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The Seventeenth Data Release of the Sloan Digital Sky Surveys : Complete Release of MaNGA, MaStar, and APOGEE-2 Data
- 2022
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Ingår i: Astrophysical Journal Supplement Series. - : Institute of Physics (IOP). - 0067-0049 .- 1538-4365. ; 259:2
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Tidskriftsartikel (refereegranskat)abstract
- This paper documents the seventeenth data release (DR17) from the Sloan Digital Sky Surveys; the fifth and final release from the fourth phase (SDSS-IV). DR17 contains the complete release of the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey, which reached its goal of surveying over 10,000 nearby galaxies. The complete release of the MaNGA Stellar Library accompanies this data, providing observations of almost 30,000 stars through the MaNGA instrument during bright time. DR17 also contains the complete release of the Apache Point Observatory Galactic Evolution Experiment 2 survey that publicly releases infrared spectra of over 650,000 stars. The main sample from the Extended Baryon Oscillation Spectroscopic Survey (eBOSS), as well as the subsurvey Time Domain Spectroscopic Survey data were fully released in DR16. New single-fiber optical spectroscopy released in DR17 is from the SPectroscipic IDentification of ERosita Survey subsurvey and the eBOSS-RM program. Along with the primary data sets, DR17 includes 25 new or updated value-added catalogs. This paper concludes the release of SDSS-IV survey data. SDSS continues into its fifth phase with observations already underway for the Milky Way Mapper, Local Volume Mapper, and Black Hole Mapper surveys.
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| 5. |
- Santana, Felipe A., et al.
(författare)
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Final Targeting Strategy for the SDSS-IV APOGEE-2S Survey
- 2021
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Ingår i: Astronomical Journal. - : American Astronomical Society. - 1538-3881 .- 0004-6256. ; 162:6
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Tidskriftsartikel (refereegranskat)abstract
- APOGEE is a high-resolution (R similar to 22,000), near-infrared, multi-epoch, spectroscopic survey of the Milky Way. The second generation of the APOGEE project, APOGEE-2, includes an expansion of the survey to the Southern Hemisphere called APOGEE-2S. This expansion enabled APOGEE to perform a fully panoramic mapping of all of the main regions of the Milky Way; in particular, by operating in the H band, APOGEE is uniquely able to probe the dust-hidden inner regions of the Milky Way that are best accessed from the Southern Hemisphere. In this paper we present the targeting strategy of APOGEE-2S, with special attention to documenting modifications to the original, previously published plan. The motivation for these changes is explained as well as an assessment of their effectiveness in achieving their intended scientific objective. In anticipation of this being the last paper detailing APOGEE targeting, we present an accounting of all such information complete through the end of the APOGEE-2S project; this includes several main survey programs dedicated to exploration of major stellar populations and regions of the Milky Way, as well as a full list of programs contributing to the APOGEE database through allocations of observing time by the Chilean National Time Allocation Committee and the Carnegie Institution for Science. This work was presented along with a companion article, Beaton et al. (2021), presenting the final target selection strategy adopted for APOGEE-2 in the Northern Hemisphere.
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| 6. |
- Stanke, T., et al.
(författare)
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The APEX Large CO Heterodyne Orion Legacy Survey (ALCOHOLS): I. Survey overview
- 2022
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 658
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Tidskriftsartikel (refereegranskat)abstract
- Context. The Orion molecular cloud complex harbours the nearest Giant Molecular Clouds (GMCs) and the nearest site of high-mass star formation. Its young star and protostar populations are thoroughly characterized. The region is therefore a prime target for the study of star formation. Aims. Here, we verify the performance of the SuperCAM 64 pixel heterodyne array on the Atacama Pathfinder Experiment (APEX). We give a descriptive overview of a set of wide-field CO(32) spectral line cubes obtained towards the Orion GMC complex, aimed at characterizing the dynamics and structure of the extended molecular gas in diverse regions of the clouds, ranging from very active sites of clustered star formation in Orion B to comparatively quiet regions in southern Orion A. In a future publication, we will characterize the full population of protostellar outflows and their feedback over an entire GMC. Methods. We present a 2.7 square degree (130 pc2) mapping survey in the 12CO(32) transition, obtained using SuperCAM on APEX at an angular resolution of 19 (7600 AU or 0.037 pc at a distance of 400 pc), covering the main sites of star formation in the Orion B cloud (L 1622, NGC 2071, NGC 2068, Ori B9, NGC 2024, and NGC 2023), and a large patch in the southern part of the L 1641 cloud in Orion A. Results. We describe CO integrated line emission and line moment maps and position-velocity diagrams for all survey fields and discuss a few sub-regions in some detail. Evidence for expanding bubbles is seen with lines splitting into double components, often in areas of optical nebulosities, most prominently in the NGC 2024 H II region, where we argue that the bulk of the molecular gas is in the foreground of the H II region. High CO(32)/CO(10) line ratios reveal warm CO along the western edge of the Orion B cloud in the NGC 2023 & NGC 2024 region facing the IC 434 H II region. We see multiple, well separated radial velocity cloud components towards several fields and propose that L 1641-S consists of a sequence of clouds at increasingly larger distances. We find a small, seemingly spherical cloud, which we term Cow Nebula globule, north of NGC 2071. We confirm that we can trace high velocity line wings out to the extremely high velocity regime in protostellar molecular outflows for the NGC 2071-IR outflow and the NGC 2024 CO jet, and identify the protostellar dust core FIR4 (rather than FIR5) as the true driving source of the NGC 2024 monopolar outflow.
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| 7. |
- Alvarez-Gutierrez, R. H., et al.
(författare)
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Filament Rotation in the California L1482 Cloud
- 2021
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Ingår i: Astrophysical Journal. - : American Astronomical Society. - 1538-4357 .- 0004-637X. ; 908:1
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Tidskriftsartikel (refereegranskat)abstract
- We analyze the gas mass distribution, the gas kinematics, and the young stellar objects of the California Molecular Cloud L1482 filament. The mean Gaia DR2 YSO distance is 511(-16)(+17) pc. In terms of the gas, the line-mass (M/L) profiles are symmetric scale-free power laws consistent with cylindrical geometry. We calculate the gravitational potential and field profiles based on these. Our IRAM 30 m multi-tracer position-velocity diagrams highlight twisting and turning structures. We measure the (CO)-O-18 velocity profile perpendicular to the southern filament ridgeline. The profile is regular, confined (projected r less than or similar to 0.4 pc), antisymmetric, and, to first order, linear, with a break at r similar to 0.25 pc. We use a simple solid-body rotation toy model to interpret it. We show that the centripetal force, compared to gravity, increases toward the break; when the ratio of forces approaches unity, the profile turns over, just before the implied filament breakup. The timescales of the inner (outer) gradients are similar to 0.7 (6.0) Myr. The timescales and relative roles of gravity to rotation indicate that the structure is stable, long lived (similar to a few times 6 Myr), and undergoing outside-in evolution. This filament has practically no star formation, a perpendicular Planck plane-of-the-sky magnetic field morphology, and 2D "zig-zag" morphology, which together with the rotation profile lead to the suggestion that the 3D shape is a "corkscrew" filament. These results, together with results in other regions, suggest evolution toward higher densities as rotating filaments shed angular momentum. Thus, magnetic fields may be an essential feature of high-mass (M similar to 10(5) M) cloud filament evolution toward cluster formation.
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| 8. |
- Stutz, Aaron Jonas, 1971-, et al.
(författare)
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Early Upper Paleolithic chronology in the Levant : new ABOx-SC accelerator mass spectrometry results from the Mughr el-Hamamah Site, Jordan
- 2015
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Ingår i: Journal of Human Evolution. - : Elsevier BV. - 0047-2484 .- 1095-8606. ; 85, s. 157-183
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Tidskriftsartikel (refereegranskat)abstract
- Methodological developments and new paleoanthropological data remain jointly central to clarifying the timing and systemic interrelationships between the Middle-Upper Paleolithic (MP-UP) archaeological transition and the broadly contemporaneous anatomically modern human-archaic biological turnover. In the recently discovered cave site of Mughr el-Hamamah, Jordan, in situ flint artifacts comprise a diagnostic early Upper Paleolithic (EUP) assemblage. Unusually well-preserved charcoal from hearths and other anthropogenic features associated with the lithic material were subjected to acid-base-wet oxidation-stepped combustion (ABOx-SC) pretreatment. This article presents the ABOx-SC accelerator mass spectrometry (AMS) radiocarbon dates on nine charcoal specimens from a single palimpsest occupation layer. Date calibration was carried out using the INTCAL13 radiocarbon calibration dataset. With the bulk of the material dating to 45-39 ka cal BP (thousands of years calibrated before present), the Mughr el-Hamamah lithic artifacts reveal important differences from penecontemporaneous sites in the region, documenting greater technological variability than previously known for this time frame in the Levant. The radiocarbon data from this EUP archaeological context highlight remaining challenges for increasing chronological precision in documenting the MP-UP transition.
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| 10. |
- Le Rouzic, E, et al.
(författare)
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Docking of HIV-1 Vpr to the nuclear envelope is mediated by the interaction with the nucleoporin hCG1
- 2002
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Ingår i: Journal of Biological Chemistry. - 0021-9258 .- 1083-351X. ; 277:47, s. 45091-45098
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Tidskriftsartikel (refereegranskat)abstract
- The HIV-1 genome contains several genes coding for auxiliary proteins, including the small Vpr protein. Vpr affects the integrity of the nuclear envelope and participates in the nuclear translocation of the preintegration complex containing the viral DNA. Here, we show by photobleaching experiments performed on living cells expressing a Vpr-green fluorescent protein fusion that the protein shuttles between the nucleus and the cytoplasm, but a significant fraction is concentrated at the nuclear envelope, supporting the hypothesis that Vpr interacts with components of the nuclear pore complex. An interaction between HIV-1 Vpr and the human nucleoporin CG1 (hCG1) was revealed in the yeast two-hybrid system, and then confirmed both in vitro and in transfected cells. This interaction does not involve the FG repeat domain of hCG1 but rather the N-terminal region of the protein. Using a nuclear import assay based on digitonin-permeabilized cells, we demonstrate that hCG1 participates in the docking of Vpr at the nuclear envelope. This association of Vpr with a component of the nuclear pore complex may contribute to the disruption of the nuclear envelope and to the nuclear import of the viral DNA.
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| 12. |
- Northcott, Paul A, et al.
(författare)
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Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma.
- 2014
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 511:7510, s. 428-428
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Tidskriftsartikel (refereegranskat)abstract
- Medulloblastoma is a highly malignant paediatric brain tumour currently treated with a combination of surgery, radiation and chemotherapy, posing a considerable burden of toxicity to the developing child. Genomics has illuminated the extensive intertumoral heterogeneity of medulloblastoma, identifying four distinct molecular subgroups. Group 3 and group 4 subgroup medulloblastomas account for most paediatric cases; yet, oncogenic drivers for these subtypes remain largely unidentified. Here we describe a series of prevalent, highly disparate genomic structural variants, restricted to groups 3 and 4, resulting in specific and mutually exclusive activation of the growth factor independent 1 family proto-oncogenes, GFI1 and GFI1B. Somatic structural variants juxtapose GFI1 or GFI1B coding sequences proximal to active enhancer elements, including super-enhancers, instigating oncogenic activity. Our results, supported by evidence from mouse models, identify GFI1 and GFI1B as prominent medulloblastoma oncogenes and implicate 'enhancer hijacking' as an efficient mechanism driving oncogene activation in a childhood cancer.
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| 14. |
- Stutz, Rebecca S., et al.
(författare)
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A mechanistic understanding of repellent function against mammalian herbivores
- 2019
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Ingår i: Ecological processes. - : Springer Science and Business Media LLC. - 2192-1709. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Background: Browsing repellents are widely used to deter large herbivores from consuming plants of ecological,economic and aesthetic importance. Understanding how these repellents function on a behavioural mechanisticlevel is critical to predicting effectiveness. Here, we illustrate how these mechanisms can be tested, by exposing amodel mammalian herbivore, the fallow deer, to different concentrations of a commercial chemical repellent(HaTe2) in two-choice feeding trials.Results:The repellent acted as a defensive chemical for the food by both reducing visitation and the amountconsumed. Deer favoured the less defended feeders before ingesting any food, suggesting that the repellentaltered olfactory and/or visual cues. Deer also consumed less of the more defended food when choosing betweenlow and high repellent feeders than no and low repellent feeders, indicating that the repellent modified flavourand/or sensation. Repellent effectiveness declined with increased exposure, suggesting that consumption had nonegative post-ingestive effects, and thus, deterrence was not caused by a conditioned aversion or irritation. Instead,this pattern suggests that deer learned, through repeated sampling of repellent-treated food, that there was noadverse physiological effect of ingesting it.Conclusions:These results imply that HaTe2 repellent will not be effective over prolonged periods or in theabsence of alternative untreated food. Understanding the mechanisms driving repellent function using two-choicetrials could help practitioners decide whether a particular repellent is likely to be effective against mammalianherbivory in their management scenario.
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| 15. |
- Stutz, Rebecca S., et al.
(författare)
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Borrowed plant defences : Deterring browsers using a forestry by-product
- 2017
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Ingår i: Forest Ecology and Management. - : Elsevier BV. - 0378-1127 .- 1872-7042. ; 390, s. 1-7
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Tidskriftsartikel (refereegranskat)abstract
- Mammalian browsers can cause ecologically and economically significant damage to important tree species, particularly at the vulnerable seedling stage. Some tree species or particular parts of trees are less preferred as a result of chemical defences - harnessing such defences could reduce the appeal of more preferred trees and thus their loss to browsing. We tested the potential of birch bark extract, a forestry by-product, to protect seedlings of Scots pine Pinus sylvestris from two globally significant browsers: moose Alces alces and red deer Cervus elaphus. We quantified the responses by captive animals to extract application as a function of both the distance between seedlings and whether the extract was applied to all or alternate seedlings. Both moose and red deer consumed pine seedlings less frequently when seedlings were treated with birch bark extract, but their responses differed when only alternate seedlings were treated. At inter-seedling distances equivalent to those used in forestry, red deer browsed untreated seedlings more frequently when alternate seedlings were treated than when none were treated (associational susceptibility), whereas moose browsed untreated seedlings less frequently with treated than untreated neighbours (associational refuge). These neighbourhood effects were not evident at inter-seedling distances three times larger or smaller than those used in forestry. There was also no significant difference in the frequency of browsing on treated seedlings in alternate compared to completely treated arrangements at any inter-seedling distance. Red deer removed significantly less foliage from treated than untreated seedlings once browsed. Browsing by moose followed a similar but non-significant trend. The relative number of untreated to treated seedlings browsed was 2:1 for red deer and 4:1 for moose. Red deer used a finer scale of selection than moose for choosing between seedlings, consistent with their smaller body mass. However, the coarser-scale of selection used by moose resulted in consumption of more untreated relative to treated seedlings. Our study highlights the potential of existing plant defensive chemistry, harvested from forestry by-products, to reduce herbivore damage to tree seedlings. We also demonstrate the need to consider both plant associational effects and the foraging strategies of the dominant herbivores in applying repellents.
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| 16. |
- Stutz, Rebecca S., et al.
(författare)
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Cohesiveness reduces foraging efficiency in a social herbivore
- 2018
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Ingår i: Animal Behaviour. - : Elsevier BV. - 0003-3472 .- 1095-8282. ; 135, s. 57-68
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Tidskriftsartikel (refereegranskat)abstract
- For social foragers, movement as a group could increase foraging efficiency through collective discovery of high-quality food sources. This would require an efficient mechanism for transferring information about food quality between individuals. Conversely, the constraints of foraging as a cohesive group could decrease efficiency; grouping may persist to serve other functions such as protection from predators. To test what drives cohesion in herbivores, we manipulated patch shape and within-patch pattern of food quality and quantified the effects on group level diet selection by a social herbivore, the fallow deer, Dama dama. We arranged feeders containing fodder in lines or blocks, and manipulated the pattern of food quality within patches by adding tannin, a plant secondary compound that decreases palatability. We quantified the relative consumption of low- and high-tannin food to compare diet selectivity at the group level between patch treatments. If group foraging evolved to increase foraging efficiency, altering the spatial arrangement of food should not affect diet selectivity because information about food location and quality is shared. We found, however, that the herd expressed different levels of selectivity between both patch shapes and food quality patterns. Deer selected better diets in blocks than lines. In lines, the herd selected better diets when quality varied between alternate feeders rather than between the two halves of the patch, suggesting a reliance on personal rather than group information. Deer consumed the most at patch centres in all treatments except in blocks with high-tannin centres, but diet selection was poorer in the latter compared to blocks with low-tannin centres. Aggregation at the centre of patches appears to have restricted exploitation of the best food. Predation pressure and/or resource variability may have favoured the evolution of a foraging strategy that prioritizes social cohesion over effective diet selection.
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| 17. |
- Stutz, Rebecca S., et al.
(författare)
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Efficient application of a browsing repellent : Can associational effects within and between plants be exploited?
- 2019
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Ingår i: European Journal of Forest Research. - : Springer Science and Business Media LLC. - 1612-4669 .- 1612-4677. ; 138:2, s. 253-262
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Tidskriftsartikel (refereegranskat)abstract
- Browsing can reduce forest productivity, particularly when the apical shoots of trees are damaged. Repellents are used widely to reduce browsing, but application is costly. To improve efficiency, it may be possible to take advantage of associational plant refuge effects, requiring repellents to be applied only to some trees or parts of trees, or reapplied less frequently. Using captive moose (Alces alces) and constructed stands of Scots pine (Pinus sylvestris), we tested for potential refuges by applying a commercial repellent (HaTe2) to all, alternate or none of the apical shoots, or all of the previous-year apical shoots. We also tested for potential refuges under field conditions, applying the repellent to all, alternate or none of the apical pine shoots in forest stands. Captive moose (two individuals in a 2.1-ha enclosure, similar to 95 individuals km(-2)) browsed 100% of trees, but were significantly less likely to browse apical shoots treated with repellent. Associational refuge was ineffective both within and between trees. In the field (0.84 moose km(-2)), only 1.3% of trees sustained browsing damage. Applying the repellent to the apical shoots of pines had no direct repellent effect nor any within-plant associational effects. Trees with treated apical shoots provided some protection for untreated neighbouring trees, but this was not biologically meaningful given the low percentage of trees browsed overall. Here, a simple captive experiment was not predictive of the browsing response observed in the field, demonstrating the need to test repellent application strategies in situ.
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| 18. |
- Thuswaldner, Sophie, 1976-, et al.
(författare)
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Identification, expression, and functional analyses of a thylakoid ATP/ADP carrier from Arabidopsis
- 2007
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Ingår i: J Biol Chem. - 0021-9258 .- 1083-351X. ; 282:12, s. 8848-59
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Tidskriftsartikel (refereegranskat)abstract
- In plants the chloroplast thylakoid membrane is the site of light-dependent photosynthetic reactions coupled to ATP synthesis. The ability of the plant cell to build and alter this membrane system is essential for efficient photosynthesis. A nucleotide translocator homologous to the bovine mitochondrial ADP/ATP carrier (AAC) was previously found in spinach thylakoids. Here we have identified and characterized a thylakoid ATP/ADP carrier (TAAC) from Arabidopsis.(i) Sequence homology with the bovine AAC and the prediction of chloroplast transit peptides indicated a putative carrier encoded by the At5g01500 gene, as a TAAC. (ii) Transiently expressed TAAC-green fluorescent protein fusion construct was targeted to the chloroplast. Western blotting using a peptide-specific antibody together with immunogold electron microscopy revealed a major location of TAAC in the thylakoid membrane. Previous proteomic analyses identified this protein in chloroplast envelope preparations. (iii) Recombinant TAAC protein specifically imports ATP in exchange for ADP across the cytoplasmic membrane of Escherichia coli. Studies on isolated thylakoids from Arabidopsis confirmed these observations. (iv) The lack of TAAC in an Arabidopsis T-DNA insertion mutant caused a 30-40% reduction in the thylakoid ATP transport and metabolism. (v) TAAC is readily expressed in dark-grown Arabidopsis seedlings, and its level remains stable throughout the greening process. Its expression is highest in developing green tissues and in leaves undergoing senescence or abiotic stress. We propose that the TAAC protein supplies ATP for energy-dependent reactions during thylakoid biogenesis and turnover in plants.
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