Ten common statistical mistakes to watch out for when writing or reviewing a manuscript

Inspired by broader efforts to make the conclusions of scientific research more robust, we have compiled a list of some of the most common statistical mistakes that appear in the scientific literature. The mistakes have their origins in ineffective experimental designs, inappropriate analyses and/or flawed reasoning. We provide advice on how authors, reviewers and readers can identify and resolve these mistakes and, we hope, avoid them in the future

Spatially resolved kinematics of the central regions of M83: hidden mass signatures and the role of supernovae

The barred grand-design spiral M83 (NGC 5236) is one of the most studied galaxies given its proximity, orientation, and particular complexity. Nonetheless, many aspects of the central regions remain controversial conveying our limited understanding of the inner gas and stellar kinematics, and ultimately of the nucleus evolution. In this work, we present AO VLT-SINFONI data of its central ~235x140 pc with an unprecedented spatial resolution of ~0.2 arcsec, corresponding to ~4 pc. We have focused our study on the distribution and kinematics of the stars and the ionised and molecular gas by studying in detail the Pa_alpha and Br_gamma emission, the H_2 1-0S(1) line at 2.122 micron and the [FeII] line at 1.644 micron, together with the CO absorption bands at 2.293 micron and 2.323 micron. Our results reveal a complex situation where the gas and stellar kinematics are totally unrelated. Supernova explosions play an important role in shaping the gas kinematics, dominated by shocks and inflows at scales of tens of parsecs that make them unsuitable to derive general dynamical properties. We propose that the location of the nucleus of M83 is unlikely to be related to the off-centre 'optical nucleus'. The study of the stellar kinematics reveals that the optical nucleus is a gravitationally bound massive star cluster with M_dyn = (1.1 \pm 0.4)x10^7 M_sun, formed by a past starburst. The kinematic and photometric analysis of the cluster yield that the stellar content of the cluster is well described by an intermediate age population of log T(yr) = 8.0\pm0.4, with a mass of M \simeq (7.8\pm2.4)x10^6 M_sun.Comment: 14 pages, 10 figures, accepted for publication in Ap

AOtools - a Python package for adaptive optics modelling and analysis

AOtools is a Python package that is open-source and aimed at providing tools for adaptive optics users and researchers. We present version 1.0, which contains tools for adaptive optics processing, including analysing data in the pupil plane, images and point spread functions in the focal plane, wavefront sensors, modelling of atmospheric turbulence, physical optical propagation of wavefronts, and conversion between frequently used adaptive optics and astronomical units. The main drivers behind AOtools is that it should be easy to install and use. To achieve this the project features extensive documentation, automated unit testing and is registered on the Python Package Index. AOtools is under continuous active development to expand the features available, and we encourage everyone involved in adaptive optics to become involved and contribute to the project

Obscuration in AGNs: near-infrared luminosity relations and dust colors

We combine two approaches to isolate the AGN luminosity at near-infrared wavelengths and relate the near-IR pure AGN luminosity to other tracers of the AGN. Using integral-field spectroscopic data of an archival sample of 51 local AGNs, we estimate the fraction of non-stellar light by comparing the nuclear equivalent width of the stellar 2.3 micron CO absorption feature with the intrinsic value for each galaxy. We compare this fraction to that derived from a spectral decomposition of the integrated light in the central arc second and find them to be consistent with each other. Using our estimates of the near-IR AGN light, we find a strong correlation with presumably isotropic AGN tracers. We show that a significant offset exists between type 1 and type 2 sources in the sense that type 1 sources are 7 (10) times brighter in the near-IR at log L_MIR = 42.5 (log L_X = 42.5). These offsets only becomes clear when treating infrared type 1 sources as type 1 AGNs. All AGNs have very red near-to-mid-IR dust colors. This, as well as the range of observed near-IR temperatures, can be explained with a simple model with only two free parameters: the obscuration to the hot dust and the ratio between the warm and hot dust areas. We find obscurations of A_V (hot) = 5 - 15 mag for infrared type 1 sources and A_V (hot) = 15 - 35 mag for type 2 sources. The ratio of hot dust to warm dust areas of about 1000 is nicely consistent with the ratio of radii of the respective regions as found by infrared interferometry.Comment: 17 pages, 10 Figures, 3 Tables, accepted by A&

On the relation of optical obscuration and X-ray absorption in Seyfert galaxies

The optical classification of a Seyfert galaxy and whether it is considered X-ray absorbed are often used interchangeably. But there are many borderline cases and also numerous examples where the optical and X-ray classifications appear to be in conflict. In this article we re-visit the relation between optical obscuration and X-ray absorption in AGNs. We make use of our "dust color" method (Burtscher et al. 2015) to derive the optical obscuration A_V and consistently estimated X-ray absorbing columns using 0.3--150 keV spectral energy distributions. We also take into account the variable nature of the neutral gas column N_H and derive the Seyfert sub-classes of all our objects in a consistent way. We show in a sample of 25 local, hard-X-ray detected Seyfert galaxies (log L_X / (erg/s) ~ 41.5 - 43.5) that there can actually be a good agreement between optical and X-ray classification. If Seyfert types 1.8 and 1.9 are considered unobscured, the threshold between X-ray unabsorbed and absorbed should be chosen at a column N_H = 10^22.3 / cm^2 to be consistent with the optical classification. We find that N_H is related to A_V and that the N_H/A_V ratio is approximately Galactic or higher in all sources, as indicated previously. But in several objects we also see that deviations from the Galactic ratio are only due to a variable X-ray column, showing that (1) deviations from the Galactic N_H/A_V can simply be explained by dust-free neutral gas within the broad line region in some sources, that (2) the dust properties in AGNs can be similar to Galactic dust and that (3) the dust color method is a robust way to estimate the optical extinction towards the sublimation radius in all but the most obscured AGNs.Comment: 7 pages, 3 figures, accepted for publication by A&A; updated PDF to include abstrac

Dynamic causal modelling of eye movements during pursuit: Confirming precision-encoding in V1 using MEG

This paper shows that it is possible to estimate the subjective precision (inverse variance) of Bayesian beliefs during oculomotor pursuit. Subjects viewed a sinusoidal target, with or without random fluctuations in its motion. Eye trajectories and magnetoencephalographic (MEG) data were recorded concurrently. The target was periodically occluded, such that its reappearance caused a visual evoked response field (ERF). Dynamic causal modelling (DCM) was used to fit models of eye trajectories and the ERFs. The DCM for pursuit was based on predictive coding and active inference, and predicts subjects' eye movements based on their (subjective) Bayesian beliefs about target (and eye) motion. The precisions of these hierarchical beliefs can be inferred from behavioural (pursuit) data. The DCM for MEG data used an established biophysical model of neuronal activity that includes parameters for the gain of superficial pyramidal cells, which is thought to encode precision at the neuronal level. Previous studies (using DCM of pursuit data) suggest that noisy target motion increases subjective precision at the sensory level: i.e., subjects attend more to the target's sensory attributes. We compared (noisy motion-induced) changes in the synaptic gain based on the modelling of MEG data to changes in subjective precision estimated using the pursuit data. We demonstrate that imprecise target motion increases the gain of superficial pyramidal cells in V1 (across subjects). Furthermore, increases in sensory precision – inferred by our behavioural DCM – correlate with the increase in gain in V1, across subjects. This is a step towards a fully integrated model of brain computations, cortical responses and behaviour that may provide a useful clinical tool in conditions like schizophrenia

Three years of harvest with the vector vortex coronagraph in the thermal infrared

For several years, we have been developing vortex phase masks based on sub-wavelength gratings, known as Annular Groove Phase Masks. Etched onto diamond substrates, these AGPMs are currently designed to be used in the thermal infrared (ranging from 3 to 13 {\mu}m). Our AGPMs were first installed on VLT/NACO and VLT/VISIR in 2012, followed by LBT/LMIRCam in 2013 and Keck/NIRC2 in 2015. In this paper, we review the development, commissioning, on-sky performance, and early scientific results of these new coronagraphic modes and report on the lessons learned. We conclude with perspectives for future developments and applications.Comment: To appear in SPIE proceedings vol. 990

Long XMM observation of the Narrow-Line Seyfert 1 galaxy IRAS13224-3809: rapid variability, high spin and a soft lag

Results are presented from a 500ks long XMM-Newton observation of the Narrow-Line Seyfert 1 galaxy IRAS13224-3809. The source is rapidly variable on timescales down to a few 100s. The spectrum shows strong broad Fe-K and L emission features which are interpreted as arising from reflection from the inner parts of an accretion disc around a rapidly spinning black hole. Assuming a power-law emissivity for the reflected flux and that the innermost radius corresponds to the innermost stable circular orbit, the black hole spin is measured to be 0.988 with a statistical precision better than one per cent. Systematic uncertainties are discussed. A soft X-ray lag of 100s confirms this scenario. The bulk of the power-law continuum source is located at a radius of 2-3 gravitational radii.Comment: 7 pages, 14 figures, submitted to MNRA

A novel flexible framework with automatic feature correspondence optimization for nonrigid registration in radiotherapy

Technical improvements in planning and dose delivery and in verification of patient positioning have substantially widened the therapeutic window for radiation treatment of cancer. However, changes in patient anatomy during the treatment limit the exploitation of these new techniques. To further improve radiation treatments, anatomical changes need to be modeled and accounted for. Non-rigid registration can be used for this purpose. This paper describes the design, the implementation and the validation of a new framework for non-rigid registration for radiotherapy applications. The core of this framework is an improved version of the Thin Plate Splines Robust Point Matching (TPS-RPM) algorithm. The TPS-RPM algorithm estimates a global correspondence and a transformation between the points that represent organs of interest belonging to two image sets. However, the algorithm does not allow for the inclusion of prior knowledge on the correspondence of subset of points and therefore, it can lead to inconsistent anatomical solutions. In this paper TPS-RPM was improved by employing a novel correspondence filter that supports simultaneous registration of multiple structures. The improved method allows for coherent organ registration and for the inclusion of user defined landmarks, lines and surfaces inside and outside of structures of interest. A procedure to generate control points form segmented organs is described. The framework parameters r and ?, which control the number of points and the non-rigidness of the transformation respectively, were optimized for three sites with different degrees of deformation: head and neck, prostate and cervix, using two cases per site. For the head and neck cases, the salivary glands were manually contoured on CT-scans, for the prostate cases the prostate and the vesicles, and for the cervix cases the cervix-uterus, the bladder and the rectum. The transformation error obtained using the best set of parameters was below 1 mm for all the studied cases. The length of the deformation vectors were on average (± 1 standard deviation) 5.8 ± 2.5 and 2.6 ± 1.1 mm for the head and neck cases, 7.2 ± 4.5 and 8.6 ± 1.9 mm for the prostate cases, and 19.0 ± 11.6 and 14.5 ± 9.3 mm for the cervix cases. Distinguishable anatomical features were identified for each case, and were used to validate the registration by calculating residual distances after transformation: 1.5 ± 0.8, 2.3 ± 1.0 and 6.3 ± 2.9 mm for the head and neck, prostate and cervix sites respectively. Finally, we demonstrated how the inclusion of these anatomical features in the registration process reduced the residual distances to 0.8 ± 0.5, 0.6 ± 0.5 and 1.3 ± 0.7 mm for the head and neck, prostate and cervix sites respectively. The inclusion of additional anatomical features produced more anatomically coherent transformations without compromising the transformation error. We concluded that the presented non-rigid registration framework is a powerful tool to simultaneously register multiple segmented organs with very different complexity