Application of stellar photometry to the analysis of microarray images

Improvements in the analysis of microarray images are critical for accurately quantifying gene expression levels. The acquisition of accurate spot intensities directly influences the results and interpretation of statistical analyses. This dissertation discusses the implementation of a novel approach to the analysis of cDNA microarray images. We use a stellar photometric model, the Moffat function, to quantify microarray spots from nylon microarray images. The inherent flexibility of the Moffat shape model makes it ideal for quantifying microarray spots. We apply our novel approach to a Wilms' tumor microarray study and compare our results with a fixed-circle segmentation approach for spot quantification. Our results suggest that different spot feature extraction methods can have an impact on the ability of statistical methods to identify differentially expressed genes. We also used the Moffat function to simulate a series of microarray images under various experimental conditions. These simulations were used to validate the performance of various statistical methods for identifying differentially expressed genes. Our simulation results indicate that tests taking into account the dependency between mean spot intensity and variance estimation, such as the smoothened t-test, can better identify differentially expressed genes, especially when the number of replicates and mean fold change are low. The analysis of the simulations also showed that overall, a rank sum test (Mann-Whitney) performed well at identifying differentially expressed genes. Previous work has suggested the strengths of nonparametric approaches for identifying differentially expressed genes. We also show that multivariate approaches, such as hierarchical and k-means cluster analysis along with principal components analysis, are only effective at classifying samples when replicate numbers and mean fold change are high. Finally, we show how our stellar shape model approach can be extended to the analysis of 2D-gel images by adapting the Moffat function to take into account the elliptical nature of spots in such images. Our results indicate that stellar shape models offer a previously unexplored approach for the quantification of 2D-gel spots. ^

Mechanical Degradation of Tungsten Alloys at Extreme Temperatures in Vacuum and Oxidation Atmospheres

Mechanical degradation of tungsten alloys at extreme temperatures in vacuum and oxidation atmospheres.

Máquinas o atmósferas: La estética de la energía en la arquitectura, 1750-2000 = From Machines to Atmospheres: The Aesthetics of Energy in Architecture, 1750-2000

La energía es ya un tema arquitectónico, pero su incorporación al proyecto ha sido hasta ahora fundamentalmente técnica, dando pie a una especie de funcionalismo ecológico cuyo destino es acaso repetir los errores de los viejos funcionalismos en su confianza de encontrar modos ‘objetivos’ de transmutar la energía en forma construida, pero sin que en tal proceso parezca haber hueco para mediaciones de tipo estético. Sin embargo, son precisamente tales mediaciones las que necesitan analizarse para que la adopción de los temas energéticos resulte fructífera en la arquitectura, y asimismo para dar cuenta de otras perspectivas complementarias —filosóficas, científicas, artísticas— que hoy forman el complejo campo semántico de la energía. Partiendo de la fecha de 1750 —que da comienzo simbólicamente al proceso de contaminaciones ‘modernas’ entre la arquitectura y otras disciplinas—, esta tesis analiza los diferentes modos con los que proyectos y edificios han expresado literal y analógicamente ciertos temas o ideales energéticos, demostrando la existencia de una ‘estética de la energía’ en la arquitectura y también de una tradición proyectual e intelectual sostenida en ella. Con este fin, se han seleccionados siete metáforas que vinculan tanto técnica como ideológicamente a la arquitectura con la energía: la metáfora de la máquina, asociada al ideal de movimiento y la autorregulación; las metáforas del arabesco, del cristal y del organismo, afines entre sí en su modo de dar cuenta del principio de la morfogénesis o energía creadora de la naturaleza; la metáfora de la actividad interna de los materiales; la metáfora del gradiente, que expresa la condición térmica y climática de la arquitectura, y, finalmente, la de la atmósfera que, recogiendo los sentidos anteriores, los actualiza en el contexto de la estética contemporánea. La selección de estas siete metáforas se ha llevado a cabo después de un barrido exhaustivo de la bibliografía precedente, y ha estructurado un relato cuyo método combina la perspectiva general —que permite cartografiar las continuidades históricas— con la cercana —que atiende a las problemas específicos de cada tema o metáfora—, complementándolas con una aproximación de sesgo iconográfico cuyo propósito es incidir en los vínculos que se dan entre lo ideológico y lo morfológico. El análisis ha puesto de manifiesto cómo detrás de cada una de estas metáforas se oculta un principio ideológico común —la justificación de la arquitectura desde planteamientos externos procedentes de la ciencia, la filosofía y el arte—, y cómo en cada uno de los casos estudiados las asimilaciones más fructíferas de la energía se han producido según mecanismos de mímesis analógica que inciden más en los procesos que en las formas que estos generan, y que en último término son de índole estética, lo cual constituye un indicio de los métodos de la arquitectura por venir. ABSTRACT Although it is already an architectural theme, the matter of incorporating energy into projects has up to now been mainly technical, giving rise to a kind of ecological functionalism which may be bound to old funcionalist mistakes in hopes of finding “objective” ways of transmuting energy into built forms without aesthetic considerations. However, it is precisely such considerations that need to be analyzed if the adoption of energy issues in architecture is to bear fruit and also to account for other complementary perspectives – philosophical, scientific, artistic – which today form the complex fabric of the energy semantic field. Beginning in 1750 – symbolic start of ‘modern’ contaminations between architecture and other disciplines –, this thesis analyzes the different ways in which projects and buildings have literally and analogically expressed certain subjects or ideals on energy, and demonstrates the existence of an “aesthetics of energy” in architecture, as well as of an intellectual and design tradition based on such aesthetics. For this purpose, seven metaphors are selected to link energy to architecture both technically and ideologically: the machine’s metaphor, associated with the ideal of mouvement and self-regulation; the arabesque, glass and the organism’s metaphors, which account for the morphogenesis principle, i.e. creative energy of nature; the metaphor linked to matter and the ideal of internal activity; the gradient’s metaphor, which expressed the thermal and climatic condition of architecture, and, finally, that of the atmosphere which, collecting the above meanings, updates them in the context of contemporary aesthetics. The selection of these seven metaphors was carried out after a thorough scan of the preceding literature, and has structured a reasoning that combines the overview method – which accounts for historical continuities – with the nearby one – which meets the specifics problems of each theme or metaphor –, both supplemented with an iconographic bias, the purpose of which is to visually express the links existing between the ideological and the morphological. So presented, the analysis shows how, behind each of these metaphors, lies a common ideological principle – the justification of architecture from scientific, philosophical and artistic “external” angles –, and how in each of the studied cases the most successful assimilation of energy were those produced by aesthetic mechanisms of analogical mimesis not focused in forms but in processes that generate them: an indication of the methods of architecture to come.

Sonic anemometry of planetary atmospheres

The application of a recently developed model of sonic anemometers measuring process has revealed that these sensors cannot be considered as absolute ones when measuring spectral characteristics of turbulent wind speed since it is demonstrated that the ratios of measured to real spectral density functions depend on the composition and temperature of the considered planetary atmosphere. The new model of the measuring process of sonic anemometers is applied to describe the measuring characteristics of these sensors as fluid/flow dependent (against the traditional hypothesis of fluid/flow independence) and hence dependent on the considered planetary atmosphere. The influence of fluid and flow characteristics (quantified via the Mach number of the flow) and the influence of the design parameters of sonic anemometers (mainly represented by time delay between pulses shots and geometry) on turbulence measurement are quantified for the atmospheres of Mars, Jupiter, and Earth. Important differences between the behavior of these sensors for the same averaged wind speed in the three considered atmospheres are detected in terms of characteristics of turbulence measurement as well as in terms of optimum values of anemometer design parameters for application on the different considered planetary atmospheres. These differences cannot be detected by traditional models of sonic anemometer measuring process based on line averaging along the sonic acoustic paths.

Optical evidence for the unification of active galactic nuclei and quasi-stellar objects.

There is a variety of optical evidence for some unification of different types of active galactic nuclei and quasi-stellar objects (QSOs). The case is very strong for the unification of at least some Seyfert galaxies, where polarization data show that the type assigned to the Seyfert galaxy must depend on viewing direction. It has been proposed that Fanaroff-Riley type 2 (FR2) radio galaxies are quasars seen in a direction from which the quasar is obscured, and there is some limited direct evidence for this picture. The broad absorption line QSOs may be normal QSOs seen from a special direction. Some of the sources observed to have high luminosities in the far infrared could be obscured QSOs and active nuclei. Mergers and interactions are likely to play an important role in nuclear activity, and active galaxies and QSOs could change their apparent types through these encounters followed by subsequent evolution.

Stellar populations in bulges of spiral galaxies

We present a few results of a work in progress tackling the radial spectroscopic properties of bulges of spiral galaxies.

A spectroscopy study of nearby late-type stars, possible members of stellar kinematic groups

Context. Nearby late-type stars are excellent targets for seeking young objects in stellar associations and moving groups. The origin of these structures is still misunderstood, and lists of moving group members often change with time and also from author to author. Most members of these groups have been identified by means of kinematic criteria, leading to an important contamination of previous lists by old field stars. Aims. We attempt to identify unambiguous moving group members among a sample of nearby-late type stars by studying their kinematics, lithium abundance, chromospheric activity, and other age-related properties. Methods. High-resolution echelle spectra (R ~ 57 000) of a sample of nearby late-type stars are used to derive accurate radial velocities that are combined with the precise Hipparcos parallaxes and proper motions to compute galactic-spatial velocity components. Stars are classified as possible members of the classical moving groups according to their kinematics. The spectra are also used to study several age-related properties for young late-type stars, i.e., the equivalent width of the lithium Li i 6707.8 Å line or the R'_HK index. Additional information like X-ray fluxes from the ROSAT All-Sky Survey or the presence of debris discs is also taken into account. The different age estimators are compared and the moving group membership of the kinematically selected candidates are discussed. Results. From a total list of 405 nearby stars, 102 have been classified as moving group candidates according to their kinematics. i.e., only ~25.2% of the sample. The number reduces when age estimates are considered, and only 26 moving group candidates (25.5% of the 102 candidates) have ages in agreement with the star having the same age as an MG member.

Li I enhancement during a long-duration stellar flare

We report the possible detection of a Li I λ6708 Å line enhancement during an unusual long-duration optical flare in the recently discovered, X-ray/EUV selected, chromospherically active binary 2RE J0743+224. The Li I equivalent width (EW) variations follow the temporal evolution of the flare and large changes are observed in the intensity of the line. The maximum Li I enhancement (40% in EW) occurs just after the maximum chromospheric emission observed in the flare. A significant increase of the Li^-6/Li^-7 isotopic ratio is also detected. No significant simultaneous variations are detected in other photospheric lines. Neither line blends nor starspots seem to be the primary cause of the observed Li I line variation. From all this we suggest that this Li I enhancement is produced by spallation reactions during the flare.

Modeling nonthermal emission from stellar bow shocks (Research Note)

Context. Runaway O- and early B-type stars passing through the interstellar medium at supersonic velocities and characterized by strong stellar winds may produce bow shocks that can serve as particle acceleration sites. Previous theoretical models predict the production of high-energy photons by nonthermal radiative processes, but their efficiency is still debated. Aims. We aim to test and explain the possibility of emission from the bow shocks formed by runaway stars traveling through the interstellar medium by using previous theoretical models. Methods. We applied our model to AE Aurigae, the first reported star with an X-ray detected bow shock, to BD+43 3654, in which the observations failed in detecting high-energy emission, and to the transition phase of a supergiant star in the late stages of its life. Results. From our analysis, we confirm that the X-ray emission from the bow shock produced by AE Aurigae can be explained by inverse Compton processes involving the infrared photons of the heated dust. We also predict low high-energy flux emission from the bow shock produced by BD+43 3654, and the possibility of high-energy emission from the bow shock formed by a supergiant star during the transition phase from blue to red supergiant. Conclusions. Bow shocks formed by different types of runaway stars are revealed as a new possible source of high-energy photons in our neighborhood.

Caught in the act: gas and stellar velocity dispersions in a fast Quenching compact star-forming galaxy at z ~ 1.7

We present Keck I MOSFIRE spectroscopy in the Y and H bands of GDN-8231, a massive, compact, star-forming galaxy at a redshift of z ~ 1.7. Its spectrum reveals both Hα and [Nii] emission lines and strong Balmer absorption lines. The Hα and Spitzer MIPS 24 μm fluxes are both weak, thus indicating a low star-formation rate of SFR≲5-10 M_⨀ yr−1. This, added to a relatively young age of ~700 Myr measured from the absorption lines, provides the first direct evidence for a distant galaxy being caught in the act of rapidly shutting down its star formation. Such quenching allows GDN-8231 to become a compact, quiescent galaxy, similar to three other galaxies in our sample, by z ~ 1.5. Moreover, the color profile of GDN-8231 shows a bluer center, consistent with the predictions of recent simulations for an early phase of inside-out quenching. Its line-of-sight velocity dispersion for the gas, σ_LOG^gas = 127 ± 32 km s^−1, is nearly 40% smaller than that of its stars, σ_LOG^* = 215 ± 35 km s^−1. High-resolution hydro-simulations of galaxies explain such apparently colder gas kinematics of up to a factor of ~1.5 with rotating disks being viewed at different inclinations and/or centrally concentrated star-forming regions. A clear prediction is that their compact, quiescent descendants preserve some remnant rotation from their star-forming progenitors.

Modeling nonthermal emission from stellar bow shocks (Research Note)

Context. Runaway O- and early B-type stars passing through the interstellar medium at supersonic velocities and characterized by strong stellar winds may produce bow shocks that can serve as particle acceleration sites. Previous theoretical models predict the production of high-energy photons by nonthermal radiative processes, but their efficiency is still debated. Aims. We aim to test and explain the possibility of emission from the bow shocks formed by runaway stars traveling through the interstellar medium by using previous theoretical models. Methods. We applied our model to AE Aurigae, the first reported star with an X-ray detected bow shock, to BD+43 3654, in which the observations failed in detecting high-energy emission, and to the transition phase of a supergiant star in the late stages of its life. Results. From our analysis, we confirm that the X-ray emission from the bow shock produced by AE Aurigae can be explained by inverse Compton processes involving the infrared photons of the heated dust. We also predict low high-energy flux emission from the bow shock produced by BD+43 3654, and the possibility of high-energy emission from the bow shock formed by a supergiant star during the transition phase from blue to red supergiant. Conclusions. Bow shocks formed by different types of runaway stars are revealed as a new possible source of high-energy photons in our neighborhood.

A VLT/FLAMES survey for massive binaries in Westerlund 1. III. The WC9d binary W239 and implications for massive stellar evolution

Context. There is growing evidence that a treatment of binarity amongst OB stars is essential for a full theory of stellar evolution. However the binary properties of massive stars – frequency, mass ratio & orbital separation – are still poorly constrained. Aims. In order to address this shortcoming we have undertaken a multiepoch spectroscopic study of the stellar population of the young massive cluster Westerlund 1. In this paper we present an investigation into the nature of the dusty Wolf-Rayet star and candidate binary W239. Methods. To accomplish this we have utilised our spectroscopic data in conjunction with multi-year optical and near-IR photometric observations in order to search for binary signatures. Comparison of these data to synthetic non-LTE model atmosphere spectra were used to derive the fundamental properties of the WC9 primary. Results. We found W239 to have an orbital period of only ~5.05 days, making it one of the most compact WC binaries yet identified. Analysis of the long term near-IR lightcurve reveals a significant flare between 2004-6. We interpret this as evidence for a third massive stellar component in the system in a long period (>6 yr), eccentric orbit, with dust production occuring at periastron leading to the flare. The presence of a near-IR excess characteristic of hot (~1300 K) dust at every epoch is consistent with the expectation that the subset of persistent dust forming WC stars are short (<1 yr) period binaries, although confirmation will require further observations. Non-LTE model atmosphere analysis of the spectrum reveals the physical properties of the WC9 component to be fully consistent with other Galactic examples. Conclusions. The simultaneous presence of both short period Wolf-Rayet binaries and cool hypergiants within Wd 1 provides compelling evidence for a bifurcation in the post-Main Sequence evolution of massive stars due to binarity. Short period O+OB binaries will evolve directly to the Wolf-Rayet phase, either due to an episode of binary mediated mass loss – likely via case A mass transfer or a contact configuration – or via chemically homogenous evolution. Conversely, long period binaries and single stars will instead undergo a red loop across the HR diagram via a cool hypergiant phase. Future analysis of the full spectroscopic dataset for Wd 1 will constrain the proportion of massive stars experiencing each pathway; hence quantifying the importance of binarity in massive stellar evolution up to and beyond supernova and the resultant production of relativistic remnants.

Astrophysical parameters of the peculiar X-ray transient IGR J11215−5952

Context. The current generation of X-ray satellites has discovered many new X-ray sources that are difficult to classify within the well-described subclasses. The hard X-ray source IGR J11215−5952 is a peculiar transient, displaying very short X-ray outbursts every 165 days. Aims. To characterise the source, we obtained high-resolution spectra of the optical counterpart, HD 306414, at different epochs, spanning a total of three months, before and around the 2007 February outburst with the combined aims of deriving its astrophysical parameters and searching for orbital modulation. Methods. We fit model atmospheres generated with the fastwind code to the spectrum, and used the interstellar lines in the spectrum to estimate its distance. We also cross-correlated each individual spectrum to the best-fit model to derive radial velocities. Results. From its spectral features, we classify HD 306414 as B0.5 Ia. From the model fit, we find Teff ≈ 24 700 K and log g ≈ 2.7, in good agreement with the morphological classification. Using the interstellar lines in its spectrum, we estimate a distance to HD 306414 d ≳ 7 kpc. Assuming this distance, we derive R∗ ≈ 40 R⊙ and Mspect ≈ 30 M⊙ (consistent, within errors, with Mevol ≈ 38 M⊙, and in good agreement with calibrations for the spectral type). Analysis of the radial velocity curve reveals that radial velocity changes are not dominated by the orbital motion, and provide an upper limit on the semi-amplitude for the optical component Kopt ≲ 11 ± 6 km   s-1. Large variations in the depth and shape of photospheric lines suggest the presence of strong pulsations, which may be the main cause of the radial velocity changes. Very significant variations, uncorrelated with those of the photospheric lines are seen in the shape and position of the Hα emission feature around the time of the X-ray outburst, but large excursions are also observed at other times. Conclusions. HD 306414 is a normal B0.5 Ia supergiant. Its radial velocity curve is dominated by an effect that is different from binary motion, and is most likely stellar pulsations. The data available suggest that the X-ray outbursts are caused by the close passage of the neutron star in a very eccentric orbit, perhaps leading to localised mass outflow.

Discussing the physical meaning of the absorption feature at 2.1 keV in 4U 1538–52

High resolution X-ray spectroscopy is a powerful tool for studying the nature of the matter surrounding the neutron star in X-ray binaries and its interaction between the stellar wind and the compact object. In particular, absorption features in their spectra could reveal the presence of atmospheres of the neutron star or their magnetic field strength. Here we present an investigation of the absorption feature at 2.1 keV in the X-ray spectrum of the high mass X-ray binary 4U 1538–52 based on our previous analysis of the XMM-Newton data. We study various possible origins and discuss the different physical scenarios in order to explain this feature. A likely interpretation is that the feature is associated with atomic transitions in an O/Ne neutron star atmosphere or of hydrogen and helium like Fe or Si ions formed in the stellar wind of the donor.