512 research outputs found
The Semantic Web and Why You Should Care
The Semantic Web is much discussed as a possible panacea for data distribution/discovery/exploration/leverage/storage etc. But what is it? What is all the fuss about? Where does this 'Linked Data' fit in? Will it all work? We attempt answer these questions, favouring scope and context over formality
Sumoylation of The Budding Yeast Kinetochore Protein Ndc10 is Required for Ndc10 Spindle Localization and Regulation of Anaphase Spindle Elongation
Posttranslational modification by the ubiquitin-like protein SUMO (small ubiquitin-like modifier) is emerging as an important regulator in many cellular processes, including genome integrity. In this study, we show that the kinetochore proteins Ndc10, Bir1, Ndc80, and Cep3, which mediate the attachment of chromosomes to spindle microtubules, are sumoylated substrates in budding yeast. Furthermore, we show that Ndc10, Bir1, and Cep3 but not Ndc80 are desumoylated upon exposure to nocodazole, highlighting the possibility of distinct roles for sumoylation in modulating kinetochore protein function and of a potential link between the sumoylation of kinetochore proteins and mitotic checkpoint function. We find that lysine to arginine mutations that eliminate the sumoylation of Ndc10 cause chromosome instability, mislocalization of Ndc10 from the mitotic spindle, abnormal anaphase spindles, and a loss of Bir1 sumoylation. These data suggest that sumoylation of Ndc10 and other kinetochore proteins play a critical role during the mitotic process
Using Song Social Tags and Topic Models to Describe and Compare Playlists
Playlists are a natural delivery method for music recommendation and discovery systems. Recommender systems offering playlists must strive to make them relevant and enjoyable. In this paper we survey many current means of generating and evaluating playlists. We present a means of comparing playlists in a reduced dimensional space through the use of aggregated tag clouds and topic models. To evaluate the fitness of this measure, we perform prototypical retrieval tasks on playlists taken from radio station logs gathered from Radio Paradise and Yes.com, using tags from Last.fm with the result showing better than random performance when using the query playlist's station as ground truth, while failing to do so when using time of day as ground truth. We then discuss possible applications for this measurement technique as well as ways it might be improved
Genetic Drift Shapes the Evolution of a Highly Dynamic Metapopulation
The dynamics of extinction and (re)colonization in habitat patches are characterizing features of dynamic metapopulations, causing them to evolve differently than large, stable populations. The propagule model, which assumes genetic bottlenecks during colonization, posits that newly founded subpopulations have low genetic diversity and are genetically highly differentiated from each other. Immigration may then increase diversity and decrease differentiation between subpopulations. Thus, older and/or less isolated subpopulations are expected to have higher genetic diversity and less genetic differentiation. We tested this theory using whole-genome pool-sequencing to characterize nucleotide diversity and differentiation in 60 subpopulations of a natural metapopulation of the cyclical parthenogen Daphnia magna. For comparison, we characterized diversity in a single, large, and stable D. magna population. We found reduced (synonymous) genomic diversity, a proxy for effective population size, weak purifying selection, and low rates of adaptive evolution in the metapopulation compared with the large, stable population. These differences suggest that genetic bottlenecks during colonization reduce effective population sizes, which leads to strong genetic drift and reduced selection efficacy in the metapopulation. Consistent with the propagule model, we found lower diversity and increased differentiation in younger and also in more isolated subpopulations. Our study sheds light on the genomic consequences of extinction-(re)colonization dynamics to an unprecedented degree, giving strong support for the propagule model. We demonstrate that the metapopulation evolves differently from a large, stable population and that evolution is largely driven by genetic drift.Peer reviewe
Analysis and Exploitation of Musician Social Networks for Recommendation and Discovery
This paper presents an extensive analysis of a sample of a social network of musicians. The network sample is first analyzed using standard complex network techniques to verify that it has similar properties to other web-derived complex networks. Content-based pairwise dissimilarity values between the musical data associated with the network sample are computed, and the relationship between those content-based distances and distances from network theory explored. Following this exploration, hybrid graphs and distance measures are constructed, and used to examine the community structure of the artist network. Finally, results of these investigations are presented and considered in the light of recommendation and discovery applications with these hybrid measures as their basis
Transnational labor regulation, reification and commodification: A critical review
Why does scholarship on transnational labor regulation
(TLR) consistently fails to search for improvements in
working conditions, and instead devotes itself to relentless
efforts for identifying administrative processes, semantics,
and amalgamations of stakeholders? This article critiques
TLR from a pro-worker perspective, through the philosophical
work of Georg Lukács, and the concepts of reification
and commodification. A set of theoretically grounded criteria
is developed and these are applied against selected
contemporary cases of TLR. In the totality that is capitalism,
reification of social relations of production conceals
completely the experiences of workers. In TLR, managerialist
and process-oriented scholarship is dominant, verifiable
outcomes and positive improvements in conditions of
employment are not sought, and worse, meaningless
procedures are celebrated as positive achievements
Pyrimidine biosynthesis is not an essential function for trypanosoma brucei bloodstream forms
<p>Background: African trypanosomes are capable of both pyrimidine biosynthesis and salvage of preformed pyrimidines from the host, but it is unknown whether either process is essential to the parasite.</p>
<p>Methodology/Principal Findings: Pyrimidine requirements for growth were investigated using strictly pyrimidine-free media, with or without single added pyrimidine sources. Growth rates of wild-type bloodstream form Trypanosoma brucei brucei were unchanged in pyrimidine-free medium. The essentiality of the de novo pyrimidine biosynthesis pathway was studied by knocking out the PYR6-5 locus that produces a fusion product of orotate phosphoribosyltransferase (OPRT) and Orotidine Monophosphate Decarboxylase (OMPDCase). The pyrimidine auxotroph was dependent on a suitable extracellular pyrimidine source. Pyrimidine starvation was rapidly lethal and non-reversible, causing incomplete DNA content in new cells. The phenotype could be rescued by addition of uracil; supplementation with uridine, 2′deoxyuridine, and cytidine allowed a diminished growth rate and density. PYR6-5−/− trypanosomes were more sensitive to pyrimidine antimetabolites and displayed increased uracil transport rates and uridine phosphorylase activity. Pyrimidine auxotrophs were able to infect mice although the infection developed much more slowly than infection with the parental, prototrophic trypanosome line.</p>
<p>Conclusions/Significance: Pyrimidine salvage was not an essential function for bloodstream T. b. brucei. However, trypanosomes lacking de novo pyrimidine biosynthesis are completely dependent on an extracellular pyrimidine source, strongly preferring uracil, and display reduced infectivity. As T. brucei are able to salvage sufficient pyrimidines from the host environment, the pyrimidine biosynthesis pathway is not a viable drug target, although any interruption of pyrimidine supply was lethal.</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
Double Spin Asymmetry of Electrons from Heavy Flavor Decays in p+p Collisions at sqrt(s)=200 GeV
We report on the first measurement of double-spin asymmetry, A_LL, of
electrons from the decays of hadrons containing heavy flavor in longitudinally
polarized p+p collisions at sqrt(s)=200 GeV for p_T= 0.5 to 3.0 GeV/c. The
asymmetry was measured at mid-rapidity (|eta|<0.35) with the PHENIX detector at
the Relativistic Heavy Ion Collider. The measured asymmetries are consistent
with zero within the statistical errors. We obtained a constraint for the
polarized gluon distribution in the proton of |Delta g/g(log{_10}x=
-1.6^+0.5_-0.4, {mu}=m_T^c)|^2 < 0.033 (1 sigma), based on a leading-order
perturbative-quantum-chromodynamics model, using the measured asymmetry.Comment: 385 authors, 17 pages, 15 figures, 5 tables. Submitted to Phys. Rev.
D. Plain text data tables for the points plotted in figures for this and
previous PHENIX publications are (or will be) publicly available at
http://www.phenix.bnl.gov/papers.htm
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