PynPoint: a modular pipeline architecture for processing and analysis of high-contrast imaging data

The direct detection and characterization of planetary and substellar companions at small angular separations is a rapidly advancing field. Dedicated high-contrast imaging instruments deliver unprecedented sensitivity, enabling detailed insights into the atmospheres of young low-mass companions. In addition, improvements in data reduction and PSF subtraction algorithms are equally relevant for maximizing the scientific yield, both from new and archival data sets. We aim at developing a generic and modular data reduction pipeline for processing and analysis of high-contrast imaging data obtained with pupil-stabilized observations. The package should be scalable and robust for future implementations and in particular well suitable for the 3-5 micron wavelength range where typically (ten) thousands of frames have to be processed and an accurate subtraction of the thermal background emission is critical. PynPoint is written in Python 2.7 and applies various image processing techniques, as well as statistical tools for analyzing the data, building on open-source Python packages. The current version of PynPoint has evolved from an earlier version that was developed as a PSF subtraction tool based on PCA. The architecture of PynPoint has been redesigned with the core functionalities decoupled from the pipeline modules. Modules have been implemented for dedicated processing and analysis steps, including background subtraction, frame registration, PSF subtraction, photometric and astrometric measurements, and estimation of detection limits. The pipeline package enables end-to-end data reduction of pupil-stabilized data and supports classical dithering and coronagraphic data sets. As an example, we processed archival VLT/NACO L' and M' data of beta Pic b and reassessed the planet's brightness and position with an MCMC analysis, and we provide a derivation of the photometric error budget.Comment: 16 pages, 9 figures, accepted for publication in A&A, PynPoint is available at https://github.com/PynPoint/PynPoin

Genomic Prediction of Single Crosses in the Early Stages of a Maize Hybrid Breeding Pipeline

Prediction of single-cross performance has been a major goal of plant breeders since the beginning of hybrid breeding. Recently, genomic prediction has shown to be a promising approach, but only limited studies have examined the accuracy of predicting single-cross performance. Moreover, no studies have examined the potential of predicting single crosses among random inbreds derived from a series of biparental families, which resembles the structure of germplasm comprising the initial stages of a hybrid maize breeding pipeline. The main objectives of this study were to evaluate the potential of genomic prediction for identifying superior single crosses early in the hybrid breeding pipeline and optimize its application. To accomplish these objectives, we designed and analyzed a novel population of single crosses representing the Iowa Stiff Stalk synthetic/non-Stiff Stalk heterotic pattern commonly used in the development of North American commercial maize hybrids. The performance of single crosses was predicted using parental combining ability and covariance among single crosses. Prediction accuracies were estimated using cross-validation and ranged from 0.28 to 0.77 for grain yield, 0.53 to 0.91 for plant height, and 0.49 to 0.94 for staygreen, depending on the number of tested parents of the single cross and genomic prediction method used. The genomic estimated general and specific combining abilities showed an advantage over genomic covariances among single crosses when one or both parents of the single cross were untested. Overall, our results suggest that genomic prediction of single crosses in the early stages of a hybrid breeding pipeline holds great potential to redesign hybrid breeding and increase its efficiency

Evolution of mud-crack patterns during repeated drying cycles

In mud, crack patterns are frequently seen with either an approximately rectilinear or hexagonal tiling. Here we show, experimentally, how a desiccation crack pattern changes from being dominated by 90° joint angles, to 120° joint angles. Layers of bentonite clay, a few mm thick, were repeatedly wetted and dried. When dried, the layers crack. These cracks visibly close when rewetted, but a similar crack pattern forms when the layer is redried, with cracks forming along the lines of previously open cracks. Time-lapse photography was used to show how the sequence in which individual cracks open is different in each generation of drying. The geometry of the crack pattern was observed after each of 25 generations of wetting and drying. The angles between cracks were found to approach 120°, with a relaxation time of approximately 4 generations. This was accompanied by a gradual change in the position of the crack vertices, as the crack pattern evolved. A simple model of crack behavior in a layer where the positions of previously open cracks define lines of weakness is developed to explain these observations

Suppression of inelastic collisions of polar 1Σ^1 \Sigma state molecules in an electrostatic field

Collisions of polar $^{1}\Sigma$ state molecules at ultralow energies are considered, within a model that accounts for long-range dipole-dipole interactions, plus rotation of the molecules. We predict a substantial suppression of dipole-driven inelastic collisions at high values of the applied electric field, namely, field values of several times $B_e/\mu$. Here $B_e$ is the rotational constant, and $\mu$ is the electric dipole moment of molecules. The sudden large drop in the inelastic cross section is attributed to the onset of degeneracy between molecular rotational levels, which dramatically alters the scattering Hamiltonian. As a result of the large ratio of elastic to inelastic collision rates, we predict that evaporative cooling may be feasible for $^{1}\Sigma$ state molecules in weak-field-seeking states, provided a large bias electric field is present

Field-linked States of Ultracold Polar Molecules

We explore the character of a novel set of ``field-linked'' states that were predicted in [A. V. Avdeenkov and J. L. Bohn, Phys. Rev. Lett. 90, 043006 (2003)]. These states exist at ultralow temperatures in the presence of an electrostatic field, and their properties are strongly dependent on the field's strength. We clarify the nature of these quasi-bound states by constructing their wave functions and determining their approximate quantum numbers. As the properties of field-linked states are strongly defined by anisotropic dipolar and Stark interactions, we construct adiabatic surfaces as functions of both the intermolecular distance and the angle that the intermolecular axis makes with the electric field. Within an adiabatic approximation we solve the 2-D Schrodinger equation to find bound states, whose energies correlate well with resonance features found in fully-converged multichannel scattering calculations

Faint Infrared Flares from the Microquasar GRS 1915+105

We present simultaneous infrared and X-ray observations of the Galactic microquasar GRS 1915+105 using the Palomar 5-m telescope and Rossi X-ray Timing Explorer on July 10, 1998 UT. Over the course of 5 hours, we observed 6 faint infrared (IR) flares with peak amplitudes of $\sim 0.3-0.6$ mJy and durations of $\sim 500-600$ seconds. These flares are associated with X-ray soft-dip/soft-flare cycles, as opposed to the brighter IR flares associated with X-ray hard-dip/soft-flare cycles seen in August 1997 by Eikenberry et al. (1998). Interestingly, the IR flares begin {\it before} the X-ray oscillations, implying an ``outside-in'' origin of the IR/X-ray cycle. We also show that the quasi-steady IR excess in August 1997 is due to the pile-up of similar faint flares. We discuss the implications of this flaring behavior for understanding jet formation in microquasars.Comment: 10 pages, 4 figures Accepted for publication in ApJ Letter

Cardiovascular Dysfunction Criteria in Critically Ill Children: The PODIUM Consensus Conference

CONTEXT Cardiovascular dysfunction is associated with poor outcomes in critically ill children. OBJECTIVE We aim to derive an evidence-informed, consensus-based definition of cardiovascular dysfunction in critically ill children. DATA SOURCES Electronic searches of PubMed and Embase were conducted from January 1992 to January 2020 using medical subject heading terms and text words to define concepts of cardiovascular dysfunction, pediatric critical illness, and outcomes of interest. STUDY SELECTION Studies were included if they evaluated critically ill children with cardiovascular dysfunction and assessment and/or scoring tools to screen for cardiovascular dysfunction and assessed mortality, functional status, organ-specific, or other patient-centered outcomes. Studies of adults, premature infants (≤36 weeks gestational age), animals, reviews and/or commentaries, case series (sample size ≤10), and non-English-language studies were excluded. Studies of children with cyanotic congenital heart disease or cardiovascular dysfunction after cardiopulmonary bypass were excluded. DATA EXTRACTION Data were abstracted from each eligible study into a standard data extraction form, along with risk-of-bias assessment by a task force member. RESULTS Cardiovascular dysfunction was defined by 9 elements, including 4 which indicate severe cardiovascular dysfunction. Cardiopulmonary arrest (>5 minutes) or mechanical circulatory support independently define severe cardiovascular dysfunction, whereas tachycardia, hypotension, vasoactive-inotropic score, lactate, troponin I, central venous oxygen saturation, and echocardiographic estimation of left ventricular ejection fraction were included in any combination. There was expert agreement (>80%) on the definition. LIMITATIONS All included studies were observational and many were retrospective. CONCLUSIONS The Pediatric Organ Dysfunction Information Update Mandate panel propose this evidence-informed definition of cardiovascular dysfunction

Applying a temporal systematics model to vector Apodizing Phase Plate coronagraphic data: TRAP4vAPP

The vector Apodizing Phase Plate (vAPP) is a pupil plane coronagraph that suppresses starlight by forming a dark hole in its point spread function (PSF). The unconventional and non-axisymmetrical PSF arising from the phase modification applied by this coronagraph presents a special challenge to post-processing techniques. We aim to implement a recently developed post-processing algorithm, temporal reference analysis of planets (TRAP) on vAPP coronagraphic data. The property of TRAP that uses non-local training pixels, combined with the unconventional PSF of vAPP, allows for more flexibility than previous spatial algorithms in selecting reference pixels to model systematic noise. Datasets from two types of vAPPs are analysed: a double grating-vAPP (dgvAPP360) that produces a single symmetric PSF and a grating-vAPP (gvAPP180) that produces two D-shaped PSFs. We explore how to choose reference pixels to build temporal systematic noise models in TRAP for them. We then compare the performance of TRAP with previously implemented algorithms that produced the best signal-to-noise ratio (S/N) in companion detections in these datasets. We find that the systematic noise between the two D-shaped PSFs is not as temporally associated as expected. Conversely, there is still a significant number of systematic noise sources that are shared by the dark hole and the bright side in the same PSF. We should choose reference pixels from the same PSF when reducing the dgvAPP360 dataset or the gvAPP180 dataset with TRAP. In these datasets, TRAP achieves results consistent with previous best detections, with an improved S/N for the gvAPP180 dataset.Comment: 15 pages, 10 figures, accepted to A&

Genetic interaction mapping informs integrative structure determination of protein complexes

Determining structures of protein complexes is crucial for understanding cellular functions. Here, we describe an integrative structure determination approach that relies on in vivo measurements of genetic interactions. We construct phenotypic profiles for point mutations crossed against gene deletions or exposed to environmental perturbations, followed by converting similarities between two profiles into an upper bound on the distance between the mutated residues. We determine the structure of the yeast histone H3-H4 complex based on similar to 500,000 genetic interactions of 350 mutants. We then apply the method to subunits Rpb1-Rpb2 of yeast RNA polymerase II and subunits RpoB-RpoC of bacterial RNA polymerase. The accuracy is comparable to that based on chemical cross-links; using restraints from both genetic interactions and cross-links further improves model accuracy and precision. The approach provides an efficient means to augment integrative structure determination with in vivo observations

The B-Star Exoplanet Abundance Study: a co-moving 16-25 Mjup companion to the young binary system HIP 79098

Wide low-mass substellar companions are known to be very rare among low-mass stars, but appear to become increasingly common with increasing stellar mass. However, B-type stars, which are the most massive stars within ~150 pc of the Sun, have not yet been examined to the same extent as AFGKM-type stars in that regard. In order to address this issue, we launched the ongoing B-star Exoplanet Abundance Study (BEAST) to examine the frequency and properties of planets, brown dwarfs, and disks around B-type stars in the Scorpius-Centaurus (Sco-Cen) association; we also analyzed archival data of B-type stars in Sco-Cen. During this process, we identified a candidate substellar companion to the B9-type spectroscopic binary HIP 79098 AB, which we refer to as HIP 79098 (AB)b. The candidate had been previously reported in the literature, but was classified as a background contaminant on the basis of its peculiar colors. Here we demonstrate that the colors of HIP 79098 (AB)b are consistent with several recently discovered young and low-mass brown dwarfs, including other companions to stars in Sco-Cen. Furthermore, we show unambiguous common proper motion over a 15-year baseline, robustly identifying HIP 79098 (AB)b as a bona fide substellar circumbinary companion at a 345+/-6 AU projected separation to the B9-type stellar pair. With a model-dependent mass of 16-25 Mjup yielding a mass ratio of <1%, HIP 79098 (AB)b joins a growing number of substellar companions with planet-like mass ratios around massive stars. Our observations underline the importance of common proper motion analysis in the identification of physical companionship, and imply that additional companions could potentially remain hidden in the archives of purely photometric surveys.Comment: 9 pages, 6 figures, accepted for publication in A&