Fine-Scale Mapping of the 5q11.2 Breast Cancer Locus Reveals at Least Three Independent Risk Variants Regulating MAP3K1

Peer reviewe

The protein sequence design problem in canonical model on 2D and 3D lattices

Abstract. In this paper we investigate the protein sequence design (PSD) problem (also known as the inverse protein folding problem) under the Canonical model 4 on 2D and 3D lattices [12, 25]. The Canonical model is specified by (i) a geometric representation of a target protein structure with amino acid residues via its contact graph, (ii) a binary folding code in which the amino acids are classified as hydrophobic (H) or polar (P), (iii) an energy function Φ defined in terms of the target structure that should favor sequences with a dense hydrophobic core and penalize those with many solvent-exposed hydrophobic residues (in the Canonical model, the energy function Φ gives an H-H residue contact in the contact graph a value of −1 and all other contacts a value of 0), and (iv) to prevent the solution from being a biologically meaningless all H sequence, the number of H residues in the sequence S is limited by fixing an upper bound λ on the ratio between H and P amino acids. The sequence S is designed by specifying which residues are H and which one

Results of the Photometric LSST Astronomical Time-series Classification Challenge (PLAsTiCC)

Next-generation surveys like the Legacy Survey of Space and Time (LSST) on the Vera C. Rubin Observatory will generate orders of magnitude more discoveries of transients and variable stars than previous surveys. To prepare for this data deluge, we developed the Photometric LSST Astronomical Time-series Classification Challenge (PLAsTiCC), a competition which aimed to catalyze the development of robust classifiers under LSST-like conditions of a non-representative training set for a large photometric test set of imbalanced classes. Over 1,000 teams participated in PLAsTiCC, which was hosted in the Kaggle data science competition platform between Sep 28, 2018 and Dec 17, 2018, ultimately identifying three winners in February 2019. Participants produced classifiers employing a diverse set of machine learning techniques including hybrid combinations and ensemble averages of a range of approaches, among them boosted decision trees, neural networks, and multi-layer perceptrons. The strong performance of the top three classifiers on Type Ia supernovae and kilonovae represent a major improvement over the current state-of-the-art within astronomy. This paper summarizes the most promising methods and evaluates their results in detail, highlighting future directions both for classifier development and simulation needs for a next generation PLAsTiCC data set

Synergies between Vera C. Rubin Observatory, Nancy Grace Roman Space Telescope, and Euclid Mission: Constraining Dark Energy with Type Ia Supernovae

We review the needs of the supernova community for improvements in survey coordination and data sharing that would significantly boost the constraints on dark energy using samples of Type Ia supernovae from the Vera C. Rubin Observatories, the \textit{Nancy Grace Roman Space Telescope}, and the \textit{Euclid} Mission. We discuss improvements to both statistical and systematic precision that the combination of observations from these experiments will enable. For example, coordination will result in improved photometric calibration, redshift measurements, as well as supernova distances. We also discuss what teams and plans should be put in place now to start preparing for these combined data sets. Specifically, we request coordinated efforts in field selection and survey operations, photometric calibration, spectroscopic follow-up, pixel-level processing, and computing. These efforts will benefit not only experiments with Type Ia supernovae, but all time-domain studies, and cosmology with multi-messenger astrophysics

Uniform Recalibration of Common Spectrophotometry Standard Stars onto the CALSPEC System using the SuperNova Integral Field Spectrograph

International audienceWe calibrate spectrophotometric optical spectra of 32 stars commonly used as standard stars, referenced to 14 stars already on the HST-based CALSPEC flux system. Observations of CALSPEC and non-CALSPEC stars were obtained with the SuperNova Integral Field Spectrograph over the wavelength range 3300 A to 9400 A as calibration for the Nearby Supernova Factory cosmology experiment. In total, this analysis used 4289 standard-star spectra taken on photometric nights. As a modern cosmology analysis, all pre-submission methodological decisions were made with the flux scale and external comparison results blinded. The large number of spectra per star allows us to treat the wavelength-by-wavelength calibration for all nights simultaneously with a Bayesian hierarchical model, thereby enabling a consistent treatment of the Type Ia supernova cosmology analysis and the calibration on which it critically relies. We determine the typical per-observation repeatability (median 14 mmag for exposures >~ 5 s), the Maunakea atmospheric transmission distribution (median dispersion of 7 mmag with uncertainty 1 mmag), and the scatter internal to our CALSPEC reference stars (median of 8 mmag). We also check our standards against literature filter photometry, finding generally good agreement over the full 12-magnitude range. Overall, the mean of our system is calibrated to the mean of CALSPEC at the level of ~ 3 mmag. With our large number of observations, careful crosschecks, and 14 reference stars, our results are the best calibration yet achieved with an integral-field spectrograph, and among the best calibrated surveys

Uniform Recalibration of Common Spectrophotometry Standard Stars onto the CALSPEC System using the SuperNova Integral Field Spectrograph

International audienceWe calibrate spectrophotometric optical spectra of 32 stars commonly used as standard stars, referenced to 14 stars already on the HST-based CALSPEC flux system. Observations of CALSPEC and non-CALSPEC stars were obtained with the SuperNova Integral Field Spectrograph over the wavelength range 3300 A to 9400 A as calibration for the Nearby Supernova Factory cosmology experiment. In total, this analysis used 4289 standard-star spectra taken on photometric nights. As a modern cosmology analysis, all pre-submission methodological decisions were made with the flux scale and external comparison results blinded. The large number of spectra per star allows us to treat the wavelength-by-wavelength calibration for all nights simultaneously with a Bayesian hierarchical model, thereby enabling a consistent treatment of the Type Ia supernova cosmology analysis and the calibration on which it critically relies. We determine the typical per-observation repeatability (median 14 mmag for exposures >~ 5 s), the Maunakea atmospheric transmission distribution (median dispersion of 7 mmag with uncertainty 1 mmag), and the scatter internal to our CALSPEC reference stars (median of 8 mmag). We also check our standards against literature filter photometry, finding generally good agreement over the full 12-magnitude range. Overall, the mean of our system is calibrated to the mean of CALSPEC at the level of ~ 3 mmag. With our large number of observations, careful crosschecks, and 14 reference stars, our results are the best calibration yet achieved with an integral-field spectrograph, and among the best calibrated surveys

Uniform Recalibration of Common Spectrophotometry Standard Stars onto the CALSPEC System using the SuperNova Integral Field Spectrograph

International audienceWe calibrate spectrophotometric optical spectra of 32 stars commonly used as standard stars, referenced to 14 stars already on the HST-based CALSPEC flux system. Observations of CALSPEC and non-CALSPEC stars were obtained with the SuperNova Integral Field Spectrograph over the wavelength range 3300 A to 9400 A as calibration for the Nearby Supernova Factory cosmology experiment. In total, this analysis used 4289 standard-star spectra taken on photometric nights. As a modern cosmology analysis, all pre-submission methodological decisions were made with the flux scale and external comparison results blinded. The large number of spectra per star allows us to treat the wavelength-by-wavelength calibration for all nights simultaneously with a Bayesian hierarchical model, thereby enabling a consistent treatment of the Type Ia supernova cosmology analysis and the calibration on which it critically relies. We determine the typical per-observation repeatability (median 14 mmag for exposures >~ 5 s), the Maunakea atmospheric transmission distribution (median dispersion of 7 mmag with uncertainty 1 mmag), and the scatter internal to our CALSPEC reference stars (median of 8 mmag). We also check our standards against literature filter photometry, finding generally good agreement over the full 12-magnitude range. Overall, the mean of our system is calibrated to the mean of CALSPEC at the level of ~ 3 mmag. With our large number of observations, careful crosschecks, and 14 reference stars, our results are the best calibration yet achieved with an integral-field spectrograph, and among the best calibrated surveys