115 research outputs found
Core Hunter II: fast core subset selection based on multiple genetic diversity measures using Mixed Replica search
BACKGROUND: Sampling core subsets from genetic resources while maintaining as much as possible the genetic diversity of the original collection is an important but computationally complex task for gene bank managers. The Core Hunter computer program was developed as a tool to generate such subsets based on multiple genetic measures, including both distance measures and allelic diversity indices. At first we investigate the effect of minimum (instead of the default mean) distance measures on the performance of Core Hunter. Secondly, we try to gain more insight into the performance of the original Core Hunter search algorithm through comparison with several other heuristics working with several realistic datasets of varying size and allelic composition. Finally, we propose a new algorithm (Mixed Replica search) for Core Hunter II with the aim of improving the diversity of the constructed core sets and their corresponding generation times. RESULTS: Our results show that the introduction of minimum distance measures leads to core sets in which all accessions are sufficiently distant from each other, which was not always obtained when optimizing mean distance alone. Comparison of the original Core Hunter algorithm, Replica Exchange Monte Carlo (REMC), with simpler heuristics shows that the simpler algorithms often give very good results but with lower runtimes than REMC. However, the performance of the simpler algorithms is slightly worse than REMC under lower sampling intensities and some heuristics clearly struggle with minimum distance measures. In comparison the new advanced Mixed Replica search algorithm (MixRep), which uses heterogeneous replicas, was able to sample core sets with equal or higher diversity scores than REMC and the simpler heuristics, often using less computation time than REMC. CONCLUSION: The REMC search algorithm used in the original Core Hunter computer program performs well, sometimes leading to slightly better results than some of the simpler methods, although it doesn’t always give the best results. By switching to the new Mixed Replica algorithm overall results and runtimes can be significantly improved. Finally we recommend including minimum distance measures in the objective function when looking for core sets in which all accessions are sufficiently distant from each other. Core Hunter II is freely available as an open source project at http://www.corehunter.org
Egorov's theorem for transversally elliptic operators on foliated manifolds and noncommutative geodesic flow
The main result of the paper is Egorov's theorem for transversally elliptic
operators on compact foliated manifolds. This theorem is applied to describe
the noncommutative geodesic flow in noncommutative geometry of Riemannian
foliations.Comment: 23 pages, no figures. Completely revised and improved version of
dg-ga/970301
The spectral shift function and spectral flow
This paper extends Krein's spectral shift function theory to the setting of
semifinite spectral triples. We define the spectral shift function under these
hypotheses via Birman-Solomyak spectral averaging formula and show that it
computes spectral flow.Comment: 47 page
Glutamine synthetase activity fuels nucleotide biosynthesis and supports growth of glutamine-restriced glioblastoma
L-Glutamine (Gln) functions physiologically to balance the carbon and nitrogen requirements of tissues. It has been proposed that in cancer cells undergoing aerobic glycolysis, accelerated anabolism is sustained by Gln-derived carbons, which replenish the tricarboxylic acid (TCA) cycle (anaplerosis). However, it is shown here that in glioblastoma (GBM) cells, almost half of the Gln-derived glutamate (Glu) is secreted and does not enter the TCA cycle, and that inhibiting glutaminolysis does not affect cell proliferation. Moreover, Gln-starved cells are not rescued by TCA cycle replenishment. Instead, the conversion of Glu to Gln by glutamine synthetase (GS; cataplerosis) confers Gln prototrophy, and fuels de novo purine biosynthesis. In both orthotopic GBM models and in patients, (13)C-glucose tracing showed that GS produces Gln from TCA-cycle-derived carbons. Finally, the Gln required for the growth of GBM tumours is contributed only marginally by the circulation, and is mainly either autonomously synthesized by GS-positive glioma cells, or supplied by astrocytes
Effects of temperature on thick branes and the fermion (quasi-)localization
Following Campos's work [Phys. Rev. Lett. 88, 141602 (2002)], we investigate
the effects of temperature on flat, de Sitter (dS), and anti-de Following
Campos's work [Phys. Rev. Lett. \textbf{88}, 141602 (2002)], we investigate the
effects of temperature on flat, de Sitter (dS), and anti-de Sitter (AdS) thick
branes in five-dimensional (5D) warped spacetime, and on the fermion
(quasi-)localization. First, in the case of flat brane, when the critical
temperature reaches, the solution of the background scalar field and the warp
factor is not unique. So the thickness of the flat thick brane is uncertain at
the critical value of the temperature parameter, which is found to be lower
than the one in flat 5D spacetime. The mass spectra of the fermion Kaluza-Klein
(KK) modes are continuous, and there is a series of fermion resonances. The
number and lifetime of the resonances are finite and increase with the
temperature parameter, but the mass of the resonances decreases with the
temperature parameter. Second, in the case of dS brane, we do not find such a
critical value of the temperature parameter. The mass spectra of the fermion KK
modes are also continuous, and there is a series of fermion resonances. The
effects of temperature on resonance number, lifetime, and mass are the same
with the case of flat brane. Last, in the case of AdS brane, {the critical
value of the temperature parameter can less or greater than the one in the flat
5D spacetime.} The spectra of fermion KK modes are discrete, and the mass of
fermion KK modes does not decrease monotonically with increasing temperature
parameter.Comment: 24 pages, 15 figures, published versio
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