Changes in the acoustic environment alter the foraging and sheltering behaviour of the cichlid Amititlania nigrofasciata

Anthropogenic noise can affect behaviour across a wide range of species in both terrestrial and aquatic environments. However, behaviours might not be affected in isolation. Therefore, a more holistic approach investigating how environmental stressors, such as noise pollution, affect different behaviours in concert is necessary. Using tank-based noise exposure experiments, we tested how changes in the acoustic environment affect the behaviour of the cichlid Amatitlania nigrofasciata. We found that exposure to anthropogenic noise affected a couple of behaviours: an increase in sheltering was accompanied by a decrease in foraging. Our results highlight the multiple negative effects of an environmental stressor on an individual's behaviour.

An unbiased genetic screen reveals the polygenic nature of the influenza virus anti-interferon response

UNLABELLED: Influenza A viruses counteract the cellular innate immune response at several steps, including blocking RIG I-dependent activation of interferon (IFN) transcription, interferon (IFN)-dependent upregulation of IFN-stimulated genes (ISGs), and the activity of various ISG products; the multifunctional NS1 protein is responsible for most of these activities. To determine the importance of other viral genes in the interplay between the virus and the host IFN response, we characterized populations and selected mutants of wild-type viruses selected by passage through non-IFN-responsive cells. We reasoned that, by allowing replication to occur in the absence of the selection pressure exerted by IFN, the virus could mutate at positions that would normally be restricted and could thus find new optimal sequence solutions. Deep sequencing of selected virus populations and individual virus mutants indicated that nonsynonymous mutations occurred at many phylogenetically conserved positions in nearly all virus genes. Most individual mutants selected for further characterization induced IFN and ISGs and were unable to counteract the effects of exogenous IFN, yet only one contained a mutation in NS1. The relevance of these mutations for the virus phenotype was verified by reverse genetics. Of note, several virus mutants expressing intact NS1 proteins exhibited alterations in the M1/M2 proteins and accumulated large amounts of deleted genomic RNAs but nonetheless replicated to high titers. This suggests that the overproduction of IFN inducers by these viruses can override NS1-mediated IFN modulation. Altogether, the results suggest that influenza viruses replicating in IFN-competent cells have tuned their complete genomes to evade the cellular innate immune system and that serial replication in non-IFN-responsive cells allows the virus to relax from these constraints and find a new genome consensus within its sequence space.

IMPORTANCE: In natural virus infections, the production of interferons leads to an antiviral state in cells that effectively limits virus replication. The interferon response places considerable selection pressure on viruses, and they have evolved a variety of ways to evade it. Although the influenza virus NS1 protein is a powerful interferon antagonist, the contributions of other viral genes to interferon evasion have not been well characterized. Here, we examined the effects of alleviating the selection pressure exerted by interferon by serially passaging influenza viruses in cells unable to respond to interferon. Viruses that grew to high titers had mutations at many normally conserved positions in nearly all genes and were not restricted to the NS1 gene. Our results demonstrate that influenza viruses have fine-tuned their entire genomes to evade the interferon response, and by removing interferon-mediated constraints, viruses can mutate at genome positions normally restricted by the interferon response.

Field testing a full-scale tidal turbine Part 2: In-line Wake Effects

Recent research has shown that higher ambient turbulence leads to better wake recovery, so turbines could be installed in closer proximity in real tidal flows than might be assumed from typical towing tank tests that do not take into account turbulent inflow conditions. The standard tools to assess flow velocities in field conditions are Doppler based sonar devices, such as Acoustic Doppler Profilers (ADPs) or Acoustic Doppler Velocimeters (ADVs). The use of these devices poses some challenges when assessing the wake of a tidal turbine. While ADPs allow the three-dimensional measurement of a velocity profile over a distance, the data is calculated as a mean of three diverging beams and with low temporal resolution. ADVs can measure with higher sampling frequency but only at a single point in the flow. During the MaRINET testing of the SCHOTTELSIT turbine at the QUB tidal test site in Portaferry, Northern Ireland, ADP and ADV measurements were successfully tested.Two methods were employed for measuring the wake: firstly, with a rigidly mounted ADP and secondly, with a submerged ADV which was streamed behind the turbine. This paper presents the experimental set-up and results and discusses limitations and challenges of the two methods used.

Energy levels, radiative rates and electron impact excitation rates for transitions in Be-like Cl XIV, K XVI and Ge XXIX

Results for energy levels, radiative rates and electron impact excitation (effective) collision strengths for transitions in Be-like Cl XIV, K XVI and Ge XXIX are reported. For the calculations of energy levels and radiative rates the general-purpose relativistic atomic structure package is adopted, while for determining the collision strengths and subsequently the excitation rates, the Dirac atomic R-matrix code is used. Oscillator strengths, radiative rates and line strengths are listed for all E1, E2, M1 and M2 transitions among the lowest 98 levels of the n ≤ 4 configurations. Furthermore, lifetimes are provided for all levels and comparisons made with available theoretical and experimental results. Resonances in the collision strengths are resolved in a fine energy mesh and averaged over a Maxwellian velocity distribution to obtain the effective collision strengths. Results obtained are listed over a wide temperature range up to 10^7.8 K, depending on the ion.

Energy levels, radiative rates, and lifetimes for transitions in W LVIII

Energy levels and radiative rates are reported for transitions in Cl-like W LVIII. Configuration interaction (CI) has been included among 44 configurations (generating 4978 levels) over a wide energy range up to 363 Ryd, and the general-purpose relativistic atomic structure package (grasp) adopted for the calculations. Since no other results of comparable complexity are available, calculations have also been performed with the flexible atomic code (fac), which help in assessing the accuracy of our results. Energies are listed for the lowest 400 levels (with energies up to ~98 Ryd), which mainly belong to the 3s²3p⁵, 3s3p⁶, 3s²3p⁴3d, 3s²3p³3d², 3s3p⁴3d², 3s²3p²3d³, and 3p⁶3d configurations, and radiative rates are provided for four types of transitions, i.e.E1, E2, M1, and M2. Our energy levels are assessed to be accurate to better than 0.5%, whereas radiative rates (and lifetimes) should be accurate to better than 20% for a majority of the strong transitions.

Energy levels, radiative rates, and lifetimes for transitions in W XL

Energy levels and radiative rates are reported for transitions in Br-like tungsten, W XL, calculated with the general-purpose relativistic atomic structure package (grasp). Configuration interaction (CI) has been included among 46 configurations (generating 4215 levels) over a wide energy range up to 213 Ryd. However, for conciseness results are only listed for the lowest 360 levels (with energies up to ~43 Ryd), which mainly belong to the 4s²4p⁵,4s²4p⁴4d,4s²4p⁴4f,4s4p⁶,4p⁶4d,4s4p⁵4d,4s²4p³4d², and 4s²4p³4d4f configurations, and provided for four types of transitions, E1, E2, M1, and M2. Comparisons are made with existing (but limited) results. However, to fully assess the accuracy of our data, analogous calculations have been performed with the flexible atomic code, including an even larger CI than in grasp. Our energy levels are estimated to be accurate to better than 0.02 Ryd, whereas results for radiative rates (and lifetimes) should be accurate to better than 20% for a majority of the strong transitions.

Energy levels, radiative rates and electron impact excitation rates for transitions in AlX

Energy levels, radiative rates and lifetimes are calculated among the lowest 98 levels of the n ≤4 configurations of Be-like Al X. The GRASP (General-purpose Relativistic Atomic Structure Package) is adopted and data are provided for all E1, E2, M1 and M2 transitions. Similar data are also obtained with the FAC (Flexible Atomic Code) to assess the accuracy of the calculations. Based on comparisons between calculations with the two codes as well as with available measurements, our listed energy levels are assessed to be accurate to better than 0.3 per cent. However, the accuracy for radiative rates and lifetimes is estimated to be about 20 per cent. Collision strengths are also calculated for which the DARC (Dirac Atomic R-matrix Code) is used. A wide energy range (up to 380 Ryd) is considered and resonances resolved in a fine energy mesh in the thresholds region. The collision strengths are subsequently averaged over a Maxwellian velocity distribution to determine effective collision strengths up to a temperature of 1.6 × 10⁷ K. Our results are compared with the previous (limited) atomic data and significant differences (up to a factor of 4) are noted for several transitions, particularly those which are not allowed in jj coupling. 

Energy levels, radiative rates and electron impact excitation rates for transitions in Si II

Energies for the lowest 56 levels, belonging to the 3s² 3p, 3s 3p², 3p³, 3s² 3d, 3s 3p 3d, 3s² 4ℓ and 3s² 5ℓ configurations of Si II, are calculated using the General-purpose Relativistic Atomic Structure Package (GRASP) code. Analogous calculations have also been performed (for up to 175 levels) using the FlexibleAtomicCode (FAC). Furthermore, radiative rates are calculated for all E1, E2, M1 and M2 transitions. Extensive comparisons are made with available theoretical and experimental energy levels, and the accuracy of the present results is assessed to be better than 0.1Ryd. Similarly, the accuracy for radiative rates (and subsequently lifetimes) is estimated to be better than 20 per cent for most of the (strong) transitions. Electron impact excitation collision strengths are also calculated, with the Dirac Atomic R-matrix Code (DARC), over a wide energy range up to 13 Ryd. Finally, to determine effective collision strengths, resonances are resolved in a fine energy mesh in the thresholds region. These collision strengths are averaged over a Maxwellian velocity distribution and results listed over a wide range of temperatures, up to 10^5.5 K. Our data are compared with earlier R-matrix calculations and differences noted, up to a factor of 2, for several transitions. Although scope remains for improvement, the accuracy for our results of collision strengths and effective collision strengths is assessed to be about 20 per cent for a majority of transitions. 

Energy levels and radiative rates for transitions in Ti VII

We report calculations of energy levels, radiative rates, oscillator strengths and line strengths for transitions among the lowest 231 levels of Ti VII. The general-purpose relativistic atomic structure package and flexible atomic code are adopted for the calculations. Radiative rates, oscillator strengths and line strengths are provided for all electric dipole (E1), magnetic dipole (M1), electric quadrupole (E2) and magnetic quadrupole (M2) transitions among the 231 levels, although calculations have been performed for a much larger number of levels (159 162). In addition, lifetimes for all 231 levels are listed. Comparisons are made with existing results and the accuracy of the data is assessed. In particular, the most recent calculations reported by Singh et al (2012 Can. J. Phys. 90 833) are found to be unreliable, with discrepancies for energy levels of up to 1 Ryd and for radiative rates of up to five orders of magnitude for several transitions, particularly the weaker ones. Based on several comparisons among a variety of calculations with two independent codes, as well as with the earlier results, our listed energy levels are estimated to be accurate to better than 1% (within 0.1 Ryd), whereas results for radiative rates and other related parameters should be accurate to better than 20%.

Energy levels and radiative rates for transitions in Ti VI

We report on calculations of energy levels, radiative rates, oscillator strengths and line strengths for transitions among the lowest 253 levels of the (1s22s22p6 ) 3s23p5 , 3s3p6 , 3s23p43d, 3s3p53d, 3s23p33d2 , 3s23p44s, 3s23p44p and 3s23p44d configurations of Ti VI. The general-purpose relativistic atomic structure package and flexible atomic code are adopted for the calculations. Radiative rates, oscillator strengths and line strengths are reported for all electric dipole (E1), magnetic dipole (M1), electric quadrupole (E2) and magnetic quadrupole (M2) transitions among the 253 levels, although calculations have been performed for a much larger number of levels. Comparisons are made with existing available results and the accuracy of the data is assessed. Additionally, lifetimes for all 253 levels are listed, although comparisons with other theoretical results are limited to only 88 levels. Our energy levels are estimated to be accurate to better than 1% (within 0.03 Ryd), whereas results for other parameters are probably accurate to better than 20%. A reassessment of the energy level data on the National Institute of Standards and Technology website for Ti VI is suggested.

Energy levels and radiative rates for transitions in Ti X

We report calculations of energy levels, radiative rates, oscillator strengths and line strengths for transitions among the lowest 345 levels of Ti X. These include 146 levels of the n 3 configurations and 86 of 3s ²4ℓ, 3s²5ℓ and 3s3p4ℓ, plus some of the 3s²6ℓ, 3p²4ℓ and 3s3p5ℓ levels. The general-purpose relativistic atomic structure package and flexible atomic code are adopted for the calculations. Radiative rates, oscillator strengths and line strengths are provided for all electric dipole (E1), magnetic dipole (M1), electric quadrupole (E2) and magnetic quadrupole (M2) transitions among the 345 levels, although calculations have been performed for a much larger number of levels. Comparisons are made with existing results and the accuracy of the data is assessed. Additionally, lifetimes for all 345 levels are listed. Extensive comparisons of lifetimes are made for the lowest 40 levels, for which discrepancies with recent theoretical work are up to 30%. Discrepancies in lifetimes are even larger, up to a factor of four, for higher excited levels. Furthermore, the effect of large configuration interaction (CI) is found to be insignificant for both the energies and lifetimes for the lowest 40 levels of Ti X which belong to the 3s²3p, 3s3p², 3s²3d, 3p³ and 3s3p3d configurations. However, the contribution of CI is more appreciable for the energy levels and radiative rates among higher excited levels. Our listed energy levels are estimated to be accurate to better than 1% (within 0.1 Ryd), whereas results for other parameters are probably accurate to better than 20%. © 2013 The Royal Swedish Academy of Sciences.

Energy levels, radiative rates and electron impact excitation rates for transitions in He-like Fe XXV, Co XXVI, Ni XXVII, Cu XXVIII and Zn XXIX

We report calculations of energy levels, radiative rates and electron impact excitation cross sections and rates for transitions in He-like Fe XXV, Co XXVI, Ni XXVII, Cu XXVIII and Zn XXIX. The grasp (general-purpose relativistic atomic structure package) is adopted for calculating energy levels and radiative rates. For determining the collision strengths and subsequently the excitation rates, the Dirac atomic R-matrix code (darc) is used. Oscillator strengths, radiative rates and line strengths are reported for all E1, E2, M1 and M2 transitions among the lowest 49 levels of each ion. Additionally, theoretical lifetimes are listed for all 49 levels of the above five ions. Collision strengths are averaged over a Maxwellian velocity distribution and the effective collision strengths obtained listed over a wide temperature range up to 10 ^7.7 K. Comparisons are made with similar data obtained using the flexible atomic code (fac) to highlight the importance of resonances, included in calculations with darc, in the determination of effective collision strengths. Discrepancies between the collision strengths from darc and fac, for some transitions, are also discussed. Finally, discrepancies between the present results of effective collision strengths with the darc code and earlier semi-relativistic R-matrix data are noted over a wide range of electron temperatures for many transitions in all ions. 

Energy levels, radiative rates and electron impact excitation rates for transitions in He-like Ga XXX, Ge XXXI, As XXXII, Se XXXIII and Br XXXIV

We report calculations of energy levels, radiative rates and electron impact excitation cross sections and rates for transitions in He-like Ga XXX, Ge XXXI, As XXXII, Se XXXIII and Br XXXIV. The grasp (general-purpose relativistic atomic structure package) is adopted for calculating energy levels and radiative rates. For determining the collision strengths, and subsequently the excitation rates, the Dirac atomic R-matrix code (darc) is used. Oscillator strengths, radiative rates and line strengths are reported for all E1, E2, M1 and M2 transitions among the lowest 49 levels of each ion. Additionally, theoretical lifetimes are provided for all 49 levels of the above five ions. Collision strengths are averaged over a Maxwellian velocity distribution and the effective collision strengths obtained listed over a wide temperature range up to 10⁸ K. Comparisons are made with similar data obtained using the flexible atomic code (fac) to highlight the importance of resonances, included in calculations with darc, in the determination of effective collision strengths. Discrepancies between the collision strengths from darc and fac, particularly for some forbidden transitions, are also discussed. Finally, discrepancies between the present results for effective collision strengths with the darc code and earlier semi-relativistic R-matrix data are noted over a wide range of electron temperatures for many transitions in all ions. © 2013 The Royal Swedish Academy of Sciences.

Energy levels, radiative rates, and electron impact excitation rates for transitions in Li-like ions with 21≤Z≤28

We report calculations of energy levels, radiative rates, and electron impact excitation rates for transitions in Li-like ions with 21≤Z≤28. The General-Purpose Relativistic Atomic Structure Package is adopted for calculating energy levels and radiative rates, while for determining the collision strengths and subsequently the excitation rates, the Dirac Atomic R-matrix Code is used. Oscillator strengths, radiative rates, and line strengths are listed for all E1, E2, M1, and M2 transitions among the lowest 24 levels of the Li-like ions considered. Collision strengths have been averaged over a Maxwellian velocity distribution, and the effective collision strengths obtained are given over a wide temperature range up to 10^7.8 K. Additionally, lifetimes are listed for all calculated levels of these ions. Finally, extensive comparisons are made with results available in the literature, as well as with our analogous calculations for all parameters with the Flexible Atomic Code, in order to assess the accuracy of the results.

Energy levels, radiative rates and electron impact excitation rates for transitions in Be-like Ti XIX

We report calculations of energy levels, radiative rates and electron impact excitation cross sections and rates for transitions in Be-like Ti XIX. The general-purpose relativistic atomic structure package is adopted for calculating energy levels and radiative rates. For determining the collision strengths and subsequently the excitation rates, the Dirac atomic R-matrix code (darc) is used. Oscillator strengths, radiative rates and line strengths are reported for all E1, E2, M1 and M2 transitions among the lowest 98 levels of the n≤ 4 configurations. Additionally, theoretical lifetimes are listed for all 98 levels. Collision strengths are averaged over a Maxwellian velocity distribution and the effective collision strengths obtained listed over a wide temperature range up to 10 ^7.7K. Comparisons are made with similar data obtained from the flexible atomic code (fac) to highlight the importance of resonances, included in calculations with darc, in the determination of effective collision strengths. Discrepancies between the collision strengths from darc and fac, particularly for forbidden transitions, are also discussed.