PDCM Finder: an open global research platform for patient-derived cancer models.

PDCM Finder (www.cancermodels.org) is a cancer research platform that aggregates clinical, genomic and functional data from patient-derived xenografts, organoids and cell lines. It was launched in April 2022 as a successor of the PDX Finder portal, which focused solely on patient-derived xenograft models. Currently the portal has over 6200 models across 13 cancer types, including rare paediatric models (17%) and models from minority ethnic backgrounds (33%), making it the largest free to consumer and open access resource of this kind. The PDCM Finder standardises, harmonises and integrates the complex and diverse data associated with PDCMs for the cancer community and displays over 90 million data points across a variety of data types (clinical metadata, molecular and treatment-based). PDCM data is FAIR and underpins the generation and testing of new hypotheses in cancer mechanisms and personalised medicine development

Improved Orbital Constraints and Hα\alpha Photometric Monitoring of the Directly Imaged Protoplanet Analog HD 142527 B

Companions embedded in the cavities of transitional circumstellar disks have been observed to exhibit excess luminosity at H$\alpha$, an indication that they are actively accreting. We report 5 years (2013-2018) of monitoring of the position and H$\alpha$ excess luminosity of the embedded, accreting low-mass stellar companion HD 142527 B from the MagAO/VisAO instrument. We use pyklip, a python implementation of the Karhounen-Loeve Image Processing algorithm, to detect the companion. Using pyklip forward modeling, we constrain the relative astrometry to $1-2 \mathrm{mas}$ precision and achieve sufficient photometric precision ($\pm0.2 \mathrm{mag}, 3\%$ error) to detect changes in the H$\alpha$ contrast of the companion over time. In order to accurately determine the relative astrometry of the companion, we conduct an astrometric calibration of the MagAO/VisAO camera against 20 years of Keck/NIRC2 images of the Trapezium cluster. We demonstrate agreement of our VisAO astrometry with other published positions for HD 142527 B, and use orbitize! to generate a posterior distribution of orbits fit to the relative astrometry of HD 142527 B. Our data suggest that the companion is close to periastron passage, on an orbit significantly misinclined with respect to both the wide circumbinary disk and the recently observed inner disk encircling HD 142527 A. We translate observed H-alpha contrasts for HD 142527 B into mass accretion rate estimates on the order of $4-9\times10^{-10} \mathrm{M_\odot}\mathrm{yr}^{-1}$. Photometric variation in the H-alpha excess of the companion suggests that the accretion rate onto the companion is variable. This work represents a significant step towards observing accretion-driven variability onto protoplanets, such as PDS 70 b\&c.Comment: Accepted to the Astronomical Journal. 32 pages, 16 figures, 8 tables, 4 appendice

The Giant Accreting Protoplanet Survey (GAPlanetS) -- Results from a Six Year Campaign to Image Accreting Protoplanets

Accreting protoplanets represent a window into planet formation processes. We report H{\alpha} differential imaging results from the deepest and most comprehensive accreting protoplanet survey to date, acquired with the Magellan Adaptive Optics (MagAO) system's VisAO camera. The fourteen transitional disks targeted are ideal candidates for protoplanet discovery due to their wide, heavily depleted central cavities, wealth of non-axisymmetric circumstellar disk features evocative of ongoing planet formation, and ongoing stellar accretion. To address the twin challenges of morphological complexity in the target systems and PSF instability, we develop novel approaches for frame selection and optimization of the Karhounen-Loeve Image Processing algorithm pyKLIP. We detect one new candidate protoplanet, CS Cha "c", at a separation of 75mas and a {\Delta}mag of 5.1 and robustly recover the HD142527 B and HD100453 B low mass stellar companions across multiple epochs. Though we cannot rule out a substantial scattered light contribution to its emission, we also recover LkCa 15 b. Its presence inside of the cleared disk cavity and consistency with a forward-modeled point source suggest that it remains a viable protoplanet candidate. The protoplanet PDS 70 c was marginally recovered under our conservative general methodology. However, through targeted optimization in H{\alpha} imagery, we tentatively recover PDS 70 c in three epochs and PDS 70 b in one epoch. Of the many other previously-reported companions and companion candidates around objects in the sample, we do not recover any additional robust candidates. However, lack of recovery at moderate H{\alpha} contrast does not rule out the presence of protoplanets at these locations, and we report limiting H{\alpha} contrasts in such cases.Comment: Accepted for publication in A

Successful Surgical Therapy of a Double Aortic Arch in a 10-Month-Old Mixed Breed Dog

A 10-month-old female spayed mixed breed dog with a suspected vascular ring anomaly was presented for exercise intolerance and wheezing. Computed tomography (CT) revealed a double aortic arch. The smaller right aortic arch was successfully ligated via right 4th intercostal thoracotomy. The patient was discharged one day postoperatively and continued to have good outcome at recheck 3.5 weeks after surgery. This is the 4th documented case of double aortic arch with a successful outcome. Preoperative CT scan was vital in preoperative planning and should be strongly recommended in all cases of suspected vascular ring anomalies with atypical presentation

The Giant Accreting Protoplanet Survey (GAPlanetS): Optimization Techniques for Robust Detections of Protoplanets

High-contrast imaging has afforded astronomers the opportunity to study light directly emitted by adolescent (tens of megayears) and “proto” (<10 Myr) planets still undergoing formation. Direct detection of these planets is enabled by empirical point-spread function (PSF) modeling and removal algorithms. The computational intensity of such algorithms, as well as their multiplicity of tunable input parameters, has led to the prevalence of ad hoc optimization approaches to high-contrast imaging results. In this work, we present a new, systematic approach to optimization vetted using data of the high-contrast stellar companion HD 142527 B from the Magellan Adaptive Optics Giant Accreting Protoplanet Survey (GAPlanetS). More specifically, we present a grid search technique designed to explore three influential parameters of the PSF subtraction algorithm pyKLIP : annuli, movement, and KL modes. We consider multiple metrics for postprocessed image quality in order to optimally recover at H α (656 nm) synthetic planets injected into contemporaneous continuum (643 nm) images. These metrics include peak (single-pixel) signal-to-noise ratio (S/N), average (multipixel average) S/N, 5 σ contrast, and false-positive fraction. We apply continuum-optimized KLIP reduction parameters to six H α direct detections of the low-mass stellar companion HD 142527 B and recover the companion at a range of separations. Relative to a single-informed, nonoptimized set of KLIP parameters applied to all data sets uniformly, our multimetric grid search optimization led to improvements in companion S/N of up to 1.2 σ , with an average improvement of 0.6 σ . Since many direct imaging detections lie close to the canonical 5 σ threshold, even such modest improvements may result in higher yields in future imaging surveys

The EurOPDX Data Portal: an open platform for patient-derived cancer xenograft data sharing and visualization.

BACKGROUND: Patient-derived xenografts (PDX) mice models play an important role in preclinical trials and personalized medicine. Sharing data on the models is highly valuable for numerous reasons - ethical, economical, research cross validation etc. The EurOPDX Consortium was established 8 years ago to share such information and avoid duplicating efforts in developing new PDX mice models and unify approaches to support preclinical research. EurOPDX Data Portal is the unified data sharing platform adopted by the Consortium. MAIN BODY: In this paper we describe the main features of the EurOPDX Data Portal ( https://dataportal.europdx.eu/ ), its architecture and possible utilization by researchers who look for PDX mice models for their research. The Portal offers a catalogue of European models accessible on a cooperative basis. The models are searchable by metadata, and a detailed view provides molecular profiles (gene expression, mutation, copy number alteration) and treatment studies. The Portal displays the data in multiple tools (PDX Finder, cBioPortal, and GenomeCruzer in future), which are populated from a common database displaying strictly mutually consistent views. (SHORT) CONCLUSION: EurOPDX Data Portal is an entry point to the EurOPDX Research Infrastructure offering PDX mice models for collaborative research, (meta)data describing their features and deep molecular data analysis according to users\u27 interests

The EurOPDX Data Portal: an open platform for patient-derived cancer xenograft data sharing and visualization

BACKGROUND: Patient-derived xenografts (PDX) mice models play an important role in preclinical trials and personalized medicine. Sharing data on the models is highly valuable for numerous reasons – ethical, economical, research cross validation etc. The EurOPDX Consortium was established 8 years ago to share such information and avoid duplicating efforts in developing new PDX mice models and unify approaches to support preclinical research. EurOPDX Data Portal is the unified data sharing platform adopted by the Consortium. MAIN BODY: In this paper we describe the main features of the EurOPDX Data Portal (https://dataportal.europdx.eu/), its architecture and possible utilization by researchers who look for PDX mice models for their research. The Portal offers a catalogue of European models accessible on a cooperative basis. The models are searchable by metadata, and a detailed view provides molecular profiles (gene expression, mutation, copy number alteration) and treatment studies. The Portal displays the data in multiple tools (PDX Finder, cBioPortal, and GenomeCruzer in future), which are populated from a common database displaying strictly mutually consistent views. (SHORT) CONCLUSION: EurOPDX Data Portal is an entry point to the EurOPDX Research Infrastructure offering PDX mice models for collaborative research, (meta)data describing their features and deep molecular data analysis according to users’ interests

Prediction of the planet yield of the MaxProtoPlanetS high-contrast survey for H-alpha protoplanets with MagAO-X based on first light contrasts

Our past GAPplanetS survey over the last 5 years with the MagAO visible AO system discovered the first examples of accreting protoplanets (by direct observation of H-alpha emission). Examples include LkCa15 b (Sallum et al. 2015) and PDS70 b (Wagner et al. 2018). In this paper we review the science performance of the newly (Dec. 2019) commissioned MagAO-X extreme AO system. In particular, we use the vAPP coronagraphic contrasts measured during MagAO-X first light. We use the Massive Accreting Gap (MAG) protoplanet model of Close 2020 to predict the H-alpha contrasts of 19 of the best transitional disk systems (ages 1-5 Myr) for the direct detection of H-alpha from accretion of hydrogen onto these protoplanets. The MAG protoplanet model applied to the observed first light MagAO-X contrasts predict a maximum yield of 46±7 planets from 19 stars (42 of these planets would be new discoveries). This suggests that there is a large, yet, unexplored reservoir of protoplanets that can be discovered with an extreme AO coronagraphic survey of 19 of the best transitional disk systems. Based on our first light contrasts we predict a healthy yield of protoplanets from our MaxProtoPlanetS survey of 19 transitional disks with MagAO-X. © 2020 SPIE.This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]