101. Nanobodies against surface biomarkers enable the analysis of tumor genetic heterogeneity in uveal melanoma Patient Derived XenograftsRonan Crepin, David Gentien, Angeline Duche, Audrey Rapinat, Cecile Reyes, Fariba Nemati, Gerald Massonnet, Didier Deacaudin, Selma Djander, Sandrine Moutel, Klervi Even Desrumeaux, Nathalie Cassoux, Sophie Piperno-Neumann, Sebastian Amigorena, Franck Perez, Sergio Roman-Roman, Ario De Marco, 2017, original scientific article Abstract: Monoclonal antibodies specific for biomarkers expressed on the surface of uveal melanoma (UM) cells would simplify the immune-capture and genomic characterization of heterogeneous tumor cells originated from patient derived xenografts (PDXs). Antibodies against four independent tumor antigens were isolated by panning a nanobody synthetic library. Such antibodies enabled flow-cytometry-based sorting of distinct cell sub-populations from UM PDXs and to analyze their genomic features. The complexity and specificity of the biochemical and genomic biomarker combinations mirrored the UM tumor polyclonality. The data showed that MUC18 is highly and universally displayed at the surface of UM cells with different genetic background and consequently represents a reliable pan-biomarker for their identification and purification. In contrast, the other three biomarkers were detected in very variable combinations in UM PDX cells. The availability of the identified nanobodies will be instrumental in developing clone-specific drug evaluation and rational clinical strategies based on accurate genomic profiling
Keywords: nanobodies, uveal melanoma, patient derived xenografts, MUC18, membrane surface biomarkers, panning, tumor polyclonality
Published in RUNG: 19.04.2017; Views: 5575; Downloads: 0
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102. Impact of atmospheric effects on the energy reconstruction of air showers observed by the surface detectors of the Pierre Auger ObservatoryA. Aab, Andrej Filipčič, Gašper Kukec Mezek, Ahmed Saleh, Samo Stanič, Marta Trini, Darko Veberič, Serguei Vorobiov, Lili Yang, Danilo Zavrtanik, Marko Zavrtanik, 2017, original scientific article Keywords: Pierre Auger Observatory (PAO), PAO Surface Detector, energy reconstruction, atmospheric effects
Published in RUNG: 16.02.2017; Views: 4304; Downloads: 0
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103. Solution-Based Fabrication of Carbon Nanotube Bumps for Flip-Chip InterconnectsXu Pingye, Fei Tong, Virginia Davis, Minseo Park, Michael Hamilton, 2014, original scientific article Keywords: Resists, Fabrication, Electrical resistance measurement, Substrates, Dispersion, Resistance, Surface treatment
Published in RUNG: 16.01.2017; Views: 4114; Downloads: 0
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104. Surface plasmon resonance properties of DC magnetron sputtered Ag nanoislands on ITO-glass and In2O3-PET substratesFei Tong, Yoonsung Chung, J Goswami, Virginia Davis, Michael Hamilton, Kim Dong-Joo, Helen Koo, Kyeong K. Lee, Minseo Park, 2014, short scientific article Keywords: Ag nanoislands, Surface plasmon resonance properties, DC magnetron sputtere, ITO-glass and In2O3-PET substrates
Published in RUNG: 16.01.2017; Views: 4176; Downloads: 0
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105. Formation of Hybrid Electronic States in FePc Chains Mediated by the Au(110) SurfaceMaria Grazia Betti, Pierluigi Gargiani, Carlo Mariani, Stefano Turchini, Nicola Zema, Sara Fortuna, Arrigo Calzolari, Stefano Fabris, 2012, original scientific article Abstract: Iron–phthalocyanine (FePc) molecules deposited on the Au(110) surface self-organize in ordered chains driven by the reconstructed Au channels. The interaction process induces a rehybridization of the electronic states localized on the central metal atom, breaking the 4-fold symmetry of the molecular orbitals of the FePc molecules. The molecular adsorption is controlled by a symmetry-determined mixing between the electronic states of the Fe metal center and of the Au substrate, as deduced by photoemission and absorption spectroscopy exploiting light polarization. DFT calculations rationalize this mixing of the Fe and Au states on the basis of symmetry arguments. The calculated electronic structure reproduces the main experimental spectral features, which are associated to a distorted molecular structure displaying a trigonal bipyramidal geometry of the ligands around the metal center.
Keywords: phthalocyanine, Au(110), gold, surface, DFT, density functional theory, calculation, simulation
Published in RUNG: 13.10.2016; Views: 4901; Downloads: 0
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106. Structural phases of ordered FePc-nanochains self-assembled on Au(110)Betti Maria Grazia, Pierluigi Gargiani, Carlo Mariani, Roberto Biagi, Jun Fujii, Giorgio Rossi, Andrea Resta, Stefano Fabris, Sara Fortuna, Xavier Torrelles, Manvendra Kumar, Maddalena Pedio, 2012, original scientific article Abstract: Iron-phthalocyanine molecules deposited on the Au(110) reconstructed channels assemble into one-dimensional molecular chains, whose spatial distribution evolves into different structural phases at increasing molecular density. The plasticity of the Au channels first induces an ordered phase with a 5×5 symmetry, followed by a second long-range ordered structure composed by denser chains with a 5×7 periodicity with respect to the bare Au surface, as observed in the low-energy electron-diffraction (LEED) and grazing incidence X-ray diffraction (GIXRD) patterns. The geometry of the FePc molecular assemblies in the Au nanorails is determined by scanning tunneling microscopy (STM). For the 5×7 phases, the GIXRD analysis identifies a “4-3” rows profile along the [001] direction in the Au surface and an on-top FePc adsorption site, further confirmed by density functional theory (DFT) calculations. The latter also reveals the electronic mixing of the interface states. The chain assembly is driven by the molecule–molecule interaction and the chains interact with the Au nanorails via the central metal atom, while the chain–chain distance in the different structural phases is primarily driven by the plasticity of the Au surface.
Keywords: STM, LEED, DFT, density functional theory, phthalocyanine, Au(110), gold, surface
Published in RUNG: 13.10.2016; Views: 4791; Downloads: 0
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107. Molecule-Driven Substrate Reconstruction in the Two-Dimensional Self-Organization of Fe-Phthalocyanines on Au(110)Sara Fortuna, Pierluigi Gargiani, Maria Grazia Betti, Carlo Mariani, Arrigo Calzolari, Silvio Modesti, Stefano Fabris, 2012, original scientific article Abstract: The structural patterns formed by molecular self-assembly at surfaces are usually controlled by the relative strengths of the intermolecular and molecule–substrate interactions. An additional steering effect is present when the substrate can easily reconstruct upon molecular adsorption, which therefore drives a self-templating effect on the metal support. This is here demonstrated for the model case of Fe-phthalocyanine molecules adsorbed on the Au(110) surface. Scanning tunneling microscopy shows that molecular adsorption promotes a local (1 × 5) surface reconstruction, which drives the assembly of molecular chains along the [11̅0] direction. The order and periodicity of the molecular assemblies are determined with low energy electron diffraction patterns. Density functional theory calculations reveal the energetic origins of the molecule-driven substrate reconstruction. Since the function of molecular overlayers at surfaces is strongly correlated to their structure, these results have implications in the design of new metal/molecular interfaces.
Keywords: self-assembly, phthalocyanine, Au(110), DFT, density functional theory, simulation, surface, recontruction
Published in RUNG: 11.10.2016; Views: 4667; Downloads: 0
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108. Oxalic acid adsorption states on the clean Cu(110) surfaceSara Fortuna, 2016, original scientific article Abstract: Carboxylic acids are known to assume a variety of configurations on metallic surfaces. In particular oxalic acid on the Cu(110) surface has been proposed to assume a number of upright configurations. Here we explore with DFT calculations the possible structures that oxalic acid can form on copper 110 at different protonation states, with particular attention at the possibility of forming structures composed of vertically standing molecules. In its fully protonated form it is capable of anchoring itself on the surface thanks to one of its hydrogen-free oxygens. We show the monodeprotonated upright molecule with two oxygens anchoring it on the surface to be the lowest energy conformation of a single oxalic molecules on the Cu(110) surface. We further show that it is possible for this configuration to form dense hexagonally arranged patterns in the unlikely scenario in which adatoms are not involved.
Keywords: oxalic acid, oxalate, cu(110), copper, surface, adsorption, density functional theory, DFT
Published in RUNG: 11.10.2016; Views: 4520; Downloads: 0
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110. Azimuthal asymmetry in the risetime of the surface detector signals of the Pierre Auger ObservatoryA. Aab, Andrej Filipčič, Gašper Kukec Mezek, Ahmed Saleh, Samo Stanič, Marta Trini, Darko Veberič, Serguei Vorobiov, Lili Yang, Danilo Zavrtanik, Marko Zavrtanik, 2016, original scientific article Abstract: The azimuthal asymmetry in the risetime of signals in Auger surface detector stations is a source of information on shower development. The azimuthal asymmetry is due to a combination of the longitudinal evolution of the shower and geometrical effects related to the angles of incidence of the particles into the detectors. The magnitude of the effect depends upon the zenith angle and state of development of the shower and thus provides a novel observable, (secθ)max, sensitive to the mass composition of cosmic rays above 3×1018 eV. By comparing measurements with predictions from shower simulations, we find for both of our adopted models of hadronic physics (QGSJETII-04 and EPOS-LHC) an indication that the mean cosmic-ray mass increases slowly with energy, as has been inferred from other studies. However, the mass estimates are dependent on the shower model and on the range of distance from the shower core selected. Thus the method has uncovered further deficiencies in our understanding of shower modeling that must be resolved before the mass composition can be inferred from (secθ)max.
Keywords: ultra-high energy cosmic rays (UHECR), UHECR mass composition, Pierre Auger Observatory, extensive air showers, Auger Surface Detector signals risetime, azimuthal symmetry
Published in RUNG: 15.04.2016; Views: 5431; Downloads: 0
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