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  • 1
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    Interplay of Ion–Water and Water–Water Interactions within the Hydration Shells of Nitrate and Carbonate Directly Probed with 2D IR Spectroscopy (2016)
    American Chemical Society (ACS)
    Details
    Publication Date: 2016-07-22
    Description: Journal of the American Chemical Society DOI: 10.1021/jacs.6b05122
    Print ISSN: 0002-7863
    Electronic ISSN: 1520-5126
    Topics: Chemistry and Pharmacology
    Published by American Chemical Society (ACS)
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  • 2
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    Anharmonic exciton dynamics and energy dissipation in liquid water from two-dimensional infrared spectroscopy (2016)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2016-09-02
    Description: Water’s extended hydrogen-bond network results in rich and complex dynamics on the sub-picosecond time scale. In this paper, we present a comprehensive analysis of the two-dimensional infrared (2D IR) spectrum of O–H stretching vibrations in liquid H 2 O and their interactions with bending and intermolecular vibrations. By exploring the dependence of the spectrum on waiting time, temperature, and laser polarization, we refine our molecular picture of water’s complex ultrafast dynamics. The spectral evolution following excitation of the O–H stretching resonance reveals vibrational dynamics on the 50–300 fs time scale that are dominated by intermolecular delocalization. These O–H stretch excitons are a result of the anharmonicity of the nuclear potential energy surface that arises from the hydrogen-bonding interaction. The extent of O–H stretching excitons is characterized through 2D depolarization measurements that show spectrally dependent delocalization in agreement with theoretical predictions. Furthermore, we show that these dynamics are insensitive to temperature, indicating that the exciton dynamics alone set the important time scales in the system. Finally, we study the evolution of the O–H stretching mode, which shows highly non-adiabatic dynamics suggestive of vibrational conical intersections. We argue that the so-called heating, commonly observed within ∼1 ps in nonlinear IR spectroscopy of water, is a nonequilibrium state better described by a kinetic temperature rather than a Boltzmann distribution. Our conclusions imply that the collective nature of water vibrations should be considered in describing aqueous solvation.
    Print ISSN: 0021-9606
    Electronic ISSN: 1089-7690
    Topics: Chemistry and Pharmacology , Physics
    Published by American Institute of Physics (AIP)
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  • 3
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    Comparison of the local binding motifs in the imidazolium-based ionic liquids [EMIM][BF4] and [EMMIM][BF4] through cryogenic ion vibrational predissociation spectroscopy: Unraveling the roles of anharmonicity and intermolecular interactions (2015)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2015-02-12
    Description: We clarify the role of the critical imidazolium C (2) H position (the central C between N atoms in the heterocycle) in the assembly motif of the [EMIM][BF 4 ] ionic liquid by analyzing the vibrational spectra of the bare EMIM + ion as well as that of the cationic [EMIM] 2 [BF 4 ] + (EMIM + = 1-ethyl-3-methylimidazolium, C 6 H 11 N 2 + ) cluster. Vibrational spectra of the cold, mass-selected ions are obtained using cryogenic ion vibrational predissociation of weakly bound D 2 molecules formed in a 10 K ion trap. The C (2) H behavior is isolated by following the evolution of key vibrational features when the C (2) hydrogen, the proposed binding location of the anion to the imidazolium ring, is replaced by either deuterium or a methyl group (i.e., in the EMMIM + analogue). Strong features in the ring CH stretching region of the bare ion are traced to Fermi resonances with overtones of lower frequency modes. Upon incorporation into the EMIM + ⋅ ⋅ ⋅ BF 4 − ⋅ ⋅ ⋅ EMIM + ternary complex, the C (2) H oscillator strength is dramatically increased, accounting for the much more complicated patterns derived from the EMIM + ring CH stretches in the light isotopomer, which are strongly suppressed in the deuterated analogue. Further changes in the spectra that occur when the C (2) H is replaced by a methyl group are consistent with BF 4 − attachment directly to the imidazolium ring in an arrangement that maximizes the electrostatic interaction between the molecular ions.
    Print ISSN: 0021-9606
    Electronic ISSN: 1089-7690
    Topics: Chemistry and Pharmacology , Physics
    Published by American Institute of Physics (AIP)
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  • 4
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    Antidepressant actions of neuritin [Neuroscience] (2012)
    National Academy of Sciences
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    Publication Date: 2012-07-11
    Description: Decreased neuronal dendrite branching and plasticity of the hippocampus, a limbic structure implicated in mood disorders, is thought to contribute to the symptoms of depression. However, the mechanisms underlying this effect, as well as the actions of antidepressant treatment, remain poorly characterized. Here, we show that hippocampal expression of neuritin, an activity-dependent gene that regulates neuronal plasticity, is decreased by chronic unpredictable stress (CUS) and that antidepressant treatment reverses this effect. We also show that viral-mediated expression of neuritin in the hippocampus produces antidepressant actions and prevents the atrophy of dendrites and spines, as well as depressive and anxiety behaviors caused by CUS. Conversely, neuritin knockdown produces depressive-like behaviors, similar to CUS exposure. The ability of neuritin to increase neuroplasticity is confirmed in models of learning and memory. Our results reveal a unique action of neuritin in models of stress and depression, and demonstrate a role for neuroplasticity in antidepressant treatment response and related behaviors.
    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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  • 5
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    An on-bead tailing/ligation approach for sequencing resin-bound RNA libraries (2012)
    Oxford University Press
    Details
    Publication Date: 2012-05-13
    Description: Nucleic acids possess the unique property of being enzymatically amplifiable, and have therefore been a popular choice for the combinatorial selection of functional sequences, such as aptamers or ribozymes. However, amplification typically requires known sequence segments that serve as primer binding sites, which can be limiting for certain applications, like the screening of on-bead libraries. Here, we report a method to amplify and sequence on-bead RNA libraries that requires not more than five known nucleotides. A key element is the attachment of the starting nucleoside to the synthesis resin via the nucleobase, which leaves the 3'-OH group accessible to subsequent enzymatic manipulations. After split-and-mix synthesis of the oligonucleotide library and deprotection, a poly(A)-tail can be efficiently added to this free 3'-hydroxyl terminus by Escherichia coli poly(A) polymerase that serves as an anchored primer binding site for reverse transcription. The cDNA is joined to a DNA adapter by T4 DNA ligase. PCR amplification yielded single-band products that could be cloned and sequenced starting from individual polystyrene beads. The method described here makes the selection of functional RNAs from on-bead RNA libraries more attractive due to increased flexibility in library design, higher yields of full-length sequence on bead and robust sequence determination.
    Keywords: Nucleic acid amplification, RNA characterisation and manipulation
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    Forests, Vol. 10, Pages 599: Comparison of Three Algorithms to Estimate Tree Stem Diameter from Terrestrial Laser Scanner Data (2019)
    MDPI
    In: Forests
    Details
    Publication Date: 2019
    Description: Terrestrial laser scanners provide accurate and detailed point clouds of forest plots, which can be used as an alternative to destructive measurements during forest inventories. Various specialized algorithms have been developed to provide automatic and objective estimates of forest attributes from point clouds. The STEP (Snakes for Tuboid Extraction from Point cloud) algorithm was developed to estimate both stem diameter at breast height and stem diameters along the bole length. Here, we evaluate the accuracy of this algorithm and compare its performance with two other state-of-the-art algorithms that were designed for the same purpose (i.e., the CompuTree and SimpleTree algorithms). We tested each algorithm against point clouds that incorporated various degrees of noise and occlusion. We applied these algorithms to three contrasting test sites: (1) simulated scenes of coniferous stands in Newfoundland (Canada), (2) test sites of deciduous stands in Phalsbourg (France), and (3) coniferous plantations in Quebec, Canada. In most cases, the STEP algorithm predicted diameter at breast height with higher R2 and lower RMSE than the other two algorithms. The STEP algorithm also achieved greater accuracy when estimating stem diameter in occluded and noisy point clouds, with mean errors in the range of 1.1 cm to 2.28 cm. The CompuTree and SimpleTree algorithms respectively produced errors in the range of 2.62 cm to 6.1 cm and 1.03 cm to 3.34 cm, respectively. Unlike CompuTree or SimpleTree, the STEP algorithm was not able to estimate trunk diameter in the uppermost portions of the trees. Our results show that the STEP algorithm is more adapted to extract DBH and stem diameter automatically from occluded and noisy point clouds. Our study also highlights that SimpleTree and CompuTree require data filtering and results corrections. Conversely, none of these procedures were applied for the implementation of the STEP algorithm.
    Electronic ISSN: 1999-4907
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by MDPI
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  • 7
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    Myelin-associated glycoprotein as a functional ligand for the Nogo-66 receptor (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-06-29
    Description: Axonal regeneration in the adult central nervous system (CNS) is limited by two proteins in myelin, Nogo and myelin-associated glycoprotein (MAG). The receptor for Nogo (NgR) has been identified as an axonal glycosyl-phosphatidyl-inositol (GPI)-anchored protein, whereas the MAG receptor has remained elusive. Here, we show that MAG binds directly, with high affinity, to NgR. Cleavage of GPI-linked proteins from axons protects growth cones from MAG-induced collapse, and dominant-negative NgR eliminates MAG inhibition of neurite outgrowth. MAG-resistant embryonic neurons are rendered MAG-sensitive by expression of NgR. MAG and Nogo-66 activate NgR independently and serve as redundant NgR ligands that may limit axonal regeneration after CNS injury.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Betty P -- Fournier, Alyson -- GrandPre, Tadzia -- Strittmatter, Stephen M -- New York, N.Y. -- Science. 2002 Aug 16;297(5584):1190-3. Epub 2002 Jun 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neurology and Section of Neurobiology, Yale University School of Medicine, New Haven, CT 06510, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12089450" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Axons/*physiology ; Binding Sites ; COS Cells ; Chick Embryo ; Cloning, Molecular ; GPI-Linked Proteins ; Ganglia, Spinal/cytology/embryology/metabolism ; Gene Library ; Ligands ; Mice ; Myelin Proteins/chemistry/metabolism/pharmacology ; Myelin-Associated Glycoprotein/chemistry/genetics/*metabolism ; Nerve Regeneration ; Neurites/*physiology ; Neurons/metabolism ; Peptide Fragments/metabolism/pharmacology ; Phosphatidylinositol Diacylglycerol-Lyase ; Protein Structure, Tertiary ; Receptors, Cell Surface/chemistry/genetics/*metabolism ; Recombinant Fusion Proteins/chemistry/metabolism ; Sialic Acids/metabolism ; Transfection ; Type C Phospholipases/metabolism
    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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  • 8
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    Fast torsional waves and strong magnetic field within the Earth's core (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-05-07
    Description: The magnetic field inside the Earth's fluid and electrically conducting outer core cannot be directly probed. The root-mean-squared (r.m.s.) intensity for the resolved part of the radial magnetic field at the core-mantle boundary is 0.3 mT, but further assumptions are needed to infer the strength of the field inside the core. Recent diagnostics obtained from numerical geodynamo models indicate that the magnitude of the dipole field at the surface of a fluid dynamo is about ten times weaker than the r.m.s. field strength in its interior, which would yield an intensity of the order of several millitesla within the Earth's core. However, a 60-year signal found in the variation in the length of day has long been associated with magneto-hydrodynamic torsional waves carried by a much weaker internal field. According to these studies, the r.m.s. strength of the field in the cylindrical radial direction (calculated for all length scales) is only 0.2 mT, a figure even smaller than the r.m.s. strength of the large-scale (spherical harmonic degree n 〈or= 13) field visible at the core-mantle boundary. Here we reconcile numerical geodynamo models with studies of geostrophic motions in the Earth's core that rely on geomagnetic data. From an ensemble inversion of core flow models, we find a torsional wave recurring every six years, the angular momentum of which accounts well for both the phase and the amplitude of the six-year signal for change in length of day detected over the second half of the twentieth century. It takes about four years for the wave to propagate throughout the fluid outer core, and this travel time translates into a slowness for Alfven waves that corresponds to a r.m.s. field strength in the cylindrical radial direction of approximately 2 mT. Assuming isotropy, this yields a r.m.s. field strength of 4 mT inside the Earth's core.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gillet, Nicolas -- Jault, Dominique -- Canet, Elisabeth -- Fournier, Alexandre -- England -- Nature. 2010 May 6;465(7294):74-7. doi: 10.1038/nature09010.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratoire de Geophysique Interne et Tectonophysique, CNRS, Universite Joseph Fourier, BP 53, 38041 Grenoble cedex 9, France. nicolas.gillet@obs.ujf-grenoble.fr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20445627" target="_blank"〉PubMed〈/a〉
    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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  • 9
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    [ASAP] Direct Observation of Ion Pairing in Aqueous Nitric Acid Using 2D Infrared Spectroscopy (2018)
    American Chemical Society (ACS)
    Details
    Publication Date: 2018-12-21
    Description: The Journal of Physical Chemistry B DOI: 10.1021/acs.jpcb.8b10019
    Electronic ISSN: 1520-5207
    Topics: Chemistry and Pharmacology , Physics
    Published by American Chemical Society (ACS)
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  • 10
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    A map of local adaptation in Arabidopsis thaliana (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-10-08
    Description: Local adaptation is critical for species persistence in the face of rapid environmental change, but its genetic basis is not well understood. Growing the model plant Arabidopsis thaliana in field experiments in four sites across the species' native range, we identified candidate loci for local adaptation from a genome-wide association study of lifetime fitness in geographically diverse accessions. Fitness-associated loci exhibited both geographic and climatic signatures of local adaptation. Relative to genomic controls, high-fitness alleles were generally distributed closer to the site where they increased fitness, occupying specific and distinct climate spaces. Independent loci with different molecular functions contributed most strongly to fitness variation in each site. Independent local adaptation by distinct genetic mechanisms may facilitate a flexible evolutionary response to changing environment across a species range.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fournier-Level, A -- Korte, A -- Cooper, M D -- Nordborg, M -- Schmitt, J -- Wilczek, A M -- New York, N.Y. -- Science. 2011 Oct 7;334(6052):86-9. doi: 10.1126/science.1209271.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21980109" target="_blank"〉PubMed〈/a〉
    Keywords: Acclimatization ; *Adaptation, Physiological ; Alleles ; Arabidopsis/*genetics/*physiology ; *Climate ; Europe ; Genes, Plant ; *Genetic Fitness ; Genetic Loci ; *Genome, Plant ; Genome-Wide Association Study ; Geography ; *Polymorphism, Single Nucleotide ; Protein Binding ; Selection, Genetic ; Temperature ; Transcription Factors/metabolism
    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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