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  • 1
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    Direct observation of quark-hadron duality in the free neutron F_{2} structure function (2015)
    American Physical Society (APS)
    Details
    Publication Date: 2015-05-27
    Description: Author(s): I. Niculescu, G. Niculescu, W. Melnitchouk, J. Arrington, M. E. Christy, R. Ent, K. A. Griffioen, N. Kalantarians, C. E. Keppel, S. Kuhn, S. Tkachenko, and J. Zhang Using the recently published data from the BONuS (Barely Off-shell Nucleon Structure) experiment at Jefferson Lab, which utilized a spectator tagging technique to extract the inclusive electron-free neutron scattering cross section, we obtain the first direct observation of quark-hadron duality in t... [Phys. Rev. C 91, 055206] Published Thu May 21, 2015
    Keywords: Hadronic Physics and QCD
    Print ISSN: 0556-2813
    Electronic ISSN: 1089-490X
    Topics: Physics
    Published by American Physical Society (APS)
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  • 2
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    eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences (2016)
    Oxford University Press
    Details
    Publication Date: 2016-01-07
    Description: eggNOG is a public resource that provides Orthologous Groups (OGs) of proteins at different taxonomic levels, each with integrated and summarized functional annotations. Developments since the latest public release include changes to the algorithm for creating OGs across taxonomic levels, making nested groups hierarchically consistent. This allows for a better propagation of functional terms across nested OGs and led to the novel annotation of 95 890 previously uncharacterized OGs, increasing overall annotation coverage from 67% to 72%. The functional annotations of OGs have been expanded to also provide Gene Ontology terms, KEGG pathways and SMART/Pfam domains for each group. Moreover, eggNOG now provides pairwise orthology relationships within OGs based on analysis of phylogenetic trees. We have also incorporated a framework for quickly mapping novel sequences to OGs based on precomputed HMM profiles. Finally, eggNOG version 4.5 incorporates a novel data set spanning 2605 viral OGs, covering 5228 proteins from 352 viral proteomes. All data are accessible for bulk downloading, as a web-service, and through a completely redesigned web interface. The new access points provide faster searches and a number of new browsing and visualization capabilities, facilitating the needs of both experts and less experienced users. eggNOG v4.5 is available at http://eggnog.embl.de .
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    Effects of sedimenting particles on the turbulence structure in a horizontal channel flow (2015)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2015-02-11
    Description: This work presents the results of experiments conducted in a horizontal channel to characterize low Reynolds number turbulent flows in the presence of small solid particles. The particle diameter relative to the integral length scale, d p / Λ x , is approximately 0.02. Particles and fluid turbulence characteristics are measured for three average solid volume fractions of approximately ϕ v = 2.0 × 10 −4 , 4.0 × 10 −4 , and 8.0 × 10 −4 under conditions where the particle number density is evolving due to deposition. The results indicate that the mean slip between particles and the fluid is important only close to the wall. Away from the wall, the particles and unladen fluid mean velocities are similar. Differences between particles and the unladen fluid statistics are more pronounced in the wall-normal velocity fluctuations than the streamwise velocity fluctuations and Reynolds shear stress due to the stronger effect of the gravitational force in the wall-normal direction. The fluid turbulent intensities show no dependency on loading, but the peak Reynolds shear stress is significantly reduced. A quadrant decomposition of the Reynolds shear stress revealed a corresponding reduction in the ejections and sweeps for the laden flow in comparison with the unladen flow. Swirling strength and vorticity root-mean-square fluctuations decayed due to the damping effect of particles. The influence of particles on the turbulence structure was examined using two-point correlations of the velocity fluctuations and swirling strength, where it was demonstrated that the wall structures are attached eddies which are more extensive (much larger) in the particle-laden flow compared to the unladen flow.
    Print ISSN: 1070-6631
    Electronic ISSN: 1089-7666
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 4
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    Nanometer resolution and coherent optical dipole coupling of two individual molecules (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-09-07
    Description: By performing cryogenic laser spectroscopy under a scanning probe electrode that induces a local electric field, we have resolved two individual fluorescent molecules separated by 12 nanometers in an organic crystal. The two molecules undergo a strong coherent dipole-dipole coupling that produces entangled sub- and superradiant states. Under intense laser illumination, both molecules are excited via a two-photon transition, and the fluorescence from this doubly excited system displays photon bunching. Our experimental scheme can be used to optically resolve molecules at the nanometer scale and to manipulate the degree of entanglement among them.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hettich, C -- Schmitt, C -- Zitzmann, J -- Kuhn, S -- Gerhardt, I -- Sandoghdar, V -- New York, N.Y. -- Science. 2002 Oct 11;298(5592):385-9. Epub 2002 Sep 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physics, University of Konstanz, 78457 Konstanz, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12215651" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 5
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    Adaptive sleep loss in polygynous pectoral sandpipers (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-08-11
    Description: The functions of sleep remain elusive. Extensive evidence suggests that sleep performs restorative processes that sustain waking brain performance. An alternative view proposes that sleep simply enforces adaptive inactivity to conserve energy when activity is unproductive. Under this hypothesis, animals may evolve the ability to dispense with sleep when ecological demands favor wakefulness. Here, we show that male pectoral sandpipers (Calidris melanotos), a polygynous Arctic breeding shorebird, are able to maintain high neurobehavioral performance despite greatly reducing their time spent sleeping during a 3-week period of intense male-male competition for access to fertile females. Males that slept the least sired the most offspring. Our results challenge the view that decreased performance is an inescapable outcome of sleep loss.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lesku, John A -- Rattenborg, Niels C -- Valcu, Mihai -- Vyssotski, Alexei L -- Kuhn, Sylvia -- Kuemmeth, Franz -- Heidrich, Wolfgang -- Kempenaers, Bart -- New York, N.Y. -- Science. 2012 Sep 28;337(6102):1654-8. Epub 2012 Aug 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Avian Sleep Group, Max Planck Institute for Ornithology, Seewiesen, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22878501" target="_blank"〉PubMed〈/a〉
    Keywords: *Adaptation, Physiological ; Animals ; Charadriiformes/*physiology ; Energy Metabolism ; Female ; Male ; *Reproduction ; *Sexual Behavior, Animal ; Sleep/*physiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 6
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    Restoration of auditory evoked responses by human ES-cell-derived otic progenitors (2012)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2012-09-14
    Description: Deafness is a condition with a high prevalence worldwide, produced primarily by the loss of the sensory hair cells and their associated spiral ganglion neurons (SGNs). Of all the forms of deafness, auditory neuropathy is of particular concern. This condition, defined primarily by damage to the SGNs with relative preservation of the hair cells, is responsible for a substantial proportion of patients with hearing impairment. Although the loss of hair cells can be circumvented partially by a cochlear implant, no routine treatment is available for sensory neuron loss, as poor innervation limits the prospective performance of an implant. Using stem cells to recover the damaged sensory circuitry is a potential therapeutic strategy. Here we present a protocol to induce differentiation from human embryonic stem cells (hESCs) using signals involved in the initial specification of the otic placode. We obtained two types of otic progenitors able to differentiate in vitro into hair-cell-like cells and auditory neurons that display expected electrophysiological properties. Moreover, when transplanted into an auditory neuropathy model, otic neuroprogenitors engraft, differentiate and significantly improve auditory-evoked response thresholds. These results should stimulate further research into the development of a cell-based therapy for deafness.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3480718/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3480718/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, Wei -- Jongkamonwiwat, Nopporn -- Abbas, Leila -- Eshtan, Sarah Jacob -- Johnson, Stuart L -- Kuhn, Stephanie -- Milo, Marta -- Thurlow, Johanna K -- Andrews, Peter W -- Marcotti, Walter -- Moore, Harry D -- Rivolta, Marcelo N -- 088719/Wellcome Trust/United Kingdom -- G0700785/Medical Research Council/United Kingdom -- G0801059/Medical Research Council/United Kingdom -- G0900919/Medical Research Council/United Kingdom -- G0900919(92659)/Medical Research Council/United Kingdom -- G20/Action on Hearing Loss/United Kingdom -- G34/Action on Hearing Loss/United Kingdom -- G44/Action on Hearing Loss/United Kingdom -- Medical Research Council/United Kingdom -- England -- Nature. 2012 Oct 11;490(7419):278-82. doi: 10.1038/nature11415. Epub 2012 Sep 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Stem Cell Biology, University of Sheffield, Sheffield S10 2TN, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22972191" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Auditory Threshold ; *Cell Differentiation ; Cell Line ; Cells, Cultured ; Cochlear Nerve/cytology/physiology ; Deafness/chemically induced/therapy ; Embryonic Stem Cells/*cytology ; *Evoked Potentials, Auditory ; Fibroblast Growth Factor 10/genetics/metabolism ; Fibroblast Growth Factor 3/genetics/metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Gerbillinae ; Hair Cells, Auditory/cytology/physiology ; Humans ; Mice ; Patch-Clamp Techniques ; Stem Cell Transplantation ; Stem Cells/*cytology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 7
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    Chemistry, Mineralogy, and Grain Properties at Namib and High Dunes, Bagnold Dune Field, Gale Crater, Mars: A Synthesis of Curiosity Rover Observations (2017)
    Wiley
    Details
    Publication Date: 2017-06-13
    Description: The Mars Science Laboratory Curiosity rover performed coordinated measurements to examine the textures and compositions of aeolian sands in the active Bagnold dune field. The Bagnold sands are rounded to subrounded, very fine- to medium- sized (~45-500 µm) with ≥6 distinct grain colors. In contrast to sands examined by Curiosity in a dust-covered, inactive bedform called Rocknest and soils at other landing sites, Bagnold sands are darker, less red, better sorted, have fewer silt-sized or smaller grains, and show no evidence for cohesion. Nevertheless, Bagnold mineralogy and Rocknest mineralogy are similar with plagioclase, olivine, and pyroxenes in similar proportions comprising 〉90% of crystalline phases, along with a substantial amorphous component (35% ± 15%). Yet, Bagnold and Rocknest bulk chemistry differ. Bagnold sands are Si-enriched relative to other soils at Gale crater, and H 2 O, S, and Cl are lower relative to all previously measured martian soils and most Gale crater rocks. Mg, Ni, Fe, and Mn are enriched in the coarse-sieved fraction of Bagnold sands, corroborated by VNIR spectra that suggest enrichment of olivine. Collectively, patterns in major element chemistry and volatile release data indicate two distinctive volatile reservoirs in martian soils: (1) amorphous components in the sand-sized fraction (represented by Bagnold) that are Si-enriched, hydroxylated alteration products and/or impact or volcanic glasses; and (2) amorphous components in the fine fraction (〈40 µm; represented by Rocknest and other bright soils) that are Fe-, S-, and Cl-enriched with low Si and adsorbed and structural H 2 O.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 8
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    STRING v9.1: protein-protein interaction networks, with increased coverage and integration (2012)
    Oxford University Press
    Details
    Publication Date: 2012-12-20
    Description: Complete knowledge of all direct and indirect interactions between proteins in a given cell would represent an important milestone towards a comprehensive description of cellular mechanisms and functions. Although this goal is still elusive, considerable progress has been made—particularly for certain model organisms and functional systems. Currently, protein interactions and associations are annotated at various levels of detail in online resources, ranging from raw data repositories to highly formalized pathway databases. For many applications, a global view of all the available interaction data is desirable, including lower-quality data and/or computational predictions. The STRING database ( http://string-db.org/ ) aims to provide such a global perspective for as many organisms as feasible. Known and predicted associations are scored and integrated, resulting in comprehensive protein networks covering 〉1100 organisms. Here, we describe the update to version 9.1 of STRING, introducing several improvements: (i) we extend the automated mining of scientific texts for interaction information, to now also include full-text articles; (ii) we entirely re-designed the algorithm for transferring interactions from one model organism to the other; and (iii) we provide users with statistical information on any functional enrichment observed in their networks.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    Cardiomyocyte proliferation in human heart growth [Medical Sciences] (2013)
    National Academy of Sciences
    Details
    Publication Date: 2013-01-23
    Description: The human heart is believed to grow by enlargement but not proliferation of cardiomyocytes (heart muscle cells) during postnatal development. However, recent studies have shown that cardiomyocyte proliferation is a mechanism of cardiac growth and regeneration in animals. Combined with evidence for cardiomyocyte turnover in adult humans, this suggests that...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 10
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    QARIP: a web server for quantitative proteomic analysis of regulated intramembrane proteolysis (2013)
    Oxford University Press
    Details
    Publication Date: 2013-06-23
    Description: Regulated intramembrane proteolysis (RIP) is a critical mechanism for intercellular communication and regulates the function of membrane proteins through sequential proteolysis. RIP typically starts with ectodomain shedding of membrane proteins by extracellular membrane-bound proteases followed by intramembrane proteolysis of the resulting membrane-tethered fragment. However, for the majority of RIP proteases the corresponding substrates and thus, their functions, remain unknown. Proteome-wide identification of RIP protease substrates is possible by mass spectrometry-based quantitative comparison of RIP substrates or their cleavage products between different biological states. However, this requires quantification of peptides from only the ectodomain or cytoplasmic domain. Current analysis software does not allow matching peptides to either domain. Here we present the QARIP ( Q uantitative A nalysis of R egulated I ntramembrane P roteolysis) web server which matches identified peptides to the protein transmembrane topology. QARIP allows determination of quantitative ratios separately for the topological domains (cytoplasmic, ectodomain) of a given protein and is thus a powerful tool for quality control, improvement of quantitative ratios and identification of novel substrates in proteomic RIP datasets. To our knowledge, the QARIP web server is the first tool directly addressing the phenomenon of RIP. The web server is available at http://webclu.bio.wzw.tum.de/qarip/ . This website is free and open to all users and there is no login requirement.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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