe are an important contributor to the dust mass in high redshift galaxies.Comment: MNRAS, accepted (18 pages with 14 figures

Genome Evolution of Wolbachia Strain wPip from the Culex pipiens Group

The obligate intracellular bacterium Wolbachia pipientis strain wPip induces cytoplasmic incompatibility (CI), patterns of crossing sterility, in the Culex pipiens group of mosquitoes. The complete sequence is presented of the 1.48-Mbp genome of wPip which encodes 1386 coding sequences (CDSs), representing the first genome sequence of a B-supergroup Wolbachia. Comparisons were made with the smaller genomes of Wolbachia strains wMel of Drosophila melanogaster, an A-supergroup Wolbachia that is also a CI inducer, and wBm, a mutualist of Brugia malayi nematodes that belongs to the D-supergroup of Wolbachia. Despite extensive gene order rearrangement, a core set of Wolbachia genes shared between the 3 genomes can be identified and contrasts with a flexible gene pool where rapid evolution has taken place. There are much more extensive prophage and ankyrin repeat encoding (ANK) gene components of the wPip genome compared with wMel and wBm, and both are likely to be of considerable importance in wPip biology. Five WO-B–like prophage regions are present and contain some genes that are identical or highly similar in multiple prophage copies, whereas other genes are unique, and it is likely that extensive recombination, duplication, and insertion have occurred between copies. A much larger number of genes encode ankyrin repeat (ANK) proteins in wPip, with 60 present compared with 23 in wMel, many of which are within or close to the prophage regions. It is likely that this pattern is partly a result of expansions in the wPip lineage, due for example to gene duplication, but their presence is in some cases more ancient. The wPip genome underlines the considerable evolutionary flexibility of Wolbachia, providing clear evidence for the rapid evolution of ANK-encoding genes and of prophage regions. This host–Wolbachia system, with its complex patterns of sterility induced between populations, now provides an excellent model for unraveling the molecular systems underlying host reproductive manipulation

Breast cancer prognosis predicted by nuclear receptor-coregulator networks

Although molecular signatures based on transcript expression in breast cancer samples have provided new insights into breast cancer classification and prognosis, there are acknowledged limitations in current signatures. To provide rational, pathway-based signatures of disrupted physiology in cancer tissues that may be relevant to prognosis, this study has directly quantitated changed gene expression, between normal breast and cancer tissue, as a basis for signature development. The nuclear receptor (NR) family of transcription factors, and their coregulators, are fundamental regulators of every aspect of metazoan life, and were rigorously quantified in normal breast tissues and ERα positive and ERα negative breast cancers. Coregulator expression was highly correlated with that of selected NR in normal breast, particularly from postmenopausal women. These associations were markedly decreased in breast cancer, and the expression of the majority of coregulators was down-regulated in cancer tissues compared with normal. While in cancer the loss of NR-coregulator associations observed in normal breast was common, a small number of NR (Rev-ERBβ, GR, NOR1, LRH-1 and PGR) acquired new associations with coregulators in cancer tissues. Elevated expression of these NR in cancers was associated with poorer outcome in large clinical cohorts, as well as suggesting the activation of ERα -related, but ERα-independent, pathways in ERα negative cancers. In addition, the combined expression of small numbers of NR and coregulators in breast cancer was identified as a signature predicting outcome in ERα negative breast cancer patients, not linked to proliferation and with predictive power superior to existing signatures containing many more genes. These findings highlight the power of predictive signatures derived from the quantitative determination of altered gene expression between normal breast and breast cancers. Taken together, the findings of this study identify networks of NR-coregulator associations active in normal breast but disrupted in breast cancer, and moreover provide evidence that signatures based on NR networks disrupted in cancer can provide important prognostic information in breast cancer patients

Antimalarial activity of the anticancer histone deacetylase inhibitor SB939

Histone deacetylase (HDAC) enzymes posttranslationally modify lysines on histone and nonhistone proteins and play crucial roles in epigenetic regulation and other important cellular processes. HDAC inhibitors (e.g., suberoylanilide hydroxamic acid [SAHA; also known as vorinostat]) are used clinically to treat some cancers and are under investigation for use against many other diseases. Development of new HDAC inhibitors for noncancer indications has the potential to be accelerated by piggy-backing onto cancer studies, as several HDAC inhibitors have undergone or are undergoing clinical trials. One such compound, SB939, is a new orally active hydroxamate-based HDAC inhibitor with an improved pharmacokinetic profile compared to that of SAHA. In this study, the in vitro and in vivo antiplasmodial activities of SB939 were investigated. SB939 was found to be a potent inhibitor of the growth of Plasmodium falciparum asexual-stage parasites in vitro (50% inhibitory concentration [IC50], 100 to 200 nM), causing hyperacetylation of parasite histone and nonhistone proteins. In combination with the aspartic protease inhibitor lopinavir, SB939 displayed additive activity. SB939 also potently inhibited the in vitro growth of exoerythrocytic-stage Plasmodium parasites in liver cells (IC50, similar to 150 nM), suggesting that inhibitor targeting to multiple malaria parasite life cycle stages may be possible. In an experimental in vivo murine model of cerebral malaria, orally administered SB939 significantly inhibited P. berghei ANKA parasite growth, preventing development of cerebral malaria-like symptoms. These results identify SB939 as a potent new antimalarial HDAC inhibitor and underscore the potential of investigating next-generation anticancer HDAC inhibitors as prospective new drug leads for treatment of malaria

A systematic study of J/psi suppression in cold nuclear matter

Based on a Glauber model, a statistical analysis of all mid-rapidity J/psi hadroproduction and leptoproduction data on nuclear targets is carried out. This allows us to determine the J/psi-nucleon inelastic cross section, whose knowledge is crucial to interpret the J/psi suppression observed in heavy-ion collisions, at SPS and at RHIC. The values of sigma are extracted from each experiment. A clear tension between the different data sets is reported. The global fit of all data gives sigma=3.4+/-0.2 mb, which is significantly smaller than previous estimates. A similar value, sigma=3.5+/-0.2 mb, is obtained when the nDS nuclear parton densities are included in the analysis, although we emphasize that the present uncertainties on gluon (anti)shadowing do not allow for a precise determination of sigma. Finally, no significant energy dependence of the J/psi-N interaction is observed, unless strong nuclear modifications of the parton densities are assumed.Comment: 25 pages, 5 figure

Engaging stakeholders in rehabilitation research: a scoping review of strategies used in partnerships and evaluation of impacts

Abstract: Purpose: To describe how stakeholder engagement has been undertaken and evaluated in rehabilitation research. Methods: A scoping review of the scientific literature using five search strategies. Quantitative and qualitative analyses using extracted data. Interpretation of results was iteratively discussed within the team, which included a parent stakeholder. Results: Searches identified 101 candidate papers; 28 were read in full to assess eligibility and 19 were included in the review. People with disabilities and their families were more frequently involved compared to other stakeholders. Stakeholders were often involved in planning and evaluating service delivery. A key issue was identifying stakeholders; strategies used to support their involvement included creating committees, organizing meetings, clarifying roles and offering training. Communication, power sharing and resources influenced how stakeholders could be engaged in the research. Perceived outcomes of stakeholder engagement included the creation of partnerships, facilitating the research process and the application of the results, and empowering stakeholders. Stakeholder engagement outcomes were rarely formally evaluated. Conclusions: There is a great interest in rehabilitation to engage stakeholders in the research process. However, further evidence is needed to identify effective strategies for meaningful stakeholder engagement that leads to more useful research that positively impacts practice. Implications for Rehabilitation Using several strategies to engage various stakeholders throughout the research process is thought to increase the quality of the research and the rehabilitation process by developing proposals and programs responding better to their needs. Engagement strategies need to be better reported and evaluated in the literature. Engagement facilitate uptake of research findings by increasing stakeholders' awareness of the evidence, the resources available and their own ability to act upon a situation. Factors influencing opportunities for stakeholder engagement need to be better understood