ALBERT

Description: On the role of tropopause folds in summertime tropospheric ozone over the eastern Mediterranean and the Middle East Dimitris Akritidis, Andrea Pozzer, Prodromos Zanis, Evangelos Tyrlis, Bojan Škerlak, Michael Sprenger, and Jos Lelieveld Atmos. Chem. Phys. Discuss., doi:10.5194/acp-2016-547,2016 Manuscript under review for ACP (discussion: open, 0 comments) We investigate the contribution of tropopause folds in the summertime tropospheric ozone pool over the eastern Mediterranean and the Middle East. For this purpose we use the EMAC atmospheric chemistry climate model and a fold identification algorithm. A clear increase of ozone is found in the middle troposphere due to fold activity. The interannual variability of near surface ozone over the eastern Mediterranean is related to that of both tropopause folds and ozone in the free troposphere.

Description: A Polarimetric Scattering Database for Non-spherical Ice Particles at MicrowaveWavelengths Yinghui Lu, Zhiyuan Jiang, Kultegin Aydin, Johannes Verlinde, Eugene E. Clothiaux, and Giovanni Botta Atmos. Meas. Tech. Discuss., doi:10.5194/amt-2016-228,2016 Manuscript under review for AMT (discussion: open, 0 comments) The database contains the complete(polarimatric) scattering information for different types of ice particles at different incident and scattered radiation directions at 4 microwave wavelengths. These results are useful for understanding the dependence of ice-particle scattering properties on ice-particle orientation with respect to the incident and scattered radiation. It is also useful in ice property retrievals, radar forward simulation.

Description: Variations in O 3 , CO, and CH 4 over the Bay of Bengal during the summer monsoon season: Ship-borne measurements and model simulations Imran A. Girach, Narendra Ojha, Prabha R. Nair, Andrea Pozzer, Yogesh K. Tiwari, K. Ravi Kumar, and Jos Lelieveld Atmos. Chem. Phys. Discuss., doi:10.5194/acp-2016-595,2016 Manuscript under review for ACP (discussion: open, 0 comments) This study presents first ship-borne measurements of trace gases over the Bay of Bengal during summer monsoon. The observed variations in trace gases are shown to be due to dynamics/transport and en-route photochemistry. Analysis of meteorological and chemical fields shows that significantly lower ozone during rainfall is associated with the downdrafts. A regional model reproduces the observed variations and revealed the rapid transport of ozone across the Bay of Bengal during an event.

Description: A comparative analysis of UV nadir-backscatter and infrared limb-emission ozone data assimilation Rossana Dragani Atmos. Chem. Phys., 16, 8539-8557, doi:10.5194/acp-16-8539-2016, 2016 We present an assessment of ultraviolet nadir-backscatter and infrared limb-emission ozone data assimilation. Understanding the differences in the impact produced by the assimilation of limb and nadir ozone data is relevant to many applications, including climate reanalysis and air quality. The results show the potential and limitations of each dataset and support the need for a more balanced long-term availability of both types of sensors than currently envisaged.

Description: Why did the storm ex-Gaston (2010) fail to redevelop during the PREDICT experiment? Thomas M. Freismuth, Blake Rutherford, Mark A. Boothe, and Michael T. Montgomery Atmos. Chem. Phys., 16, 8511-8519, doi:10.5194/acp-16-8511-2016, 2016 Numerical model analyses are used to investigate the role of dry, environmental air in the failed redevelopment of a tropical cyclone (ex-Gaston, 2010). As early as 12:00 UTC 2 September 2010, a dry layer at and above 600 hPa results in a decrease in the vertical mass flux and vertical, relative vorticity. The intrusion of dry air led to a reduction in vorticity and a compromised pouch at these middle levels. This study supports work looking at the role of dry air in moist convection.

Description: Thermal infrared laser heterodyne spectro-radiometry for solar occultation atmospheric CO 2 measurements Alex Hoffmann, Neil A. Macleod, Marko Huebner, and Damien Weidmann Atmos. Meas. Tech. Discuss., doi:10.5194/amt-2016-142,2016 Manuscript under review for AMT (discussion: open, 0 comments) This paper focuses on the demonstration and assessment of thermal infrared laser heterodyne spectro-radiometry for the remote sensing of carbon dioxide (CO 2 ). A research instrument has been developed and operated from the ground using direct sunlight to measure CO 2 to a high precision. This technology would enable the development of high-performance miniature ground-based sounders to complement existing measurement networks and contribute to the improvement of global carbon emission assessment.

Description: A Polarimetric Scattering Database for Non-spherical Ice Particles at MicrowaveWavelengths Yinghui Lu, Zhiyuan Jiang, Kultegin Aydin, Johannes Verlinde, Eugene E. Clothiaux, and Giovanni Botta Atmos. Meas. Tech. Discuss., doi:10.5194/amt-2016-228,2016 Manuscript under review for AMT (discussion: open, 0 comments) The database contains the complete(polarimatric) scattering information for different types of ice particles at different incident and scattered radiation directions at 4 microwave wavelengths. These results are useful for understanding the dependence of ice-particle scattering properties on ice-particle orientation with respect to the incident and scattered radiation. It is also useful in ice property retrievals, radar forward simulation.

Description: Chemical Characteristics of Marine Fine Aerosols over Sea and at Offshore Islands during Three Cruise Sampling Campaigns in the Taiwan Strait– Sea Salts and Anthropogenic Particles Tsung-Chang Li, Chung-Shin Yuan, Chung-Hsuang Hung, Hsun-Yu Lin, Hu-Ching Huang, and Chon-Lin Lee Atmos. Chem. Phys. Discuss., doi:10.5194/acp-2016-384,2016 Manuscript under review for ACP (discussion: open, 0 comments) This manuscript is significant because it is important to establish data on the background physicochemical characteristics of atmospheric fine particles, as well as their spatial distributions and seasonal variations given various meteorological conditions, and the results of this study will be very much valuable for clarifying the transportation PM 2.5 over sea and at the offshore islands at the Taiwan Strait, which can further fill the the important blank for the global atmospheric research.

Description: Evaluation of Machine Learning Algorithms for Classification of Primary Biological Aerosol using a new UV-LIF spectrometer Simon Ruske, David O. Topping, Virginia E. Foot, Paul H. Kaye, Warren R. Stanley, Ian Crawford, Andrew P. Morse, and Martin W. Gallagher Atmos. Meas. Tech. Discuss., doi:10.5194/amt-2016-214,2016 Manuscript under review for AMT (discussion: open, 0 comments) Particles such as Bacteria, Pollen and Fungal spores have important implications within the environment and public health sectors. Here we evaluate the performance of various different methods for distinguishing between these different types of particles using a new instrument. We demonstrate that there may be better alternatives to the currently used methods which can be further investigated in future research.

Description: Identification of the cloud base height over the central Himalayan region: Intercomparison of Ceilometer and Doppler Lidar K. K. Shukla, K. Niranjan Kumar, D. V. Phanikumar, R. K. Newsom, V. R. Kotamarthi, T. B. M. J. Ouarda, and M. V. Ratnam Atmos. Meas. Tech. Discuss., doi:10.5194/amt-2016-162,2016 Manuscript under review for AMT (discussion: open, 0 comments) Estimation of Cloud base height was carried out by using various ground based instruments (Doppler Lidar and Ceilometer) and satellite datasets (MODIS) over central Himalayan region for the first time. The present study demonstrates the potential of Doppler Lidar in precise estimation of cloud base height and updraft velocities. More such deployments will be invaluable inputs for regional weather prediction models over complex Himalayan terrains.

Description: It is well known that land snails can be dispersed by birds, both by attachment to the body (ectozoochory) and by passing intact and alive through the bird's digestive tract (endozoochory). Endozoochory has, however, only been recorded for very small species. We examined the possibility that larger species (up to c . 17 mm in maximum shell dimension) could survive passage through a bird's digestive system. Live Alinda biplicata , Cochlodina laminata (both Clausiliidae) and Discus rotundatus (Discidae) were fed to 10 bird species (Corvidae, Turdidae, Sturnidae and Columbidae) in 14 experimental trials. Of 720 snails offered, 14 passed intact through the birds, of which nine were alive (eight clausiliids and one D. rotundatus ); thus more than 1% of all snails offered survived ingestion. In an additional experiment, some A. biplicata and C. laminata remained attached to birds' legs by pedal adhesion in simulated flight trials where the birds' legs oscillated at the maximum rate achieved during flight.

Description: Cephalopods show excellent camouflaged body patterning, but they also use body patterning for communication. It is not known whether body patterning responses can be shaped by learning. Here, we tested the hypothesis that cuttlefish ( Sepia officinalis ) can be conditioned to change their body pattern for a food reward. Cuttlefish were placed in a tank (all black or all white) and allowed to acclimate and settle into camouflaged body patterning (matching the tank colour). In each trial, a contrasting probe (white or black) was inserted into the tank. Experimental cuttlefish received a food reward if they broke camouflage (e.g. displayed light body patterning in the black tank or displayed dark body patterning in the white tank) within 15 s of the insertion of the probe; control cuttlefish received food rewards at random intervals. Experimental cuttlefish changed their body patterning more quickly and more consistently in response to the probe than did control cuttlefish, but only when they were trained in the black tank. We conclude that cuttlefish body patterning is not entirely innate, can be shaped by individual experience and appears to be more flexible than previous research has suggested.

Description: On the role of tropopause folds in summertime tropospheric ozone over the eastern Mediterranean and the Middle East Dimitris Akritidis, Andrea Pozzer, Prodromos Zanis, Evangelos Tyrlis, Bojan Škerlak, Michael Sprenger, and Jos Lelieveld Atmos. Chem. Phys. Discuss., doi:10.5194/acp-2016-547,2016 Manuscript under review for ACP (discussion: open, 0 comments) We investigate the contribution of tropopause folds in the summertime tropospheric ozone pool over the eastern Mediterranean and the Middle East. For this purpose we use the EMAC atmospheric chemistry climate model and a fold identification algorithm. A clear increase of ozone is found in the middle troposphere due to fold activity. The interannual variability of near surface ozone over the eastern Mediterranean is related to that of both tropopause folds and ozone in the free troposphere.

Description: Increased nitrate and decreased δ 15 N–NO 3 − in the Greenland Arctic after 1940 attributed to North American oil burning Nathan J. Chellman, Meredith G. Hastings, and Joseph R. McConnell The Cryosphere Discuss., doi:10.5194/tc-2016-163,2016 Manuscript under review for TC (discussion: open, 0 comments) This manuscript analyzes the changing sources of nitrate deposition to Greenland since 1760 CE using a dataset consisting of sub-seasonally resolved nitrogen isotopes of nitrate and source tracers. Correlations amongst ion concentration, source tracers, and the δ 15 N–NO 3 − provide evidence of the impact of biomass burning and fossil fuel combustion emissions of nitrogen oxides and suggest that oil combustion is the likely driver of increased nitrate concentration in Greenland ice since 1940 CE.

Description: Inversion of geothermal heat flux in a thermomechanically coupled nonlinear Stokes ice sheet model Hongyu Zhu, Noemi Petra, Georg Stadler, Tobin Isaac, Thomas J. R. Hughes, and Omar Ghattas The Cryosphere, 10, 1477-1494, doi:10.5194/tc-10-1477-2016, 2016 We study how well the basal geothermal heat flux can be inferred from surface velocity observations using a thermomechanically coupled nonlinear Stokes ice sheet model. The prospects and limitations of this inversion is studied in two and three dimensional model problems. We also argue that a one-way coupled approach for the adjoint equations motivated by staggered solvers for forward multiphysics problems can lead to an incorrect gradient and premature termination of the optimization iteration.

Description: Increased nitrate and decreased δ 15 N–NO 3 − in the Greenland Arctic after 1940 attributed to North American oil burning Nathan J. Chellman, Meredith G. Hastings, and Joseph R. McConnell The Cryosphere Discuss., doi:10.5194/tc-2016-163,2016 Manuscript under review for TC (discussion: open, 0 comments) This manuscript analyzes the changing sources of nitrate deposition to Greenland since 1760 CE using a dataset consisting of sub-seasonally resolved nitrogen isotopes of nitrate and source tracers. Correlations amongst ion concentration, source tracers, and the δ 15 N–NO 3 − provide evidence of the impact of biomass burning and fossil fuel combustion emissions of nitrogen oxides and suggest that oil combustion is the likely driver of increased nitrate concentration in Greenland ice since 1940 CE.

Description: To refine the 3-D seismic velocity model in the greater Parkfield, California region, a new data set including regular earthquakes, shots, quarry blasts and low-frequency earthquakes (LFEs) was assembled. Hundreds of traces of each LFE family at two temporary arrays were stacked with time–frequency domain phase weighted stacking method to improve signal-to-noise ratio. We extend our model resolution to lower crustal depth with LFE data. Our result images not only previously identified features but also low velocity zones (LVZs) in the area around the LFEs and the lower crust beneath the southern Rinconada Fault. The former LVZ is consistent with high fluid pressure that can account for several aspects of LFE behaviour. The latter LVZ is consistent with a high conductivity zone in magnetotelluric studies. A new Vs model was developed with S picks that were obtained with a new autopicker. At shallow depth, the low Vs areas underlie the strongest shaking areas in the 2004 Parkfield earthquake. We relocate LFE families and analyse the location uncertainties with the NonLinLoc and tomoDD codes. The two methods yield similar results.

Description: Improving the inter-hemispheric gradient of total column atmospheric CO 2 and CH 4 in simulations with the ECMWF semi-Lagrangian atmospheric global model Anna Agusti-Panareda, Michail Diamantakis, Victor Bayona, Friedrich Klappenbach, and Andre Butz Geosci. Model Dev. Discuss., doi:10.5194/gmd-2016-143,2016 Manuscript under review for GMD (discussion: open, 0 comments) This paper demonstrates how important mass fixers can be in the simulation of long-lived greenhouse gases using transport models based on the highly efficient semi-lagrangian advection scheme. Mass fixers can have a large impact on the representation of the inter-hemispheric gradient of CO 2 and CH 4 , a crucial feature of their distribution. This work is relevant for models simulating atmospheric composition that use semi-lagrangian advection schemes both for climate and air quality applications.

Description: We have monitored the massive binary star Carinae with the CTIO/Small and Moderate Aperture Research Telescope System 1.5 m telescope and CHIRON spectrograph from the previous apastron passage of the system through the recent 2014.6 periastron passage. Our monitoring has resulted in a large, homogeneous data set with an unprecedented time-sampling, spectral resolving power, and signal to noise. This allowed us to investigate temporal variability previously unexplored in the system and discover a kinematic structure in the P Cygni absorption troughs of neutral helium wind lines. The features observed occurred prior to the periastron passage and are seen as we look through the trailing arm of the wind–wind collision shock cone. We show that the bulk of the variability is repeatable across the last five periastron passages, and that the absorption occurs in the inner 230 au of the system. In addition, we found an additional, high-velocity absorption component superimposed on the P Cygni absorption troughs that has been previously unobserved in these lines, but which bears resemblance to the observations of the He i 10830 Å feature across previous cycles. Through a comparison of the current smoothed particle hydrodynamical simulations, we show that the observed variations are likely caused by instabilities in the wind–wind collision region in our line of sight, coupled with stochastic variability related to clumping in the winds.

Description: We investigated the typical environment and physical properties of ‘red discs’ and ‘blue bulges’, comparing those to the ‘normal’ objects in the blue cloud and red sequence. Our sample is composed of cluster members and field galaxies at z ≤ 0.1, so that we can assess the impact of the local and global environment. We find that disc galaxies display a strong dependence on environment, becoming redder for higher densities. This effect is more pronounced for objects within the virial radius, being also strong related to the stellar mass. We find that local and global environment affect galaxy properties, but the most effective parameter is stellar mass. We find evidence for a scenario where ‘blue discs’ are transformed into ‘red discs’ as they grow in mass and move to the inner parts of clusters. From the metallicity differences of red and blue discs, and the analysis of their star formation histories, we suggest the quenching process is slow. We estimate a quenching time-scale of ~2–3 Gyr. We also find from the sSFR– M * plane that ‘red discs’ gradually change as they move into clusters. The ‘blue bulges’ have many similar properties than ‘blue discs’, but some of the former show strong signs of asymmetry. The high asymmetry ‘blue bulges’ display enhanced recent star formation compared to their regular counterparts. That indicates some of these systems may have increased their star formation due to mergers. None the less, there may not be a single evolutionary path for these blue early-type objects.

Description: We study the dependence of the estimated size and geometry of the medium on the time-averaged spectral model assumed and on the frequency of the kHz quasi-periodic oscillation (QPO) in the framework of a thermal Comptonization model. We use the high-quality time lag and rms obtained during 1996 March 3 observation of 4U 1608–52 by RXTE as well as other observations of the source at different QPO frequencies where a single time lag between two broad energy bands has been reported. We compare the results obtained when assuming that the time-averaged spectra are represented by the spectrally degenerate ‘hot ( kT b ≥ 1 keV)’ and ‘cold ( kT b ≤ 0.5 keV)’ seed spectral models where T b is seed source temperature. We find that for the ‘hot-seed’ model the medium size is in the range of 0.3–2.0 km and the size decreases with increasing QPO frequency. On the other hand, for the ‘cold-seed’ model, the range for the sizes is much larger 0.5–20 km and hence perhaps show no variation with QPO frequency. Our results emphasize the need for broad-band spectral information combined with high-frequency timing to lift this degeneracy. We further compare the rms as a function of energy for the upper kHz QPO, and indeed we find that the driver for this QPO should be temperature variations of the corona identical to the lower kHz QPO. However, the time lag reported for the upper kHz QPO is hard, which if confirmed would challenge the simple Comptonization model presented here.

Description: We describe a statistical approach for measuring the influence that a galaxy's closest companion has on the galaxy's properties out to arbitrarily wide separations. We begin by identifying the closest companion for every galaxy in a large spectroscopic sample of Sloan Digital Sky Survey galaxies. We then characterize the local environment of each galaxy by using the number of galaxies within 2 Mpc and by determining the isolation of the galaxy pair from other neighbouring galaxies. We introduce a sophisticated algorithm for creating a statistical control sample for each galaxy, matching on stellar mass, redshift, local density and isolation. Unlike traditional studies of close galaxy pairs, this approach is effective in a wide range of environments, regardless of how faraway the closest companion is (although a very distant closest companion is unlikely to have a measurable influence on the galaxy in question). We apply this methodology to measurements of galaxy asymmetry, and find that the presence of nearby companions drives a clear enhancement in galaxy asymmetries. The asymmetry excess peaks at the smallest projected separations (〈10 kpc), where the mean asymmetry is enhanced by a factor of 2.0 ± 0.2. Enhancements in mean asymmetry decline as pair separation increases, but remain statistically significant (1–2) out to projected separations of at least 50 kpc.

Description: The collimation of a Poynting-flux dominated jet by a wind emanating from the surface of an accretion flow is computed using a semi-analytic model. The injection of the disc wind is treated as a boundary condition in the equatorial plane, and its evolution is followed by invoking a prescribed geometry of streamlines. Solutions are obtained for a wide range of disc wind parameters. It is found that jet collimation generally occurs when the total wind power exceeds about 10 percents of the jet power. For moderate wind powers, we find gradual collimation. For strong winds, we find rapid collimation followed by focusing of the jet, after which it remains narrow over many Alfvén crossing times before becoming conical. We estimate that in the later case, the jet's magnetic field may be dissipated by the current-driven kink instability over a distance of a few hundreds gravitational radii. We apply the model to M87 and show that the observed parabolic shape of the radio jet within the Bondi radius can be reproduced provided that the wind injection zone extends to several hundreds gravitational radii, and that its total power is about one-third of the jet power. The radio spectrum can be produced by synchrotron radiation of relativistically hot, thermal electrons in the sheath flow surrounding the inner jet.

Description: We use ~100 cosmological galaxy formation ‘zoom-in’ simulations using the smoothed particle hydrodynamics code gasoline to study the effect of baryonic processes on the mass profiles of cold dark matter haloes. The haloes in our study range from dwarf ( M 200  ~ 10 10 M ) to Milky Way ( M 200  ~ 10 12 M ) masses. Our simulations exhibit a wide range of halo responses, primarily varying with mass, from expansion to contraction, with up to factor ~10 changes in the enclosed dark matter mass at 1 per cent of the virial radius. Confirming previous studies, the halo response is correlated with the integrated efficiency of star formation: SF ( M star / M 200 )/( b / m ). In addition, we report a new correlation with the compactness of the stellar system: R r 1/2 / R 200 . We provide an analytic formula depending on SF and R for the response of cold dark matter haloes to baryonic processes. An observationally testable prediction is that, at fixed mass, larger galaxies experience more halo expansion, while the smaller galaxies more halo contraction. This diversity of dark halo response is captured by a toy model consisting of cycles of adiabatic inflow (causing contraction) and impulsive gas outflow (causing expansion). For net outflow, or equal inflow and outflow fractions, f , the overall effect is expansion, with more expansion with larger f . For net inflow, contraction occurs for small f (large radii), while expansion occurs for large f (small radii), recovering the phenomenology seen in our simulations. These regularities in the galaxy formation process provide a step towards a fully predictive model for the structure of cold dark matter haloes.

Description: The strongest transitions of Zn and Cr ii are the most sensitive to relative variations in the fine-structure constant (α/α) among the transitions commonly observed in quasar absorption spectra. They also lie within just 40 Å of each other (rest frame), so they are resistant to the main systematic error affecting most previous measurements of α/α: long-range distortions of the wavelength calibration. While Zn and Cr ii absorption is normally very weak in quasar spectra, we obtained high signal-to-noise, high-resolution echelle spectra from the Keck and Very Large Telescopes of nine rare systems where it is strong enough to constrain α/α from these species alone. These provide 12 independent measurements (three quasars were observed with both telescopes) at redshifts 1.0–2.4, 11 of which pass stringent reliability criteria. These 11 are all consistent with α/α = 0 within their individual uncertainties of 3.5–13 parts per million (ppm), with a weighted mean α/α = 0.4 ± 1.4 stat ± 0.9 sys  ppm (1 statistical and systematic uncertainties), indicating no significant cosmological variations in α. This is the first statistical sample of absorbers that is resistant to long-range calibration distortions (at the 〈1 ppm level), with a precision comparable to previous large samples of ~150 (distortion-affected) absorbers. Our systematic error budget is instead dominated by much shorter range distortions repeated across echelle orders of individual spectra.

Description: We use the eagle suite of cosmological hydrodynamical simulations to study how the H i content of present-day galaxies depends on their environment. We show that eagle reproduces observed H i mass–environment trends very well, while semi-analytic models typically overpredict the average H i masses in dense environments. The environmental processes act primarily as an on/off switch for the H i content of satellites with M * 〉 10 9 M . At a fixed M * , the fraction of H i -depleted satellites increase with increasing host halo mass M 200 in response to stronger environmental effects, while at a fixed M 200 it decreases with increasing satellite M * as the gas is confined by deeper gravitational potentials. H i -depleted satellites reside mostly, but not exclusively, within the virial radius r 200 of their host halo. We investigate the origin of these trends by focusing on three environmental mechanisms: ram pressure stripping by the intragroup medium, tidal stripping by the host halo and satellite–satellite encounters. By tracking back in time the evolution of the H i -depleted satellites, we find that the most common cause of H i removal is satellite encounters. The time-scale for H i removal is typically less than 0.5 Gyr. Tidal stripping occurs in haloes of M 200 〈 10 14 M within 0.5 x r 200 , while the other processes act also in more massive haloes, generally within r 200 . Conversely, we find that ram pressure stripping is the most common mechanism that disturbs the H i morphology of galaxies at redshift z = 0. This implies that H i removal due to satellite–satellite interactions occurs on shorter time-scales than the other processes.

Description: We present the first numerical simulations in coupled dark energy cosmologies with high enough resolution to investigate the effects of the coupling on galactic and subgalactic scales. We choose two constant couplings and a time-varying coupling function and we run simulations of three Milky Way-sized haloes (~10 12  M ), a lower mass halo (6 x 10 11  M ) and a dwarf galaxy halo (5 x 10 9  M ). We resolve each halo with several million dark matter particles. On all scales, the coupling causes lower halo concentrations and a reduced number of substructures with respect to cold dark matter (CDM). We show that the reduced concentrations are not due to different formation times. We ascribe them to the extra terms that appear in the equations describing the gravitational dynamics. On the scale of the Milky Way satellites, we show that the lower concentrations can help in reconciling observed and simulated rotation curves, but the coupling values necessary to have a significant difference from CDM are outside the current observational constraints. On the other hand, if other modifications to the standard model allowing a higher coupling (e.g. massive neutrinos) are considered, coupled dark energy can become an interesting scenario to alleviate the small-scale issues of the CDM model.

Description: The correlation between radio spectral index and redshift has been exploited to discover high-redshift radio galaxies, but its underlying cause is unclear. It is crucial to characterize the particle acceleration and loss mechanisms in high-redshift radio galaxies to understand why their radio spectral indices are steeper than their local counterparts. Low-frequency information on scales of ~1 arcsec are necessary to determine the internal spectral index variation. In this paper we present the first spatially resolved studies at frequencies below 100 MHz of the z = 2.4 radio galaxy 4C 43.15 which was selected based on its ultrasteep spectral index (α 〈 –1; S ~ α ) between 365 MHz and 1.4 GHz. Using the International Low Frequency Array Low Band Antenna we achieve subarcsecond imaging resolution at 55 MHz with very long baseline interferometry techniques. Our study reveals low-frequency radio emission extended along the jet axis, which connects the two lobes. The integrated spectral index for frequencies 〈500 MHz is –0.83. The lobes have integrated spectral indices of –1.31 ± 0.03 and –1.75 ± 0.01 for frequencies ≥1.4 GHz, implying a break frequency between 500 MHz and 1.4 GHz. These spectral properties are similar to those of local radio galaxies. We conclude that the initially measured ultrasteep spectral index is due to a combination of the steepening spectrum at high frequencies with a break at intermediate frequencies.

Description: We examine a sample of 1495 galaxies in the CANDELS fields to determine the evolution of two-component galaxies, including bulges and discs, within massive galaxies at the epoch 1 〈  z  〈 3 when the Hubble sequence forms. We fit all of our galaxies’ light profiles with a single Sérsic fit, as well as with a combination of exponential and Sérsic profiles. The latter is done in order to describe a galaxy with an inner and an outer component, or bulge and disc component. We develop and use three classification methods (visual, F -test and the residual flux fraction) to separate our sample into one-component galaxies (disc/spheroids-like galaxies) and two-component galaxies (galaxies formed by an ‘inner part’ or bulge and an ‘outer part’ or disc). We then compare the results from using these three different ways to classify our galaxies. We find that the fraction of galaxies selected as two-component galaxies increases on average 50 per cent from the lowest mass bin to the most massive galaxies, and decreases with redshift by a factor of 4 from z  = 1 to 3. We find that single Sérsic ‘disc-like’ galaxies have the highest relative number densities at all redshifts, and that two-component galaxies have the greatest increase and become at par with Sérsic discs by z  = 1. We also find that the systems we classify as two-component galaxies have an increase in the sizes of their outer components, or ‘discs’, by about a factor of 3 from z  = 3 to 1.5, while the inner components or ‘bulges’ stay roughly the same size. This suggests that these systems are growing from the inside out, whilst the bulges or protobulges are in place early in the history of these galaxies. This is also seen to a lesser degree in the growth of single ‘disc-like’ galaxies versus ‘spheroid-like’ galaxies over the same epoch.

Description: Using the idea of regularization of singularities due to the variability of the fundamental constants in cosmology we study the cyclic universe models. We find two models of oscillating and non-singular mass density and pressure (‘non-singular’ bounce) regularized by varying gravitational constant G despite the scale factor evolution is oscillating and having sharp turning points (‘singular’ bounce). Both violating (big-bang) and non-violating (phantom) null energy condition models appear. Then, we extend this idea on to the multiverse containing cyclic individual universes with either growing or decreasing entropy though leaving the net entropy constant. In order to get an insight into the key idea, we consider the doubleverse with the same geometrical evolution of the two ‘parallel’ universes with their physical evolution [physical coupling constants c ( t ) and G ( t )] being different. An interesting point is that there is a possibility to exchange the universes at the point of maximum expansion – the fact which was already noticed in quantum cosmology. Similar scenario is also possible within the framework of Brans–Dicke theory where varying G ( t ) is replaced by the dynamical Brans–Dicke field ( t ) though these theories are slightly different.

Description: In the thermal dark matter (DM) paradigm, primordial interactions between DM and Standard Model particles are responsible for the observed DM relic density. In Bœhm et al., we showed that weak-strength interactions between DM and radiation (photons or neutrinos) can erase small-scale density fluctuations, leading to a suppression of the matter power spectrum compared to the collisionless cold DM (CDM) model. This results in fewer DM subhaloes within Milky Way-like DM haloes, implying a reduction in the abundance of satellite galaxies. Here we use very high-resolution N -body simulations to measure the dynamics of these subhaloes. We find that when interactions are included, the largest subhaloes are less concentrated than their counterparts in the collisionless CDM model and have rotation curves that match observational data, providing a new solution to the ‘too big to fail’ problem.

Description: The recent discovery of the gravitational wave source GW150914 has revealed a coalescing binary black hole (BBH) with masses of ~30 M . Previous proposals for the origin of such a massive binary include Population III (PopIII) stars. PopIII stars are efficient producers of BBHs and of a gravitational wave background (GWB) in the 10–100 Hz band, and also of ionizing radiation in the early Universe. We quantify the relation between the amplitude of the GWB ( gw ) and the electron scattering optical depth ( e ), produced by PopIII stars, assuming that f esc 10 per cent of their ionizing radiation escapes into the intergalactic medium. We find that PopIII stars would produce a GWB that is detectable by the future O5 LIGO/Virgo if e 0.07, consistent with the recent Planck measurement of e = 0.055 ± 0.09. Moreover, the spectral index of the background from PopIII BBHs becomes as small as dln gw /dln f 0.3 at f 30 Hz, which is significantly flatter than the value ~2/3 generically produced by lower redshift and less-massive BBHs. A detection of the unique flattening at such low frequencies by the O5 LIGO/Virgo will indicate the existence of a high-chirp mass, high-redshift BBH population, which is consistent with the PopIII origin. A precise characterization of the spectral shape near 30–50 Hz by the Einstein Telescope could also constrain the PopIII initial mass function and star formation rate.

Description: We employ very high resolution simulations of isolated Milky Way-like galaxies to study the effect of triaxial dark matter haloes on exponential stellar discs. Non-adiabatic halo shape changes can trigger two-armed grand-design spiral structures which extend all the way to the edge of the disc. Their pattern speed coincides with the inner Lindblad resonance indicating that they are kinematic density waves which can persist up to several Gyr. In dynamically cold discs, grand-design spirals are swing amplified and after a few Gyr can lead to the formation of (multi-armed) transient recurrent spirals. Stellar discs misaligned to the principal planes of the host triaxial halo develop characteristic integral shaped warps, but otherwise exhibit very similar spiral structures as aligned discs. For the grand-design spirals in our simulations, their strength dependence with radius is determined by the torque on the disc, suggesting that by studying grand-design spirals without bars it may be possible to set constraints on the tidal field and host dark matter halo shape.

Description: Intrinsic galaxy shape and angular momentum alignments can arise in cosmological large-scale structure due to tidal interactions or galaxy formation processes. Cosmological hydrodynamical simulations have recently come of age as a tool to study these alignments and their contamination to weak gravitational lensing. We probe the redshift and luminosity evolution of intrinsic alignments in Horizon-AGN between z = 0 and 3 for galaxies with an r -band absolute magnitude of M r ≤ –20. Alignments transition from being radial at low redshifts and high luminosities, dominated by the contribution of ellipticals, to being tangential at high redshift and low luminosities, where discs dominate the signal. This cannot be explained by the evolution of the fraction of ellipticals and discs alone: intrinsic evolution in the amplitude of alignments is necessary. The alignment amplitude of elliptical galaxies alone is smaller in amplitude by a factor of ~=2, but has similar luminosity and redshift evolution as in current observations and in the non-linear tidal alignment model at projected separations of 1 Mpc. Alignments of discs are null in projection and consistent with current low-redshift observations. The combination of the two populations yields an overall amplitude a factor of ~=4 lower than observed alignments of luminous red galaxies with a steeper luminosity dependence. The restriction on accurate galaxy shapes implies that the galaxy population in the simulation is complete only to M r ≤ –20. Higher resolution simulations will be necessary to avoid extrapolation of the intrinsic alignment predictions to the range of luminosities probed by future surveys.

Description: The spins of stellar-mass black holes (BHs) and the power outputs of their jets are measurable quantities. Unfortunately, the currently employed methods do not agree and the results are controversial. Two major issues concern the measurements of BH spin and beam (jet) power. The former issue can be resolved by future observations. But the latter issue can be resolved now, if we pay attention to what is expected from theoretical considerations. The question of whether a correlation has been found between the power outputs of few objects and the spins of their BHs is moot because BH beam power does not scale with the square of the spin of the BH. We show that the theoretical BH beam power is a strongly non-linear function of spin that cannot be approximated by a quadratic relation, as is generally stated when the influence of the magnetic field is not accounted for in the Blandford & Znajek model. The BH beam power of ballistic jets should scale a lot more steeply with BH spin irrespective of the magnetic field assumed to thread the horizon and the spin range considered. This behaviour may already be visible in the analyses of radio observations by Narayan & McClintock and Russell et al. In agreement with previous studies, we also find that the power output that originates in the inner regions of the surrounding accretion discs is higher than that from the BHs and it cannot be ignored in investigations of continuous compact jets from these systems.

Description: We present deep spectroscopy of three Galactic planetary nebulae (PNe) with large abundance discrepancy factors: NGC 6153, M 1-42 and Hf 2-2. The spectra were obtained with Very Large Telescope/Ultraviolet and Visual Echelle Spectrograph and cover the whole optical range (3040–11 000 Å) with a spectral resolution of ~20 000. For all three PNe, several hundred emission lines were detected and identified, with more than 70 per cent of them as permitted lines. Most of these permitted lines are excited by recombination. Numerous weak optical recombination lines (ORLs) of O ii , C ii , N ii and Ne ii were detected in the spectra and accurate fluxes measured. Line flux tables were compiled and ready for use by the community of nebular astrophysics. These ORLs were critically analysed using the effective recombination coefficients recently calculated for the optical recombination spectrum of N ii and O ii under the physical conditions of photoionized gaseous nebulae. Plasma diagnostics based on the heavy element ORLs were carried out using the new atomic data. Elemental abundances derived from the ORLs were systematically higher than those derived from the collisionally excited lines (CELs) by a factor of ~11, 22 and 80 for NGC 6153, M 1-42 and Hf 2-2, respectively. The electron temperatures derived from the heavy element ORLs are systematically lower than those derived from the CELs. These ORL versus CEL abundance and temperature discrepancies, previously observed in the three PNe through deep spectroscopy with medium to low spectral resolution, are thus confirmed by our analysis of the deep echelle spectra using the new atomic data.

Description: The birth of the first luminous sources and the ensuing epoch of reionization are best studied via the redshifted 21-cm emission line, the signature of the first two imprinting the last. In this work, we present a fully Bayesian method, hibayes , for extracting the faint, global (sky-averaged) 21-cm signal from the much brighter foreground emission. We show that a simplified (but plausible) Gaussian model of the 21-cm emission from the Cosmic Dawn epoch (15 z 30), parametrized by an amplitude $A_{\rm H\,\small {I}}$ , a frequency peak $\nu _{\rm H\,\small {I}}$ and a width $\sigma _{\rm H\,\small {I}}$ , can be extracted even in the presence of a structured foreground frequency spectrum (parametrized as a seventh-order polynomial), provided sufficient signal-to-noise (400 h of observation with a single dipole). We apply our method to an early, 19-min-long observation from the Large aperture Experiment to detect the Dark Ages, constraining the 21-cm signal amplitude and width to be $-890 \lt A_{\rm H\,\small {I}} \lt 0$ mK and $\sigma _{\rm H\,\small {I}} \gt 6.5$ MHz (corresponding to z 〉 1.9 at redshift z ~= 20) respectively at the 95-per cent confidence level in the range 13.2 〈 z 〈 27.4 (100 〉 〉 50 MHz).

Description: Several dedicated surveys focusing on early-type galaxies (ETGs) reveal that significant fractions of them are detectable in all interstellar medium phases studied to date. We select ETGs from the Herschel Reference Survey that have both far-infrared Herschel and either H  i or CO detection (or both). We derive their star formation rates (SFRs), stellar masses and dust masses via modelling their spectral energy distributions. We combine these with literature information on their atomic and molecular gas properties, in order to relate their star formation, total gas mass and dust mass on global scales. The ETGs deviate from the dust mass–SFR relation and the Schmidt–Kennicutt relation that SDSS star-forming galaxies define: compared to SDSS galaxies, ETGs have more dust at the same SFR, or less SFR at the same dust mass. When placing them in the M * –SFR plane, ETGs show a much lower specific SFR as compared to normal star-forming galaxies. ETGs show a large scatter compared to the Schmidt–Kennicutt relation found locally within our Galaxy, extending to lower SFRs and gas mass surface densities. Using an ETG's SFR and the Schmidt–Kennicutt law to predict its gas mass leads to an underestimate. ETGs have similar observed-gas-to-modelled-dust mass ratios to star-forming galaxies of the same stellar mass, as well as they exhibit a similar scatter.

Description: We report on the identification of the new Galactic Centre (GC) transient Swift J174540.7–290015 as a likely low-mass X-ray binary located at only 16 arcsec from Sgr A * . This transient was detected on 2016 February 6, during the Swift GC monitoring, and it showed long-term spectral variations compatible with a hard- to soft-state transition. We observed the field with XMM–Newton on February 26 for 35 ks, detecting the source in the soft state, characterized by a low level of variability and a soft X-ray thermal spectrum with a high energy tail (detected by INTEGRAL up to ~50 keV), typical of either accreting neutron stars or black holes. We observed: (i) a high column density of neutral absorbing material, suggesting that Swift J174540.7–290015 is located near or beyond the GC and; (ii) a sub-Solar iron abundance, therefore we argue that iron is depleted into dust grains. The lack of detection of Fe K absorption lines, eclipses or dipping suggests that the accretion disc is observed at a low inclination angle. Radio (Very Large Array) observations did not detect any radio counterpart to Swift J174540.7–290015. No evidence for X-ray or radio periodicity is found. The location of the transient was observed also in the near-infrared (near-IR) with gamma-ray burst optical near-IR detector at MPG/European Southern Observatory La Silla 2.2 m telescope and VLT/ NaCo pre- and post-outburst. Within the Chandra error region, we find multiple objects that display no significant variations.

Description: This is the first of two papers describing the observations and cataloguing of deep 3-GHz observations of the Lockman Hole North using the Karl G. Jansky Very Large Array. The aim of this paper is to investigate, through the use of simulated images, the uncertainties and accuracy of source-finding routines, as well as to quantify systematic effects due to resolution, such as source confusion and source size. While these effects are not new, this work is intended as a particular case study that can be scaled and translated to other surveys. We use the simulations to derive uncertainties in the fitted parameters, as well as bias corrections for the actual catalogue (presented in Paper II). We compare two different source-finding routines, OBIT and AEGEAN, and two different effective resolutions, 8 and 2.75  arcsec. We find that the two routines perform comparably well, with OBIT being slightly better at de-blending sources, but slightly worse at fitting resolved sources. We show that 30–70 per cent of sources are missed or fit inaccurately once the source size becomes larger than the beam, possibly explaining source count errors in high-resolution surveys. We also investigate the effect of blending, finding that any sources with separations smaller than the beam size are fit as single sources. We show that the use of machine-learning techniques can correctly identify blended sources up to 90 per cent of the time, and prior-driven fitting can lead to a 70 per cent improvement in the number of de-blended sources.

Description: We present evidence for a small glitch in the spin evolution of the millisecond pulsar J0613–0200, using the EPTA Data Release 1.0, combined with Jodrell Bank analogue filterbank times of arrival (TOAs) recorded with the Lovell telescope and Effelsberg Pulsar Observing System TOAs. A spin frequency step of 0.82(3) nHz and frequency derivative step of –1.6(39)  x  10 –19 Hz s –1 are measured at the epoch of MJD 50888(30). After PSR B1821–24A, this is only the second glitch ever observed in a millisecond pulsar, with a fractional size in frequency of / = 2.5(1)  x  10 –12 , which is several times smaller than the previous smallest glitch. PSR J0613–0200 is used in gravitational wave searches with pulsar timing arrays, and is to date only the second such pulsar to have experienced a glitch in a combined 886 pulsar-years of observations. We find that accurately modelling the glitch does not impact the timing precision for pulsar timing array applications. We estimate that for the current set of millisecond pulsars included in the International Pulsar Timing Array, there is a probability of ~50 per cent that another glitch will be observed in a timing array pulsar within 10 years.

Description: We exploit Atacama Large Interferometer Array (ALMA) 870 μm observations to measure the star formation rates (SFRs) of eight X-ray detected active galactic nuclei (AGNs) in a z 3.1 protocluster, four of which reside in extended Lyα haloes (often termed Lyman-alpha blobs: LABs). Three of the AGNs are detected by ALMA and have implied SFRs of 220–410 M  yr –1 ; the non-detection of the other five AGNs places SFR upper limits of 210 M  yr –1 . The mean SFR of the protocluster AGNs (110–210 M  yr –1 ) is consistent (within a factor of 0.7–2.3) with that found for co-eval AGNs in the field, implying that the galaxy growth is not significantly accelerated in these systems. However, when also considering ALMA data from the literature, we find evidence for elevated mean SFRs (up-to a factor of 5.9 over the field) for AGNs at the protocluster core, indicating that galaxy growth is significantly accelerated in the central regions of the protocluster. We also show that all of the four protocluster LABs are associated with an ALMA counterpart within the extent of their Lyα emission. The SFRs of the ALMA sources within the LABs (150–410 M  yr –1 ) are consistent with those expected for co-eval massive star-forming galaxies in the field. Furthermore, the two giant LABs (with physical extents of 100 kpc) do not host more luminous star formation than the smaller LABs, despite being an order of magnitude brighter in Lyα emission. We use these results to discuss star formation as the power source of LABs.

Description: We present the discovery of a new, peculiar form of double-periodic pulsation in RR Lyrae stars. In four, long-period ( P 〉 0.6 d) stars observed by the Optical Gravitational Lensing Experiment, and classified as fundamental mode pulsators (RRab), we detect additional, low-amplitude variability, with period shorter than fundamental mode period. The period ratios fall in a range similar to double-mode fundamental and first overtone RR Lyrae stars (RRd), with the exception of one star, in which the period ratio is significantly lower and nearly exactly equals 0.7. Although period ratios are fairly different for the four stars, the light-curve shapes corresponding to the dominant, fundamental mode are very similar. The peak-to-peak amplitudes and amplitude ratios (Fourier parameters R 21 and R 31 ) are among the highest observed in RRab stars of similar period, while Fourier phases ( 21 and 31 ) are among the lowest observed in RRab stars. If the additional variability is interpreted as due to radial first overtone, then, the four stars are the most extreme RRd variables of the longest pulsation periods known. Indeed, the observed period ratios can be well modelled with high-metallicity pulsation models. However, at such long pulsation periods, first overtone is typically damped. Five other candidates, with weak signature of additional variability, sharing the same characteristics, were also detected and are briefly discussed.

Description: The Laser Interferometer Gravitational-Wave Observatory (LIGO) detection of gravitational waves that take away 5 per cent of the total mass of two merging black holes points out on the importance of considering varying gravitational mass of a system in the framework of the Einstein general theory of relativity. We calculate the acceleration of a particle in the non-stationary field of a quasi-spherical system composed of a large number of objects emitting gravitational waves. It is shown that reduction of the gravitational mass of the system due to emitting gravitational waves leads to a repulsive gravitational force that diminishes with time but never disappears. This repulsive force may be related to the observed expansion of the Universe.

Description: Radiative feedback is an important consequence of cluster formation in giant molecular clouds (GMCs) in which newly formed clusters heat and ionize their surrounding gas. The process of cluster formation, and the role of radiative feedback, has not been fully explored in different GMC environments. We present a suite of simulations which explore how the initial gravitational boundedness, and radiative feedback, affect cluster formation. We model the early evolution (〈5 Myr) of turbulent, 10 6 M clouds with virial parameters ranging from 0.5 to 5. To model cluster formation, we use cluster sink particles, coupled to a raytracing scheme, and a custom subgrid model which populates a cluster via sampling an initial mass function (IMF) with an efficiency of 20 per cent per free-fall time. We find that radiative feedback only decreases the cluster particle formation efficiency by a few per cent. The initial virial parameter plays a much stronger role in limiting cluster formation, with a spread of cluster formation efficiencies of 37–71 per cent for the most unbound to the most bound model. The total number of clusters increases while the maximum mass cluster decreases with an increasing initial virial parameter, resulting in steeper mass distributions. The star formation rates in our cluster particles are initially consistent with observations but rise to higher values at late times. This suggests that radiative feedback alone is not responsible for dispersing a GMC over the first 5 Myr of cluster formation.

Description: Large redshift surveys capable of measuring the baryon acoustic oscillation (BAO) signal have proven to be an effective way of measuring the distance–redshift relation in cosmology. Building off the work in Zhu et al., we develop a technique to directly constrain the distance–redshift relation from BAO measurements without splitting the sample into redshift bins. We apply the redshift weighting technique in Zhu et al. to the clustering of galaxies from 1000 Quick particle mesh (QPM) mock simulations after reconstruction and achieve a 0.75 per cent measurement of the angular diameter distance D A at z = 0.64 and the same precision for Hubble parameter H at z = 0.29. These QPM mock catalogues mimic the clustering and noise level of the Baryon Oscillation Spectroscopic Survey Data Release 12 (DR12). We compress the correlation functions in the redshift direction on to a set of weighted correlation functions. These estimators give unbiased D A and H measurements across the entire redshift range of the combined sample. We demonstrate the effectiveness of redshift weighting in improving the distance and Hubble parameter estimates. Instead of measuring at a single ‘effective’ redshift as in traditional analyses, we report our D A and H measurements at all redshifts. The measured fractional error of D A ranges from 1.53 per cent at z = 0.2 to 0.75 per cent at z = 0.64. The fractional error of H ranges from 0.75 per cent at z = 0.29 to 2.45 per cent at z = 0.7. Our measurements are consistent with a Fisher forecast to within 10–20 per cent depending on the pivot redshift. We further show the results are robust against the choice of fiducial cosmologies, galaxy bias models, and redshift–space distortions streaming parameters.

Description: The dwarf spheroidal galaxies (dSphs) in the Milky Way are the primary targets in the indirect searches for particle dark matter. To set robust constraints on candidate dark matter particles, understanding the dark halo structure of these systems is of substantial importance. In this paper, we first evaluate the astrophysical factors for dark matter annihilation and decay for 24 dSphs, taking into account a non-spherical dark halo, using generalized axisymmetric mass models based on axisymmetric Jeans equations. First, from a fitting analysis of the most recent kinematic data available, our axisymmetric mass models are a much better fit than previous spherical ones, thus, our work should be the most realistic and reliable estimator for astrophysical factors. Secondly, we find that among analysed dSphs, the ultra-faint dwarf galaxies Triangulum II and Ursa Major II are the most promising but large uncertain targets for dark matter annihilation while the classical dSph Draco is the most robust and detectable target for dark matter decay. It is also found that the non-sphericity of luminous and dark components influences the estimate of astrophysical factors, even though these factors largely depend on the sample size, the prior range of parameters and the spatial extent of the dark halo. Moreover, owing to these effects, the constraints on the dark matter annihilation cross-section are more conservative than those of previous spherical works. These results are important for optimizing and designing dark matter searches in current and future multi-messenger observations by space and ground-based telescopes.

Description: Invertebrate animal species that can withstand temperatures as high as 37°C, the human body temperature, are limited. In the present study, we utilized the two-spotted cricket, Gryllus bimaculatus , which lives in tropical and subtropical regions, as an animal model of human pathogenic bacterial infection. Injection of Pseudomonas aeruginosa or Staphylococcus aureus into the hemolymph killed crickets. Injected P. aeruginosa or S. aureus proliferated in the hemolymph until the cricket died. The ability of these pathogenic bacteria to kill the crickets was blocked by the administration of antibiotics. S. aureus gene-knockout mutants of virulence factors, including cvfA, agr and srtA , exhibited decreased killing ability compared with the parent strain. The dose at which 50% of crickets were killed by P. aeruginosa or S. aureus was not decreased at 37°C compared with that at 27°C. Injection of Listeria monocytogenes , which upregulates toxin expression at 37°C, killed crickets, and the dose at which 50% of crickets were killed was decreased at 37°C compared with that at 27°C. These findings suggest that the two-spotted cricket is a useful model animal for evaluating the virulence properties of various human pathogenic bacteria at variable temperature including 37°C.

Description: We investigate how nightside cooling and surface friction affect surface temperatures and large-scale circulation for tidally locked Earth-like planets. For each scenario, we vary the orbital period between P rot = 1 and 100 d and capture changes in climate states. We find drastic changes in climate states for different surface friction scenarios. For very efficient surface friction ( t s,fric = 0.1 d), the simulations for short rotation periods ( P rot ≤ 10 d) show predominantly standing extratropical Rossby waves. These waves lead to climate states with two high-latitude westerly jets and unperturbed meridional direct circulation. In most other scenarios, simulations with short rotation periods exhibit instead dominance by standing tropical Rossby waves. Such climate states have a single equatorial westerly jet, which disrupts direct circulation. Experiments with weak surface friction ( t s,fric = 10–100 d) show decoupling between surface temperatures and circulation, which leads to strong cooling of the nightside. The experiment with t s,fric = 100 d assumes climate states with easterly flow (retrograde rotation) for medium and slow planetary rotations P rot = 12–100 d. We show that an increase of nightside cooling efficiency by one order of magnitude compared to the nominal model leads to a cooling of the nightside surface temperatures by 80–100 K. The dayside surface temperatures only drop by 25 K at the same time. The increase in thermal forcing suppresses the formation of extratropical Rossby waves on small planets ( R P = 1 R Earth ) in the short rotation period regime ( P rot ≤ 10 d).

Description: sUAS and their application in observing geomorphological processes Jozef Gallik and Lenka Bolešová Solid Earth, 7, 1033-1042, doi:10.5194/se-7-1033-2016, 2016 Technology is moving ahead very fast, and so researchers have new possibilities for their research. We tried to demonstrate benefits of using remote-sensing technology (Phantom 1 drone) such as its accuracy in the terrain, easy access to hardly accessible areas, and the possibility to collect data even during unfavourable weather conditions. The high mountainous environment provided us great conditions for testing the drone as a device for very easy and accurate mapping of natural phenomena.

Description: Response of seasonal soil freeze depth to climate change across China Xiaoqing Peng, Oliver W. Frauenfeld, Tingjun Zhang, Kang Wang, Bin Cao, Xinyue Zhong, Hang Su, and Cuicui Mu The Cryosphere Discuss., doi:10.5194/tc-2016-129,2016 Manuscript under review for TC (discussion: open, 0 comments) Previous researches paid more attention on the permafrost, e.g. active layer thickness, soil temperature, permafrost area extent, and associated with permafrost degradation leading other changes. However, seasonally frozen ground, vast area extent, did not focus by so much attention. Here, we combined more than 800 observation station data and gridded data to investigate soil freeze depth across China. The results indicate that soil freeze depth increase with climate warming.

Description: Slight glacier reduction over the northwestern Tibetan Plateau despite significant recent warming Yetang Wang, Shugui Hou, Wenling An, Hongxi Pang, and Yaping Liu The Cryosphere Discuss., doi:10.5194/tc-2016-165,2016 Manuscript under review for TC (discussion: open, 0 comments) This study further confirms "Pamir–Karakoram–Western-Kunlun-Mountain (northwestern Tibetan Plateau) Glacier Anomaly". Slight glacier reduction over the northwestern Tibetan Plateau may result from more accumulation from increased precipitation in winter which to great extent protects it from mass reductions under climate warming during 1961–2000. Warming slowdown since 2000 happening at this region may further mitigate glacier mass reduction.

Description: Response of seasonal soil freeze depth to climate change across China Xiaoqing Peng, Oliver W. Frauenfeld, Tingjun Zhang, Kang Wang, Bin Cao, Xinyue Zhong, Hang Su, and Cuicui Mu The Cryosphere Discuss., doi:10.5194/tc-2016-129,2016 Manuscript under review for TC (discussion: open, 0 comments) Previous researches paid more attention on the permafrost, e.g. active layer thickness, soil temperature, permafrost area extent, and associated with permafrost degradation leading other changes. However, seasonally frozen ground, vast area extent, did not focus by so much attention. Here, we combined more than 800 observation station data and gridded data to investigate soil freeze depth across China. The results indicate that soil freeze depth increase with climate warming.

Description: There are various ways of achieving an enlarged understanding of a concept of interest. One way is by giving its proper definition. Another is by giving something else a proper definition and then using it to model or formally represent the original concept. Between the two we find varying shades of grey. We might open up a concept by a direct lexical definition of the predicate that expresses it, or by a theory whose theorems define it implicitly. At the other end of the spectrum, the modelling-this-as-that option also admits of like variation, ranging from models rooted in formal representability theorems to models conceived of as having only heuristic value. There exist on both sides of this divide further differences still. In one of them, both the definiendum and definiens of a definition are words or phrases of some common natural language. In others, the item of interest is a natural language expression and its representation is furnished by the artificial linguistic system that models it. The modern history of these approaches is both very large and growing. Much of this evolution has given too short a shrift to the history of the demotion of ‘intuitive’ concepts in favour of the artificially contrived ones intended to model them. A working assumption of this article is that in the absence of a good understanding of what motivated the modelling-turn in the foundations of mathematics and the intuitive theory of truth, the whole notion of formal representability will have been inadequately understood. In the interests of space, I will concentrate on seminal issues in set theory as dealt with by Russell and Frege, and in the theory of truth in natural languages as dealt with by Tarski. The nub of the present focus is the representational role of model theory in the logics of formalized languages.

Description: An important distinction is that between selective abductions , which select an optimal candidate from given multitude of possible explanations, and creative abductions , which introduce new theoretical concepts and models. The article focuses on creative abductions, which are essential for scientific progress, although they are rarely discussed in the literature. Scientifically, fruitful creative abductions are demarcated from purely speculative abductions by means of three virtues which are possessed by the former but not by the latter: (i) providing unification , (ii) detecting common causes and (iii) generating novel predictions by means of which they can be independently tested . Based on historical examples it is demonstrated that common cause abduction from correlated dispositions is the fundamental abductive operation by which new theoretical concepts and models are scientifically generated. Statistical factor analysis can be regarded as a statistical generalization of common cause abduction.

Description: This article investigates the appropriateness of LP-based reasoning to machine ethics, an interdisciplinary field of inquiry that emerges from the need of imbuing autonomous agents with the capacity for moral decision making. The first contribution of the article is that of identifying morality viewpoints, as studied in moral philosophy and psychology, which are amenable to computational modelling, and then mapping them to appropriate LP-based reasoning features. The identified viewpoints are covered by two morality themes: moral permissibility and the dual-process model. In the second contribution, various LP-based reasoning features are applied to model these identified morality viewpoints, via classic moral examples taken offthe-shelf from the literature. For this purpose, our Q UALM system, which features a combination of LP abduction, updating and counterfactuals, supported by LP tabling mechanisms, are mainly employed. The applications are also supported by other existing LP-based systems, featuring preference handling and probabilistic reasoning, which complement Q UALM in addressing the morality viewpoints in question.

Description: Effect of tropical cyclones on the stratosphere–troposphere exchange observed using satellite observations over the north Indian Ocean M. Venkat Ratnam, S. Ravindra Babu, S. S. Das, G. Basha, B. V. Krishnamurthy, and B. Venkateswararao Atmos. Chem. Phys., 16, 8581-8591, doi:10.5194/acp-16-8581-2016, 2016 The impact of cyclones that occurred over the north Indian Ocean during 2007–2013 on the STE process is quantified using satellite observations. It is shown that cyclones have a significant impact on the tropopause structure, ozone and water vapour budget, and consequentially STE in the UTLS region. The cross-tropopause mass flux from the stratosphere to the troposphere for cyclonic storms is found to be 0.05 ± 0.29 × 10 −3  kg m −2 , and for very severe cyclonic storms it is 0.5 ± 1.07 × 10 −3  kg m −2 .

Description: Using detailed modelling, we analyse the spectra observed from the sample galaxies at z  ~ 0.8 presented by Ly et al., constraining the models by the [O iii ]5007+4959/[O iii ]4363 line ratios. Composite models (shock + photoionization) are adopted. Shock velocities ≥100 km s –1 and pre-shock densities n 0  ~ 200 cm –3 characterize the gas surrounding the starburst (SB), while n 0 are higher by a factor of 1.5–10 in the AGN emitting gas. SB effective temperatures are similar to those of quiescent galaxies ( T * ~ 4–7  x  10 4  K). Cloud geometrical thicknesses in the SB are ≤10 16  cm, indicating major fragmentation, while in AGN they reach 〉10 pc. O/H are about solar for all the objects, except for a few AGN clouds with O/H = 0.3–0.5 solar. SB models reproduce most of the data within the observational errors. About half of the objects’ spectra are well fitted by an accreting AGN. Some galaxies show multiple radiation sources, such as SB + AGN, or a double AGN.

Description: We present a method of comparing the Galactic systems realized by two astrometric catalogues. The systematic differences between positions and proper motions are represented by vector spherical harmonics. To extract the signal from the noise, we use a statistical criterion adapted to using healpix data pixelization to determine the significance of all the accessible harmonics. We also use a new analytical method that includes the magnitude equation in the vector spherical harmonics technique. The influence of the magnitude equation on the determination of the mutual orientation and rotation of the PPMXL and UCAC4 Galactic reference frames has been found in the range of J magnitudes from 10.25 to 15.75 mag. The angles of mutual orientation and the rates of mutual rotation of the Galactic frames under consideration depend on magnitude and can reach the level of 10 mas in orientation and 0.7 mas yr –1 for spin. We make a kinematic study of the low degree harmonics in the representation of the systematic differences between the Galactic proper motions. We have found that, averaged over the magnitude range, the biases of the Oort constants due to systematic differences of proper motions between the two catalogues, which are as large as 〈 A 〉 = 1.60 ± 0.41 and 〈 B 〉 = –1.91 ± 0.32 km s –1 kpc –1 , are greater than the standard errors of their evaluation in the systems of these catalogues. The theoretical equations used in this paper are based on real vector harmonics. We present a set of formulae to convert them into the complex function formalism.

Description: We present a way of searching for non-transiting exoplanets with dusty tails. In the transiting case, the extinction by dust during the transit removes more light from the beam than is scattered into it. Thus, the forward scattering component of the light is best seen either just prior to ingress, or just after egress, but with reduced amplitude over the larger peak that is obscured by the transit. This picture suggests that it should be equally productive to search for positive-going peaks in the flux from non-transiting exoplanets with dusty tails. We discuss what amplitudes are expected for different orbital inclination angles. The signature of such objects should be distinct from normal transits, starspots, and most – but not all – types of stellar pulsations.

Description: We present results from three-dimensional, numerical relativity simulations of a tilted black hole-thick accretion disc system. The simulations are analysed using tracer particles in the disc which are advected with the flow. Such tracers, which we employ in these new simulations for the first time, provide a powerful means to analyse in detail the complex dynamics of tilted black hole–torus systems. We show how its use helps to gain insight into the overall dynamics of the system, discussing the origin of the observed black hole precession and the development of a global non-axisymmetric m = 1 mode in the disc. Our three-dimensional simulations show the presence of quasi-periodic oscillations (QPOs) in the instantaneous accretion rate, with frequencies in a range compatible with those observed in low-mass X-ray binaries with either a black hole or a neutron star component. The frequency ratio of the dominant low-frequency peak and the first overtone is o 1 / f ~ 1.9, a frequency ratio not attainable when modelling the QPOs as p -mode oscillations in axisymmetric tori.

Description: We present a multiwavelength investigation of the young stellar population and star formation activities around the H ii region Sharpless 311. Using our deep near-infrared observations and archival Spitzer -IRAC observations, we have detected a total of 125 young stellar objects (YSOs) in an area of ~86 arcmin 2 . The YSO sample includes eight Class I and 117 Class II candidate YSOs. The mass completeness of the identified YSO sample is estimated to be 1.0 M . The ages and masses of the majority of the candidate YSOs are estimated to be in the range ~0.1–5 Myr and ~0.3–6 M , respectively. The 8-μm image of S311 displays an approximately spherical cavity around the ionizing source, which was possibly created by the expansion of the H ii region. The spatial distribution of the candidate YSOs reveals that a significant number of them are distributed systematically along the 8-μm emission with a majority clustered around the eastern border of the H ii region. Four clumps/compact H ii regions are detected in the radio continuum observations at 1280 MHz, which may have been formed during the expansion of the H ii region. The estimated dynamical age of the region, main-sequence lifetime of the ionizing source, the spatial distribution and ages of the candidate YSOs indicate triggered star formation in the complex.

Description: Variation of CCN activity during new particle formation events in the North China Plain Nan Ma, Chunsheng Zhao, Jiangchuan Tao, Zhijun Wu, Simonas Kecorius, Zhibin Wang, Johannes Größ, Hongjian Liu, Yuxuan Bian, Ye Kuang, Monique Teich, Gerald Spindler, Konrad Müller, Dominik van Pinxteren, Hartmut Herrmann, Min Hu, and Alfred Wiedensohler Atmos. Chem. Phys., 16, 8593-8607, doi:10.5194/acp-16-8593-2016, 2016 New particle formation (NPF) is one of main sources of cloud condensation nuclei (CCN) in the atmosphere. Based on in situ measurements, we found that CCN activity of newly formed particles largely differs in different NPF events. It is therefore difficult to find a simple parameterization of CCN activity for NPF events. Using a fixed size-resolved activation ratio curve or critical diameter is very likely to result in large biases up to 50 % in the calculated N CCN during NPF events.

Description: Real time retrieval of volcanic cloud particles and SO 2 by satellite using an improved simplified approach Sergio Pugnaghi, Lorenzo Guerrieri, Stefano Corradini, and Luca Merucci Atmos. Meas. Tech., 9, 3053-3062, doi:10.5194/amt-9-3053-2016, 2016 Volcanic plume removal (VPR) is a procedure developed to retrieve the ash optical depth, effective radius and mass, and sulfur dioxide mass contained in a volcanic cloud from the thermal radiance at 8.7, 11, and 12 µm. It is based on an estimation of a virtual image representing what the sensor would have seen in a multispectral thermal image if the volcanic cloud were not present. Ash and sulfur dioxide were retrieved by the first version of the VPR using a very simple atmospheric model that ignored the layer above the volcanic cloud. This new version takes into account the layer of atmosphere above the cloud as well as thermal radiance scattering along the line of sight of the sensor. In addition to improved results, the new version also offers an easier and faster preliminary preparation and includes other types of volcanic particles (andesite, obsidian, pumice, ice crystals, and water droplets). As in the previous version, a set of parameters regarding the volcanic area, particle types, and sensor is required to run the procedure. However, in the new version, only the mean plume temperature is required as input data. In this work, a set of parameters to compute the volcanic cloud transmittance in the three quoted bands, for all the aforementioned particles, for both Mt. Etna (Italy) and Eyjafjallajökull (Iceland) volcanoes, and for the Terra and Aqua MODIS instruments is presented. Three types of tests are carried out to verify the results of the improved VPR. The first uses all the radiative transfer simulations performed to estimate the above mentioned parameters. The second one makes use of two synthetic images, one for Mt. Etna and one for Eyjafjallajökull volcanoes. The third one compares VPR and Look-Up Table (LUT) retrievals analyzing the true image of Eyjafjallajökull volcano acquired by MODIS aboard the Aqua satellite on 11 May 2010 at 14:05 GMT.

Description: Temperature-dependence of aerosol optical depth over the southeastern US Tero Mielonen, Anca Hienola, Thomas Kühn, Joonas Merikanto, Antti Lipponen, Tommi Bergman, Hannele Korhonen, Pekka Kolmonen, Larisa Sogacheva, Darren Ghent, Antti Arola, Gerrit de Leeuw, and Harri Kokkola Atmos. Chem. Phys. Discuss., doi:10.5194/acp-2016-625,2016 Manuscript under review for ACP (discussion: open, 0 comments) We studied the temperature dependence of AOD and its radiative effects over the southeastern US. We used spaceborne observations of AOD, LST and tropospheric NO 2 with simulations of ECHAM-HAMMOZ. The level of AOD in this region is governed by anthropogenic emissions but the temperature dependency is most likely caused by BVOC emissions. According to the observations and simulations, the regional clear-sky DRE for biogenic aerosols is −0.43 ± 0.88 W/m 2 /K and −0.86 ± 0.06 W/m 2 /K, respectively.

Description: Stratospheric Air Sub-sampler (SAS) and its application to analysis of Δ 17 O(CO 2 ) from small air samples collected with an AirCore Dorota Janina Mrozek, Carina van der Veen, Magdalena E. G. Hofmann, Huilin Chen, Rigel Kivi, Pauli Heikkinen, and Thomas Röckmann Atmos. Meas. Tech. Discuss., doi:10.5194/amt-2016-124,2016 Manuscript under review for AMT (discussion: open, 0 comments) Stratospheric Air Sub-sampler (SAS) is a device to collect and to store the stratospheric profile of air collected with an AirCore (Karion et al, 2010) in numerous sub-samples. The sub-samples (each of 25 mL at ambient temperature and pressure) can be later introduced to the continuous flow systems to measure for example the isotopic composition of CO 2 . The performance of the coupled system is demonstrated for a set of air samples from an AirCore flight in November 2014 near Sodankylä, Finland.

Description: Real time retrieval of volcanic cloud particles and SO 2 by satellite using an improved simplified approach Sergio Pugnaghi, Lorenzo Guerrieri, Stefano Corradini, and Luca Merucci Atmos. Meas. Tech., 9, 3053-3062, doi:10.5194/amt-9-3053-2016, 2016 Volcanic plume removal (VPR) is a procedure developed to retrieve the ash optical depth, effective radius and mass, and sulfur dioxide mass contained in a volcanic cloud from the thermal radiance at 8.7, 11, and 12 µm. It is based on an estimation of a virtual image representing what the sensor would have seen in a multispectral thermal image if the volcanic cloud were not present. Ash and sulfur dioxide were retrieved by the first version of the VPR using a very simple atmospheric model that ignored the layer above the volcanic cloud. This new version takes into account the layer of atmosphere above the cloud as well as thermal radiance scattering along the line of sight of the sensor. In addition to improved results, the new version also offers an easier and faster preliminary preparation and includes other types of volcanic particles (andesite, obsidian, pumice, ice crystals, and water droplets). As in the previous version, a set of parameters regarding the volcanic area, particle types, and sensor is required to run the procedure. However, in the new version, only the mean plume temperature is required as input data. In this work, a set of parameters to compute the volcanic cloud transmittance in the three quoted bands, for all the aforementioned particles, for both Mt. Etna (Italy) and Eyjafjallajökull (Iceland) volcanoes, and for the Terra and Aqua MODIS instruments is presented. Three types of tests are carried out to verify the results of the improved VPR. The first uses all the radiative transfer simulations performed to estimate the above mentioned parameters. The second one makes use of two synthetic images, one for Mt. Etna and one for Eyjafjallajökull volcanoes. The third one compares VPR and Look-Up Table (LUT) retrievals analyzing the true image of Eyjafjallajökull volcano acquired by MODIS aboard the Aqua satellite on 11 May 2010 at 14:05 GMT.

Description: Evaluation of IWV from the numerical weather prediction WRF model with PPP GNSS processing for Bulgaria Tzvetan Simeonov, Dmitry Sidorov, Felix Norman Teferle, Georgi Milev, and Guergana Guerova Atmos. Meas. Tech. Discuss., doi:10.5194/amt-2016-152,2016 Manuscript under review for AMT (discussion: open, 0 comments) Global Navigation Satellite Systems (GNSS) meteorology is an established operational service providing hourly updated GNSS tropospheric products to the National Meteorologic Services (NMS) in Europe. In the last decade through the ground-based GNSS network densification and new processing strategies like Precise Point Positioning (PPP) it has become possible to obtain sub-hourly tropospheric products for monitoring severe weather events. In this work one year (January–December 2013) of sub-hourly GNSS tropospheric products (Zenith Total Delay) are computed using the PPP strategy for seven stations in Bulgaria. In order to take advantage of the sub-hourly GNSS data to derive Integrated Water Vapour (IWV) surface pressure and temperature with similar temporal resolution is required. As the surface observations are on 3 hourly basis the first step is to compare the surface pressure and temperature from numerical weather prediction model Weather Forecasting and Research (WRF) with observations at three synoptic stations in Bulgaria. The mean difference between the two data-sets for 1) surface pressure is less than 0.5 hPa and the correlation is over 0.989, 2) temperature the largest mean difference is 1.1 °C and the correlation coefficient is over 0.957 and 3) IWV mean difference is in range 0.1–1.1 mm. The evaluation of WRF on annual bases shows IWV underestimation between 0.5 and 1.5 mm at five stations and overestimation at Varna and Rozhen. Varna and Rozhen have also much smaller correlation 0.9 and 0.76. The study of the monthly IWV variation shows that at those locations the GNSS IWV has unexpected drop in April and March respectively. The reason for this drop is likely problems with station raw data. At the remaining 5 stations a very good agreement between GNSS and WRF is observed with high correlation during the cold part of 2013 i.e. March, October and December (0.95) and low correlation during the warm part of 2013 i.e. April to August (below 0.9). The diurnal cycle of the WRF model shows a dry bias in the range of 0.5-1.5 mm. Between 00 and 01 UTC the GNSS IWV tends to be underestimate IWV which is likely due to the processing window used. The precipitation efficiency from GNSS and WRF show very good agreement on monthly bases with a maximum in May-June and minimum in August–September. The annual precipitation efficiency in 2013 at Lovech and Burgas is about 6 %.

Description: Contrasting radiation and soil heat fluxes in Arctic shrub and wet sedge tundra Inge Juszak, Werner Eugster, Monique M. P. D. Heijmans, and Gabriela Schaepman-Strub Biogeosciences, 13, 4049-4064, doi:10.1594/PANGAEA.860561, 2016 Changes in Arctic vegetation composition and structure feed back to climate and permafrost. Using field observations at a Siberian tundra site, we find that dwarf shrubs absorb more solar radiation than wet sedges and thus amplify surface warming, especially during snow melt. On the other hand, permafrost thaw was enhanced below sedges as a consequence of high soil moisture. Standing dead sedge leaves affected the radiation budget strongly and deserve more scientific attention.

Description: The detailed, atomistic-level understanding of molecular signaling along the tumor-suppressive Hippo signaling pathway that controls tissue homeostasis by balancing cell proliferation and death through apoptosis is a promising avenue for the discovery of novel anticancer drug targets. The activation of kinases such as Mammalian STE20-Like Protein Kinases 1 and 2 (MST1 and MST2)—modulated through both homo- and heterodimerization (e.g. interactions with Ras association domain family, RASSF, enzymes)—is a key upstream event in this pathway and remains poorly understood. On the other hand, RASSFs (such as RASSF1A or RASSF5) act as important apoptosis activators and tumor suppressors, although their exact regulatory roles are also unclear. We present recent molecular studies of signaling along the Ras-RASSF-MST pathway, which controls growth and apoptosis in eukaryotic cells, including a variety of modern molecular modeling and simulation techniques. Using recently available structural information, we discuss the complex regulatory scenario according to which RASSFs perform dual signaling functions, either preventing or promoting MST2 activation, and thus control cell apoptosis. Here, we focus on recent studies highlighting the special role being played by the specific interactions between the helical Salvador/RASSF/Hippo (SARAH) domains of MST2 and RASSF1a or RASSF5 enzymes. These studies are crucial for integrating atomistic-level mechanistic information about the structures and conformational dynamics of interacting proteins, with information available on their system-level functions in cellular signaling.

Description: Big-data-based edge biomarker is a new concept to characterize disease features based on biomedical big data in a dynamical and network manner, which also provides alternative strategies to indicate disease status in single samples. This article gives a comprehensive review on big-data-based edge biomarkers for complex diseases in an individual patient, which are defined as biomarkers based on network information and high-dimensional data. Specifically, we firstly introduce the sources and structures of biomedical big data accessible in public for edge biomarker and disease study. We show that biomedical big data are typically ‘small-sample size in high-dimension space', i.e. small samples but with high dimensions on features (e.g. omics data) for each individual, in contrast to traditional big data in many other fields characterized as ‘large-sample size in low-dimension space', i.e. big samples but with low dimensions on features. Then, we demonstrate the concept, model and algorithm for edge biomarkers and further big-data-based edge biomarkers. Dissimilar to conventional biomarkers, edge biomarkers, e.g. module biomarkers in module network rewiring-analysis, are able to predict the disease state by learning differential associations between molecules rather than differential expressions of molecules during disease progression or treatment in individual patients. In particular, in contrast to using the information of the common molecules or edges (i.e.molecule-pairs) across a population in traditional biomarkers including network and edge biomarkers, big-data-based edge biomarkers are specific for each individual and thus can accurately evaluate the disease state by considering the individual heterogeneity. Therefore, the measurement of big data in a high-dimensional space is required not only in the learning process but also in the diagnosing or predicting process of the tested individual. Finally, we provide a case study on analyzing the temporal expression data from a malaria vaccine trial by big-data-based edge biomarkers from module network rewiring-analysis. The illustrative results show that the identified module biomarkers can accurately distinguish vaccines with or without protection and outperformed previous reported gene signatures in terms of effectiveness and efficiency.

Description: Molecular interrogation of a biological sample through DNA sequencing, RNA and microRNA profiling, proteomics and other assays, has the potential to provide a systems level approach to predicting treatment response and disease progression, and to developing precision therapies. Large publicly funded projects have generated extensive and freely available multi-assay data resources; however, bioinformatic and statistical methods for the analysis of such experiments are still nascent. We review multi-assay genomic data resources in the areas of clinical oncology, pharmacogenomics and other perturbation experiments, population genomics and regulatory genomics and other areas, and tools for data acquisition. Finally, we review bioinformatic tools that are explicitly geared toward integrative genomic data visualization and analysis. This review provides starting points for accessing publicly available data and tools to support development of needed integrative methods.

Description: One of the major challenges in biology concerns the integration of data across length and time scales into a consistent framework: how do macroscopic properties and functionalities arise from the molecular regulatory networks—and how can they change as a result of mutations? Morphogenesis provides an excellent model system to study how simple molecular networks robustly control complex processes on the macroscopic scale despite molecular noise, and how important functional variants can emerge from small genetic changes. Recent advancements in three-dimensional imaging technologies, computer algorithms and computer power now allow us to develop and analyse increasingly realistic models of biological control. Here, we present our pipeline for image-based modelling that includes the segmentation of images, the determination of displacement fields and the solution of systems of partial differential equations on the growing, embryonic domains. The development of suitable mathematical models, the data-based inference of parameter sets and the evaluation of competing models are still challenging, and current approaches are discussed.

Description: Owing greatly to the advancement of next-generation sequencing (NGS), the amount of NGS data is increasing rapidly. Although there are many NGS applications, one of the most commonly used techniques ‘RNA sequencing (RNA-seq)’ is rapidly replacing microarray-based techniques in laboratories around the world. As more and more of such techniques are standardized, allowing technicians to perform these experiments with minimal hands-on time and reduced experimental/operator-dependent biases, the bottleneck of such techniques is clearly visible; that is, data analysis. Further complicating the matter, increasing evidence suggests most of the genome is transcribed into RNA; however, the majority of these RNAs are not translated into proteins. These RNAs that do not become proteins are called ‘noncoding RNAs (ncRNAs)’. Although some time has passed since the discovery of ncRNAs, their annotations remain poor, making analysis of RNA-seq data challenging. Here, we examine the current limitations of RNA-seq analysis using case studies focused on the detection of novel transcripts and examination of their characteristics. Finally, we validate the presence of novel transcripts using biological experiments, showing novel transcripts can be accurately identified when a series of filters is applied. In conclusion, novel transcripts that are identified from RNA-seq must be examined carefully before proceeding to biological experiments.

Description: Functional genomics has enormous potential to facilitate our understanding of normal and disease-specific physiology. In the past decade, intensive research efforts have been focused on modeling functional relationship networks, which summarize the probability of gene co-functionality relationships. Such modeling can be based on either expression data only or heterogeneous data integration. Numerous methods have been deployed to infer the functional relationship networks, while most of them target the global (non-context-specific) functional relationship networks. However, it is expected that functional relationships consistently reprogram under different tissues or biological processes. Thus, advanced methods have been developed targeting tissue-specific or developmental stage-specific networks. This article brings together the state-of-the-art functional relationship network modeling methods, emphasizes the need for heterogeneous genomic data integration and context-specific network modeling and outlines future directions for functional relationship networks.

Description: Identification of drug–target interactions is an important process in drug discovery. Although high-throughput screening and other biological assays are becoming available, experimental methods for drug–target interaction identification remain to be extremely costly, time-consuming and challenging even nowadays. Therefore, various computational models have been developed to predict potential drug–target associations on a large scale. In this review, databases and web servers involved in drug–target identification and drug discovery are summarized. In addition, we mainly introduced some state-of-the-art computational models for drug–target interactions prediction, including network-based method, machine learning-based method and so on. Specially, for the machine learning-based method, much attention was paid to supervised and semi-supervised models, which have essential difference in the adoption of negative samples. Although significant improvements for drug–target interaction prediction have been obtained by many effective computational models, both network-based and machine learning-based methods have their disadvantages, respectively. Furthermore, we discuss the future directions of the network-based drug discovery and network approach for personalized drug discovery based on personalized medicine, genome sequencing, tumor clone-based network and cancer hallmark-based network. Finally, we discussed the new evaluation validation framework and the formulation of drug–target interactions prediction problem by more realistic regression formulation based on quantitative bioactivity data.

Description: Atherosclerosis is one of the principle pathologies of cardiovascular disease with blood cholesterol a significant risk factor. The World Health Organization estimates that approximately 2.5 million deaths occur annually because of the risk from elevated cholesterol, with 39% of adults worldwide at future risk. Atherosclerosis emerges from the combination of many dynamical factors, including haemodynamics, endothelial damage, innate immunity and sterol biochemistry. Despite its significance to public health, the dynamics that drive atherosclerosis remain poorly understood. As a disease that depends on multiple factors operating on different length scales, the natural framework to apply to atherosclerosis is mathematical and computational modelling. A computational model provides an integrated description of the disease and serves as an in silico experimental system from which we can learn about the disease and develop therapeutic hypotheses. Although the work completed in this area to date has been limited, there are clear signs that interest is growing and that a nascent field is establishing itself. This article discusses the current state of modelling in this area, bringing together many recent results for the first time. We review the work that has been done, discuss its scope and highlight the gaps in our understanding that could yield future opportunities.

Description: We present Bioinformatics Autodiscovery of Training Materials (BATMat), an open-source, Google-based, targeted, automatic search tool for training materials related to bioinformatics. BATMat helps gain access with one click to filtered and portable information containing links to existing materials (when present). It also offers functionality to sort results according to source site or title. Availability: http://imbatmat.com Contact: piar301@gmail.com

Description: Holocene hydrological changes in the Rhône River (NW Mediterranean) as recorded in the marine mud belt Maria-Angela Bassetti, Serge Berné, Marie-Alexandrine Sicre, Bernard Dennielou, Yoann Alonso, Roselyne Buscail, Bassem Jalali, Bertil Hebert, and Christophe Menniti Clim. Past, 12, 1539-1553, doi:10.5194/cp-12-1539-2016, 2016 This work represents the first attempt to decipher the linkages between rapid climate changes and continental Holocene paleohydrology in the NW Mediterranean shallow marine setting. Between 11 and 4 ka cal BP, terrigenous input increased and reached a maximum at 7 ka cal BP, probably as a result of a humid phase. From ca. 4 ka cal BP to the present, enhanced variability in the land-derived material is possibly due to large-scale atmospheric circulation and rainfall patterns in western Europe.

Description: Occurrence of entomopathogenic fungi on phylloplanes in Tilia x europaea crowns between 1 and 13 m was assessed in urban parks. Prevalence of fungal infections in ladybirds (Coleoptera: Coccinellidae) collected from Tilia x europaea was assessed to determine whether fungi found on phylloplanes also occurred as infections in ladybirds. Isaria spp. was most abundant on phylloplanes (mean colony forming units (CFU) per leaf ± SE, 0.33 ± 0.03) followed by Beauveria spp. (0.22 ± 0.02 CFU per leaf) and Lecanicillium spp. (0.19 ± 0.02 CFU per leaf). Densities of inoculum were higher in inner crowns and decreased with height, although Lecanicillium spp. peaked at 5–7 m. Upper phylloplane surfaces harboured higher densities of Isaria spp. and Beauveria spp. than lower surfaces, whereas Lecanicillium spp. was equally distributed. Most prevalent on ladybirds were Isaria spp. (20.6% Harmonia axyridis ; 4.8% natives), Lecanicillium spp. (13.6% H. axyridis ; 4.8% natives), with fewer Beauveria spp. infections (2.6% H. axyridis ). Molecular identification revealed Beauveria bassiana , B. pseudobassiana , Isaria farinosa and Lecanicillium muscarium among isolates of both tree and ladybird origin. Tilia x europaea phylloplanes support a diverse assemblage of entomopathogenic fungal species with a different prevalence in coccinellids compared to their relative abundance in this habitat.

Description: Sulfate-reducing prokaryotes (SRPs) and antibiotic resistance genes (ARGs) in sediments could be biomarkers for evaluating the environmental impacts of human activities, although factors governing their distribution are not clear yet. By using metagenomic approach, this study investigated the distributions of SRPs and ARGs in marine sediments collected from 12 different coastal locations of Hong Kong, which exhibited different pollution levels and were classified into two groups based on sediment parameters. Our results showed that relative abundances of major SRP genera to total prokaryotes were consistently lower in the more seriously polluted sediments ( P -value 〈 0.05 in 13 of 20 genera), indicating that the relative abundance of SRPs is a negatively correlated biomarker for evaluating human impacts. Moreover, a unimodel distribution pattern for SRPs along with the pollution gradient was observed. Although total ARGs were enriched in sediments from the polluted sites, distribution of single major ARG types could be explained neither by individual sediment parameters nor by corresponding concentration of antibiotics. It supports the hypothesis that the persistence of ARGs in sediments may not need the selection of antibiotics. In summary, our study provided important hints of the niche differentiation of SRPs and behavior of ARGs in marine coastal sediment.

Description: The aftershock distribution of the 1933 Sanriku-oki outer trench earthquake is estimated by using modern relocation methods and a newly developed velocity structure to examine the spatial extent of the source-fault and the possibility of a triggered interplate seismicity. In this study, we first examined the regional data quality of the 1933 earthquake based on smoked-paper records and then relocated the earthquakes by using the 3-D velocity structure and double-difference method. The improvements of hypocentre locations using these methods were confirmed by the examination of recent earthquakes that are accurately located based on ocean bottom seismometer data. The results show that the 1933 aftershocks occurred under both the outer- and inner-trench-slope regions. In the outer-trench-slope region, aftershocks are distributed in a ~280-km-long area and their depths are shallower than 50 km. Although we could not constrain the fault geometry from the hypocentre distribution, the depth distribution suggests the whole lithosphere is probably not under deviatoric tension at the time of the 1933 earthquake. The occurrence of aftershocks under the inner trench slope was also confirmed by an investigation of waveform frequency difference between outer and inner trench earthquakes as recorded at Mizusawa. The earthquakes under the inner trench slope were shallow (depth less double equals30 km) and the waveforms show a low-frequency character similar to the waveforms of recent, precisely located earthquakes in the same area. They are also located where recent activity of interplate thrust earthquakes is high. These suggest that the 1933 outer-trench-slope main shock triggered interplate earthquakes, which is an unusual case in the order of occurrence in contrast with the more common pairing of a large initial interplate shock with subsequent outer-slope earthquakes. The off-trench earthquakes are distributed about 80 km width in the trench perpendicular direction. This wide width cannot be explained from a single high-angle fault confined at a shallow depth (depth less double equals50 km). The upward motion of the 1933 tsunami waveform records observed at Sanriku coast also cannot be explained from a single high-angle west-dipping normal fault. If we consider additional fault, involvement of high-angle, east-dipping normal faults can better explain the tsunami first motion and triggering of the aftershock in a wide area under the outer trench slope. Therefore multiple off-trench normal faults may have activated during the 1933 earthquake. We also relocated recent (2001–2012) seismicity by the same method. The results show that the present seismicity in the outer-trench-slope region can be divided into several groups along the trench. Comparison of the 1933 rupture dimensions based on our aftershock relocations with the morphologies of fault scarps in the outer trench slope suggest that the rupture was limited to the region where fault scarps are largely trench parallel and cross cut the seafloor spreading fabric. These findings imply that bending geometry and structural segmentation of the incoming plate largely controls the spatial extent of the 1933 seismogenic faulting. In this shallow rupture model for this largest outer trench earthquake, triggered seismicity in the forearc and structural control of faulting represent an important deformation styles for off-trench and shallow megathrust zones.

Description: Effects of Multiple Doppler Radar data assimilation on the numerical simulation of a Flash Flood Event during the HyMeX campaign Ida Maiello, Sabrina Gentile, Rossella Ferretti, Luca Baldini, Nicoletta Roberto, Errico Picciotti, Pier Paolo Alberoni, and Frank S. Marzano Hydrol. Earth Syst. Sci. Discuss., doi:10.5194/hess-2016-320,2016 Manuscript under review for HESS (discussion: open, 0 comments) An analysis to evaluate the impact of assimilating multiple radar data with a three dimensional variational (3D-Var) system on a heavy precipitation event is presented. The main goal is to establish a general methodology to quantitatively assess the performance of flash-flood numerical weather prediction at mesoscale. In this respect, during the first Special Observation Period (SOP1) of HyMeX (Hydrological cycle in the Mediterranean Experiment) campaign several Intensive Observing Periods (IOPs) were launched and nine occurred in Italy. Among them IOP4 is chosen for this study because of its low predictability. This event hit central Italy on 14 September 2012 producing heavy precipitation and causing several damages. Data taken from three C-band radars running operationally during the event are assimilated to improve high resolution initial conditions. In order to evaluate the impact of the assimilation procedure at different horizontal resolution and to assess the impact of assimilating multiple radars data, several experiments using Weather Research and Forecasting (WRF) model are performed. Finally, the statistical indexes as accuracy, equitable threat score, false alarm ratio and frequency bias are used to objectively compare the experiments, using rain gauges data as benchmark.

Description: Model-based study of the role of rainfall and land use–land cover in the changes in the occurrence and intensity of Niger red floods in Niamey between 1953 and 2012 Claire Casse, Marielle Gosset, Théo Vischel, Guillaume Quantin, and Bachir Alkali Tanimoun Hydrol. Earth Syst. Sci., 20, 2841-2859, doi:10.5194/hess-20-2841-2016, 2016 Since 1950, the Niger River basin has overcome drastic changes. In Niamey city, the highest river levels and the longest flooded period ever recorded occurred in 2003, 2010, 2012 and 2013, with heavy casualties and property damage. The reasons for these changes, and the relative role of climate versus Land Use Land Cover changes are still debated and are investigated in this paper using observations and modelling. We conclude on the successive role of cover and then rainfall variability.

Description: Upscaling instantaneous to daily evapotranspiration using modelled daily shortwave radiation for remote sensing applications: an Artificial Neural Network approach Loise Wandera, Kaninska Mallick, Gerard Kiely, Olivier Roupsard, Matthias Peichl, and Vicenzo Magliulo Hydrol. Earth Syst. Sci. Discuss., doi:10.5194/hess-2016-344,2016 Manuscript under review for HESS (discussion: open, 0 comments) Upscaling instantaneous to daily evapotranspiration (ET i to ET d ) is one of the central challenge in regional vegetation water use mapping using polar orbiting satellites. Here we developed a robust ET i upscaling for global studies using the ratio between daily and instantaneous global radiation (R Sd /R Si ). Using data from 126 FLUXNET tower sites this study demonstrated R Sd /R si ratio to be the most robust factor explaining ET d /ET i variability across variable sky conditions and multiple biomes.

Description: 4-D imaging of sub-second dynamics in pore-scale processes using real-time synchrotron X-ray tomography Katherine J. Dobson, Sophia B. Coban, Samuel A. McDonald, Joanna N. Walsh, Robert C. Atwood, and Philip J. Withers Solid Earth, 7, 1059-1073, doi:10.5194/se-7-1059-2016, 2016 State-of-the-art synchrotron x-ray imaging was used to observe micron scale transport processes in real time. The 20 Hz 3-D image acquisition rates give experimental data free from motion artefacts, and suitable for detailed quantitative analysis of the dynamic fluid distribution, flow pathways and processes. The method marks a major breakthrough in our ability to capture both sub-second and lower frequency non-equilibrium process in many geological or engineering systems.

Description: Alpine tectonic wedging and crustal delamination in the Cantabrian Mountains (NW Spain) Jorge Gallastegui, Javier A. Pulgar, and Josep Gallart Solid Earth, 7, 1043-1057, doi:10.5194/se-7-1043-2016, 2016 We present the interpretation of deep seismic reflection profile ESCIN-2 across the boundary between the Cantabrian Mountains and the Cenozoic Duero Basin (NW Spain). 2-D seismic modelling allowed us to construct a N-S geological cross section which is compatible with the rest of the geophysical data. This profile shows the importance of the N-S Alpine deformation. A wedge of Cantabrian margin crust indented southwards into the delaminated Iberian crust, forcing its northward subduction.

Description: NGC 6946, known as the Fireworks galaxy because of its high supernova rate and high star formation, is embedded in a very extended H i halo. Its northern spiral arm is well detached from the galactic main body. We found that this arm contains a large (~300 pc in size) Red Ellipse, named according to a strong contamination of the Hα emission line on its optical images. The ellipse is accompanied by a short parallel arc and a few others still smaller and less regular; a bright star cluster is seen inside these features. The complicated combination of arcs seems to be unique; it is only a bit similar to some SNRs. However, the long-slit spectral data obtained with the Russian 6-m telescope did not confirm the origin of the nebula as a result of a single SN outburst. The emission-line spectrum corresponds to the photoionization by young hot stars with a small contribution of shock ionization. The most likely explanation of the Red Ellipse is a superbubble created by a collective feedback of massive stars in the star cluster located in the NE side of the Red Ellipse. However, the very regular elliptical shape of the nebulae seems strange.

Description: Gravity is believed to be important on multiple physical scales in molecular clouds. However, quantitative constraints on gravity are still lacking. We derive an analytical formula which provides estimates on multiscale gravitational energy distribution using the observed surface density probability distribution function (PDF). Our analytical formalism also enables one to convert the observed column density PDF into an estimated volume density PDF, and to obtain average radial density profile ( r ). For a region with $N_{\rm col} \sim N^{-\gamma _{\rm N}}$ , the gravitational energy spectra is $E_{\rm p}(k)\sim k^{-4(1 - 1/\gamma _{\rm N})}$ . We apply the formula to observations of molecular clouds, and find that a scaling index of –2 of the surface density PDF implies that ~ r –2 and E p ( k ) ~ k –2 . The results are valid from the cloud scale (a few parsec) to around ~ 0.1 pc. Because of the resemblance the scaling index of the gravitational energy spectrum and the that of the kinetic energy power spectrum of the Burgers turbulence (where E ~ k –2 ), our result indicates that gravity can act effectively against turbulence over a multitude of physical scales. This is the critical scaling index which divides molecular clouds into two categories: clouds like Orion and Ophiuchus have shallower power laws, and the amount of gravitational energy is too large for turbulence to be effective inside the cloud. Because gravity dominates, we call this type of cloud g-type clouds. On the other hand, clouds like the California molecular cloud and the Pipe nebula have steeper power laws, and turbulence can overcome gravity if it can cascade effectively from the large scale. We call this type of cloud t-type clouds. The analytical formula can be used to determine if gravity is dominating cloud evolution when the column density PDF can be reliably determined.

Description: Studying local earthquakes in the area Baltic-Bothnia Megashear using the data of the POLENET/LAPNET temporary array Olga Usoltseva and Elena Kozlovskaya Solid Earth, 7, 1095-1108, doi:10.5194/se-7-1095-2016, 2016 We address the problem of seismicity in the intraplate area of northern Fennoscandia using the information on local events recorded by the POLENET/LAPNET seismic array. We relocate the seismic events, calculate a 3-D tomographic P wave velocity model of the uppermost crust and investigate a focal mechanism of the event. Our results demonstrate that the Baltic-Bothnia Megashear is an important large-scale, reactivated tectonic structure that has to be taken into account when estimating seismic hazard.

Description: Studying local earthquakes in the area Baltic-Bothnia Megashear using the data of the POLENET/LAPNET temporary array Olga Usoltseva and Elena Kozlovskaya Solid Earth, 7, 1095-1108, doi:10.5194/se-7-1095-2016, 2016 We address the problem of seismicity in the intraplate area of northern Fennoscandia using the information on local events recorded by the POLENET/LAPNET seismic array. We relocate the seismic events, calculate a 3-D tomographic P wave velocity model of the uppermost crust and investigate a focal mechanism of the event. Our results demonstrate that the Baltic-Bothnia Megashear is an important large-scale, reactivated tectonic structure that has to be taken into account when estimating seismic hazard.

Description: Combined deep sampling and mass-based approaches to assess soil carbon and nitrogen losses due to land-use changes in karst area of southwestern China Yecui Hu, Zhangliu Du, Qibing Wang, and Guichun Li Solid Earth, 7, 1075-1084, doi:10.5194/se-7-1075-2016, 2016 We quantified the SOC and TN losses induced by land-use changes in a typical karst region of southwestern China. Converting from natural forest to croplands greatly led to SOC and TN losses (as higher as 37.8 %), but the magnitude depended on sampling depth and calculation method. We recommend to account for SOC and TN stocks on equivalent soil mass basis together with deep sampling. This study has significant implications on the projected land management in the degraded karst areas.

Description: Experimental sand burial affects seedling survivorship, morphological traits, and biomass allocation of Ulmus pumila var. sabulosa in the Horqin Sandy Land, China Jiao Tang, Carlos Alberto Busso, Deming Jiang, Ala Musa, Dafu Wu, Yongcui Wang, and Chunping Miao Solid Earth, 7, 1085-1094, doi:10.5194/se-7-1085-2016, 2016 In order to test the tolerance of sandy elm after emergence, an experiment was conducted to evaluate the changes of survivorship, morphological traits and biomass allocation buried by various experimental burial depths. The results showed that partial sand burial did not influence survivorship but increased seedling height, diameter, taproot length, total biomass, and relative growth rates. It decreased total leaf area and changed biomass allocation, transferring more biomass to aboveground.

Description: Characteristics of an avalanche-feeding and partially debris-covered glacier and its response to atmospheric warming in Mt. Tomor, Tian Shan, China Puyu Wang, Zhongqin Li, and Huilin Li The Cryosphere Discuss., doi:10.5194/tc-2016-138,2016 Manuscript under review for TC (discussion: open, 0 comments) A cirque-valley glacier with complex topography and partially debris-covered area was investigated in the Mt. Tomor, Tian Shan. The glacier is analogous to temperate one on movement and temperature regimes. The strongest ablation and most significant terminus retreat and area reduction occurred at the end of last century and the beginning of this century. Since inhibition of debris cover to melting, it is expected to keep shrinkage in the coming decades, but the terminus retreat is to be slower.

Description: Birds can be classified into altricial and precocial. The hatchlings of altricial birds are almost naked, whereas those of precocial birds are covered with natal down. This regulatory divergence is thought to reflect environmental adaptation, but the molecular basis of the divergence is unclear. To address this issue, we chose the altricial zebra finch and the precocial chicken as the model animals. We noted that zebra finch hatchlings show natal down growth suppressed anterior dorsal (AD) skin but partially down-covered posterior dorsal (PD) skin. Comparing the transcriptomes of AD and PD skins, we found that the feather growth promoter SHH (sonic hedgehog) was expressed higher in PD skin than in AD skin. Moreover, the data suggested that the FGF (fibroblast growth factor)/Mitogen-activated protein kinase (MAPK) signaling pathway is involved in natal down growth suppression and that FGF16 is a candidate upstream signaling suppressor. Ectopic expression of FGF16 on chicken leg skin showed downregulation of SHH , upregulation of the feather growth suppressor FGF10 , and suppression of feather bud elongation, similar to the phenotype found in zebra finch embryonic AD skin. Therefore, we propose that FGF16 -related signals suppress natal down elongation and cause the naked AD skin in zebra finch. Our study provides insights into the regulatory divergence in natal down formation between precocial and altricial birds.

Description: The cadherin–catenin complex (CCC) mediates cell–cell adhesion in bilaterian animals by linking extracellular cadherin-based adhesions to the actin cytoskeleton. However, it is unknown whether the basic organization of the complex is conserved across all metazoans. We tested whether protein interactions and actin-binding properties of the CCC are conserved in a nonbilaterian animal, the sea anemone Nematostella vectensis . We demonstrated that N. vectensis has a complete repertoire of cadherin–catenin proteins, including two classical cadherins, one α-catenin, and one β-catenin. Using size-exclusion chromatography and multi-angle light scattering, we showed that α-catenin and β-catenin formed a heterodimer that bound N. vectensis Cadherin-1 and -2. Nematostella vectensis α-catenin bound F-actin with equivalent affinity as either a monomer or an α/β-catenin heterodimer, and its affinity for F-actin was, in part, regulated by a novel insert between the N- and C-terminal domains. Nematostella vectensis α-catenin inhibited Arp2/3 complex-mediated nucleation of actin filaments, a regulatory property previously thought to be unique to mammalian αE-catenin. Thus, despite significant differences in sequence, the key interactions of the CCC are conserved between bilaterians and cnidarians, indicating that the core function of the CCC as a link between cell adhesions and the actin cytoskeleton is ancestral in the eumetazoans.

Description: Nucleotide insertions/deletions are ubiquitous in eukaryotic genomes, and the resulting hemizygous (unpaired) DNA has significant, heritable effects on adjacent DNA. However, little is known about the genetic behavior of insertion DNA. Here, we describe a binary transgenic system to study the behavior of insertion DNA during meiosis. Transgenic Arabidopsis lines were generated to carry two different defective reporter genes on nonhomologous chromosomes, designated as "recipient" and "donor" lines. Double hemizygous plants (harboring unpaired DNA) were produced by crossing between the recipient and the donor, and double homozygous lines (harboring paired DNA) via self-pollination. The transfer of the donor’s unmutated sequence to the recipient generated a functional β-glucuronidase gene, which could be visualized by histochemical staining and corroborated by polymerase chain reaction amplification and sequencing. More than 673 million seedlings were screened, and the results showed that meiotic ectopic recombination in the hemizygous lines occurred at a frequency 〉6.49-fold higher than that in the homozygous lines. Gene conversion might have been exclusively or predominantly responsible for the gene correction events. The direct measurement of ectopic recombination events provided evidence that an insertion, in the absence of an allelic counterpart, could scan the entire genome for homologous counterparts with which to pair. Furthermore, the unpaired (hemizygous) architectures could accelerate ectopic recombination between itself and interchromosomal counterparts. We suggest that the ectopic recombination accelerated by hemizygous architectures may be a general mechanism for interchromosomal recombination through ubiquitously dispersed repeat sequences in plants, ultimately contributing to genetic renovation and eukaryotic evolution.

Description: Adaptation of a complex trait often requires the accumulation of many modifications to finely tune its underpinning molecular components to novel environmental requirements. The investigation of cis -acting regulatory modifications can be used to pinpoint molecular systems partaking in such complex adaptations. Here, we identify cis -acting modifications with the help of an interspecific crossing scheme designed to distinguish modifications derived in each of the two sister species, Arabidopsis halleri and A. lyrata . Allele-specific expression levels were assessed in three environmental conditions chosen to reflect interspecific ecological differences: cold exposure, dehydration, and standard conditions. The functions described by Gene Ontology categories enriched in cis -acting mutations are markedly different in A. halleri and A. lyrata , suggesting that polygenic adaptation reshaped distinct polygenic molecular functions in the two species. In the A. halleri lineage, an excess of cis -acting changes affecting metal transport and homeostasis was observed, confirming that the well-known heavy metal tolerance of this species is the result of polygenic selection. In A. lyrata , we find a marked excess of cis -acting changes among genes showing a transcriptional response to cold stress in the outgroup species A. thaliana . The adaptive relevance of these changes will have to be validated. We finally observed that polygenic molecular functions enriched in derived cis -acting changes are more constrained at the amino acid level. Using the distribution of cis -acting variation to tackle the polygenic basis of adaptation thus reveals the contribution of mutations of small effect to Darwinian adaptation.