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The Low Frequency Array (LOFAR) is an international radio telescope array, consisting of 38 stations in the Netherlands and 14 international stations spread over Europe. Here we present an observation method to study the jovian decametric radio emissions from several LOFAR stations (here DE604, FR606 and IE613), at high temporal and spectral resolution. This method is based on prediction tools, such as radio emission simulations and probability maps, and data processing. We report an observation of Io-induced decametric emission from June 2021, and a first case study of the substructures that compose the macroscopic emissions (called millisecond bursts). The study of these bursts make it possible to determine the electron populations at the origin of these emissions. We then present several possible future avenues for study based on these observations. The methodology and study perspectives described in this paper can be applied to new observations of jovian radio emissions induced by Io, but also by Ganymede or Europa, or jovian auroral radio emissions., Comment: 7 pages, 3 figures, submitted to the Royal Astronomical Society Techniques and Instruments journal

We simulate possible stellar coronal mass ejection (CME) scenarios over the magnetic cycle of $\epsilon$ Eridani (18 Eridani; HD 22049). We use three separate epochs from 2008, 2011, and 2013, and estimate the radio emission frequencies associated with these events. These stellar eruptions have proven to be elusive, although a promising approach to detect and characterise these phenomena are low-frequency radio observations of potential type II bursts as CME induced shocks propagate through the stellar corona. Stellar type II radio bursts are expected to emit below 450 MHz, similarly to their solar counterparts. We show that the length of time these events remain above the ionospheric cutoff is not necessarily dependent on the stellar magnetic cycle, but more on the eruption location relative to the stellar magnetic field. We find that these type II bursts would remain within the frequency range of LOFAR for a maximum of 20-30 minutes post-eruption for the polar CMEs, (50 minutes for 2nd harmonics). We find evidence of slower equatorial CMEs, which result in slightly longer observable windows for the 2008 and 2013 simulations. Stellar magnetic geometry and strength has a significant effect on the detectability of these events. We place the CMEs in the context of the stellar mass-loss rate (27-48 $\times$ solar mass-loss rate), showing that they can amount to 3-50% of the stellar wind mass-loss rate for $\epsilon$ Eridani. Continuous monitoring of likely stellar CME candidates with low-frequency radio telescopes will be required to detect these transient events., Comment: 17 pages, 11 figures. Accepted for publication in ApJ

MAORY is the adaptive optics module for ELT providing two gravity invariant ports with the same optical quality for two different client instruments. It enable high angular resolution observations in the near infrared over a large field of view (~1 arcmin2 ) by real time compensation of the wavefront distortions due to atmospheric turbulence. Wavefront sensing is performed by laser and natural guide stars while the wavefront sensor compensation is performed by an adaptive deformable mirror in MAORY which works together with the telescope's adaptive and tip tilt mirrors M4 and M5 respectively., Comment: 4 pages, 4 figures

Surveys have shown that up to one tenth of all ultracool dwarfs (UCDs) are appreciable radio emitters, with their emission attributed to a combination of gyrosynchrotron radiation and the electron cyclotron maser instability (ECMI). 2M J0746+2000AB is a close stellar binary comprised of an L0 and L1.5 dwarf that was previously identified as a source of 5 GHz radio emission. We used very-long-baseline interferometry (VLBI) to precisely track the radio emission over seven epochs in 2010-2017, and found both components to be radio emitters -- the first such system identified -- with the secondary component as the dominant source of emission in all epochs. The previously identified 2.07 h periodic bursts were confirmed to originate from the secondary component, although an isolated burst was also identified from the primary component. We additionally fitted the VLBI absolute astrometric positions jointly with existing relative orbital astrometry derived from optical/IR observations with Markov-chain Monte Carlo (MCMC) methods to determine the orbital parameters of the two components. We found the masses of the primary and secondary optical components to be 0.0795 +/- 0.0003 Msun and 0.0756 +/- 0.0003 Msun, respectively, representing the most precise mass estimates of any UCDs to date. Finally, we place a 3-sigma upper limit of 0.9 Mjup au on the mass and separation of planets orbiting either of the two components., Comment: 14 pages, 7 figures, 5 tables; ApJ, accepted

Systems biology approaches to the integrative study of cells, organs and organisms offer the best means of understanding in a holistic manner the diversity of molecular assays that can be now be implemented in a high throughput manner. Such assays can sample the genome, epigenome, proteome, metabolome and microbiome contemporaneously, allowing us for the first time to perform a complete analysis of physiological activity. The central problem remains empowering the scientific community to actually implement such an integration, across seemingly diverse data types and measurements. One promising solution is to apply semantic techniques on a self-consistent and implicitly correct ontological representation of these data types. In this paper we describe how we have applied one such solution, based around the InterMine data warehouse platform which uses as its basis the Sequence Ontology, to facilitate a systems biology analysis of virulence in the apicomplexan pathogen $Toxoplasma~gondii$, a common parasite that infects up to half the worlds population, with acute pathogenic risks for immuno-compromised individuals or pregnant mothers. Our solution, which we named `toxoMine', has provided both a platform for our collaborators to perform such integrative analyses and also opportunities for such cyberinfrastructure to be further developed, particularly to take advantage of possible semantic similarities of value to knowledge discovery in the Omics enterprise. We discuss these opportunities in the context of further enhancing the capabilities of this powerful integrative platform., Comment: To appear in the Proceedings of the 2016 IEEE Tenth International Conference on Semantic Computing (ICSC 2016)

A fraction of very low mass stars and brown dwarfs are known to be radio active, in some cases producing periodic pulses. Extensive studies of two such objects have also revealed optical periodic variability and the nature of this variability remains unclear. Here we report on multi-epoch optical photometric monitoring of six radio detected dwarfs, spanning the $\sim$M8 - L3.5 spectral range, conducted to investigate the ubiquity of periodic optical variability in radio detected ultracool dwarfs. This survey is the most sensitive ground-based study carried out to date in search of periodic optical variability from late-type dwarfs, where we obtained 250 hours of monitoring, delivering photometric precision as low as $\sim$0.15%. Five of the six targets exhibit clear periodicity, in all cases likely associated with the rotation period of the dwarf, with a marginal detection found for the sixth. Our data points to a likely association between radio and optical periodic variability in late-M/early-L dwarfs, although the underlying physical cause of this correlation remains unclear. In one case, we have multiple epochs of monitoring of the archetype of pulsing radio dwarfs, the M9 TVLM 513-46546, spanning a period of 5 years, which is sufficiently stable in phase to allow us to establish a period of 1.95958 $\pm$ 0.00005 hours. This phase stability may be associated with a large-scale stable magnetic field, further strengthening the correlation between radio activity and periodic optical variability. Finally, we find a tentative spin-orbit alignment of one component of the very low mass binary LP 349-25., Comment: Accepted to The Astrophysical Journal; 22 pages; 12 figures

The ominous warnings of a `data deluge' in the life sciences from high-throughput DNA sequencing data are being supplanted by a second deluge, of cliches bemoaning our collective scientific fate unless we address the genomic data `tsunami'. It is imperative that we explore the many facets of the genome, not just sequence but also transcriptional and epigenetic variability, integrating these observations in order to attain a genuine understanding of how genes function, towards a goal of genomics-based personalized medicine. Determining any individual's genomic properties requires comparison to many others, sifting out the specific from the trends, requiring access to the many in order to yield information relevant to the few. This is the central big data challenge in genomics that still requires some sort of resolution. Is there a practical, feasible way of directly connecting the scientific community to this data universe? The best answer could be in the stars overhead., Comment: 11 pages, 1 figure, accepted for publication in Genome Biology

Studies of solar-type binaries have found coplanarity between the equatorial and orbital planes of systems with $<$40 AU separation. By comparison, the alignment of the equatorial and orbital axes in the substellar regime, and the associated implications for formation theory, are relatively poorly constrained. Here we present the discovery of the rotation period of 3.32 $\pm$ 0.15 hours from 2MASS J0746+20A - the primary component of a tight (2.7 AU) ultracool dwarf binary system (L0+L1.5). The newly discovered period, together with the established period via radio observations of the other component, and the well constrained orbital parameters and rotational velocity measurements, allow us to infer alignment of the equatorial planes of both components with the orbital plane of the system to within 10 degrees. This result suggests that solar-type binary formation mechanisms may extend down into the brown dwarf mass range, and we consider a number of formation theories that may be applicable in this case. This is the first such observational result in the very low mass binary regime. In addition, the detected period of 3.32 $\pm$ 0.15 hours implies that the reported radio period of 2.07 $\pm$ 0.002 hours is associated with the secondary star, not the primary, as was previously claimed. This in turn refutes the claimed radius of 0.78 $\pm$ 0.1 $R_{J}$ for 2MASS J0746+20A, which we demonstrate to be 0.99 $\pm$ 0.03 $R_{J}$., Comment: Article accepted in Astronomy & Astrophysics section 7 - Stellar structure and evolution of Astronomy and Astrophysics; 9 pages; 6 figures

We present an inverse mapping approach to determining the emission height of the optical photons from pulsars, which is directly constrained by empirical data. The model discussed is for the case of the Crab pulsar. Our method, using the optical Stokes parameters, determines the most likely geometry for emission including magnetic field inclination angle ($\alpha$), observers line of sight angle ($\chi$) and emission height. We discuss the computational implementation of the approach, along with any physical assumptions made. We find that the most likely emission altitude is at 20% of the light cylinder radius above the stellar surface, in the open field region. We also present a general treatment of the expected polarisation from synchrotron source with a truncated power law spectrum of particles., Comment: 17 pages 16 figures; accepted for publication in MNRAS

This work presents a highly optimized computational framework for the Discrete Dipole Approximation, a numerical method for calculating the optical properties associated with a target of arbitrary geometry that is widely used in atmospheric, astrophysical and industrial simulations. Core optimizations include the bit-fielding of integer data and iterative methods that complement a new Discrete Fourier Transform (DFT) kernel, which efficiently calculates the matrix vector products required by these iterative solution schemes. The new kernel performs the requisite 3-D DFTs as ensembles of 1-D transforms, and by doing so, is able to reduce the number of constituent 1-D transforms by 60% and the memory by over 80%. The optimizations also facilitate the use of parallel techniques to further enhance the performance. Complete OpenMP-based shared-memory and MPI-based distributed-memory implementations have been created to take full advantage of the various architectures. Several benchmarks of the new framework indicate extremely favorable performance and scalability. OpenDDA is available following the usual open source regulations from http://www.opendda.org, Comment: 29 pages, 5 figures

We show that observations of pulsars with pulsed optical emission indicate that the peak flux scales according to the magnetic field strength at the light cylinder. The derived relationships indicate that the emission mechanism is common across all of the observed pulsars with periods ranging from 33ms to 385 ms and ages of 1000-300,000 years. It is noted that similar trends exist for $\gamma$ ray pulsars. Furthermore the model proposed by Pacini (1971) and developed by Pacini and Salvati (1983,1987) still has validity and gives an adequate explanation of the optical phenomena., Comment: 23 pages, 6 figures, accepted for publication in the Astrophysical Journal

Observations of the 5 confirmed optical pulsars indicate that the peak emission scales according to the outer field strength. We show that this gives gives further confirmation that a simple phenomenological models such as Pacini and Salvati (1987) still have validity. Furthermore we show that the Crab pulsar exhibits unpulsed emission which further complicates any studies of the thermal emission from Isolated Neutron Stars., Comment: 4 pages, 3 figures, to appear in the Proceedings of IAU Colloquium 177 : "Pulsar Astronomy - 2000 & Beyond", Ed. Kramer, Wex & Wielebinski, ASP conf.Series. Uses newpasp.sty

Using the high speed 2-d TRIFFID photometer, we have obtained phase resolved photometry of the Crab pulsar in UBV that allows us to flux the unpulsed light curve component. Following de-extinction, weighted least-square fitting indicates a power-law exponent of alpha = -0.62 +/- 0.49. This is steeper than that reported for the peak components and its origin remains unclear with respect to contemporary magnetospheric theory., Comment: 2 pages, 2 figures, to appear in the Proceedings of IAU Colloquium 177 : "Pulsar Astronomy - 2000 & Beyond", Ed. Kramer, Wex & Wielebinski, ASP conf.Series. Uses newpasp.sty

PSR B0656+14's high energy emission is consistent with that of combined magnetospheric and thermal (surface & polar cap) emission. Uncertainties with the radio-derived distance and X-ray instrumentation sensitivities complicate a definitive thermal characterisation however. A re-analysis of combined ROSAT/EUVE archival data in conjunction with integrated & phase-resolved optical photometry is shown to constrain this characterisation., Comment: 2 pages, 2 figures, to appear in the Proceedings of IAU Colloquium 177 : "Pulsar Astronomy - 2000 & Beyond", Ed. Kramer, Wex & Wielebinski, ASP conf.Series. Uses newpasp.sty