Computational multifocus fluorescence microscopy for three-dimensional visualization of multicellular tumor spheroids

Significance: Three-dimensional (3D) visualization of multicellular tumor spheroids (MCTS) in fluorescence microscopy can rapidly provide qualitative morphological information about the architecture of these cellular aggregates, which can recapitulate key aspects of their in vivo counterpart. Aim: The present work is aimed at overcoming the shallow depth-of-field (DoF) limitation in fluorescence microscopy while achieving 3D visualization of thick biological samples under study. Approach: A custom-built fluorescence microscope with an electrically focus-tunable lens was developed to optically sweep in-depth the structure of MCTS. Acquired multifocus stacks were combined by means of postprocessing algorithms performed in the Fourier domain. Results: Images with relevant characteristics as extended DoF, stereoscopic pairs as well as reconstructed viewpoints of MCTS were obtained without segmentation of the focused regions or estimation of the depth map. The reconstructed images allowed us to observe the 3D morphology of cell aggregates. Conclusions: Computational multifocus fluorescence microscopy can provide 3D visualization in MCTS. This tool is a promising development in assessing the morphological structure of different cellular aggregates while preserving a robust yet simple optical setup

A Role for Both Conformational Selection and Induced Fit in Ligand Binding by the LAO Protein

Molecular recognition is determined by the structure and dynamics of both a protein and its ligand, but it is difficult to directly assess the role of each of these players. In this study, we use Markov State Models (MSMs) built from atomistic simulations to elucidate the mechanism by which the Lysine-, Arginine-, Ornithine-binding (LAO) protein binds to its ligand. We show that our model can predict the bound state, binding free energy, and association rate with reasonable accuracy and then use the model to dissect the binding mechanism. In the past, this binding event has often been assumed to occur via an induced fit mechanism because the protein's binding site is completely closed in the bound state, making it impossible for the ligand to enter the binding site after the protein has adopted the closed conformation. More complex mechanisms have also been hypothesized, but these have remained controversial. Here, we are able to directly observe roles for both the conformational selection and induced fit mechanisms in LAO binding. First, the LAO protein tends to form a partially closed encounter complex via conformational selection (that is, the apo protein can sample this state), though the induced fit mechanism can also play a role here. Then, interactions with the ligand can induce a transition to the bound state. Based on these results, we propose that MSMs built from atomistic simulations may be a powerful way of dissecting ligand-binding mechanisms and may eventually facilitate a deeper understanding of allostery as well as the prediction of new protein-ligand interactions, an important step in drug discovery

Structural importance of Stone-Thrower-Wales defects in rolled and flat graphenes from surface-enhanced Raman scattering

We first survey the historical aspects of the term Stone-Thrower-Wales (STW) defect and its experimental identification. Physicochemical properties associated with the STW defect have been extensively investigated theoretically as well. However, it is difficult to verify the predicted properties by means of experiments. Here we demonstrate an experimental way to probe the vibrational properties of STW defects in single-wall carbon nanotubes (SWCNTs) using surface-enhanced Raman scattering (SEAS). We also performed density functional theory calculations to support our interpretation of the SERS spectra. The characteristic fluctuations of peak intensities and frequencies are ascribed to dynamic motion of an STW defect in the hexagonal SWCNT lattice. The role of an STW defect at edges is also discussed in terms of its relevance to the stability and O-2 reactivity of flat and curved graphene structures.ArticleCARBON. 50(9):3274-3279 (2012)journal articl

Electronic wave functions and optical transitions in (In,Ga)As/GaP quantum dots

Robert, Cédric et al.We study the complex electronic band structure of low In content InGaAs/GaP quantum dots. A supercell extended-basis tight-binding model is used to simulate the electronic and the optical properties of a pure GaAs/GaP quantum dot modeled at the atomic level. Transitions between hole states confined into the dots and several XZ-like electronic states confined by the strain field in the GaP barrier are found to play the main role on the optical properties. Especially, the calculated radiative lifetime for such indirect transitions is in good agreement with the photoluminescence decay time measured in time-resolved photoluminescence in the µs range. Photoluminescence experiments under hydrostatic pressure are also presented. The redshift of the photoluminescence spectrum with pressure is also in good agreement with the nature of the electronic confined states simulated with the tight-binding model.A.R.G. and M.I.A. acknowledge support from the Spanish Ministry of Economy and Competitiveness (MINECO) through Grant No. MAT2009-09480 (PIEZOHM) and Severo Ochoa Excellence Centre Award (No. SEV-2015-0496). M.O.N. acknowledges financial support from the Russian Foundation for Basic Research. This research is supported by “Region Bretagne” through the PONANT project including ´ FEDER funds. This paper is also supported by the OPTOSI Agence Nationale pour la Recherche Project No. 12-BS03- 002-02. This work has been performed using HPC resources of GENCI CINES, TGCC/CCRT, and IDRIS under the allocation No. 2013-[x2013096724].Peer reviewe

A tetraiodo cuprate NHC-MIC biscarbene proligand: coordination chemistry and preliminary catalysis

La preparación de una sal híbrida conteniendo cationes imidazolio/triazolio [NHC-MIC]²+ fue llevada a cabo en tres pasos sintéticos utilizando la cicloadición de azida-alquino catalizada por cobre (CuAAC) y la subsecuente N-metilación del 1,2,-3 triazol. Deprotonación selectiva de la sal mixta con NaH en presencia de un precursor metálico (M= Pd, Rh) permite la síntesis de NHC-metálicos conteniendo fragmentos catiónicos de tipo triazolio [NHC∙(M)-MIC]+. La subsecuente deprotonación del triazolio con KOᵗBu en presencia de Mpermite entonces la síntesis de complejos inusuales tipo quelato conteniendo carbenos clásicos tipo NHC y carbenos mesoiónicos MIC con estructura general [NHC∙(M)∙MIC]+MX₂-. Todos los compuestos han sido caracterizados mediante RMN de ¹H y ¹³C, FT-IR y cristalografía de rayos-X de monocristal. Estudios catalíticos preliminares de los nuevos complejos en procesos de formación de α-cetoamidas serán discutidos.A novel linked imidazolium/triazolium salt [NHC-MIC]²+ was preparedin three synthetic stepsusing copper catalyzed alkyne azide cycloaddition (CuAAC) and N-methylation protocols. Metallation of the imidazolium moiety using KHMDS in presence of a metallic precursor (M = Pd, Rh) yields NHC-anchored/pendent triazolium species [NHC∙(M)-MIC]+ in good yields. The subsequent deprotonation of the triazolium fragment with KOᵗBu in presence of one equivalent of M delivers the rare chelating mixed classical NHC/mesionic biscarbene complexes with the general formula [NHC∙(M)∙MIC]+MX₂-. All the complexes were fully characterized by ¹H and ¹³C NMR, FT-IR and single crystal X-ray diffraction. Preliminary catalytic performances of the new complexes in the oxidativepreparation of α-ketoamides will be discussed

History-sensitive versus future-sensitive approaches to security in distributed systems

We consider the use of aspect-oriented techniques as a flexible way to deal with security policies in distributed systems. Recent work suggests to use aspects for analysing the future behaviour of programs and to make access control decisions based on this; this gives the flavour of dealing with information flow rather than mere access control. We show in this paper that it is beneficial to augment this approach with history-based components as is the traditional approach in reference monitor-based approaches to mandatory access control. Our developments are performed in an aspect-oriented coordination language aiming to describe the Bell-LaPadula policy as elegantly as possible. Furthermore, the resulting language has the capability of combining both history- and future-sensitive policies, providing even more flexibility and power.Comment: In Proceedings ICE 2010, arXiv:1010.530

Many-Exciton Quantum Dynamics in a Ruddlesden-Popper Tin Iodide

We present a study on the many-body exciton interactions in a prototype Ruddlesden-Popper metal halide (RPMH), namely \ce{(PEA)2SnI4} (PEA = phenylethylammine), using coherent two-dimensional electronic spectroscopy. The optical dephasing times of the third-order polarization observed in these systems are determined by exciton many-body interactions and lattice fluctuations. We investigate the excitation-induced dephasing (EID) and observe a significant reduction of the contribution to the dephasing time with increasing excitation density as compared to its lead counterpart \ce{(PEA)2PbI4}, which we have previously reported [A.~R.~Srimath~Kandada~\textit{et~al.}, J.\ Chem.\ Phys.\ \textbf{153}, 164706 (2020)]. Surprisingly, we find that the EID interaction parameter is four orders of magnitude higher in \ce{(PEA)2SnI4} than that in \ce{(PEA)2PbI4}. This increase in the EID rate may be due to exciton localization arising from a more strongly statically disordered lattice in the tin derivative. This is supported by the observation of multiple closely spaced exciton states and the broadening of the linewidth with increasing population time (spectral diffusion), which suggests a static disordered structure relative to the highly dynamic lead-halide. Additionally, we find that the exciton nonlinear coherent lineshape shows evidence of a biexcitonic state with low binding energy ($<10$\,meV) not observed in the lead system. We model the lineshapes based on a stochastic scattering theory that accounts for the interaction with a non-stationary population of dark background excitations. Our study provides evidence of differences in the exciton quantum dynamics between tin- and lead-based RPMHs and links them to the exciton-exciton interaction strength and the static disorder aspect of the crystalline structure.Comment: Submitted for publicatio

Cellular automaton supercolliders

Gliders in one-dimensional cellular automata are compact groups of non-quiescent and non-ether patterns (ether represents a periodic background) translating along automaton lattice. They are cellular-automaton analogous of localizations or quasi-local collective excitations travelling in a spatially extended non-linear medium. They can be considered as binary strings or symbols travelling along a one-dimensional ring, interacting with each other and changing their states, or symbolic values, as a result of interactions. We analyse what types of interaction occur between gliders travelling on a cellular automaton `cyclotron' and build a catalog of the most common reactions. We demonstrate that collisions between gliders emulate the basic types of interaction that occur between localizations in non-linear media: fusion, elastic collision, and soliton-like collision. Computational outcomes of a swarm of gliders circling on a one-dimensional torus are analysed via implementation of cyclic tag systems

High-resolution stable isotope stratigraphy of the upper Cambrian and Ordovician in the Argentine Precordillera: Carbon isotope excursions and correlations

We report the occurrence of important carbon isotope excursions in early Paleozoic formations of the Eastern and Central Argentine Precordillera. The Steptoean positive isotope carbon excursion (SPICE) is known from North America, Kazakhstan, South China, Australia and South America, and the negative isotope carbon excursion (SNICE) has been described for the first time in South America. We report here the record of the SPICE and SNICE in a single section in the Eastern Precordillera. In the Central Precordillera, a minor middle Darriwilian positive carbon isotope excursion (MDICE) and a late Sandbian positive isotope carbon excursion, the GICE (~ + 3‰; C. bicornis biozone) are reported from two sections. One pre-GICE positive carbon-isotope excursion (Sandbian Sa1, N. gracilis biozone) in the Central Precordillera with a δ13C peak of ~ + 2‰ is, perhaps, equivalent to the positive Spechts Ferry δ13C excursion of North America. A positive δ13C excursion (~ 6‰; N. persculptus biozone) recorded at the base of the late Hirnantian La Chilca Formation probably corresponds to HICE. These carbon-isotope excursions resulted from more than one factor where paleoceanographic events probably played a major role: (a) sea-level fall and vigorous fluctuations in the Steptoean (SPICE), (b) sea-level rise in the Sunwaptan (SNICE), (c) important transgression in the Sandbian (pre-GICE and GICE), and (d) sea-level fall in the late Hirnantian (HICE). In the Darriwilian and Sandbian stages, organic burial has led to a large 12C sequestration in the deep anoxic ocean with saline bottom water, recorded by the graptoliferous black shales of the Gualcamayo and Los Azules formations in Central Precordillera, helped the building of the MDICE and GICE anomalies. δ18O values for the Upper Cambrian carbonates are likely near-primary isotope signals that point to progressive cooling from the SPICE to the SNICE, whereas for Sandbian carbonates they suggest strong temperature fluctuations. The δ13C peak of the GICE coincides with a cooler period with temperatures warming up towards the late Hirnantian to Rhuddanian. The Upper Cambrian to the Middle Ordovician of the Precordillera recorded a decrease of seawater 87Sr/86Sr ratios in accordance to the global picture. This decrease probably reflects the influence of widespread volcanic activity from arc terranes in low-latitude settings along eastern margins of Laurentia and in the Argentine Precordillera in the Early to Middle Ordovician. Five carbonate samples (from San Juan, Gualcamayo and Los Azules formations) yielded εNd values that along seven already published values seem to plot along the Nd isotopic evolution trend of the Iapetus Ocean. Together, the record of global Upper Cambrian and Ordovician carbon-isotope excursions in the Argentine Precordillera is a valuable proxy in refining Early Paleozoic stratigraphy, establishing of regional/global high-resolution correlations, and sea-level change history in South America.Fil: Sial, A. N.. Universidade Federal de Pernambuco; BrasilFil: Peralta, Silvio Heriberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Juan; ArgentinaFil: Gaucher, C.. No especifíca;Fil: Toselli, Alejandro Jose. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Instituto Superior de Correlación Geológica. Universidad Nacional de Tucumán. Facultad de Ciencias Naturales e Instituto Miguel Lillo. Departamento de Geología. Cátedra Geología Estructural. Instituto Superior de Correlación Geológica; ArgentinaFil: Ferreira, V. P.. Universidade Federal de Pernambuco; BrasilFil: Frei, R.. Universidad de Copenhagen; DinamarcaFil: Parada, M. A.. Universidad de Chile; ChileFil: Pimentel, M. M.. Universidade Federal do Rio Grande do Sul; BrasilFil: Silva Pereira, Natan. Universidade Federal de Pernambuco; Brasi