ALBERT

Description: We present an implementation of smoothed particle hydrodynamics (SPH) with improved accuracy for simulations of galaxies and the large-scale structure. In particular, we implement and test a vast majority of SPH improvement in the developer version of gadget -3. We use the Wendland kernel functions, a particle wake-up time-step limiting mechanism and a time-dependent scheme for artificial viscosity including high-order gradient computation and shear flow limiter. Additionally, we include a novel prescription for time-dependent artificial conduction, which corrects for gravitationally induced pressure gradients and improves the SPH performance in capturing the development of gas-dynamical instabilities. We extensively test our new implementation in a wide range of hydrodynamical standard tests including weak and strong shocks as well as shear flows, turbulent spectra, gas mixing, hydrostatic equilibria and self-gravitating gas clouds. We jointly employ all modifications; however, when necessary we study the performance of individual code modules. We approximate hydrodynamical states more accurately and with significantly less noise than standard gadget -SPH. Furthermore, the new implementation promotes the mixing of entropy between different fluid phases, also within cosmological simulations. Finally, we study the performance of the hydrodynamical solver in the context of radiative galaxy formation and non-radiative galaxy cluster formation. We find galactic discs to be colder and more extended and galaxy clusters showing entropy cores instead of steadily declining entropy profiles. In summary, we demonstrate that our improved SPH implementation overcomes most of the undesirable limitations of standard gadget -SPH, thus becoming the core of an efficient code for large cosmological simulations.

Description: We present constraints on the origins of fast radio bursts (FRBs) using large cosmological simulations. We calculate contributions to FRB dispersion measures (DMs) from the Milky Way, from the Local Universe, from cosmological large-scale structure, and from potential FRB host galaxies, and then compare these simulations to the DMs of observed FRBs. We find that the Milky Way contribution has previously been underestimated by a factor of ~2, and that the foreground-subtracted DMs are consistent with a cosmological origin, corresponding to a source population observable to a maximum redshift z  ~ 0.6–0.9. We consider models for the spatial distribution of FRBs in which they are randomly distributed in the Universe, track the star formation rate of their host galaxies, track total stellar mass, or require a central supermassive black hole. Current data do not discriminate between these possibilities, but the predicted DM distributions for different models will differ considerably once we begin detecting FRBs at higher DMs and higher redshifts. We additionally consider the distribution of FRB fluences, and show that the observations are consistent with FRBs being standard candles, each burst producing the same radiated isotropic energy. The data imply a constant isotropic burst energy of ~7  x  10 40  erg if FRBs are embedded in host galaxies, or ~9  x  10 40  erg if FRBs are randomly distributed. These energies are 10–100 times larger than had previously been inferred. Within the constraints of the available small sample of data, our analysis favours FRB mechanisms for which the isotropic radiated energy has a narrow distribution in excess of 10 40  erg.

Description: Mammalian nonsense-mediated mRNA decay (NMD) is a eukaryotic surveillance mechanism that degrades mRNAs containing premature translation termination codons. Phosphorylation of the essential NMD effector UPF1 by the phosphoinositide-3-kinase-like kinase (PIKK) SMG-1 is a key step in NMD and occurs when SMG-1, its two regulatory factors SMG-8 and SMG-9, and UPF1 form a complex at a terminating ribosome. Electron cryo-microscopy of the SMG-1–8–9-UPF1 complex shows the head and arm architecture characteristic of PIKKs and reveals different states of UPF1 docking. UPF1 is recruited to the SMG-1 kinase domain and C-terminal insertion domain, inducing an opening of the head domain that provides access to the active site. SMG-8 and SMG-9 interact with the SMG-1 C-insertion and promote high-affinity UPF1 binding to SMG-1–8–9, as well as decelerated SMG-1 kinase activity and enhanced stringency of phosphorylation site selection. The presence of UPF2 destabilizes the SMG-1–8–9-UPF1 complex leading to substrate release. Our results suggest an intricate molecular network of SMG-8, SMG-9 and the SMG-1 C-insertion domain that governs UPF1 substrate recruitment and phosphorylation by SMG-1 kinase, an event that is central to trigger mRNA decay.

Description: We have simulated the formation of a massive galaxy cluster ( $M_{200}^{\rm crit}$ = 1.1 x 10 15 h –1 M ) in a cold dark matter universe using 10 different codes ( ramses , 2 incarnations of arepo and 7 of gadget ), modelling hydrodynamics with full radiative subgrid physics. These codes include smoothed-particle hydrodynamics (SPH), spanning traditional and advanced SPH schemes, adaptive mesh and moving mesh codes. Our goal is to study the consistency between simulated clusters modelled with different radiative physical implementations – such as cooling, star formation and thermal active galactic nucleus (AGN) feedback. We compare images of the cluster at z = 0, global properties such as mass, and radial profiles of various dynamical and thermodynamical quantities. We find that, with respect to non-radiative simulations, dark matter is more centrally concentrated, the extent not simply depending on the presence/absence of AGN feedback. The scatter in global quantities is substantially higher than for non-radiative runs. Intriguingly, adding radiative physics seems to have washed away the marked code-based differences present in the entropy profile seen for non-radiative simulations in Sembolini et al.: radiative physics + classic SPH can produce entropy cores, at least in the case of non cool-core clusters. Furthermore, the inclusion/absence of AGN feedback is not the dividing line -as in the case of describing the stellar content – for whether a code produces an unrealistic temperature inversion and a falling central entropy profile. However, AGN feedback does strongly affect the overall stellar distribution, limiting the effect of overcooling and reducing sensibly the stellar fraction.

Description: The Anatolian Plate is composed of different lithospheric blocks and ribbon continents amalgamated during the closure of the Paleotethys Ocean and Neotethys Ocean along a subduction margin. Using ambient noise tomography, we investigate the crustal and uppermost mantle shear wave velocity structure of the Anatolian Plate. A total of 215 broad-band seismic stations were used spanning 7 yr of recording to compute 13 778 cross-correlations and obtain Rayleigh wave dispersion measurements for periods between 8 and 40 s. We then perform a shear wave inversion to calculate the seismic velocity structure of the crust and uppermost mantle. Our results show that the overall crustal shear wave velocities of the Anatolian crust are low (~3.4 km s –1 ), indicative of a felsic overall composition. We find that prominent lateral seismic velocity gradients correlate with Tethyan suture zones, supporting the idea that the neotectonic structures of Turkey are exploiting the lithospheric weaknesses associated with the amalgamation of Anatolia. Anomalously slow shear wave velocities (~3.15 km s –1 at 25 km) are located in the western limb of the Isparta Angle in southwestern Turkey. In the upper crust, we find that these low shear wave velocities correlate well with the projected location of a carbonate platform unit (Bey Dağlari) beneath the Lycian Nappe complex. In the lower crust and upper mantle of this region, we propose that the anomalously slow velocities are due to the introduction of aqueous fluids related to the underplating of accretionary material from the underthrusting of a buoyant, attenuated continental fragment similar to the Eratosthenes seamount. We suggest that this fragment controlled the location of the formation of the Subduction-Transform Edge Propagator fault in the eastern Aegean Sea during rapid slab rollback of the Aegean Arc in early Miocene times. Lastly, we observe that the uppermost mantle beneath continental Anatolia is generally slow (~4.2 km s –1 ), indicating higher than usual temperatures consistent with the influx of asthenosphere to shallow depths as a result of the segmentation and break-up of the subducting African lithosphere.

Description: Many animals communicate through acoustic signaling, and "acoustic space" may be viewed as a limited resource that organisms compete for. If acoustic signals overlap, the information in them is masked, so there should be selection toward strategies that reduce signal overlap. The extent to which animals are able to partition acoustic space in acoustically diverse habitats such as tropical forests is poorly known. Here, we demonstrate that a single cicada species plays a major role in the frequency and timing of acoustic communication in a neotropical wet forest bird community. Using an automated acoustic monitor, we found that cicadas vary the timing of their signals throughout the day and that the frequency range and timing of bird vocalizations closely track these signals. Birds significantly avoid temporal overlap with cicadas by reducing and often shutting down vocalizations at the onset of cicada signals that utilize the same frequency range. When birds do vocalize at the same time as cicadas, the vocalizations primarily occur at nonoverlapping frequencies with cicada signals. Our results greatly improve our understanding of the community dynamics of acoustic signaling and reveal how patterns in biotic noise shape the frequency and timing of bird vocalizations in tropical forests.

Description: : Pharmacogenomics holds great promise for the development of biomarkers of drug response and the design of new therapeutic options, which are key challenges in precision medicine. However, such data are scattered and lack standards for efficient access and analysis, consequently preventing the realization of the full potential of pharmacogenomics. To address these issues, we implemented PharmacoGx , an easy-to-use, open source package for integrative analysis of multiple pharmacogenomic datasets. We demonstrate the utility of our package in comparing large drug sensitivity datasets, such as the Genomics of Drug Sensitivity in Cancer and the Cancer Cell Line Encyclopedia. Moreover, we show how to use our package to easily perform Connectivity Map analysis. With increasing availability of drug-related data, our package will open new avenues of research for meta-analysis of pharmacogenomic data. Availability and implementation : PharmacoGx is implemented in R and can be easily installed on any system. The package is available from CRAN and its source code is available from GitHub. Contact : bhaibeka@uhnresearch.ca or benjamin.haibe.kains@utoronto.ca Supplementary information: Supplementary data are available at Bioinformatics online.

Description: How a galaxy regulates its supernovae (SNe) energy into different interstellar/circumgalactic medium components strongly affects galaxy evolution. Based on the JVLA D-configuration C- (6 GHz) and L -band (1.6 GHz) continuum observations, we perform statistical analysis comparing multiwavelength properties of the Continuum Haloes in Nearby Galaxies – an EVLA Survey galaxies. The high-quality JVLA data and edge-on orientation enable us for the first time to include the halo into the energy budget for a complete radio-flux-limited sample. We find tight correlations of L radio with the mid-IR-based star formation rate (SFR). The normalization of our I 1.6 GHz /W Hz –1 –SFR relation is ~2–3times of those obtained for face-on galaxies, probably a result of enhanced IR extinction at high inclination. We also find tight correlations between L radio and the SNe energy injection rate $\dot{E}_{\rm SN(Ia+CC)}$ , indicating the energy loss via synchrotron radio continuum accounts for ~1 of $\dot{E}_{\rm SN}$ , comparable to the energy contained in cosmic ray electrons. The integrated C -to- L -band spectral index is α ~ 0.5–1.1 for non-active galactic nucleus galaxies, indicating a dominance by the diffuse synchrotron component. The low-scatter L radio –SFR/ $L_{\rm radio}\text{-}\dot{E}_{\rm SN (Ia+CC)}$ relationships have superlinear logarithmic slopes at ~2 in L band (1.132 ± 0.067/1.175 ± 0.102) while consistent with linear in C band (1.057 ± 0.075/1.100 ± 0.123). The superlinearity could be naturally reproduced with non-calorimeter models for galaxy discs. Using Chandra halo X-ray measurements, we find sublinear L X – L radio relations. These results indicate that the observed radio halo of a starburst galaxy is close to electron calorimeter, and a galaxy with higher SFR tends to distribute an increased fraction of SNe energy into radio emission (than X-ray).