Multi-band high resolution spectroscopy rules out the hot Jupiter BD+20 1790b - First data from the GIARPS Commissioning

Context. Stellar activity is currently challenging the detection of young planets via the radial velocity (RV) technique. Aims. We attempt to definitively discriminate the nature of the RV variations for the young active K5 star BD+20 1790, for which visible (VIS) RV measurements show divergent results on the existence of a substellar companion. Methods. We compare VIS data with high precision RVs in the near infrared (NIR) range by using the GIANO - B and IGRINS spectrographs. In addition, we present for the first time simultaneous VIS-NIR observations obtained with GIARPS (GIANO - B and HARPS - N) at Telescopio Nazionale Galileo (TNG). Orbital RVs are achromatic, so the RV amplitude does not change at different wavelengths, while stellar activity induces wavelength-dependent RV variations, which are significantly reduced in the NIR range with respect to the VIS. Results. The NIR radial velocity measurements from GIANO - B and IGRINS show an average amplitude of about one quarter with respect to previously published VIS data, as expected when the RV jitter is due to stellar activity. Coeval multi-band photometry surprisingly shows larger amplitudes in the NIR range, explainable with a mixture of cool and hot spots in the same active region. Conclusions. In this work, the claimed massive planet around BD+20 1790 is ruled out by our data. We exploited the crucial role of multi- wavelength spectroscopy when observing young active stars: thanks to facilities like GIARPS that provide simultaneous observations, this method can reach its maximum potential.Comment: 12 pages, 7 figure

The PRIDE database and related tools and resources in 2019: improving support for quantification data

The PRoteomics IDEntifications (PRIDE) database (https://www.ebi.ac.uk/pride/) is the world's largest data repository of mass spectrometry-based proteomics data, and is one of the founding members of the global ProteomeXchange (PX) consortium. In this manuscript, we summarize the developments in PRIDE resources and related tools since the previous update manuscript was published in Nucleic Acids Research in 2016. In the last 3years, public data sharing through PRIDE (as part of PX) has definitely become the norm in the field. In parallel, data re-use of public proteomics data has increased enormously, with multiple applications. We first describe the new architecture of PRIDE Archive, the archival component of PRIDE. PRIDE Archive and the related data submission framework have been further developed to support the increase in submitted data volumes and additional data types. A new scalable and fault tolerant storage backend, Application Programming Interface and web interface have been implemented, as a part of an ongoing process. Additionally, we emphasize the improved support for quantitative proteomics data through the mzTab format. At last, we outline key statistics on the current data contents and volume of downloads, and how PRIDE data are starting to be disseminated to added-value resources including Ensembl, UniProt and Expression Atlas

Method for Independent Estimation of the False Localization Rate for Phosphoproteomics

Phosphoproteomic methods are commonly employed to identify and quantify phosphorylation sites on proteins. In recent years, various tools have been developed, incorporating scores or statistics related to whether a given phosphosite has been correctly identified or to estimate the global false localization rate (FLR) within a given data set for all sites reported. These scores have generally been calibrated using synthetic datasets, and their statistical reliability on real datasets is largely unknown, potentially leading to studies reporting incorrectly localized phosphosites, due to inadequate statistical control. In this work, we develop the concept of scoring modifications on a decoy amino acid, that is, one that cannot be modified, to allow for independent estimation of global FLR. We test a variety of amino acids, on both synthetic and real data sets, demonstrating that the selection can make a substantial difference to the estimated global FLR. We conclude that while several different amino acids might be appropriate, the most reliable FLR results were achieved using alanine and leucine as decoys. We propose the use of a decoy amino acid to control false reporting in the literature and in public databases that re-distribute the data. Data are available via ProteomeXchange with identifier PXD028840

GIARPS: commissioning and first scientific results

GIARPS (GIAno \& haRPS) is a project devoted to have on the same focal station of the Telescopio Nazionale Galileo (TNG) both high resolution spectrographs, HARPS-N (VIS) and GIANO-B (NIR), working simultaneously. This could be considered the first and unique worldwide instrument providing cross-dispersed echelle spectroscopy at a resolution of 50,000 in the NIR range and 115,000 in the VIS and over in a wide spectral range ($0.383 - 2.45\ \mu$m) in a single exposure. The science case is very broad, given the versatility of such an instrument and its large wavelength range. A number of outstanding science cases encompassing mainly extra-solar planet science starting from rocky planets search and hot Jupiters to atmosphere characterization can be considered. Furthermore both instruments can measure high precision radial velocities by means the simultaneous thorium technique (HARPS-N) and absorbing cell technique (GIANO-B) in a single exposure. Other science cases are also possible. GIARPS, as a brand new observing mode of the TNG started after the moving of GIANO-A (fiber fed spectrograph) from Nasmyth-A to Nasmyth-B where it was re-born as GIANO-B (no more fiber feed spectrograph). The official Commissioning finished on March 2017 and then it was offered to the community. Despite the work is not finished yet. In this paper we describe the preliminary scientific results obtained with GIANO-B and GIARPS observing mode with data taken during commissioning and first open time observations.Comment: 10 pages, 11 figures, Telescopes and Astronomical instrumentation, SPIE Conf. 201

BioContainers: An open-source and community-driven framework for software standardization

Motivation BioContainers (biocontainers.pro) is an open-source and community-driven framework which provides platform independent executable environments for bioinformatics software. BioContainers allows labs of all sizes to easily install bioinformatics software, maintain multiple versions of the same software and combine tools into powerful analysis pipelines. BioContainers is based on popular open-source projects Docker and rkt frameworks, that allow software to be installed and executed under an isolated and controlled environment. Also, it provides infrastructure and basic guidelines to create, manage and distribute bioinformatics containers with a special focus on omics technologies. These containers can be integrated into more comprehensive bioinformatics pipelines and different architectures (local desktop, cloud environments or HPC clusters). Availability and Implementation The software is freely available at github.com/BioContainers/.publishedVersio

SIFAP2: a new versatile configuration at the TNG for the MPPC based photometer

The quality of SiFAP (Silicon Fast Astronomical Photometer) at the TNG has already shown its ability to easily detect optical pulses from transitional millisecond pulsars and from other slower neutron stars. Up to now the photometer based on Silicon Photo Multipliers manufactured by Hamamatsu Photonics (MPPC, Multi Pixel Photon Counter) was mounted (on and manually aligned with) a MOS mask at the F/11 focal plane of the telescope. In order to have a more versatile instrument with the possibility to remotely center and point several targets during the night we have decided to build a new mechanical support for the MPPCs and mount it on the Namsyth Interface (NI), where originally OIG and later GIANO were hosted. The MPPC module devoted to observe the target will be placed at the center of the FoV (on-axis), while the reference signal will be collected from a peripheral star in the FoV (Field of view) by means of the MPPC module that will be set at this position by a combination of a linear stage movement and a derotator angle. At the same time we have introduced the option for a polarimetric mode, with a 3rd MPPC module and a polarizing cube beam-splitter that separates the states between this and the on axis MPPC. SiFAP has been developed with 3 independent custom electronic chains for data acquisition, exploiting the 3 different outputs (analog, digital, USB pre-processed) provided by the MPPCs modules. The electronic chain fed by the analog output is able to tag a single photon ToA (Time of Arrival) with a time resolution of 25 ns, while the remaining electronic chains can integrate the signal into time bins from 100 ms down to 20 μs. The absolute time is provided by a GPS unit with a time resolution of 25 ns at 50% of the rising edge of the 1PPS (1 Pulse Per Second) signal which is linked to the UTC (Universal Time Coordinated). Apart from the versatility with the remotely controlled on sky configuration of the MPPCs, the mounting of SiFAP2 at the NI allows for a permanent hosting of the instrument, readily available for observations. The new polarimetric mode will then offer other scientific opportunities that have not been explored so far in high-temporal resolution astronomy

Investigating the origin of optical and X-ray pulsations of the transitional millisecond pulsar PSR J1023+0038

Context. PSR J1023+0038 is the first millisecond pulsar that was ever observed as an optical and UV pulsar. So far, it is the only optical transitional millisecond pulsar. The rotation- and accretion-powered emission mechanisms hardly individually explain the observed characteristics of optical pulsations. A synergistic model, combining these standard emission processes, was proposed to explain the origin of the X-ray/UV/optical pulsations. Aims: We study the phase lag between the pulses in the optical and X-ray bands to gain insight into the physical mechanisms that cause it. Methods: We performed a detailed timing analysis of simultaneous or quasi-simultaneous observations in the X-ray band, acquired with the XMM-Newton and NICER satellites, and in the optical band, with the fast photometers SiFAP2 (mounted at the 3.6 m Telescopio Nazionale Galileo) and Aqueye+ (mounted at the 1.8 m Copernicus Telescope). We estimated the time lag of the optical pulsation with respect to that in the X-rays by modeling the folded pulse profiles with two harmonic components. Results: Optical pulses lag the X-ray pulses by ∼150 μs in observations acquired with instruments (NICER and Aqueye+) whose absolute timing uncertainty is much smaller than the measured lag. We also show that the phase lag between optical and X-ray pulsations lies in a limited range of values, δϕ ∈ (0 − 0.15), which is maintained over timescales of about five years. This indicates that both pulsations originate from the same region, and it supports the hypothesis of a common emission mechanism. Our results are interpreted in the shock-driven mini pulsar nebula scenario. This scenario suggests that optical and X-ray pulses are produced by synchrotron emission from the shock that formed within a few light cylinder radii away (∼100 km) from the pulsar, where its striped wind encounters the accretion disk inflow