A New High Contrast Imaging Program at Palomar Observatory

We describe a new instrument that forms the core of a long-term high contrast imaging program at the 200-inch Hale Telescope at Palomar Observatory. The primary scientific thrust is to obtain images and low-resolution spectroscopy of brown dwarfs and young Jovian mass exoplanets in the vicinity of stars within 50 parsecs of the Sun. The instrument is a microlens-based integral field spectrograph integrated with a diffraction limited, apodized-pupil Lyot coronagraph, mounted behind the Palomar adaptive optics system. The spectrograph obtains imaging in 23 channels across the J and H bands (1.06 - 1.78 microns). In addition to obtaining spectra, this wavelength resolution allows suppression of the chromatically dependent speckle noise, which we describe. We have recently installed a novel internal wave front calibration system that will provide continuous updates to the AO system every 0.5 - 1.0 minutes by sensing the wave front within the coronagraph. The Palomar AO system is undergoing an upgrade to a much higher-order AO system ("PALM-3000"): a 3388-actuator tweeter deformable mirror working together with the existing 241-actuator mirror. This system will allow correction with subapertures as small as 8cm at the telescope pupil using natural guide stars. The coronagraph alone has achieved an initial dynamic range in the H-band of 2 X 10^-4 at 1 arcsecond, without speckle noise suppression. We demonstrate that spectral speckle suppression is providing a factor of 10-20 improvement over this bringing our current contrast at an arcsecond to ~2 X 10^-5. This system is the first of a new generation of apodized pupil coronagraphs combined with high-order adaptive optics and integral field spectrographs (e.g. GPI, SPHERE, HiCIAO), and we anticipate this instrument will make a lasting contribution to high contrast imaging in the Northern Hemisphere for years.Comment: Accepted to PASP: 12 pages, 12 figure

Real-time wavefront control for the PALM-3000 high order adaptive optics system

We present a cost-effective scalable real-time wavefront control architecture based on off-the-shelf graphics processing units hosted in an ultra-low latency, high-bandwidth interconnect PC cluster environment composed of modules written in the component-oriented language of nesC. We demonstrate the architecture is capable of supporting the most computation and memory intensive wavefront reconstruction method (vector-matrix-multiply) at frame rates up to 2 KHz with latency under 250 &mgr;s for the PALM-3000 adaptive optics systems, a state-of-the-art upgrade on the 5.1 meter Hale Telescope that consists of a 64x64 subaperture Shack-Hartmann wavefront sensor and a 3368 active actuator high order deformable mirror in series with a 349 actuator "woofer" DM. This architecture can easily scale up to support larger AO systems at higher rates and lower latency

A Close Companion Search Around L Dwarfs Using Aperture Masking Interferometry and Palomar Laser Guide Star Adaptive Optics

We present a close companion search around 16 known early L dwarfs using aperture masking interferometry with Palomar laser guide star adaptive optics (LGS AO). The use of aperture masking allows the detection of close binaries, corresponding to projected physical separations of 0.6-10.0 AU for the targets of our survey. This survey achieved median contrast limits of ΔK ~ 2.3 for separations between 1.2λ/D-4λ/D and ΔK ~ 1.4 at 2/3λ/D. We present four candidate binaries detected with moderate-to-high confidence (90%-98%). Two have projected physical separations less than 1.5 AU. This may indicate that tight-separation binaries contribute more significantly to the binary fraction than currently assumed, consistent with spectroscopic and photometric overluminosity studies. Ten targets of this survey have previously been observed with the Hubble Space Telescope as part of companion searches. We use the increased resolution of aperture masking to search for close or dim companions that would be obscured by full aperture imaging, finding two candidate binaries. This survey is the first application of aperture masking with LGS AO at Palomar. Several new techniques for the analysis of aperture masking data in the low signal-to-noise regime are explored

Know The Star, Know the Planet. IV. A Stellar Companion to the Host star of the Eccentric Exoplanet HD 8673b

HD 8673 hosts a massive exoplanet in a highly eccentric orbit (e=0.723). Based on two epochs of speckle interferometry a previous publication identified a candidate stellar companion. We observed HD 8673 multiple times with the 10 m Keck II telescope, the 5 m Hale telescope, the 3.63 m AEOS telescope and the 1.5m Palomar telescope in a variety of filters with the aim of confirming and characterizing the stellar companion. We did not detect the candidate companion, which we now conclude was a false detection, but we did detect a fainter companion. We collected astrometry and photometry of the companion on six epochs in a variety of filters. The measured differential photometry enabled us to determine that the companion is an early M dwarf with a mass estimate of 0.33-0.45 M?. The companion has a projected separation of 10 AU, which is one of the smallest projected separations of an exoplanet host binary system. Based on the limited astrometry collected, we are able to constrain the orbit of the stellar companion to a semi-major axis of 35{60 AU, an eccentricity ? 0.5 and an inclination of 75{85?. The stellar companion has likely strongly in uenced the orbit of the exoplanet and quite possibly explains its high eccentricity.Comment: Accepted to the Astronomical Journal, 6 Pages, 5 Figure

Exome sequencing reveals independent SGCD deletions causing limb girdle muscular dystrophy in Boston terriers

Background: Limb-girdle muscular dystrophies (LGMDs) are a heterogeneous group of inherited autosomal myopathies that preferentially affect voluntary muscles of the shoulders and hips. LGMD has been clinically described in several breeds of dogs, but the responsible mutations are unknown. The clinical presentation in dogs is characterized by marked muscle weakness and atrophy in the shoulder and hips during puppyhood. Methods: Following clinical evaluation, the identification of the dystrophic histological phenotype on muscle histology, and demonstration of the absence of sarcoglycan-sarcospan complex by immunostaining, whole exome sequencing was performed on five Boston terriers: one affected dog and its three family members and one unrelated affected dog. Results: Within sarcoglycan-delta (SGCD), a two base pair deletion segregating with LGMD in the family was discovered, and a deletion encompassing exons 7 and 8 was found in the unrelated dog. Both mutations are predicted to cause an absence of SGCD protein, confirmed by immunohistochemistry. The mutations are private to each family. Conclusions: Here, we describe the first cases of canine LGMD characterized at the molecular level with the classification of LGMD2F.Peer reviewe

Socioeconomic Status and Prevalence of Obesity and Diabetes in a Mexican American Community, Cameron County, Texas, 2004-2007

Rates of obesity and diabetes in this border community are among the highest in the United States. Belonging to the lower socioeconomic stratum significantly increased the likelihood of having undiagnosed diabetes and, in patients too young to be eligible for Medicare, the overall risk of developing diabetes. Modest improvement in income has a beneficial effect on health in this racial/ethnic minority community

Design and performance of the PALM-3000 3.5 kHz upgrade

PALM-3000 (P3K), the second-generation adaptive optics (AO) instrument for the 5.1 meter Hale telescope at Palomar Observatory, underwent a significant upgrade to its wavefront sensor (WFS) arm and real-time control (RTC) system in late 2019. Main features of this upgrade include an EMCCD WFS camera capable of 3.5 kHz framerates and advanced Digital Signal Processor (DSP) boards to replace the aging GPU based real-time control system. With this upgrade P3K is able to maintain a lock on natural guide stars fainter than mV=16. Here we present the design and on-sky re-commissioning results of the upgraded system

Comparing sensitivity to change using the 6-item versus the 17-item Hamilton Depression Rating Scale in the GUIDED randomized controlled trial

BACKGROUND: Previous research suggests that the 17-item Hamilton Depression Rating Scale (HAM-D17) is less sensitive in detecting differences between active treatment and placebo for major depressive disorder (MDD) than is the HAM-D6 scale, which focuses on six core depression symptoms. Whether HAM-D6 shows greater sensitivity when comparing two active MDD treatment arms is unknown. METHODS: This post hoc analysis used data from the intent-to-treat (ITT) cohort (N = 1541) of the Genomics Used to Improve DEpression Decisions (GUIDED) trial, a rater- and patient-blinded randomized controlled trial. GUIDED compared combinatorial pharmacogenomics-guided care with treatment as usual (TAU) in patients with MDD. Percent of symptom improvement, response rate and remission rate from baseline to week 8 were evaluated using both scales. Analyses were performed for the full cohort and for the subset of patients who at baseline were taking medications predicted by the test to have moderate or significant gene-drug interactions. A Mokken scale analysis was conducted to compare the homogeneity of HAM-D17 with that of HAM-D6. RESULTS: At week 8, the guided-care arm demonstrated statistically significant benefit over TAU when the HAM-D6 (∆ = 4.4%, p = 0.023) was used as the continuous measure of symptom improvement, but not when using the HAM-D17 (∆ = 3.2%, p = 0.069). Response rates increased significantly for guided-care compared with TAU when evaluated using both HAM-D6 (∆ = 7.0%, p = 0.004) and HAM-D17 (∆ = 6.3%, p = 0.007). Remission rates also were significantly greater for guided-care versus TAU using both measures (HAM-D6 ∆ = 4.6%, p = 0.031; HAM-D17 ∆ = 5.5%, p = 0.005). Patients in the guided-care arm who at baseline were taking medications predicted to have gene-drug interactions showed further increased benefit over TAU at week 8 for symptom improvement (∆ = 7.3%, p = 0.004) response (∆ = 10.0%, p = 0.001) and remission (∆ = 7.9%, p = 0.005) using HAM-D6. All outcomes showed continued improvement through week 24. Mokken scale analysis demonstrated the homogeneity and unidimensionality of HAM-D6, but not of HAM-D17, across treatment arms. CONCLUSIONS: The HAM-D6 scale identified a statistically significant difference in symptom improvement between combinatorial pharmacogenomics-guided care and TAU, whereas the HAM-D17 did not. The demonstrated utility of pharmacogenomics-guided treatment over TAU as detected by the HAM-D6 highlights its value for future biomarker-guided trials comparing active treatment arms. TRIAL REGISTRATION: Clinicaltrials.gov: NCT02109939. Registered 10 April 2014

Microbiome function predicts amphibian chytridiomycosis disease dynamics

[Background] The fungal pathogenBatrachochytrium dendrobatidis (Bd) threatens amphibian biodiversity and ecosystem stability worldwide. Amphibian skin microbial community structure has been linked to the clinical outcome of Bd infections, yet its overall functional importance is poorly understood. [Methods] Microbiome taxonomic and functional profiles were assessed using high-throughput bacterial 16S rRNA and fungal ITS2 gene sequencing, bacterial shotgun metagenomics and skin mucosal metabolomics. We sampled 56 wild midwife toads (Alytes obstetricans) from montane populations exhibiting Bd epizootic or enzootic disease dynamics. In addition, to assess whether disease-specific microbiome profiles were linked to microbe-mediated protection or Bd-induced perturbation, we performed a laboratory Bd challenge experiment whereby 40 young adult A. obstetricans were exposed to Bd or a control sham infection. We measured temporal changes in the microbiome as well as functional profiles of Bd-exposed and control animals at peak infection. [Results] Microbiome community structure and function differed in wild populations based on infection history and in experimental control versus Bd-exposed animals. Bd exposure in the laboratory resulted in dynamic changes in microbiome community structure and functional differences, with infection clearance in all but one infected animal. Sphingobacterium, Stenotrophomonas and an unclassified Commamonadaceae were associated with wild epizootic dynamics and also had reduced abundance in laboratory Bd-exposed animals that cleared infection, indicating a negative association with Bd resistance. This was further supported by microbe-metabolite integration which identified functionally relevant taxa driving disease outcome, of which Sphingobacterium and Bd were most influential in wild epizootic dynamics. The strong correlation between microbial taxonomic community composition and skin metabolome in the laboratory and field is inconsistent with microbial functional redundancy, indicating that differences in microbial taxonomy drive functional variation. Shotgun metagenomic analyses support these findings, with similar disease-associated patterns in beta diversity. Analysis of differentially abundant bacterial genes and pathways indicated that bacterial environmental sensing and Bd resource competition are likely to be important in driving infection outcomes. [Conclusions] Bd infection drives altered microbiome taxonomic and functional profiles across laboratory and field environments. Our application of multi-omics analyses in experimental and field settings robustly predicts Bd disease dynamics and identifies novel candidate biomarkers of infection. [MediaObject not available: see fulltext.]K.A.B. was funded by a CASE studentship from NERC, NERC Biomolecular Analysis Facility grant (NBAF939) and an E.P. Abraham Junior Research Fellowship from St Hilda’s College, University of Oxford. M.C.F and T.W.J.G. were funded by NERC award NE/E006701/1 and the Biodiversa project RACE: Risk Assessment of Chytridiomycosis to European Amphibian Biodiversity. T.W.J.G was also funded by Research England and NERC NE/S000062/1. D.S.S. and A.L. received funding through the project People, Pollution, and Pathogens financed through the call “Mountains as Sentinels of Change” by the Belmont-Forum (ANR-15-MASC-0001 - P3, DFG-SCHM3059/6-1, NERC-1633948, NSFC-41661144004). D.S.S. holds the AXA Chair for Functional Mountain Ecology funded by the AXA Research Fund through the project GloMEc and M.C.F. is a fellow in the CIFAR ‘Fungal Kingdoms’ Program

Design and implementation of the PALM-3000 real-time control system

This paper reflects, from a computational perspective, on the experience gathered in designing and implementing realtime control of the PALM-3000 adaptive optics system currently in operation at the Palomar Observatory. We review the algorithms that serve as functional requirements driving the architecture developed, and describe key design issues and solutions that contributed to the system's low compute-latency. Additionally, we describe an implementation of dense matrix-vector-multiplication for wavefront reconstruction that exceeds 95% of the maximum sustained achievable bandwidth on NVIDIA Geforce 8800GTX GPU