Computational KIR copy number discovery reveals interaction between inhibitory receptor burden and survival.

Natural killer (NK) cells have increasingly become a target of interest for immunotherapies. NK cells express killer immunoglobulin-like receptors (KIRs), which play a vital role in immune response to tumors by detecting cellular abnormalities. The genomic region encoding the 16 KIR genes displays high polymorphic variability in human populations, making it difficult to resolve individual genotypes based on next generation sequencing data. As a result, the impact of polymorphic KIR variation on cancer phenotypes has been understudied. Currently, labor-intensive, experimental techniques are used to determine an individual's KIR gene copy number profile. Here, we develop an algorithm to determine the germline copy number of KIR genes from whole exome sequencing data and apply it to a cohort of nearly 5000 cancer patients. We use a k-mer based approach to capture sequences unique to specific genes, count their occurrences in the set of reads derived from an individual and compare the individual's k-mer distribution to that of the population. Copy number results demonstrate high concordance with population copy number expectations. Our method reveals that the burden of inhibitory KIR genes is associated with survival in two tumor types, highlighting the potential importance of KIR variation in understanding tumor development and response to immunotherapy

The filter wheel and filters development for the X-IFU instruments onboard Athena

Athena is the large mission selected by ESA in 2013 to investigate the science theme "Hot and Energetic Universe" and presently scheduled for launch in 2028. One of the two instruments located at the focus of the 12 m-long Athena telescope is the X-ray Integral Field Unit (X-IFU). This is an array of TES microcalorimeters that will be operated at temperatures of 50 mK in order to perform high resolution spectroscopy with an energy resolution down to 2.5 eV at energies < 7 keV. In order to cope with the large dynamical range of X-ray fluxes spanned by the celestial objects Athena will be observing, the X-IFU will be equipped with a filter wheel. This will allow the user to fine tune the instrument set-up based on the nature of the target, thus optimizing the scientific outcomes of the observation. A few positions of the filter wheel will also be used to host a calibration source and to allow the measurement of the instrument intrinsic background

The filter wheel and filters development for the X-IFU instruments on-board Athena

Athena is the large mission selected by ESA in 2013 to investigate the science theme “Hot and Energetic Universe” and presently scheduled for launch in 2028. One of the two instruments located at the focus of the 12 m-long Athena telescope is the X-ray Integral Field Unit (X-IFU). This is an array of TES microcalorimeters that will be operated at temperatures of 50 mK in order to perform high resolution spectroscopy with an energy resolution down to 2.5 eV at energies < 7 keV. In order to cope with the large dynamical range of X-ray fluxes spanned by the celestial objects Athena will be observing, the X-IFU will be equipped with a filter wheel. This will allow the user to fine tune the instrument set-up based on the nature of the target, thus optimizing the scientific outcomes of the observation. A few positions of the filter wheel will also be used to host a calibration source and to allow the measurement of the instrument intrinsic background

Altered thymic differentiation and modulation of arthritis by invariant NKT cells expressing mutant ZAP70

Various subsets of invariant natural killer T (iNKT) cells with different cytokine productions develop in the mouse thymus, but the factors driving their differentiation remain unclear. Here we show that hypomorphic alleles of Zap70 or chemical inhibition of Zap70 catalysis leads to an increase of IFN-gamma-producing iNKT cells (NKT1 cells), suggesting that NKT1 cells may require a lower TCR signal threshold. Zap70 mutant mice develop IL-17-dependent arthritis. In a mouse experimental arthritis model, NKT17 cells are increased as the disease progresses, while NKT1 numbers negatively correlates with disease severity, with this protective effect of NKT1 linked to their IFN-gamma expression. NKT1 cells are also present in the synovial fluid of arthritis patients. Our data therefore suggest that TCR signal strength during thymic differentiation may influence not only IFN-gamma production, but also the protective function of iNKT cells in arthritis

ESPRESSO: The next European exoplanet hunter

The acronym ESPRESSO stems for Echelle SPectrograph for Rocky Exoplanets and Stable Spectroscopic Observations; this instrument will be the next VLT high resolution spectrograph. The spectrograph will be installed at the Combined-Coud\'e Laboratory of the VLT and linked to the four 8.2 m Unit Telescopes (UT) through four optical Coud\'e trains. ESPRESSO will combine efficiency and extreme spectroscopic precision. ESPRESSO is foreseen to achieve a gain of two magnitudes with respect to its predecessor HARPS, and to improve the instrumental radial-velocity precision to reach the 10 cm/s level. It can be operated either with a single UT or with up to four UTs, enabling an additional gain in the latter mode. The incoherent combination of four telescopes and the extreme precision requirements called for many innovative design solutions while ensuring the technical heritage of the successful HARPS experience. ESPRESSO will allow to explore new frontiers in most domains of astrophysics that require precision and sensitivity. The main scientific drivers are the search and characterization of rocky exoplanets in the habitable zone of quiet, nearby G to M-dwarfs and the analysis of the variability of fundamental physical constants. The project passed the final design review in May 2013 and entered the manufacturing phase. ESPRESSO will be installed at the Paranal Observatory in 2016 and its operation is planned to start by the end of the same year.Comment: 12 pages, figures included, accepted for publication in Astron. Nach

The Next Generation Transit Survey—Prototyping Phase

We present the prototype telescope for the Next Generation Transit Survey, which was built in the UK in 2008/2009 and tested on La Palma in the Canary Islands in 2010. The goals for the prototype system were severalfold: to determine the level of systematic noise in an NGTS-like system; demonstrate that we can perform photometry at the (sub) millimagnitude level on transit timescales across a wide-field; show that it is possible to detect transiting super-Earth and Neptune-sized exoplanets and prove the technical feasibility of the proposed planet survey. We tested the system for around 100 nights and met each of the goals above. Several key areas for improvement were highlighted during the prototyping phase. They have been subsequently addressed in the final NGTS facility, which was recently commissioned at ESO Cerro Paranal, Chile

VIS: the visible imager for Euclid

Euclid-VIS is the large format visible imager for the ESA Euclid space mission in their Cosmic Vision program, scheduled for launch in 2020. Together with the near infrared imaging within the NISP instrument, it forms the basis of the weak lensing measurements of Euclid. VIS will image in a single r+i+z band from 550-900 nm over a field of view of ~0.5 deg2. By combining 4 exposures with a total of 2260 sec, VIS will reach to V=24.5 (10σ) for sources with extent ~0.3 arcsec. The image sampling is 0.1 arcsec. VIS will provide deep imaging with a tightly controlled and stable point spread function (PSF) over a wide survey area of 15000 deg2 to measure the cosmic shear from nearly 1.5 billion galaxies to high levels of accuracy, from which the cosmological parameters will be measured. In addition, VIS will also provide a legacy dataset with an unprecedented combination of spatial resolution, depth and area covering most of the extra-Galactic sky. Here we will present the results of the study carried out by the Euclid Consortium during the period up to the Preliminary Design Review. © (2014) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only

The Next Generation Transit Survey (NGTS)

© 2017 The Author(s) Published by Oxford University Press on behalf of the Royal Astronomical Society. We describe the Next Generation Transit Survey (NGTS), which is a ground-based project searching for transiting exoplanets orbiting bright stars. NGTS builds on the legacy of previous surveys, most notably WASP, and is designed to achieve higher photometric precision and hence find smaller planets than have previously been detected from the ground. It also operates in red light,maximizing sensitivity to late K and earlyMdwarf stars. The survey specifications call for photometric precision of 0.1 per cent in red light over an instantaneous field of view of 100 deg 2 , enabling the detection of Neptune-sized exoplanets around Sun-like stars and super-Earths around M dwarfs. The survey is carried out with a purpose-built facility at Cerro Paranal, Chile, which is the premier site of the European Southern Observatory (ESO). An array of twelve 20 cm f/2.8 telescopes fitted with back-illuminated deep-depletion CCD cameras is used to survey fields intensively at intermediateGalactic latitudes. The instrument is also ideally suited to ground-based photometric follow-up of exoplanet candidates from space telescopes such as TESS, Gaia and PLATO. We present observations that combine precise autoguiding and the superb observing conditions at Paranal to provide routine photometric precision of 0.1 per cent in 1 h for stars with I-band magnitudes brighter than 13. We describe the instrument and data analysis methods as well as the status of the survey, which achieved first light in 2015 and began full-survey operations in 2016. NGTS data will be made publicly available through the ESO archive

Revisiting Proxima with ESPRESSO

We aim to confirm the presence of Proxima b using independent measurements obtained with the new ESPRESSO spectrograph, and refine the planetary parameters taking advantage of its improved precision. We analysed 63 spectroscopic ESPRESSO observations of Proxima taken during 2019. We obtained radial velocity measurements with a typical radial velocity photon noise of 26 cm/s. We ran a joint MCMC analysis on the time series of the radial velocity and full-width half maximum of the cross-correlation function to model the planetary and stellar signals present in the data, applying Gaussian process regression to deal with stellar activity. We confirm the presence of Proxima b independently in the ESPRESSO data. The ESPRESSO data on its own shows Proxima b at a period of 11.218 $\pm$ 0.029 days, with a minimum mass of 1.29 $\pm$ 0.13 Me. In the combined dataset we measure a period of 11.18427 $\pm$ 0.00070 days with a minimum mass of 1.173 $\pm$ 0.086 Me. We find no evidence of stellar activity as a potential cause for the 11.2 days signal. We find some evidence for the presence of a second short-period signal, at 5.15 days with a semi-amplitude of merely 40 cm/s. If caused by a planetary companion, it would correspond to a minimum mass of 0.29 $\pm$ 0.08 Me. We find that the FWHM of the CCF can be used as a proxy for the brightness changes and that its gradient with time can be used to successfully detrend the radial velocity data from part of the influence of stellar activity. The activity-induced radial velocity signal in the ESPRESSO data shows a trend in amplitude towards redder wavelengths. Velocities measured using the red end of the spectrograph are less affected by activity, suggesting that the stellar activity is spot-dominated. The data collected excludes the presence of extra companions with masses above 0.6 Me at periods shorter than 50 days.Comment: 25 pages, 26 figure