Fully flexible analysis of behavioural sequences based on parametric survival models with frailties—A tutorial

Recent automated systems allow collecting continuous data on individual animals with high accuracy over a long time. During this time, animals can be traced across different (discrete) types of behavioural states, with the duration in each state being known. Nevertheless, analyses of such sequences of states or behaviours may prove difficult. Classic Markov-chain methods have limitations in respect to incorporating “memory” (effects of past states), the duration in the states and accounting for dependencies. Dependencies occur in many data sets, where, for example a variety of individuals from different groups are observed and/or when an experiment is divided in different crossover treatment phases. So-called parametric survival analysis with frailties can incorporate aforementioned aspects in one coherent model. The time spent in a specific state (performing a specific behaviour) can be modelled in dependence of the subsequent state (transition probabilities) while incorporating how these transitions are influenced by experimental treatments. In addition, prior states can be used as predictor variables (accounting for past behaviour). Finally, random effects can be included to account for dependencies according to, for example individual identity, group/farm/laboratory or experimental period. Using interactions between random and fixed effects, the within- and between-subject variability of the transition probabilities can be estimated to indicate variation between and consistency within individual subjects (individuality and personality). Moreover, relative hazards describing transitions from one state to several potential follow-up states can be estimated. Behavioural sequences and their modulation by experimental situations can be studied accordingly. Using two exemplary data sets, the data type and structure adequate for parametric survival analysis are introduced and advice is given on how to specify and run such models. Overall, parametric survival analysis with frailties presents a modern and versatile approach that can revive sequential analysis. This will facilitate more detailed use of behavioural data and accordingly detect more subtle aspects of behaviour.Ministerie van Economische Zaken en Klimaat http://dx.doi.org/10.13039/501100016238Bundesamt für Lebensmittelsicherheit und Veterinärwesen http://dx.doi.org/10.13039/501100006454Peer Reviewe

Measurement of the Surface Gravity of η\eta Boo

Direct angular size measurements of the G0IV subgiant $\eta$ Boo from the Palomar Testbed Interferometer are presented, with limb-darkened angular size of $\theta_{LD}= 2.1894^{+0.0055}_{-0.0140}$ mas, which indicate a linear radius of $R=2.672 \pm 0.028 R_\odot$. A bolometric flux estimate of $F_{BOL} = 22.1 \pm 0.28\times 10^{-7}$ erg cm$^{-2}$s$^{-1}$ is computed, which indicates an effective temperature of $T_{EFF}=6100 \pm 28$ K and luminosity of $L = 8.89 \pm 0.16 L_\odot$ for this object. Similar data are established for a check star, HD 121860. The $\eta$ Boo results are compared to, and confirm, similar parameters established by the {\it MOST} asteroseismology satellite. In conjunction with the mass estimate from the {\it MOST} investigation, a surface gravity of $\log g=3.817 \pm 0.016$ [cm s$^{-2}$] is established for $\eta$ Boo.Comment: To appear in March 1, 2007 ApJ v657 n

« Le problème, c’est qu’elle est mal baisée »: la lutte contre le sexisme en milieu médical menée par les étudiant·e·s en médecine [« Her problem is she hasn't been laid »: medical students fighting against sexist behaviours during training and clinical practice]

In 2018, a survey conducted by and among medical students in Lausanne revealed that they were witnesses and victims of numerous sexist behaviours during their training and clinical practice. The collected testimonies included accounts of sexual assault, sexual advances and microaggressions that have personal and professional impact on the victims. The CLASH was created with the aim of eradicating these incidents and changing the medical culture through the creation of an awareness-raising campaign, the implementation of a support hotline for victims and the introduction of a practical course during the medical curriculum. Further action at institutional and political level as well as large-scale studies are needed to ensure non-discriminatory training for all in the future

The night-sky at the Calar Alto Observatory

We present a characterization of the main properties of the night-sky at the Calar Alto observatory for the time period between 2004 and 2007. We use optical spectrophotometric data, photometric calibrated images taken in moonless observing periods, together with the observing conditions regularly monitored at the observatory, such as atmospheric extinction and seeing. We derive, for the first time, the typical moonless night-sky optical spectrum for the observatory. The spectrum shows a strong contamination by different pollution lines, in particular from Mercury lines, which contribution to the sky-brightness in the different bands is of the order of ~0.09 mag, ~0.16 mag and ~0.10 mag in B, V and R respectively. The zenith-corrected values of the moonless night-sky surface brightness are 22.39, 22.86, 22.01, 21.36 and 19.25 mag arcsec^-2 in U, B, V, R and I, which indicates that Calar Alto is a particularly dark site for optical observations up to the I-band. The fraction of astronomical useful nights at the observatory is ~70%, with a ~30% of photometric nights. The typical extinction at the observatory is k_V~0.15 mag in the Winter season, with little dispersion. In summer the extinction has a wider range of values, although it does not reach the extreme peaks observed at other sites. The median seeing for the last two years (2005-6) was ~0.90", being smaller in the Summer (~0.87") than in the Winter (~0.96"). We conclude in general that after 26 years of operations Calar Alto is still a good astronomical site, being a natural candidate for future large aperture optical telescopes.Comment: 16 pages, 5 figures, accepted for publishing in the Publications of Astronomical Society of the Pacific (PASP

Improved Color-Temperature Relations and Bolometric Corrections for Cool Stars

We present new grids of colors and bolometric corrections for F-K stars having 4000 K < Teff < 6500 K, 0.0 < log g < 4.5 and -3.0 < [Fe/H] < 0.0. A companion paper extends these calculations into the M giant regime. Colors are tabulated for Johnson U-V and B-V; Cousins V-R and V-I; Johnson-Glass V-K, J-K and H-K; and CIT/CTIO V-K, J-K, H-K and CO. We have developed these color-temperature (CT) relations by convolving synthetic spectra with photometric filter-transmission-profiles. The synthetic spectra have been computed with the SSG spectral synthesis code using MARCS stellar atmosphere models as input. Both of these codes have been improved substantially, especially at low temperatures, through the incorporation of new opacity data. The resulting synthetic colors have been put onto the observational systems by applying color calibrations derived from models and photometry of field stars which have Teffs determined by the infrared-flux method. The color calibrations have zero points and slopes which change most of the original synthetic colors by less than 0.02 mag and 5%, respectively. The adopted Teff scale (Bell & Gustafsson 1989) is confirmed by the extraordinary agreement between the predicted and observed angular diameters of the field stars. We have also derived empirical CT relations from the field-star photometry. Except for the coolest dwarfs (Teff < 5000 K), our calibrated, solar-metallicity model colors are found to match these and other empirical relations quite well. Our calibrated, 4 Gyr, solar-metallicity isochrone also provides a good match to color-magnitude diagrams of M67. We regard this as evidence that our calibrated colors can be applied to many astrophysical problems, including modelling the integrated light of galaxies. (abridged)Comment: To appear in the March 2000 issue of the Astronomical Journal. 72 pages including 16 embedded postscript figures (one page each) and 6 embedded postscript tables (18 pages total

EK Eridani: the tip of the iceberg of giants which have evolved from magnetic Ap stars

We observe the slowly-rotating, active, single giant, EK Eri, to study and infer the nature of its magnetic field directly. We used the spectropolarimeter NARVAL at the Telescope Bernard Lyot, Pic du Midi Observatory, and the Least Square Deconvolution method to create high signal-to-noise ratio Stokes V profiles. We fitted the Stokes V profiles with a model of the large-scale magnetic field. We studied the classical activity indicators, the CaII H and K lines, the CaII infrared triplet, and H\alpha line. We detected the Stokes V signal of EK Eri securely and measured the longitudinal magnetic field Bl for seven individual dates spanning 60% of the rotational period. The measured longitudinal magnetic field of EK Eri reached about 100 G and was as strong as fields observed in RSCVn or FK Com type stars: this was found to be extraordinary when compared with the weak fields observed at the surfaces of slowly-rotating MS stars or any single red giant previously observed with NARVAL. From our modeling, we infer that the mean surface magnetic field is about 270 G, and that the large scale magnetic field is dominated by a poloidal component. This is compatible with expectations for the descendant of a strongly magnetic Ap star.Comment: 8 pages, 6 figures. Accepted for publication in A&

Annotation of two large contiguous regions from the Haemonchus contortus genome using RNA-seq and comparative analysis with Caenorhabditis elegans

The genomes of numerous parasitic nematodes are currently being sequenced, but their complexity and size, together with high levels of intra-specific sequence variation and a lack of reference genomes, makes their assembly and annotation a challenging task. Haemonchus contortus is an economically significant parasite of livestock that is widely used for basic research as well as for vaccine development and drug discovery. It is one of many medically and economically important parasites within the strongylid nematode group. This group of parasites has the closest phylogenetic relationship with the model organism Caenorhabditis elegans, making comparative analysis a potentially powerful tool for genome annotation and functional studies. To investigate this hypothesis, we sequenced two contiguous fragments from the H. contortus genome and undertook detailed annotation and comparative analysis with C. elegans. The adult H. contortus transcriptome was sequenced using an Illumina platform and RNA-seq was used to annotate a 409 kb overlapping BAC tiling path relating to the X chromosome and a 181 kb BAC insert relating to chromosome I. In total, 40 genes and 12 putative transposable elements were identified. 97.5% of the annotated genes had detectable homologues in C. elegans of which 60% had putative orthologues, significantly higher than previous analyses based on EST analysis. Gene density appears to be less in H. contortus than in C. elegans, with annotated H. contortus genes being an average of two-to-three times larger than their putative C. elegans orthologues due to a greater intron number and size. Synteny appears high but gene order is generally poorly conserved, although areas of conserved microsynteny are apparent. C. elegans operons appear to be partially conserved in H. contortus. Our findings suggest that a combination of RNA-seq and comparative analysis with C. elegans is a powerful approach for the annotation and analysis of strongylid nematode genomes

The radius and effective temperature of the binary Ap star beta CrB from CHARA/FLUOR and VLT/NACO observations

The prospects for using asteroseismology of rapidly oscillating Ap (roAp) stars are hampered by the large uncertainty in fundamental stellar parameters. Results in the literature for the effective temperature (Teff) often span a range of 1000 K. Our goal is to reduce systematic errors and improve the Teff calibration of Ap stars based on new interferometric measurements. We obtained long-baseline interferometric observations of beta CrB using the CHARA/FLUOR instrument. To disentangle the flux contributions of the two components of this binary star, we obtained VLT/NACO adaptive optics images. We determined limb darkened angular diameters of 0.699+-0.017 mas for beta CrB A (from interferometry) and 0.415+-0.017 mas for beta CrB B (from surface brightness- color relations), corresponding to radii of 2.63+-0.09 Rsun (3.4 percent uncertainty) and 1.56+-0.07 Rsun (4.5 percent). The combined bolometric flux of the A and B components was determined from satellite UV data, spectrophotometry in the visible and broadband data in the infrared. The flux from the B component constitutes 16+-4 percent of the total flux and was determined by fitting an ATLAS9 model atmosphere to the broad-band NACO J and K magnitudes. Combining the flux of the A component with its measured angular diameter, we determine the effective temperature Teff(A) = 7980+-180 K (2.3 percent). Our new interferometric and imaging data enable a nearly model-independent determination of the effective temperature of beta CrB A. Including our recent study of alpha Cir, we now have direct Teff measurements of two of the brightest roAp stars, providing a strong benchmark for an improved calibration of the Teff scale for Ap stars. This will support the use of potentially strong constraints imposed by asteroseismic studies of roAp stars.Comment: 7 pages, accepted by A&

Determining the Physical Properties of the B Stars II. Calibration of Synthetic Photometry

We present a new calibration of optical (UBV, Stromgren, uvby-beta, and Geneva) and near IR (Johnson RIJHK and 2MASS) photometry for B and early A stars derived from Kurucz (1991) Atlas model atmospheres. Our sample of stars consists of 45 normal, nearby B and early A stars which have high quality, low resolution IUE spectra and accurate Hipparcos parallaxes. The calibration is unique because it relies only on the UV spectral energy distributions, the absolute flux calibration of the V filter and the Hipparcos distances to determine the appropriate model atmospheres for the program stars. These models are then used to calibrate the synthetic photometry. We compare our results with previous, well accepted results and provide a thorough discussion of the random errors and systematic effects affecting the calibration. In particular, we demonstrate the influence of vsini on surface gravities derived from fitting model atmospheres. Finally, we discuss some of our intended applications of this new calibration.Comment: 56 pages, 11 Figures, electronic tables not included. To appear in AJ, March 200

Large-scale wind structures in OB supergiants: a search for rotationally modulated H\alpha variability

We present the results of a long-term monitoring campaign of the H\alpha line in a sample of bright OB-supergiants (O7.5-B9) that aims at detecting rotationally modulated changes potentially related to the existence of large-scale wind structures. A total of 22 objects were monitor ed during 36 nights spread over 6 months in 2001-2002. Coordinated broad-band photometric observations were also obtained for some targets. Conspicuous evidence for variability in H\alpha is found for the stars displaying a feature contaminated by wind emission. Most changes take place on a daily time-scale, although hourly variations are also occasionally detected. Convincing evidence for a cyclical pattern of variability in H\alpha has been found in 2 stars: HD 14134 and HD 42087 (periodic signals are also detected in other stars, but independent confirmation is required). Rotational modulation is suggested from the similarity between the observed recurrence time-scales (in the range 13-25 days) and estimated periods of stellar rotation. We call attention to the atypical case of HD 14134 which exhibits a clear 12.8-d periodicity both in the photometric and in the spectroscopic data sets. This places this object among a handful of early-type stars where one may observe a clear link between extended wind structures and photospheric disturbances. Further modelling may test the hypothesis that azimuthally-extended wind streams are responsible for the patterns of spectral variability in our target stars.Comment: 18 pages, accepted for publication in MNRA