The non-uniform, dynamic atmosphere of Betelgeuse observed at mid-infrared wavelengths

We present an interferometric study of the continuum surface of the red supergiant star Betelgeuse at 11.15 microns wavelength, using data obtained with the Berkeley Infrared Spatial Interferometer each year between 2006 and 2010. These data allow an investigation of an optically thick layer within 1.4 stellar radii of the photosphere. The layer has an optical depth of ~1 at 11.15 microns, and varies in temperature between 1900 K and 2800 K and in outer radius between 1.16 and 1.36 stellar radii. Electron-hydrogen atom collisions contribute significantly to the opacity of the layer. The layer has a non-uniform intensity distribution that changes between observing epochs. These results indicate that large-scale surface convective activity strongly influences the dynamics of the inner atmosphere of Betelgeuse, and mass-loss processes.Comment: 13 pages, 5 figures, in press (ApJ

Building A High Performance Parallel File System Using Grid Datafarm and ROOT I/O

Sheer amount of petabyte scale data foreseen in the LHC experiments require a careful consideration of the persistency design and the system design in the world-wide distributed computing. Event parallelism of the HENP data analysis enables us to take maximum advantage of the high performance cluster computing and networking when we keep the parallelism both in the data processing phase, in the data management phase, and in the data transfer phase. A modular architecture of FADS/ Goofy, a versatile detector simulation framework for Geant4, enables an easy choice of plug-in facilities for persistency technologies such as Objectivity/DB and ROOT I/O. The framework is designed to work naturally with the parallel file system of Grid Datafarm (Gfarm). FADS/Goofy is proven to generate 10^6 Geant4-simulated Atlas Mockup events using a 512 CPU PC cluster. The data in ROOT I/O files is replicated using Gfarm file system. The histogram information is collected from the distributed ROOT files. During the data replication it has been demonstrated to achieve more than 2.3 Gbps data transfer rate between the PC clusters over seven participating PC clusters in the United States and in Japan.Comment: Talk from the 2003 Computing in High Energy and Nuclear Physics (CHEP03), La Jolla, Ca, USA, March 2003, 4 pages, PDF. PSN TUDT01

Response network analysis of differential gene expression in human epithelial lung cells during avian influenza infections

<p>Abstract</p> <p>Background</p> <p>The recent emergence of the H5N1 influenza virus from avian reservoirs has raised concern about future influenza strains of high virulence emerging that could easily infect humans. We analyzed differential gene expression of lung epithelial cells to compare the response to H5N1 infection with a more benign infection with Respiratory Syncytial Virus (RSV). These gene expression data are then used as seeds to find important nodes by using a novel combination of the Gene Ontology database and the Human Network of gene interactions. Additional analysis of the data is conducted by training support vector machines (SVM) with the data and examining the orientations of the optimal hyperplanes generated.</p> <p>Results</p> <p>Analysis of gene clustering in the Gene Ontology shows no significant clustering of genes unique to H5N1 response at 8 hours post infection. At 24 hours post infection, however, a number of significant gene clusters are found for nodes representing "immune response" and "response to virus" terms. There were no significant clusters of genes in the Gene Ontology for the control (Mock) or RSV experiments that were unique relative to the H5N1 response. The genes found to be most important in distinguishing H5N1 infected cells from the controls using SVM showed a large degree of overlap with the list of significantly regulated genes. However, though none of these genes were members of the GO clusters found to be significant.</p> <p>Conclusions</p> <p>Characteristics of H5N1 infection compared to RSV infection show several immune response factors that are specific for each of these infections. These include faster timescales within the cell as well as a more focused activation of immunity factors. Many of the genes that are found to be significantly expressed in H5N1 response relative to the control experiments are not found to cluster significantly in the Gene Ontology. These genes are, however, often closely linked to the clustered genes through the Human Network. This may suggest the need for more diverse annotations of these genes and verification of their action in immune response.</p

Distributed Management of Massive Data: an Efficient Fine-Grain Data Access Scheme

This paper addresses the problem of efficiently storing and accessing massive data blocks in a large-scale distributed environment, while providing efficient fine-grain access to data subsets. This issue is crucial in the context of applications in the field of databases, data mining and multimedia. We propose a data sharing service based on distributed, RAM-based storage of data, while leveraging a DHT-based, natively parallel metadata management scheme. As opposed to the most commonly used grid storage infrastructures that provide mechanisms for explicit data localization and transfer, we provide a transparent access model, where data are accessed through global identifiers. Our proposal has been validated through a prototype implementation whose preliminary evaluation provides promising results

The close circumstellar environment of Betelgeuse - Adaptive optics spectro-imaging in the near-IR with VLT/NACO

Context: Betelgeuse is one the largest stars in the sky in terms of angular diameter. Structures on the stellar photosphere have been detected in the visible and near-infrared as well as a compact molecular environment called the MOLsphere. Mid-infrared observations have revealed the nature of some of the molecules in the MOLsphere, some being the precursor of dust. Aims: Betelgeuse is an excellent candidate to understand the process of mass loss in red supergiants. Using diffraction-limited adaptive optics (AO) in the near-infrared, we probe the photosphere and close environment of Betelgeuse to study the wavelength dependence of its extension, and to search for asymmetries. Methods: We obtained AO images with the VLT/NACO instrument, taking advantage of the "cube" mode of the CONICA camera to record separately a large number of short-exposure frames. This allowed us to adopt a "lucky imaging" approach for the data reduction, and obtain diffraction-limited images over the spectral range 1.04-2.17 $\mu$m in 10 narrow-band filters. Results: In all filters, the photosphere of Betelgeuse appears partly resolved. We identify an asymmetric envelope around the star, with in particular a relatively bright "plume" extending in the southwestern quadrant up to a radius of approximately six times the photosphere. The CN molecule provides an excellent match to the 1.09 mic bandhead in absorption in front of the stellar photosphere, but the emission spectrum of the plume is more difficult to interpret. Conclusions: Our AO images show that the envelope surrounding Betelgeuse has a complex and irregular structure. We propose that the southwestern plume is linked either to the presence of a convective hot spot on the photosphere, or to the rotation of the star.Comment: 12 pages. Astronomy and Astrophysics (2009) in pres

Radiative hydrodynamics simulations of red supergiant stars: II. simulations of convection on Betelgeuse match interferometric observations

Context. The red supergiant (RSG) Betelgeuse is an irregular variable star. Convection may play an important role in understanding this variability. Interferometric observations can be interpreted using sophisticated simulations of stellar convection. Aims. We compare the visibility curves and closure phases obtained from our 3D simulation of RSG convection with CO5BOLD to various interferometric observations of Betelgeuse from the optical to the H band in order to characterize and measure the convection pattern on this star. Methods. We use 3D radiative-hydrodynamics (RHD) simulation to compute intensity maps in different filters and we thus derive interferometric observables using the post-processing radiative transfer code OPTIM3D. The synthetic visibility curves and closure phases are compared to observations. Results. We provide a robust detection of the granulation pattern on the surface of Betelgeuse in the optical and in the H band based on excellent fits to the observed visibility points and closure phases. Moreover, we determine that the Betelgeuse surface in the H band is covered by small to medium scale (5-15 mas) convection-related surface structures and a large (30 mas) convective cell. In this spectral region, H2O molecules are the main absorbers and contribute to the small structures and to the position of the first null of the visibility curve (i.e. the apparent stellar radius).Comment: 11 pages, Accepted for publication on A&

The molecular and dusty composition of Betelgeuse's inner circumstellar environment

The study of the atmosphere of red supergiant stars in general and of Betelgeuse (alpha Orionis) in particular is of prime importance to understand dust formation and how mass is lost to the interstellar medium in evolved massive stars. A molecular shell, the MOLsphere (Tsuji, 2000a), in the atmosphere of Betelgeuse has been proposed to account for the near- and mid-infrared spectroscopic observations of Betelgeuse. The goal is to further test this hypothesis and to identify some of the molecules in this MOLsphere. We report on measurements taken with the mid-infrared two-telescope beam combiner of the VLTI, MIDI, operated between 7.5 and 13.5 $\mu$m. The data are compared to a simple geometric model of a photosphere surrounded by a warm absorbing and emitting shell. Physical characteristics of the shell are derived: size, temperature and optical depth. The chemical constituents are determined with an analysis consistent with available infrared spectra and interferometric data. We are able to account for the measured optical depth of the shell in the N band, the ISO-SWS spectrum and K and L band interferometric data with a shell whose inner and outer radii are given by the above range and with the following species: H2O, SiO and Al2O3. These results confirm the MOLsphere model. We bring evidence for more constituents and for the presence of species participating in the formation of dust grains in the atmosphere of the star, i.e. well below the distance at which the dust shell is detected. We believe these results bring key elements to the understanding of mass loss in Betelgeuse and red supergiants in general and bring support to the dust-driven scenario.Comment: 11 pages, 10 figures, accepted for publication in A&

De Novo Growth Zone Formation from Fission Yeast Spheroplasts

Eukaryotic cells often form polarized growth zones in response to internal or external cues. To understand the establishment of growth zones with specific dimensions we used fission yeast, which grows as a rod-shaped cell of near-constant width from growth zones located at the cell tips. Removing the cell wall creates a round spheroplast with a disorganized cytoskeleton and depolarized growth proteins. As spheroplasts recover, new growth zones form that resemble normal growing cell tips in shape and width, and polarized growth resumes. Regulators of the GTPase Cdc42, which control width in exponentially growing cells, also control spheroplast growth zone width. During recovery the Cdc42 scaffold Scd2 forms a polarized patch in the rounded spheroplast, demonstrating that a growth zone protein can organize independent of cell shape. Rga4, a Cdc42 GTPase activating protein (GAP) that is excluded from cell tips, is initially distributed throughout the spheroplast membrane, but is excluded from the growth zone after a stable patch of Scd2 forms. These results provide evidence that growth zones with normal width and protein localization can form de novo through sequential organization of cellular domains, and that the size of these growth zones is genetically controlled, independent of preexisting cell shape

Identification of Genes Affecting the Toxicity of Anti-Cancer Drug Bortezomib by Genome-Wide Screening in S. pombe

Bortezomib/PS-341/Velcade, a proteasome inhibitor, is widely used to treat multiple myeloma. While several mechanisms of the cytotoxicity of the drug were proposed, the actual mechanism remains elusive. We aimed to identify genes affecting the cytotoxicity of Bortezomib in the fission yeast S.pombe as the drug inhibits this organism's cell division cycle like proteasome mutants. Among the 2815 genes screened (covering 56% of total ORFs), 19 genes, whose deletions induce strong synthetic lethality with Bortezomib, were identified. The products of the 19 genes included four ubiquitin enzymes and one nuclear proteasome factor, and 13 of them are conserved in humans. Our results will provide useful information for understanding the actions of Bortezomib within cells

Trends in incidence and mortality of tuberculosis in Japan : a population-based study, 1997–2016

Japan is still a medium-burden tuberculosis (TB) country. We aimed to examine trends in newly notified active TB incidence and TB-related mortality in the last two decades in Japan. This is a population-based study using Japanese Vital Statistics and Japan Tuberculosis Surveillance from 1997 to 2016. We determined active TB incidence and mortality rates (per 100 000 population) by sex, age and disease categories. Joinpoint regression was applied to calculate the annual percentage change (APC) in age-adjusted mortality rates and to identify the years showing significant trend changes. Crude and age-adjusted incidence rates reduced from 33.9 to 13.9 and 37.3 to 11.3 per 100 000 population, respectively. Also, crude and age-adjusted mortality rates reduced from 2.2 to 1.5 and 2.8 to 1.0 per 100 000 population, respectively. Average APC in the incidence and mortality rates showed significant decline both in men (−6.2% and −5.4%, respectively) and women (−5.7% and −4.6%, respectively). Age-specific analysis demonstrated decreases in incidence and mortality rates for every age category, except for the incidence trend in the younger population. Although trends in active TB incidence and mortality rates in Japan have favourably decreased, the rate of decline is far from achieving TB elimination by 2035