A. J. Connolly

McGill University, Montréal, Quebec, Canada

Are you A. J. Connolly?

Claim your profile

Publications (311)1068.49 Total impact

  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The Large Synoptic Survey Telescope (LSST) is a large-aperture, wide-field, ground-based survey system that will image the sky in six optical bands from 320 to 1050 nm, uniformly covering approximately $18,000$deg$^2$ of the sky over 800 times. The LSST is currently under construction on Cerro Pach\'on in Chile, and expected to enter operations in 2022. Once operational, the LSST will explore a wide range of astrophysical questions, from discovering "killer" asteroids to examining the nature of Dark Energy. The LSST will generate on average 15 TB of data per night, and will require a comprehensive Data Management system to reduce the raw data to scientifically useful catalogs and images with minimum human intervention. These reductions will result in a real-time alert stream, and eleven data releases over the 10-year duration of LSST operations. To enable this processing, the LSST project is developing a new, general-purpose, high-performance, scalable, well documented, open source data processing software stack for O/IR surveys. Prototypes of this stack are already capable of processing data from existing cameras (e.g., SDSS, DECam, MegaCam), and form the basis of the Hyper-Suprime Cam (HSC) Survey data reduction pipeline.
    Preview · Article · Dec 2015
  • [Show abstract] [Hide abstract]
    ABSTRACT: Rationale: Genetic variation at the chromosome 9p21 cardiovascular risk locus has been associated with peripheral artery disease (PAD), but its mechanism remains unknown. Objective: To determine whether this association is secondary to an increase in atherosclerosis, or is the result of a separate angiogenesis-related mechanism. Methods and results: Quantitative evaluation of human vascular samples revealed that carriers of the 9p21 risk allele possess a significantly higher burden of immature intraplaque microvessels than carriers of the ancestral allele, irrespective of lesion size or patient comorbidity. To determine whether aberrant angiogenesis also occurs under non-atherosclerotic conditions, we performed femoral artery ligation surgery in mice lacking the 9p21 candidate gene, Cdkn2b. These animals developed advanced hind-limb ischemia and digital auto-amputation, secondary to a defect in the capacity of the Cdkn2b-deficient smooth muscle cell (SMC) to support the developing neovessel. Microarray studies identified impaired TGFβ signaling in cultured CDKN2B-deficient cells, as well as TGFβ1 upregulation in the vasculature of 9p21 risk allele carriers. Molecular signaling studies indicated that loss of CDKN2B impairs the expression of the inhibitory factor, SMAD-7, which promotes downstream TGFβ activation. Ultimately, this manifests in the upregulation of a poorly studied effector molecule, TGFβ1-induced-1, which is a TGFβ-'rheostat' known to have antagonistic effects on the EC and SMC. Dual knockdown studies confirmed the reversibility of the proposed mechanism, in vitro. Conclusions: These results suggest that loss of CDKN2B may not only promote cardiovascular disease through the development of atherosclerosis, but may also impair TGFβ signaling and hypoxic neovessel maturation.
    No preview · Article · Nov 2015 · Circulation Research
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Tissue engineering approaches may improve survival and functional benefits from human embryonic stem cell-derived cardiomyocte (ESC-CM) transplantation, thereby potentially preventing dilative remodelling and progression to heart failure. Assessment of transport stability, long term survival, structural organisation, functional benefits, and teratoma risk of engineered heart muscle (EHM) in a chronic myocardial infarction (MI) model. We constructed EHMs from ESC-CMs and released them for transatlantic shipping following predefined quality control criteria. Two days of shipment did not lead to adverse effects on cell viability or contractile performance of EHMs (n=3, P=0.83, P=0.87). After ischemia / reperfusion (I/R) injury, EHMs were implanted onto immunocompromised rat hearts at 1 month to simulate chronic ischemia. Bioluminescence imaging (BLI) showed stable engraftment with no significant cell loss between week 2 and 12 (n=6, P=0.67), preserving up to 25% of the transplanted cells. Despite high engraftment rates and attenuated disease progression (change in ejection fraction for EHMs -6.7±1.4% vs control -10.9±1.5%, n>12, P=0.05), we observed no difference between EHMs containing viable or non-viable human cardiomyocytes in this chronic xenotransplantation model (n>12, P=0.41). Grafted cardiomyocytes showed enhanced sarcomere alignment and increased connexin 43 expression at 220 days after transplantation. No teratomas or tumors were found in any of the animals (n=14) used for long-term monitoring. EHM transplantation led to high engraftment rates, long term survival, and progressive maturation of human cardiomyocytes. However, cell engraftment was not correlated with functional improvements in this chronic MI model. Most importantly, the safety of this approach was demonstrated by the lack of tumor or teratoma formation.
    Full-text · Article · Aug 2015 · Circulation Research
  • [Show abstract] [Hide abstract]
    ABSTRACT: Pulmonary arterial hypertension (PAH) is a devastating disorder characterized by progressive elevation of the pulmonary pressures that, in the absence of therapy, results in chronic right-heart failure and premature death. The vascular pathology of PAH is characterized by progressive loss of small (diameter, less than 50 μm) peripheral pulmonary arteries along with abnormal medial thickening, neointimal formation, and intraluminal narrowing of the remaining pulmonary arteries. Vascular pathology correlates with disease severity, given that hemodynamic effects and disease outcomes are worse in patients with advanced compared with lower-grade lesions. Novel imaging tools are urgently needed that demonstrate the extent of vascular remodeling in PAH patients during diagnosis and treatment monitoring. Optical coherence tomography (OCT) is a catheter-based intravascular imaging technique used to obtain high-resolution 2D and 3D cross-sectional images of coronary arteries, thus revealing the extent of vascular wall pathology due to diseases such as atherosclerosis and in-stent restenosis; its utility as a diagnostic tool in the assessment of the pulmonary circulation is unknown. Here we show that OCT provides high-definition images that capture the morphology of pulmonary arterial walls in explanted human lungs and during pulmonary arterial catheterization of an adult pig. We conclude that OCT may facilitate the evaluation of patients with PAH by disclosing the degree of wall remodeling present in pulmonary vessels. Future studies are warranted to determine whether this information complements the hemodynamic and functional assessments routinely performed in PAH patients, facilitates treatment selection, and improves estimates of prognosis and outcome.
    No preview · Article · Jul 2015 · Comparative medicine
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Many scientific data-intensive applications perform iterative computations on array data. There exist multiple engines specialized for array processing. These engines efficiently support various types of operations, but none includes native support for iterative processing. In this paper, we develop a model for iterative array computations and a series of optimizations. We evaluate the benefits of an optimized, native support for iterative array processing on the SciDB engine and real workloads from the astronomy domain.
    Preview · Article · May 2015

  • No preview · Article · Jan 2015 · The Thoracic and Cardiovascular Surgeon
  • [Show abstract] [Hide abstract]
    ABSTRACT: Objective: Rupture and dissection of aortic root aneurysms remain the leading causes of death in patients with the Marfan syndrome, a hereditary connective tissue disorder that affects 1 in 5000 individuals worldwide. In the present study, we use a Marfan mouse model (Fbn1(C1039G/+)) to investigate the biological importance of apoptosis during aneurysm development in Marfan syndrome. Approach and results: Using in vivo single-photon emission computed tomographic-imaging and ex vivo autoradiography for Tc99m-annexin, we discovered increased apoptosis in the Fbn1(C1039G/+) ascending aorta during early aneurysm development peaking at 4 weeks. Immunofluorescence colocalization studies identified smooth muscle cells (SMCs) as the apoptotic cell population. As biological proof of concept that early aortic wall apoptosis plays a role in aneurysm development in Marfan syndrome, Fbn1(C1039G/+) mice were treated daily from 2 to 6 weeks with either (1) a pan-caspase inhibitor, Q-VD-OPh (20 mg/kg), or (2) vehicle control intraperitoneally. Q-VD-OPh treatment led to a significant reduction in aneurysm size and decreased extracellular matrix degradation in the aortic wall compared with control mice. In vitro studies using Fbn1(C1039G/+) ascending SMCs showed that apoptotic SMCs have increased elastolytic potential compared with viable cells, mostly because of caspase activity. Moreover, in vitro (1) cell membrane isolation, (2) immunofluorescence staining, and (3) scanning electron microscopy studies illustrate that caspases are expressed on the exterior cell surface of apoptotic SMCs. Conclusions: Caspase inhibition attenuates aneurysm development in an Fbn1(C1039G/+) Marfan mouse model. Mechanistically, during apoptosis, caspases are expressed on the cell surface of SMCs and likely contribute to elastin degradation and aneurysm development in Marfan syndrome.
    No preview · Article · Oct 2014 · Arteriosclerosis Thrombosis and Vascular Biology
  • [Show abstract] [Hide abstract]
    ABSTRACT: The LSST will, over a 10-year period, produce a multi-color, multi-epoch survey of more than 18000 square degrees of the southern sky. It will generate a multi-petabyte archive of images and catalogs of astrophysical sources from which a wide variety of high-precision statistical studies can be undertaken. To accomplish these goals, the LSST project has developed a suite of modeling and simulation tools for use in validating that the design and the as-delivered components of the LSST system will yield data products with the required statistical properties. In this paper we describe the development, and use of the LSST simulation framework, including the generation of simulated catalogs and images for targeted trade studies, simulations of the observing cadence of the LSST, the creation of large-scale simulations that test the procedures for data calibration, and use of end-to-end image simulations to evaluate the performance of the system as a whole.
    No preview · Conference Paper · Aug 2014
  • [Show abstract] [Hide abstract]
    ABSTRACT: We describe the Metrics Analysis Framework (MAF), an open-source python framework developed to provide a user-friendly, customizable, easily-extensible set of tools for analyzing data sets. MAF is part of the Large Synoptic Survey Telescope (LSST) Simulations effort. Its initial goal is to provide a tool to evaluate LSST Operations Simulation (OpSim) simulated surveys to help understand the effects of telescope scheduling on survey performance, however MAF can be applied to a much wider range of datasets. The building blocks of the framework are Metrics (algorithms to analyze a given quantity of data), Slicers (subdividing the overall data set into smaller data slices as relevant for each Metric), and Database classes (to access the dataset and read data into memory). We describe how these building blocks work together, and provide an example of using MAF to evaluate different dithering strategies. We also outline how users can write their own custom Metrics and use these within the framework.
    No preview · Conference Paper · Jul 2014
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The requirement and influence of the peripheral nervous system on tissue replacement in mammalian appendages remain largely undefined. To explore this question, we have performed genetic lineage tracing and clonal analysis of individual cells of mouse hind limb tissues devoid of nerve supply during regeneration of the digit tip, normal maintenance, and cutaneous wound healing. We show that cellular turnover, replacement, and cellular differentiation from presumed tissue stem/progenitor cells within hind limb tissues remain largely intact independent of nerve and nerve-derived factors. However, regenerated digit tips in the absence of nerves displayed patterning defects in bone and nail matrix. These nerve-dependent phenotypes mimic clinical observations of patients with nerve damage resulting from spinal cord injury and are of significant interest for translational medicine aimed at understanding the effects of nerves on etiologies of human injury.
    Full-text · Article · Jun 2014 · Proceedings of the National Academy of Sciences
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: -Ascending aortic dissection and rupture remain a life-threatening complication in patients with Marfan syndrome (MFS). The extracellular matrix provides strength and elastic recoil to the aortic wall, thereby preventing radial expansion. We have previously shown that ascending aortic aneurysm formation in Marfan mice (Fbn1(C1039G/+)) is associated with decreased aortic wall elastogenesis and increased elastin breakdown. In this study, we test the feasibility of quantifying aortic wall elastin content using magnetic resonance imaging (MRI) with a gadolinium-based elastin-specific contrast agent (ESMA) in Fbn1(C1039G/+) mice. -Ascending aorta elastin content was measured in 32-week-old Fbn1(C1039G/+) mice and wild-type (WT) (n=9 and n=10, respectively) using 7T MRI with a T1-mapping sequence. Significantly lower enhancement (i.e., lower R1 values, where R1=1/T1) was detected post-ESMA in Fbn1(C1039G/+) compared to WT ascending aortas (1.15±0.07 vs. 1.36±0.05, p<0.05). Post-ESMA R1 values correlated with ascending aortic wall gadolinium content directly measured by inductively coupled mass spectroscopy (p=0.006). -Herein, we demonstrate that MRI with ESMA accurately measures elastin bound gadolinium within the aortic wall and detects a decrease in aortic wall elastin in Marfan mice compared to WT controls. This approach has translational potential for non-invasively assessing aneurysm tissue changes and risk, as well as monitoring elastin content in response to therapeutic interventions.
    Preview · Article · May 2014 · Circulation Cardiovascular Imaging
  • Pramod Gupta · Andrew J. Connolly · Jeffrey P. Gardner
    [Show abstract] [Hide abstract]
    ABSTRACT: Future astronomical surveys will produce data on similar to 10(8) objects per night. In order to characterize and classify these sources, we will require algorithms that scale linearly with the size of the data, that can be easily parallelized and where the speedup of the parallel algorithm will be linear in the number of processing cores. In this paper, we present such an algorithm and apply it to the question of colour selection of quasars. We use non-parametric Bayesian classification and a binning algorithm implemented with hash tables (BASH tables). We show that this algorithm's run time scales linearly with the number of test set objects and is independent of the number of training set objects. We also show that it has the same classification accuracy as other algorithms. For current data set sizes, it is up to three orders of magnitude faster than commonly used naive kernel-density-estimation techniques and it is estimated to be about eight times faster than the current fastest algorithm using dual kd-trees for kernel density estimation. The BASH table algorithm scales linearly with the size of the test set data only, and so for future larger data sets, it will be even faster compared to other algorithms which all depend on the size of the test set and the size of the training set. Since it uses linear data structures, it is easier to parallelize compared to tree-based algorithms and its speedup is linear in the number of cores unlike tree-based algorithms whose speedup plateaus after a certain number of cores. Moreover, due to the use of hash tables to implement the binning, the memory usage is very small. While our analysis is for the specific problem of selection of quasars, the ideas are general and the BASH table algorithm can be applied to any density-estimation problem involving sparse high-dimensional data sets. Since sparse high-dimensional data sets are a common type of scientific data set, this method has the potential to be useful in a broad range of machine-learning applications in astrophysics.
    No preview · Article · Feb 2014 · Monthly Notices of the Royal Astronomical Society
  • Jake Vander Plas · A. J. Connolly · Z. Ivezic
    [Show abstract] [Hide abstract]
    ABSTRACT: As astronomical data sets grow in size and complexity, automated machine learning and data mining methods are becoming an increasingly fundamental component of research in the field. The astroML project (http://astroML.org) provides a common repository for practical examples of the data mining and machine learning tools used and developed by astronomical researchers, written in Python. The astroML module contains a host of general-purpose data analysis and machine learning routines, loaders for openly-available astronomical datasets, and fast implementations of specific computational methods often used in astronomy and astrophysics. The associated website features hundreds of examples of these routines being used for analysis of real astronomical datasets, while the associated textbook provides a curriculum resource for graduate-level courses focusing on practical statistics, machine learning, and data mining approaches within Astronomical research. This poster will highlight several of the more powerful and unique examples of analysis performed with astroML, all of which can be reproduced in their entirety on any computer with the proper packages installed.
    No preview · Article · Jan 2014
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: With upcoming all sky surveys such as LSST poised to generate a deep digital movie of the optical sky, variability-based AGN selection will enable the construction of highly-complete catalogs with minimum contamination. In this study, we generate $g$-band difference images and construct light curves for QSO/AGN candidates listed in SDSS Stripe 82 public catalogs compiled from different methods, including spectroscopy, optical colors, variability, and X-ray detection. Image differencing excels at identifying variable sources embedded in complex or blended emission regions such as Type II AGNs and other low-luminosity AGNs that may be omitted from traditional photometric or spectroscopic catalogs. To separate QSOs/AGNs from other sources using our difference image light curves, we explore several light curve statistics and parameterize optical variability by the characteristic damping timescale ($\tau$) and variability amplitude. By virtue of distinguishable variability parameters of AGNs, we are able to select them with high completeness of 93.4% and efficiency (i.e., purity) of 71.3%. Based on optical variability, we also select highly variable blazar candidates, whose infrared colors are consistent with known blazars. One third of them are also radio detected. With the X-ray selected AGN candidates, we probe the optical variability of X-ray detected optically-extended sources using their difference image light curves for the first time. A combination of optical variability and X-ray detection enables us to select various types of host-dominated AGNs. Contrary to the AGN unification model prediction, two Type II AGN candidates (out of 6) show detectable variability on long-term timescales like typical Type I AGNs. This study will provide a baseline for future optical variability studies of extended sources.
    Full-text · Article · Dec 2013 · The Astrophysical Journal
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: This document presents (off-line) computing requrements and challenges for Cosmic Frontier science, covering the areas of data management, analysis, and simulations. We invite contributions to extend the range of covered topics and to enhance the current descriptions.
    Full-text · Article · Nov 2013

  • No preview · Article · Oct 2013 · Circulation Journal
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The quantity and quality of cosmic structure observations have greatly accelerated in recent years. Further leaps forward will be facilitated by imminent projects, which will enable us to map the evolution of dark and baryonic matter density fluctuations over cosmic history. The way that these fluctuations vary over space and time is sensitive to the nature of dark matter and dark energy. Dark energy and gravity both affect how rapidly structure grows; the greater the acceleration, the more suppressed the growth of structure, while the greater the gravity, the more enhanced the growth. While distance measurements also constrain dark energy, the comparison of growth and distance data tests whether General Relativity describes the laws of physics accurately on large scales. Modified gravity models are able to reproduce the distance measurements but at the cost of altering the growth of structure (these signatures are described in more detail in the accompanying paper on Novel Probes of Gravity and Dark Energy). Upcoming surveys will exploit these differences to determine whether the acceleration of the Universe is due to dark energy or to modified gravity. To realize this potential, both wide field imaging and spectroscopic redshift surveys play crucial roles. Projects including DES, eBOSS, DESI, PFS, LSST, Euclid, and WFIRST are in line to map more than a 1000 cubic-billion-light-year volume of the Universe. These will map the cosmic structure growth rate to 1% in the redshift range 0<z<2, over the last 3/4 of the age of the Universe.
    Full-text · Article · Sep 2013 · Astroparticle Physics
  • [Show abstract] [Hide abstract]
    ABSTRACT: In this demonstration, we present AscotDB, a new tool for the analysis of telescope image data. AscotDB results from the integration of ASCOT, a Web-based tool for the collaborative analysis of telescope images and their metadata, and SciDB, a parallel array processing engine. We demonstrate the novel data exploration supported by this integrated tool on a 1 TB dataset comprising scientifically accurate, simulated telescope images. We also demonstrate novel iterative-processing features that we added to SciDB in order to support this use-case.
    No preview · Article · Aug 2013 · Proceedings of the VLDB Endowment

  • No preview · Article · May 2013
  • [Show abstract] [Hide abstract]
    ABSTRACT: Most quasars are known to be variable and they show larger variability on longer timescales of months to years. In this study, we generate g-band difference images and construct light curves for QSO/AGN candidates listed in Stripe 82 public catalogs complied from different methods, including spectroscopy, colors, variability, and X-ray detection. To separate QSOs/AGNs from other (non-)variable sources, we quantify their variability in the characteristic timescales (τ) and amplitude (SF∞) using the first-order structure function (SF) for the damped random walk (DRW) model. We find that QSOs occupy a specific region in the SF parameter space, enabling us to identify them with high efficiency and completeness. Since difference imaging excels at identifying variable sources embedded in complex or blended emission regions, it is one of the best tools to examine the variability of active nuclei surrounded by host galaxy emission, i.e. type II AGNs, and lower-luminosity AGNs. For the first time, we probe the variability of X-ray detected extended sources using their difference imaging light curves. Contrary to the AGN unification model prediction, some type II AGNs show detectable variability on long-term timescales like typical QSOs/AGNs.
    No preview · Article · Jan 2013

Publication Stats

29k Citations
1,068.49 Total Impact Points


  • 2015
    • McGill University
      Montréal, Quebec, Canada
  • 2003-2015
    • Stanford University
      • • Department of Medicine
      • • Division of Cardiovascular Medicine
      Stanford, California, United States
    • Palo Alto Medical Foundation
      Palo Alto, California, United States
    • The University of Tokyo
      • Institute for Cosmic Ray Research
      Tokyo, Tokyo-to, Japan
  • 2007-2014
    • University of Washington Seattle
      • Department of Astronomy
      Seattle, Washington, United States
  • 2012
    • Space Telescope Science Institute
      Baltimore, Maryland, United States
  • 2006-2012
    • Stanford Medicine
      • • Department of Pathology
      • • Department of Developmental Biology
      Stanford, California, United States
    • Lawrence Berkeley National Laboratory
      Berkeley, California, United States
    • Princeton University
      • Department of Astrophysical Sciences
      Princeton, New Jersey, United States
  • 2010
    • Vanderbilt University
      • Department of Physics and Astronomy
      Нашвилл, Michigan, United States
  • 2009
    • American University Washington D.C.
      Washington, Washington, D.C., United States
    • University of Illinois, Urbana-Champaign
      • Department of Astronomy
      Urbana, Illinois, United States
  • 2000-2008
    • University of Pittsburgh
      • Physics and Astronomy
      Pittsburgh, PA, United States
  • 1996-2008
    • Johns Hopkins University
      • Department of Physics and Astronomy
      Baltimore, MD, United States
  • 2005
    • Massachusetts Institute of Technology
      • Department of Physics
      Cambridge, Massachusetts, United States
  • 2001-2003
    • Carnegie Mellon University
      • Department of Physics
      Pittsburgh, Pennsylvania, United States
    • Fermi National Accelerator Laboratory (Fermilab)
      Batavia, Illinois, United States
  • 2002
    • University of Chicago
      • Department of Astronomy and Astrophysics
      Chicago, Illinois, United States
    • University of Santiago, Chile
      • Departamento de Economía
      CiudadSantiago, Santiago, Chile
  • 1999
    • Eötvös Loránd University
      • Department of Physics of Complex Systems
      Budapeŝto, Budapest, Hungary
  • 1992-1997
    • University of California, San Francisco
      • • Cardiovascular Research Institute
      • • Department of Pathology
      San Francisco, CA, United States