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Author |
Ames, S.K.; Gardner, S.N.; Marti, J.M.; Slezak, T.R.; Gokhale, M.B.; Allen, J.E. |
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Title  |
Using populations of human and microbial genomes for organism detection in metagenomes |
Type |
Journal Article |
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Year |
2015 |
Publication |
Genome Research |
Abbreviated Journal |
Genome Res. |
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Volume |
25 |
Issue |
7 |
Pages |
1056-1067 |
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Abstract |
Identifying causative disease agents in human patients from shotgun metagenomic sequencing (SMS) presents a powerful tool to apply when other targeted diagnostics fail. Numerous technical challenges remain, however, before SMS can move beyond the role of research tool. Accurately separating the known and unknown organism content remains difficult, particularly when SMS is applied as a last resort. The true amount of human DNA that remains in a sample after screening against the human reference genome and filtering nonbiological components left from library preparation has previously been underreported. In this study, we create the most comprehensive collection of microbial and reference-free human genetic variation available in a database optimized for efficient metagenomic search by extracting sequences from GenBank and the 1000 Genomes Project. The results reveal new human sequences found in individual Human Microbiome Project (HMP) samples. Individual samples contain up to 95% human sequence, and 4% of the individual HMP samples contain 10% or more human reads. Left unidentified, human reads can complicate and slow down further analysis and lead to inaccurately labeled microbial taxa and ultimately lead to privacy concerns as more human genome data is collected. |
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Address |
[Ames, Sasha K.; Gokhale, Maya B.] Lawrence Livermore Natl Lab, Ctr Appl Sci Comp, Livermore, CA 94550 USA, Email: allen99@llnl.gov |
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Publisher |
Cold Spring Harbor Lab Press, Publications Dept |
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Language |
English |
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ISSN |
1088-9051 |
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Notes |
WOS:000357356900012 |
Approved |
no |
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Is ISI |
yes |
International Collaboration |
yes |
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Call Number |
IFIC @ pastor @ |
Serial |
2295 |
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Author |
Dorado-Morales, P.; Vilanova, C.; Pena-Garay, C.; Marti, J.M.; Porcar, M. |
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Title |
Unveiling Bacterial Interactions through Multidimensional Scaling and Dynamics Modeling |
Type |
Journal Article |
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Year |
2015 |
Publication |
Scientific Reports |
Abbreviated Journal |
Sci Rep |
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Volume |
5 |
Issue |
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Pages |
18396 - 6pp |
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Keywords |
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Abstract |
We propose a new strategy to identify and visualize bacterial consortia by conducting replicated culturing of environmental samples coupled with high-throughput sequencing and multidimensional scaling analysis, followed by identification of bacteria-bacteria correlations and interactions. We conducted a proof of concept assay with pine-tree resin-based media in ten replicates, which allowed detecting and visualizing dynamical bacterial associations in the form of statistically significant and yet biologically relevant bacterial consortia. |
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Address |
[Dorado-Morales, Pedro; Vilanova, Cristina; Porcar, Manuel] Univ Valencia, Cavanilles Inst Biodivers & Evolutionary Biol, Valencia 46020, Spain, Email: manuel.porcar@uv.es |
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Publisher |
Nature Publishing Group |
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English |
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Edition |
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ISSN |
2045-2322 |
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Notes |
WOS:000366483800002 |
Approved |
no |
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Is ISI |
yes |
International Collaboration |
no |
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Call Number |
IFIC @ pastor @ |
Serial |
2483 |
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Author |
de Azcarraga, J.A.; Fedoruk, S.; Izquierdo, J.M.; Lukierski, J. |
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Title |
Two-twistor particle models and free massive higher spin fields |
Type |
Journal Article |
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Year |
2015 |
Publication |
Journal of High Energy Physics |
Abbreviated Journal |
J. High Energy Phys. |
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Volume |
04 |
Issue |
4 |
Pages |
010 - 39pp |
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Keywords |
Field Theories in Lower Dimensions; Higher Spin Symmetry; Extended Supersymmetry; Space-Time Symmetries |
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Abstract |
We present D = 3 and D = 4 world-line models for massive particles moving in a new type of enlarged spacetime, with D-1 additional vector coordinates, which after quantization lead to towers of massive higher spin (HS) free fields. Two classically equivalent formulations are presented: one with a hybrid spacetime/bispinor variables and a second described by a free two-twistor dynamics with constraints. After first quantization in the D = 3 and D = 4 cases, the wave functions satisfying a massive version of Vasiliev's free unfolded equations are given as functions on the SL(2, R) and SL(2, C) group manifolds respectively, which describe arbitrary on-shell momenta and spin degrees of freedom. Further we comment on the D = 6 case, and possible supersymmetric extensions are mentioned as well. Finally, the description of interactions and the Ads/crr duality are briefly considered for massive IHS fields. |
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Address |
[de Azcarraga, J. A.] Univ Valencia, Dept Theoret Phys, E-46100 Burjassot, Valencia, Spain, Email: j.a.de.azcarraga@ific.uv.es; |
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Publisher |
Springer |
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English |
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Series Issue |
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Edition |
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ISSN |
1029-8479 |
ISBN |
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Area |
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Expedition |
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Conference |
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Notes |
WOS:000356852000010 |
Approved |
no |
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Is ISI |
yes |
International Collaboration |
yes |
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Call Number |
IFIC @ pastor @ |
Serial |
2293 |
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Author |
ATLAS Collaboration (Aad, G. et al); Cabrera Urban, S.; Castillo Gimenez, V.; Costa, M.J.; Ferrer, A.; Fiorini, L.; Fuster, J.; Garcia, C.; Garcia Navarro, J.E.; Gonzalez de la Hoz, S.; Hernandez Jimenez, Y.; Higon-Rodriguez, E.; Irles Quiles, A.; Kaci, M.; King, M.; Lacasta, C.; Lacuesta, V.R.; Marti-Garcia, S.; Mitsou, V.A.; Moles-Valls, R.; Oliver Garcia, E.; Pedraza Lopez, S.; Perez Garcia-Estañ, M.T.; Romero Adam, E.; Ros, E.; Salt, J.; Sanchez Martinez, V.; Soldevila, U.; Sanchez, J.; Torro Pastor, E.; Valero, A.; Valladolid Gallego, E.; Valls Ferrer, J.A.; Vos, M. |
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Title |
Two-particle Bose-Einstein correlations in pp collisions at root s=0.9 and 7 TeV measured with the ATLAS detector |
Type |
Journal Article |
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Year |
2015 |
Publication |
European Physical Journal C |
Abbreviated Journal |
Eur. Phys. J. C |
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Volume |
75 |
Issue |
10 |
Pages |
466 - 25pp |
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Abstract |
The paper presents studies of Bose-EinsteinCorrelations (BEC) for pairs of like-sign charged particles measured in the kinematic range p(T) > 100 MeV and |eta| < 2.5 in proton-proton collisions at centre-of-mass energies of 0.9 and 7 TeV with the ATLAS detector at the CERN Large Hadron Collider. The integrated luminosities are approximately 7 μb(-1), 190 μb(-1) and 12.4 nb(-1) for 0.9 TeV, 7 TeV minimum-bias and 7 TeV high-multiplicity data samples, respectively. The multiplicity dependence of the BEC parameters characterizing the correlation strength and the correlation source size are investigated for charged-particle multiplicities of up to 240. A saturation effect in the multiplicity dependence of the correlation source size parameter is observed using the high-multiplicity 7 TeV data sample. The dependence of the BEC parameters on the average transverse momentum of the particle pair is also investigated. |
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Address |
[Jackson, P.; Lee, L.; Soni, N.; White, M. J.] Univ Adelaide, Dept Phys, Adelaide, SA, Australia, Email: atlas.publications@cern.ch |
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Corporate Author |
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Thesis |
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Publisher |
Springer |
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Editor |
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Language |
English |
Summary Language |
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Original Title |
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ISSN |
1434-6044 |
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Notes |
WOS:000366309300001 |
Approved |
no |
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Is ISI |
yes |
International Collaboration |
yes |
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Call Number |
IFIC @ pastor @ |
Serial |
2497 |
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Author |
Barenboim, G.; Vives, O. |
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Title |
Transplanckian inflation as gravity echoes |
Type |
Journal Article |
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Year |
2015 |
Publication |
Physics Letters B |
Abbreviated Journal |
Phys. Lett. B |
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Volume |
748 |
Issue |
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Pages |
336-342 |
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Keywords |
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Abstract |
In this work, we show that, in the presence of non-minimal coupling to gravity, it is possible to generate sizeable tensor modes in single-field models without transplanckian field values. These transplanckian field values apparently needed in Einstein gravity to accommodate the experimental results may only be due to our insistence of imposing a minimal coupling of the inflaton field to gravity in a model with non-minimal couplings. We present three simple single-field models that prove that it is possible to accommodatea large tensor-to-scalar ratio without requiring transplanckian field values within the slow-roll regime. |
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Address |
[Barenboim, G.] Univ Valencia, Dept Fis Teor, CSIC, E-46100 Burjassot, Spain, Email: Gabriela.Barenboim@uv.es |
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Publisher |
Elsevier Science Bv |
Place of Publication |
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Editor |
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Language |
English |
Summary Language |
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Original Title |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
0370-2693 |
ISBN |
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Conference |
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Notes |
WOS:000359146200050 |
Approved |
no |
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Is ISI |
yes |
International Collaboration |
no |
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Call Number |
IFIC @ pastor @ |
Serial |
2357 |
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