Encouraging responsible reporting practices in the Instructions to Authors of neuroscience and physiology journals: There is room to improve

Journals can substantially influence the quality of research reports by including responsible reporting practices in their Instructions to Authors. We assessed the extent to which 100 journals in neuroscience and physiology required authors to report methods and results in a rigorous and transparent way. For each journal, Instructions to Authors and any referenced reporting guideline or checklist were downloaded from journal websites. Twenty-two questions were developed to assess how journal Instructions to Authors address fundamental aspects of rigor and transparency in five key reporting areas. Journal Instructions to Authors and all referenced external guidelines and checklists were audited against these 22 questions. Of the full sample of 100 Instructions to Authors, 34 did not reference any external reporting guideline or checklist. Reporting whether clinical trial protocols were pre-registered was required by 49 journals and encouraged by 7 others. Making data publicly available was encouraged by 64 journals; making (processing or statistical) code publicly available was encouraged by *30 of the journals. Other responsible reporting practices were mentioned by less than 20 of the journals. Journals can improve the quality of research reports by mandating, or at least encouraging, the responsible reporting practices highlighted here

Signatures of Star-planet interactions

Planets interact with their host stars through gravity, radiation and magnetic fields, and for those giant planets that orbit their stars within $\sim$10 stellar radii ($\sim$0.1 AU for a sun-like star), star-planet interactions (SPI) are observable with a wide variety of photometric, spectroscopic and spectropolarimetric studies. At such close distances, the planet orbits within the sub-alfv\'enic radius of the star in which the transfer of energy and angular momentum between the two bodies is particularly efficient. The magnetic interactions appear as enhanced stellar activity modulated by the planet as it orbits the star rather than only by stellar rotation. These SPI effects are informative for the study of the internal dynamics and atmospheric evolution of exoplanets. The nature of magnetic SPI is modeled to be strongly affected by both the stellar and planetary magnetic fields, possibly influencing the magnetic activity of both, as well as affecting the irradiation and even the migration of the planet and rotational evolution of the star. As phase-resolved observational techniques are applied to a large statistical sample of hot Jupiter systems, extensions to other tightly orbiting stellar systems, such as smaller planets close to M dwarfs become possible. In these systems, star-planet separations of tens of stellar radii begin to coincide with the radiative habitable zone where planetary magnetic fields are likely a necessary condition for surface habitability.Comment: Accepted for publication in the handbook of exoplanet

Seasonal winter forecasts and the stratosphere

Published© 2016 Royal Meteorological Society. We investigate seasonal forecasts of the winter North Atlantic Oscillation (NAO) and their relationship with the stratosphere. Climatological frequencies of sudden stratospheric warming (SSW) and strong polar vortex (SPV) events are well represented and the predicted risk of events varies between 25 and 90% from winter to winter, indicating predictability beyond the deterministic range. The risk of SSW and SPV events relates to predicted NAO as expected, with NAO shifts of -6.5 and +4.8hPa in forecast members containing SSW and SPV events. Most striking of all is that forecast skill of the surface winter NAO vanishes from these hindcasts if members containing SSW events are excluded.This work was supported by the Joint DECC/Defra Met Office Hadley Centre Climate Programme (GA01101), the UK Public Weather Service research program and the European Union Framework 7 SPECS project. The contribution of AYK is funded by FMI’s tenure track program and the Academy of Finland under grant 286298

Fragment Flow and the Nuclear Equation of State

We use the Boltzmann-Uehling-Uhlenbeck model with a momentum-dependent nuclear mean field to simulate the dynamical evolution of heavy ion collisions. We re-examine the azimuthal anisotropy observable, proposed as sensitive to the equation of state of nuclear matter. We obtain that this sensitivity is maximal when the azimuthal anisotropy is calculated for nuclear composite fragments, in agreement with some previous calculations. As a test case we concentrate on semi-central $^{197}{\rm Au}\ +\ ^{197}{\rm Au}$ collisions at 400 $A$ MeV.Comment: 12 pages, ReVTeX 3.0. 12 Postscript figures, uuencoded and appende

Recent trends in molecular diagnostics of yeast infections : from PCR to NGS

The incidence of opportunistic yeast infections in humans has been increasing over recent years. These infections are difficult to treat and diagnose, in part due to the large number and broad diversity of species that can underlie the infection. In addition, resistance to one or several antifungal drugs in infecting strains is increasingly being reported, severely limiting therapeutic options and showcasing the need for rapid detection of the infecting agent and its drug susceptibility profile. Current methods for species and resistance identification lack satisfactory sensitivity and specificity, and often require prior culturing of the infecting agent, which delays diagnosis. Recently developed high-throughput technologies such as next generation sequencing or proteomics are opening completely new avenues for more sensitive, accurate and fast diagnosis of yeast pathogens. These approaches are the focus of intensive research, but translation into the clinics requires overcoming important challenges. In this review, we provide an overview of existing and recently emerged approaches that can be used in the identification of yeast pathogens and their drug resistance profiles. Throughout the text we highlight the advantages and disadvantages of each methodology and discuss the most promising developments in their path from bench to bedside

Risk factors for influenza-related complications in children during the 2009/10 pandemic: a UK primary care cohort study using linked routinely collected data.

Primary care clinicians have a central role in managing influenza/influenza-like illness (ILI) during influenza pandemics. This study identifies risk factors for influenza-related complications in children presenting with influenza/ILI in primary care. We conducted a cohort study using routinely collected linked data from the Clinical Practice Research Datalink on children aged 17 years and younger who presented with influenza/ILI during the 2009/10 pandemic. We calculated odds ratios (ORs) for potential risk factors in relation to influenza-related complications, complications requiring intervention, pneumonia, all-cause hospitalisation and hospitalisation due to influenza-related complications within 30 days of presentation. Analyses were adjusted for potential confounders including age, vaccination and socio-economic deprivation. Asthma was a risk factor for influenza-related complications (adjusted OR 1.48, 95% confidence interval (CI) 1.21-1.80, P < 0.001), complications requiring intervention (adjusted OR 1.44, 95% CI 1.11-1.88; P = 0.007), pneumonia (adjusted OR 1.64, 95% CI 1.07-2.51, P = 0.024) and hospitalisation due to influenza-related complications (adjusted OR 2.46, 95% CI 1.09-5.56, P = 0.031). Neurological conditions were risk factors for all-cause hospitalisation (adjusted OR 4.25, 95% CI 1.50-12.07, P = 0.007) but not influenza-related complications (adjusted OR 1.46, 95% CI 0.83-2.56, P = 0.189). Community-based early interventions to prevent influenza-related clinical deterioration should therefore be primarily targeted at children with asthma and neurological conditions

Dioxin Toxicity In Vivo Results from an Increase in the Dioxin-Independent Transcriptional Activity of the Aryl Hydrocarbon Receptor

The Aryl hydrocarbon receptor (Ahr) is the nuclear receptor mediating the toxicity of dioxins -widespread and persistent pollutants whose toxic effects include tumor promotion, teratogenesis, wasting syndrome and chloracne. Elimination of Ahr in mice eliminates dioxin toxicity but also produces adverse effects, some seemingly unrelated to dioxin. Thus the relationship between the toxic and dioxin-independent functions of Ahr is not clear, which hampers understanding and treatment of dioxin toxicity. Here we develop a Drosophila model to show that dioxin actually increases the in vivo dioxin-independent activity of Ahr. This hyperactivation resembles the effects caused by an increase in the amount of its dimerisation partner Ahr nuclear translocator (Arnt) and entails an increased transcriptional potency of Ahr, in addition to the previously described effect on nuclear translocation. Thus the two apparently different functions of Ahr, dioxin-mediated and dioxin-independent, are in fact two different levels (hyperactivated and basal, respectively) of a single function

Chirped pulse Raman amplification in warm plasma: towards controlling saturation

Stimulated Raman backscattering in plasma is potentially an efficient method of amplifying laser pulses to reach exawatt powers because plasma is fully broken down and withstands extremely high electric fields. Plasma also has unique nonlinear optical properties that allow simultaneous compression of optical pulses to ultra-short durations. However, current measured efficiencies are limited to several percent. Here we investigate Raman amplification of short duration seed pulses with different chirp rates using a chirped pump pulse in a preformed plasma waveguide. We identify electron trapping and wavebreaking as the main saturation mechanisms, which lead to spectral broadening and gain saturation when the seed reaches several millijoules for durations of 10&apos;s - 100&apos;s fs for 250 ps, 800 nm chirped pump pulses. We show that this prevents access to the nonlinear regime and limits the efficiency, and interpret the experimental results using slowly-varying-amplitude, current-averaged particle-in-cell simulations. We also propose methods for achieving higher efficiencies.close0