Accelerating Bayesian hierarchical clustering of time series data with a randomised algorithm

We live in an era of abundant data. This has necessitated the development of new and innovative statistical algorithms to get the most from experimental data. For example, faster algorithms make practical the analysis of larger genomic data sets, allowing us to extend the utility of cutting-edge statistical methods. We present a randomised algorithm that accelerates the clustering of time series data using the Bayesian Hierarchical Clustering (BHC) statistical method. BHC is a general method for clustering any discretely sampled time series data. In this paper we focus on a particular application to microarray gene expression data. We define and analyse the randomised algorithm, before presenting results on both synthetic and real biological data sets. We show that the randomised algorithm leads to substantial gains in speed with minimal loss in clustering quality. The randomised time series BHC algorithm is available as part of the R package BHC, which is available for download from Bioconductor (version 2.10 and above) via http://bioconductor.org/packages/2.10/bioc/html/BHC.html. We have also made available a set of R scripts which can be used to reproduce the analyses carried out in this paper. These are available from the following URL. https://sites.google.com/site/randomisedbhc/

Aggressive presentation of breast implant-associated ALK-1 negative anaplastic large cell lymphoma with bilateral axillary lymph node involvement

We recently encountered a unique case of breast silicone implant-associated ALK-1 negative anaplastic large cell lymphoma (ALCL) in a female with a remote history of breast carcinoma, which presented as a sinusoidal infiltrate in an axillary lymph node (LN) and had a highly complex karyotype

The Role of a Hot Gas Environment on the Evolution of Galaxies

Most spiral galaxies are found in galaxy groups with low velocity dispersions; most E/S0 galaxies are found in galaxy groups with relatively high velocity dispersions. The mass of the hot gas we can observe in the E/S0 groups via their thermal X-ray emission is, on average, as much as the baryonic mass of the galaxies in these groups. By comparison, galaxy clusters have as much or more hot gas than stellar mass. Hot gas in S-rich groups, however, is of low enough temperature for its X-ray emission to suffer heavy absorption due to Galactic HI and related observational effects, and hence is hard to detect. We postulate that such lower temperature hot gas does exist in low velocity dispersion, S-rich groups, and explore the consequences of this assumption. For a wide range of metallicity and density, hot gas in S-rich groups can cool in far less than a Hubble time. If such gas exists and can cool, especially when interacting with HI in existing galaxies, then it can help link together a number of disparate observations, both Galactic and extragalactic, that are otherwise difficult to understand.Comment: 16 pages with one figure. ApJ Letters, in pres

Long-lived space observatories for astronomy and astrophysics

NASA's plan to build and launch a fleet of long-lived space observatories that include the Hubble Space Telescope (HST), the Gamma Ray Observatory (GRO), the Advanced X Ray Astrophysics Observatory (AXAF), and the Space Infrared Telescope Facility (SIRTF) are discussed. These facilities are expected to have a profound impact on the sciences of astronomy and astrophysics. The long-lived observatories will provide new insights about astronomical and astrophysical problems that range from the presence of planets orbiting nearby stars to the large-scale distribution and evolution of matter in the universe. An important concern to NASA and the scientific community is the operation and maintenance cost of the four observatories described above. The HST cost about $1.3 billion (1984 dollars) to build and is estimated to require$160 million (1986 dollars) a year to operate and maintain. If HST is operated for 20 years, the accumulated costs will be considerably more than those required for its construction. Therefore, it is essential to plan carefully for observatory operations and maintenance before a long-lived facility is constructed. The primary goal of this report is to help NASA develop guidelines for the operations and management of these future observatories so as to achieve the best possible scientific results for the resources available. Eight recommendations are given

SU(3) Predictions for Weak Decays of Doubly Heavy Baryons -- including SU(3) breaking terms

We find expressions for the weak decay amplitudes of baryons containing two b quarks (or one b and one c quark -- many relationship are the same) in terms of unknown reduced matrix elements. This project was originally motivated by the request of the FNAL Run II b Physics Workshop organizers for a guide to experimentalists in their search for as yet unobserved hadrons. We include an analysis of linear SU(3) breaking terms in addition to relationships generated by unbroken SU(3) symmetry, and relate these to expressions in terms of the complete set of possible reduced matrix elements.Comment: 49 page

Reconnection Outflows and Current Sheet Observed with Hinode/XRT in the 2008 April 9 "Cartwheel CME" Flare

Supra-arcade downflows (SADs) have been observed with Yohkoh/SXT (soft X-rays (SXR)), TRACE (extreme ultra-violet (EUV)), SoHO/LASCO (white light), SoHO/SUMER (EUV spectra), and Hinode/XRT (SXR). Characteristics such as low emissivity and trajectories which slow as they reach the top of the arcade are consistent with post-reconnection magnetic flux tubes retracting from a reconnection site high in the corona until they reach a lower-energy magnetic configuration. Viewed from a perpendicular angle, SADs should appear as shrinking loops rather than downflowing voids. We present XRT observations of supra-arcade downflowing loops (SADLs) following a coronal mass ejection (CME) on 2008 April 9 and show that their speeds and decelerations are consistent with those determined for SADs. We also present evidence for a possible current sheet observed during this flare that extends between the flare arcade and the CME. Additionally, we show a correlation between reconnection outflows observed with XRT and outgoing flows observed with LASCO.Comment: 32 pages, 23 figures, Accepted for publication by the Astrophysical Journal (Oct. 2010

Fate of lesion-related side branches after coronary artery stenting

AbstractObjectives. The aim of this study was to assess the immediate and long-term patency of lesion-associated side branches after coronary artery stenting.Background. The possible adverse effects related to implantation of coronary stents are not completely known. An important potential complication of stenting is side branch occlusion due to mechanical obstruction or thrombosis.Methods. Serial coronary angiography was performed in 153 patients (167 lesions) at baseline, after conventional balloon angioplasty, immediately after Palmaz-Schatz stent placement and at 6 months. The patency of side branches, where present, was analysed at each of these points.Results. Of 167 lesions stented, 57 stent placements spanned 66 side branches with a diameter ≥1 mm. Twenty-seven (41%) of these side branches had ≥50% ostial stenosis before standard balloon angioplasty. Six side branches became occluded after standard balloon angioplasty and remained occluded after stenting. Of the 60 side branches patent after conventional angioplasty, 57 (95%) remained patent immediately after stenting. All three side branches that became occluded after stenting had ≥50% ostial stenosis at baseline. All 60 side branches, including the 3 initially occluded after stenting, were patent at 6-month follow-up.Conclusions. These findings demonstrate that 1) acute side branch occlusion due to coronary stenting occurs infrequently; 2) when side branch occlusion occurs, it is associated with intrinsic ostial disease; and 3) the patency of side branch ostia is well maintained at long-term follow-up

Predicting functional gains in a stroke trial.

A number of therapies in development for patients with central nervous system injury aim to reduce disability by improving function of surviving brain elements rather than by salvaging tissue. The current study tested the hypothesis that, after adjusting for a number of clinical assessments, a measure of brain function at baseline would improve prediction of behavioral gains after treatment.Twenty-four patients with chronic stroke underwent baseline clinical and functional MRI assessments, received 6 weeks of rehabilitation therapy with or without investigational motor cortex stimulation, and then had repeat assessments. Thirteen baseline clinical/radiological measures were evaluated for ability to predict subsequent trial-related gains.Across all patients, bivariate analyses found that greater trial-related functional gains were predicted by (1) smaller infarct volume, (2) greater baseline clinical status, and (3) lower degree of activation in stroke-affected motor cortex on baseline functional MRI. When these 3 variables were further assessed using multivariate linear regression modeling, only lower motor cortex activation and greater clinical status at baseline remained significant predictors. Note that lower baseline motor cortex activation was also associated with larger increases in motor cortex activation after treatment.Lower motor cortex activity at baseline predicted greater behavioral gains after therapy, even after controlling for a number of clinical assessments. The boosts in cortical activity that paralleled behavioral gains suggest that in some patients, low baseline cortical activity represents underuse of surviving cortical resources. A measure of brain function might be important for optimal clinical decision-making in the context of a restorative intervention

The first super-Earth Detection from the High Cadence and High Radial Velocity Precision Dharma Planet Survey

The Dharma Planet Survey (DPS) aims to monitor about 150 nearby very bright FGKM dwarfs (within 50 pc) during 2016$-$2020 for low-mass planet detection and characterization using the TOU very high resolution optical spectrograph (R$\approx$100,000, 380-900nm). TOU was initially mounted to the 2-m Automatic Spectroscopic Telescope at Fairborn Observatory in 2013-2015 to conduct a pilot survey, then moved to the dedicated 50-inch automatic telescope on Mt. Lemmon in 2016 to launch the survey. Here we report the first planet detection from DPS, a super-Earth candidate orbiting a bright K dwarf star, HD 26965. It is the second brightest star ($V=4.4$ mag) on the sky with a super-Earth candidate. The planet candidate has a mass of 8.47$\pm0.47M_{\rm Earth}$, period of $42.38\pm0.01$ d, and eccentricity of $0.04^{+0.05}_{-0.03}$. This RV signal was independently detected by Diaz et al. (2018), but they could not confirm if the signal is from a planet or from stellar activity. The orbital period of the planet is close to the rotation period of the star (39$-$44.5 d) measured from stellar activity indicators. Our high precision photometric campaign and line bisector analysis of this star do not find any significant variations at the orbital period. Stellar RV jitters modeled from star spots and convection inhibition are also not strong enough to explain the RV signal detected. After further comparing RV data from the star's active magnetic phase and quiet magnetic phase, we conclude that the RV signal is due to planetary-reflex motion and not stellar activity.Comment: 13 pages, 17 figures, Accepted for publication in MNRA