182 research outputs found
The Pan-STARRS Moving Object Processing System
We describe the Pan-STARRS Moving Object Processing System (MOPS), a modern
software package that produces automatic asteroid discoveries and
identifications from catalogs of transient detections from next-generation
astronomical survey telescopes. MOPS achieves > 99.5% efficiency in producing
orbits from a synthetic but realistic population of asteroids whose
measurements were simulated for a Pan-STARRS4-class telescope. Additionally,
using a non-physical grid population, we demonstrate that MOPS can detect
populations of currently unknown objects such as interstellar asteroids.
MOPS has been adapted successfully to the prototype Pan-STARRS1 telescope
despite differences in expected false detection rates, fill-factor loss and
relatively sparse observing cadence compared to a hypothetical Pan-STARRS4
telescope and survey. MOPS remains >99.5% efficient at detecting objects on a
single night but drops to 80% efficiency at producing orbits for objects
detected on multiple nights. This loss is primarily due to configurable MOPS
processing limits that are not yet tuned for the Pan-STARRS1 mission.
The core MOPS software package is the product of more than 15 person-years of
software development and incorporates countless additional years of effort in
third-party software to perform lower-level functions such as spatial searching
or orbit determination. We describe the high-level design of MOPS and essential
subcomponents, the suitability of MOPS for other survey programs, and suggest a
road map for future MOPS development.Comment: 57 Pages, 26 Figures, 13 Table
Identification and differential production of ubiquinone-8 in the bacterial predator Bdellovibrio bacteriovorus
Bdellovibrio bacteriovorus 109J, a predatory bacterium with potential as a bacterial control agent, can exist in several lifestyles that differ both in predatory capacity and color. We determined that levels of ubiquinone-8 contribute to the distinctive but variable yellow color of different types of Bdellovibrio cells. Steady-state ubiquinone-8 concentrations did not differ markedly between conventional predatory and host-independent B. bacteriovorus despite upregulation of a suite of ubiquinone-8 synthesis genes in host-independent cells. In contrast, in spatially organized B. bacteriovorus films, the yellow inner regions contain significantly higher ubiquinone-8 concentrations than the off-white outer regions. Correspondingly, RT-PCR analysis reveals that the inner region, previously shown to consist primarily of active predators, clearly expresses two ubiquinone biosynthesis genes, while the outer region, composed mainly of quiescent or stalled bdelloplasts, expresses those genes weakly or not at all. Moreover, B. bacteriovorus cells in the inner region of week-old interfacial films, which are phenotypically attack-phase, have much higher UQ8 levels than regular attack-phase bdellovibrios, most likely because their âtrappedâ state prevents a high expenditure of energy to power flagellar motion
Global Connectivity of Southern Ocean Ecosystems
Southern Ocean ecosystems are globally important. Processes in the Antarctic atmosphere, cryosphere, and the Southern Ocean directly influence global atmospheric and oceanic systems. Southern Ocean biogeochemistry has also been shown to have global importance. In contrast, ocean ecological processes are often seen as largely separate from the rest of the global system. In this paper, we consider the degree of ecological connectivity at different trophic levels, linking Southern Ocean ecosystems with the global ocean, and their importance not only for the regional ecosystem but also the wider Earth system. We also consider the human system connections, including the role of Southern Ocean ecosystems in supporting society, culture, and economy in many nations, influencing public and political views and hence policy. Rather than Southern Ocean ecosystems being defined by barriers at particular oceanic fronts, ecological changes are gradual due to cross-front exchanges involving oceanographic processes and organism movement. Millions of seabirds and hundreds of thousands of cetaceans move north out of polar waters in the austral autumn interacting in food webs across the Southern Hemisphere, and a few species cross the equator. A number of species migrate into the east and west ocean-basin boundary current and continental shelf regions of the major southern continents. Human travel in and out of the Southern Ocean region includes fisheries, tourism, and scientific vessels in all ocean sectors. These operations arise from many nations, particularly in the Northern Hemisphere, and are important in local communities as well as national economic, scientific, and political activities. As a result of the extensive connectivity, future changes in Southern Ocean ecosystems will have consequences throughout the Earth system, affecting ecosystem services with socio-economic impacts throughout the world. The high level of connectivity also means that changes and policy decisions in marine ecosystems outside the Southern Ocean have consequences for ecosystems south of the Antarctic Polar Front. Knowledge of Southern Ocean ecosystems and their global connectivity is critical for interpreting current change, projecting future change impacts, and identifying integrated strategies for conserving and managing both the Southern Ocean and the broader Earth system
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Association of the tumor necrosis factor-alpha promoter polymorphism with change in triacylglycerol response to sequential meals
Background: Reported associations between Tumor Necrosis Factor-alpha (TNFA) and the postprandial
triacylglycerol (TAG) response have been inconsistent, which could be due to variations in the TNFA gene, meal fat composition or participantâs body weight. Hence, we investigated the association of TNFA polymorphism
(â308G â A) with body mass index (BMI) and postprandial lipaemia and also determined the impact of BMI on the
association of the polymorphism with postprandial lipaemia.
Methods: The study participants (n = 230) underwent a sequential meal postprandial study. Blood samples were taken
at regular intervals after a test breakfast (t = 0, 49 g fat) and lunch (t =330 min, 29 g fat) to measure fasting and
postprandial lipids, glucose and insulin. The Metabolic Challenge Study (MECHE) comprising 67 Irish participants who
underwent a 54 g fat oral lipid tolerance test was used as a replication cohort. The impact of genotype on postprandial
responses was determined using general linear model with adjustment for potential confounders.
Results: The -308G â A polymorphism showed a significant association with BMI (P = 0.03) and fasting glucose
(P = 0.006), where the polymorphism explained 13 % of the variation in the fasting glucose. A 30 % higher incremental
area under the curve (IAUC) was observed for the postprandial TAG response in the GG homozygotes than A-allele
carriers (P = 0.004) and the genotype explained 19 % of the variation in the IAUC. There was a non-significant trend in
the impact of BMI on the association of the genotype with TAG IAUC (P = 0.09). These results were not statistically
significant in the MECHE cohort, which could be due to the differences in the sample size, meal composition, baseline
lipid profile, allelic diversity and postprandial characterisation of participants across the two cohorts.
Conclusions: Our findings suggest that TNFA -308G â A polymorphism may be an important candidate for BMI,
fasting glucose and postprandial TAG response. Further studies are required to investigate the mechanistic effects of
the polymorphism on glucose and TAG metabolism, and determine whether BMI is an important variable which
should be considered in the design of future studies.
Trial registration: NCT01172951
Structure of the germline genome of Tetrahymena thermophila and relationship to the massively rearranged somatic genome
The germline genome of the binucleated ciliate Tetrahymena thermophila undergoes programmed chromosome breakage and massive DNA elimination to generate the somatic genome. Here, we present a complete sequence assembly of the germline genome and analyze multiple features of its structure and its relationship to the somatic genome, shedding light on the mechanisms of genome rearrangement as well as the evolutionary history of this remarkable germline/soma differentiation. Our results strengthen the notion that a complex, dynamic, and ongoing interplay between mobile DNA elements and the host genome have shaped Tetrahymena chromosome structure, locally and globally. Non-standard outcomes of rearrangement events, including the generation of short-lived somatic chromosomes and excision of DNA interrupting protein-coding regions, may represent novel forms of developmental gene regulation. We also compare Tetrahymenas germline/soma differentiation to that of other characterized ciliates, illustrating the wide diversity of adaptations that have occurred within this phylum.</p
The Long-Baseline Neutrino Experiment: Exploring Fundamental Symmetries of the Universe
The preponderance of matter over antimatter in the early Universe, the
dynamics of the supernova bursts that produced the heavy elements necessary for
life and whether protons eventually decay --- these mysteries at the forefront
of particle physics and astrophysics are key to understanding the early
evolution of our Universe, its current state and its eventual fate. The
Long-Baseline Neutrino Experiment (LBNE) represents an extensively developed
plan for a world-class experiment dedicated to addressing these questions. LBNE
is conceived around three central components: (1) a new, high-intensity
neutrino source generated from a megawatt-class proton accelerator at Fermi
National Accelerator Laboratory, (2) a near neutrino detector just downstream
of the source, and (3) a massive liquid argon time-projection chamber deployed
as a far detector deep underground at the Sanford Underground Research
Facility. This facility, located at the site of the former Homestake Mine in
Lead, South Dakota, is approximately 1,300 km from the neutrino source at
Fermilab -- a distance (baseline) that delivers optimal sensitivity to neutrino
charge-parity symmetry violation and mass ordering effects. This ambitious yet
cost-effective design incorporates scalability and flexibility and can
accommodate a variety of upgrades and contributions. With its exceptional
combination of experimental configuration, technical capabilities, and
potential for transformative discoveries, LBNE promises to be a vital facility
for the field of particle physics worldwide, providing physicists from around
the globe with opportunities to collaborate in a twenty to thirty year program
of exciting science. In this document we provide a comprehensive overview of
LBNE's scientific objectives, its place in the landscape of neutrino physics
worldwide, the technologies it will incorporate and the capabilities it will
possess.Comment: Major update of previous version. This is the reference document for
LBNE science program and current status. Chapters 1, 3, and 9 provide a
comprehensive overview of LBNE's scientific objectives, its place in the
landscape of neutrino physics worldwide, the technologies it will incorporate
and the capabilities it will possess. 288 pages, 116 figure
Structural and biochemical insights into the function and evolution of sulfoquinovosidases
An estimated 10 billion tonnes of sulfoquinovose (SQ) are produced and degraded each year. Prokaryotic sulfoglycolytic pathways catabolize sulfoquinovose (SQ) liberated from plant sulfolipid, or its delipidated form α-d-sulfoquinovosyl glycerol (SQGro), through the action of a sulfoquinovosidase (SQase), but little is known about the capacity of SQ glycosides to support growth. Structural studies of the first reported SQase (Escherichia coli YihQ) have identified three conserved residues that are essential for substrate recognition, but crossover mutations exploring active-site residues of predicted SQases from other organisms have yielded inactive mutants casting doubt on bioinformatic functional assignment. Here, we show that SQGro can support the growth of E. coli on par with d-glucose, and that the E. coli SQase prefers the naturally occurring diastereomer of SQGro. A predicted, but divergent, SQase from Agrobacterium tumefaciens proved to have highly specific activity toward SQ glycosides, and structural, mutagenic, and bioinformatic analyses revealed the molecular coevolution of catalytically important amino acid pairs directly involved in substrate recognition, as well as structurally important pairs distal to the active site. Understanding the defining features of SQases empowers bioinformatic approaches for mapping sulfur metabolism in diverse microbial communities and sheds light on this poorly understood arm of the biosulfur cycle
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