The 13th Data Release of the Sloan Digital Sky Survey: First Spectroscopic Data from the SDSS-IV Survey Mapping Nearby Galaxies at Apache Point Observatory

The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) began observations in July 2014. It pursues three core programs: APOGEE-2,MaNGA, and eBOSS. In addition, eBOSS contains two major subprograms: TDSS and SPIDERS. This paper describes the first data release from SDSS-IV, Data Release 13 (DR13), which contains new data, reanalysis of existing data sets and, like all SDSS data releases, is inclusive of previously released data. DR13 makes publicly available 1390 spatially resolved integral field unit observations of nearby galaxies from MaNGA,the first data released from this survey. It includes new observations from eBOSS, completing SEQUELS. In addition to targeting galaxies and quasars, SEQUELS also targeted variability-selected objects from TDSS and X-ray selected objects from SPIDERS. DR13 includes new reductions ofthe SDSS-III BOSS data, improving the spectrophotometric calibration and redshift classification. DR13 releases new reductions of the APOGEE-1data from SDSS-III, with abundances of elements not previously included and improved stellar parameters for dwarf stars and cooler stars. For the SDSS imaging data, DR13 provides new, more robust and precise photometric calibrations. Several value-added catalogs are being released in tandem with DR13, in particular target catalogs relevant for eBOSS, TDSS, and SPIDERS, and an updated red-clump catalog for APOGEE.This paper describes the location and format of the data now publicly available, as well as providing references to the important technical papers that describe the targeting, observing, and data reduction. The SDSS website, http://www.sdss.org, provides links to the data, tutorials and examples of data access, and extensive documentation of the reduction and analysis procedures. DR13 is the first of a scheduled set that will contain new data and analyses from the planned ~6-year operations of SDSS-IV.PostprintPeer reviewe

The 13th Data Release of the Sloan Digital Sky Survey: First Spectroscopic Data from the SDSS-IV Survey Mapping Nearby Galaxies at Apache Point Observatory

The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) began observations in 2014 July. It pursues three core programs: the Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2), Mapping Nearby Galaxies at APO (MaNGA), and the Extended Baryon Oscillation Spectroscopic Survey (eBOSS). As well as its core program, eBOSS contains two major subprograms: the Time Domain Spectroscopic Survey (TDSS) and the SPectroscopic IDentification of ERosita Sources (SPIDERS). This paper describes the first data release from SDSS-IV, Data Release 13 (DR13). DR13 makes publicly available the first 1390 spatially resolved integral field unit observations of nearby galaxies from MaNGA. It includes new observations from eBOSS, completing the Sloan Extended QUasar, Emission-line galaxy, Luminous red galaxy Survey (SEQUELS), which also targeted variability-selected objects and X-ray-selected objects. DR13 includes new reductions of the SDSS-III BOSS data, improving the spectrophotometric calibration and redshift classification, and new reductions of the SDSS-III APOGEE-1 data, improving stellar parameters for dwarf stars and cooler stars. DR13 provides more robust and precise photometric calibrations. Value-added target catalogs relevant for eBOSS, TDSS, and SPIDERS and an updated red-clump catalog for APOGEE are also available. This paper describes the location and format of the data and provides references to important technical papers. The SDSS web site, http://www.sdss.org, provides links to the data, tutorials, examples of data access, and extensive documentation of the reduction and analysis procedures. DR13 is the first of a scheduled set that will contain new data and analyses from the planned ~6 yr operations of SDSS-IV

Internal kinematics and structure of the bulge globular cluster NGC 6569

In the context of a project aimed at characterizing the properties of star clusters in the Galactic bulge, here we present the determination of the internal kinematics and structure of the massive globular cluster NGC 6569. The kinematics has been studied by means of an unprecedented spectroscopic dataset acquired in the context of the ESO-VLT Multi-Instrument Kinematic Survey (MIKiS) of Galactic globular clusters, combining the observations from four different spectrographs. We measured the line-of-sight velocity of a sample of almost 1300 stars distributed between ~0.8" and 770" from the cluster center. From a sub-sample of high-quality measures, we determined the velocity dispersion profile of the system over its entire radial extension (from ~ 5" to ~ 200" from the center), finding the characteristic behavior usually observed in globular clusters, with a constant inner plateau and a declining trend at larger radii. The projected density profile of the cluster has been obtained from resolved star counts, by combining high-resolution photometric data in the center, and the Gaia EDR3 catalog radially extended out to ~20' for a proper sampling of the Galactic field background. The two profiles are properly reproduced by the same King model, from which we estimated updated values of the central velocity dispersion, main structural parameters (such as the King concentration, the core, half-mass, and tidal radii), total mass, and relaxation times. Our analysis also reveals a hint of ordered rotation in an intermediate region of the cluster (40"<r<90", corresponding to $2 r_c<r<4.5 r_c$), but additional data are required to properly assess this possibility.Comment: Accepted for publication in The Astrophysical Journal; 21 pages, 10 figures, 4 table

Remote sensing of bark beetle damage in urban forests at individual tree level using a novel hyperspectral camera from UAV and aircraft

Climate-related extended outbreaks and range shifts of destructive bark beetle species pose a serious threat to urban boreal forests in North America and Fennoscandia. Recent developments in low-cost remote sensing technologies offer an attractive means for early detection and management of environmental change. They are of great interest to the actors responsible for monitoring and managing forest health. The objective of this investigation was to develop, assess, and compare automated remote sensing procedures based on novel, low-cost hyperspectral imaging technology for the identification of bark beetle infestations at the individual tree level in urban forests. A hyperspectral camera based on a tunable Fabry-Perot interferometer was operated from a small, unmanned airborne vehicle (UAV) platform and a small Cessna-type aircraft platform. This study compared aspects of using UAV datasets with a spatial extent of a few hectares (ha) and a ground sample distance (GSD) of 10-12 cm to the aircraft data covering areas of several km(2) and having a GSD of 50 cm. An empirical assessment of the automated identification of mature Norway spruce (Picea abies L. Karst.) trees suffering from infestation (representing different colonization phases) by the European spruce bark beetle (Ips typographus L.) was carried out in the urban forests of Lahti, a city in southern Finland. Individual spruces were classified as healthy, infested, or dead. For the entire test area, the best aircraft data results for overall accuracy were 79% (Cohen's kappa: 0.54) when using three crown color classes (green as healthy, yellow as infested, and gray as dead). For two color classes (healthy, dead) in the same area, the best overall accuracy was 93% (kappa: 0.77). The finer resolution UAV dataset provided better results, with an overall accuracy of 81% (kappa: 0.70), compared to the aircraft results of 73% (kappa: 0.56) in a smaller sub-area. The results showed that novel, low-cost remote sensing technologies based on individual tree analysis and calibrated remote sensing imagery offer great potential for affordable and timely assessments of the health condition of vulnerable urban forests.Peer reviewe

The 13th data release of the Sloan Digital Sky Survey: first spectroscopic data from the SDSS-IV survey mapping nearby galaxies at Apache Point Observatory

The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) began observations in 2014 July. It pursues three core programs: the Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2), Mapping Nearby Galaxies at APO (MaNGA), and the Extended Baryon Oscillation Spectroscopic Survey (eBOSS). As well as its core program, eBOSS contains two major subprograms: the Time Domain Spectroscopic Survey (TDSS) and the SPectroscopic IDentification of ERosita Sources (SPIDERS). This paper describes the first data release from SDSS-IV, Data Release 13 (DR13). DR13 makes publicly available the first 1390 spatially resolved integral field unit observations of nearby galaxies from MaNGA. It includes new observations from eBOSS, completing the Sloan Extended QUasar, Emission-line galaxy, Luminous red galaxy Survey (SEQUELS), which also targeted variability-selected objects and X-ray-selected objects. DR13 includes new reductions of the SDSS-III BOSS data, improving the spectrophotometric calibration and redshift classification, and new reductions of the SDSS-III APOGEE-1 data, improving stellar parameters for dwarf stars and cooler stars. DR13 provides more robust and precise photometric calibrations. Value-added target catalogs relevant for eBOSS, TDSS, and SPIDERS and an updated red-clump catalog for APOGEE are also available. This paper describes the location and format of the data and provides references to important technical papers. The SDSS web site, http://www.sdss.org, provides links to the data, tutorials, examples of data access, and extensive documentation of the reduction and analysis procedures. DR13 is the first of a scheduled set that will contain new data and analyses from the planned ~6 yr operations of SDSS-IV

Integrating OLAP and Ranking: The Ranking-Cube Methodology

Recent years have witnessed an enormous growth of data in business, industry, and Web applications. Database search often returns a large collection of results, which poses challenges to both efficient query processing and effective digest of the query results. To address this problem, ranked search has been introduced to database systems. We study the problem of On-Line Analytical Processing (OLAP) of ranked queries, where ranked queries are conducted in the arbitrary subset of data defined by multi-dimensional selections. While pre-computation and multi-dimensional aggregation is the standard solution for OLAP, materializing dynamic ranking results is unrealistic because the ranking criteria are not known until the query time. To overcome such difficulty, we develop a new ranking cube method that performs semi on-line materialization and semi online computation in this thesis. Its complete life cycle, including cube construction, incremental maintenance, and query processing, is also discussed. We further extend the ranking cube in three dimensions. First, how to answer queries in high-dimensional data. Second, how to answer queries which involves joins over multiple relations. Third, how to answer general preference queries (besides ranked queries, such as skyline queries). Our performance studies show that ranking-cube is orders of magnitude faster than previous approaches

Exploring the internal kinematics of Galactic Globular Cluster cores

Globular clusters (GCs) are traditionally described as simple quasi-relaxed non-rotating stellar systems, characterized by spherical symmetry and isotropy in velocity space. However, recent studies have shown deviations from isotropic velocity distributions and significant internal rotation in many GCs, suggesting that their internal structure and kinematics are more complex than previously thought. The aim of this thesis is to investigate the internal kinematics of Galactic Globular Clusters (GGCs) as part of the Multi-Instrument Kinematic Survey (MIKiS), which exploits the capabilities of different ESO-VLT spectrographs to obtain comprehensive velocity dispersion (VD) and rotation profiles of GGCs. Moreover, this thesis has the particular goal of unraveling the kinematics of GC cores, which are still largely unexplored, by taking advantage of the exceptional spatial resolution of the adaptive-optics assisted integral-field spectrograph MUSE/NFM. The thesis presents a thorough kinematic study of three GGCs NGC 1904, NGC 6440, and NGC 6569. By combining the data sets acquired with four different spectrographs, we obtained the radial velocity (RV) of more than 1000 individual stars in each cluster, sampling from the innermost to the outermost regions. This allowed us to obtain the entire VD profile of each cluster and exclude the presence of an intermediate-mass black hole in the core of NGC 1904, at odds with previous findings obtained from integrated-light spectra. The studies also revealed signatures of internal rotation in each of the GCs studied. These results, supported by those of N-body simulations, prove that GCs were born with a significant initial rotation that they gradually lost through internal two-body relaxation and angular momentum loss carried away by escaping stars. Furthermore, we derived the structural parameters of NGC 6440 and NGC 6569, obtaining a comprehensive overview of the internal kinematics and structure of these GCs, which is necessary to properly reconstruct the evolutionary history of these systems

Wide-Field Fluorescence Hyperspectral Imaging to Quantify Cell Populations in Spheroids Formed and Cultured in Microfluidic Chips

Le cancer de l'ovaire a le taux de mortalité le plus élevé de tous les cancers gynécologiques. Malgré les avancements en techniques de chirurgie et les développements en chimiothérapie au cours de la dernière décennie, son taux de survie après cinq ans demeure inférieur à 45%, en raison du diagnostic tardif de ce cancer et du phénomène de résistance aux médicaments. Les patients présentant un cancer épithélial de l'ovaire (CÉO), la forme la plus courante de la maladie, répondent généralement bien au traitement de chimiothérapie standard à base de platine et de taxane. Cependant, une forte proportion de patients rechute et cette récurrence se révèle souvent résistante au traitement standard. Une des hypothèses de cette résistance chez le CÉO est que son instabilité génétique élevée se traduit par une hétérogénéité clonale dans les tumeurs, où le nombre de clones (populations de cellules identiques) dans les tumeurs augmente avec le temps, créant de nouvelles mutations présentant différents niveaux de sensibilité aux traitements. Par exemple, le premier traitement de chimiothérapie d'une patiente peut tuer les clones sensibles et laisser une faible population de cellules résistantes qui finiront par croître et provoquer une rechute du cancer. Il est donc nécessaire d'étudier l'hétérogénéité clonale et ses effets sur la résistance aux médicaments. Divers modèles de cancer in vitro ont été développés pour la recherche en laboratoire. Le modèle le plus simple et le plus courant est la culture en monocouches bi-dimensionnelles (2D), pour laquelle les cellules cancéreuses adhèrent à une surface, comme les boîtes de pétri, et croissent en monocouche. Le modèle le plus réaliste consiste à utiliser directement les tumeurs de patients, car elles incluent le microenvironnement complet du cancer en trois dimensions (3D). Cependant, comme le tissu du patient est souvent disponible en quantités limitées, le nombre d’expériences qu’il est possible de faire est aussi limité. Les sphéroïdes sont des agrégats de cellules 3D formés in vitro et représentent un compromis idéal entre la simplicité, leur composition cellulaire étant connue et contrôlée, et le réalisme, car ils imitent mieux la nature 3D des tumeurs humaines que la culture en monocouches 2D. Les sphéroïdes peuvent facilement être utilisés pour étudier l'hétérogénéité clonale car plusieurs lignées cellulaires peuvent être mélangées à des ratios précis pour former des sphéroïdes de coculture. La communauté microfluidique a mis au point des puces microfluidiques qui peuvent facilement former et traiter des centaines de sphéroïdes. Dans ce projet, les puces microfluidiques sont utilisées pour réduire le travail en laboratoire en formant des dizaines de sphéroïdes en une seule étape et en les piégeant en place, de sorte que les changements de milieu de culture et de médicaments peuvent être rapidement effectués. L’un des principaux avantages de l’utilisation de sphéroïdes comme modèle de cancer in vitro est que des centaines de sphéroïdes de coculture identiques peuvent être utilisés pour étudier facilement diverses conditions. Cependant, l'analyse de la réponse dynamique de chacune des populations de cellules composant ce grand nombre de sphéroïdes reste un défi. Les études utilisent souvent la morphologie cellulaire, les marqueurs immunologiques ou les marqueurs fluorescents pour identifier les populations cellulaires. Mais beaucoup de ces techniques reposent sur l'observation directe de chaque cellule composant le sphéroïde et nécessitent soit une digestion du sphéroïde en une suspension cellulaire, soit une coupe du sphéroïde en fines tranches. Pour analyser des échantillons 3D intacts, des techniques de microscopie telles que la microscopie confocale, multiphotonique et à feuilles de lumière (light sheet microscopy) ont été développées. Bien qu'elles présentent de nombreux avantages, ces techniques ne sont pas adaptées pour analyser un haut nombre de sphéroïdes en une seule acquisition ou ne peuvent pas analyser les sphéroïdes de diamètres supérieurs à 70-100 µm. Au cours de ce doctorat, un système d'imagerie hyperspectrale (HSI) en fluorescence à large champ a été conçu, construit et validé pour l’étude de sphéroïdes en coculture. Le système HSI a été spécifiquement conçu pour imager plusieurs sphéroïdes en une seule acquisition et pour l'imagerie in situ de sphéroïdes dans des puces microfluidiques. La conception du système HSI, présentée dans l’article 1, repose sur l’utilisation d’un filtre accordable à cristaux liquides et d’une caméra à dispositif à transfert de charges à multiplication d’électrons (EMCCD) pour l’imagerie des sphéroïdes dans un champ de vision de 7,25 mm de diamètre. Un algorithme d'analyse d'image a également été développé pour compenser toute réponse du système influençant l'intensité de fluorescence mesurée pour chaque sphéroïde présent dans l'image. Une étape finale de quantification pour compenser les propriétés optiques de l'échantillon a également été développée et validée à l'aide de fantômes optiques. L'article 2 présente une méthodologie pour étudier l'hétérogénéité clonale et sa relation avec la réponse au traitement. Deux lignées cellulaires fluorescentes ont été dérivées de la même lignée cellulaire du cancer de l'ovaire et ont été utilisées pour former des sphéroïdes de coculture avec différents ratios d'ensemencement cellulaire initiaux. Les résultats montrent que le système HSI permet de suivre la croissance de chaque population cellulaire et sa réponse aux médicaments en fonction du temps, y compris pour les populations occupant seulement 10% des sphéroïdes. L’accaparement d’un clone par rapport à l’autre dans les sphéroïdes a également été observé lorsqu'une forte dose de chimiothérapie était utilisée pour traiter les sphéroïdes. Le système HSI a également pu mettre en évidence différentes dynamiques de réponse au médicament entre les deux populations de cellules. L'imagerie hyperspectrale en fluorescence à champ large est une technique idéale pour l'imagerie de plusieurs sphéroïdes en une seule acquisition. Sa résolution spectrale permet de quantifier un plus grand nombre de fluorophores que les cubes de filtres de microscopie standards. L'imagerie hyperspectrale pourrait également être utilisée pour étudier les sphéroïdes de coculture constitués de différents types de cellules, tels que les cellules épithéliales et stromales ou les cellules cancéreuses et immunitaires.----------ABSTRACT Ovarian cancer has the highest mortality rate of all gynecological cancers. Despite advancement in surgery and chemotherapy over the past decade, its five-year survival rate is still less than 45%, due to late diagnosis and drug resistance. Patients presenting epithelial ovarian cancer (EOC), the most common form of the disease, usually respond well to the standard platinum- and taxane-based chemotherapy treatment. However, a high proportion of patient relapses, and this recurring cancer is often found to be resistant to the standard treatment. One hypothesis for this drug resistance in EOC is that its known high genetic instability translates into clonal heterogeneity in tumours, where the number of clones (i.e. populations of identical cells) in tumours increases over time as new mutations create new clones of various drug sensitivity levels. A patient’s first chemotherapy treatment can kill the sensitive clones and leave a small population of resistant cells that will eventually grow and cause a cancer relapse. There is a need to study clonal heterogeneity and its effect on drug resistance. Various in vitro cancer models were developed to research cancer treatments. The simplest and more common model is the 2D monolayer culture, where cancer cells adhere to a surface, such as petri dishes, and grow in a monolayer. The most realistic model involves using actual patient tumours, as they include the complete cancer microenvironment in three dimensions (3D). However, limited patient tissue is usually available to perform large experiment repetitions. Spheroids are 3D cell aggregated formed in vitro and represent an ideal compromise between simplicity, as the cell composition is known and controlled, and realism, as they better mimic the 3D nature of human tumours compared to monolayer 2D culture. Spheroids can easily be used to study clonal heterogeneity as multiple cell lines can be mixed at specific ratios to form co-culture spheroids. The microfluidic community has developed microfluidic chips that can easily form and treat hundreds of spheroids. Here, microfluidic chips are used to reduce laboratory work by forming 120 spheroids in a single step and trap the spheroids in place so that medium and drug changes can be quickly done. One of the main advantages of using spheroid as an in vitro cancer model is that hundreds of identical co-culture spheroids can be made to easily study various conditions. However, analyzing the dynamic response of individual cell populations of this large number of spheroids is still a ix challenge. Researchers often use cell morphology, immunostains or fluorescent markers to identify cell populations. But many of these techniques rely on the direct observation of each cell in the spheroid and require either spheroid digestion into a single cell suspension or spheroid slicing into thin tissue slices. To analyze intact 3D samples, microscopy techniques such as confocal, multiphoton, and light sheet microscopy were developed. While they present many advantages, these techniques are either not adapted to analyze many spheroids in a single acquisition or cannot analyze up to the centre spheroids larger than 70-100 μm in diameter. In this dissertation, a wide-field fluorescence hyperspectral imaging (HSI) system was designed, build and validated for co-culture spheroid research. The HSI system was specifically designed to image multiple spheroids in a single acquisition and for in situ imaging of spheroids in microfluidic chips. The HSI system design, presented in Article 1, is based on the use of a liquid crystal tunable filter and an electron-multiplying charged-coupled device camera to image spheroids in a 7.25 mmin diameter field of view. An image analysis algorithm was also developed to compensate for any system response influencing the measured fluorescence intensity from each spheroid present in the image. A final quantification step to compensate for the optical properties of the sample was also developed and validated using optical phantoms. Article 2 presents a methodology to study clonal heterogeneity and its relation to treatment response. Two fluorescent cell lines were derived from the same ovarian cancer cell line and used to form co-culture spheroids with various initial cell seeding ratios. Results show that the HSI system was able to follow each cell population growth and response to drugs over time, including for populations occupying only 10% of the spheroid. The onset of a clonal takeover was also observed when a high dose of chemotherapy drug was used to treat the spheroids. The HSI system was also able to highlight different response rates to the drug between the two cell populations. Wide-field fluorescence hyperspectral imaging is an ideal technique to images multiple spheroids in a single acquisition. Its spectral resolution can quantify a larger number of fluorophores than standard microscopy filter sets. Hyperspectral imaging could also be used to study co-culture spheroids made of different cell types, such as epithelial and stromal cells, or cancer and immune cells