MSO-GP: 3-D segmentation of large and complex conjoined tree structures.

Robust segmentation of large and complex conjoined tree structures in 3-D is a major challenge in computer vision. This is particularly true in computational biology, where we often encounter large data structures in size, but few in number, which poses a hard problem for learning algorithms. We show that merging multiscale opening with geodesic path propagation, can shed new light on this classic machine vision challenge, while circumventing the learning issue by developing an unsupervised visual geometry approach (digital topology/morphometry). The novelty of the proposed MSO-GP method comes from the geodesic path propagation being guided by a skeletonization of the conjoined structure that helps to achieve robust segmentation results in a particularly challenging task in this area, that of artery-vein separation from non-contrast pulmonary computed tomography angiograms. This is an important first step in measuring vascular geometry to then diagnose pulmonary diseases and to develop image-based phenotypes. We first present proof-of-concept results on synthetic data, and then verify the performance on pig lung and human lung data with less segmentation time and user intervention needs than those of the competing methods.

Ultrafast symmetry-breaking charge separation in Perylenemonoimide-embedded multichromophores: impact of regioisomerism.

Symmetry-breaking charge separation (SB-CS) has recently evolved as an emerging concept offering its potential to the latest generation of organic photovoltaics. However there are several concerns that need to be addressed to reach the state-of-the-art in SB-CS chemistry, for instance, the desirable molecular geometry, interchromophoric distance and extent of electronic coupling. To shed light on those features, it is reported herein, that ortho-functionalized perylene monoimide (PMI) constituted regioisomeric dimer and trimer derivatives with varied molecular twisting and electronic conjugation have been synthesized. In steady-state photophysical studies, all the dimers and trimer derivatives exhibit a larger bathochromic shift in the emission spectra and a significant reduction of fluorescence quantum yield in polar DMF. Among the series of multichromophores, ortho- and self-coupled dimers display the strikingly different optical feature of SB-CS with a very fast charge separation rate (τCS = 80.2 ps) upon photoexcitation in DMF, which is unveiled by femtosecond transient absorption (fs-TA) studies. The SB-CS for two dimers is well-supported by the formation of PMI˙+ and PMI˙- bands in the fs-TA spectra. Further analysis of fs-TA data revealed that, among the other multichromophores the trimer also exhibits a clear charge separation, whereas SB-CS signatures are less prominent, but can not be completely disregarded, for the meta- and para-dimers. Additionally, the charge separation dynamics of those above-mentioned PMI derivatives are devoid of a kinetically favorable excimer or triplet formation. The evidence of a profound charge transfer phenomenon in the ortho-dimer is characterized by density functional theory (DFT) calculations on excited state electronic structures. The excitonic communications in the excited state electronic arrangements unravel the key role of dihedral twisting in SB-CS. The thermodynamic feasibility of CS (ΔGCS) and activation barrier (ΔG≠) of the derivatives in DMF are established from the Rehm-Weller equation and Marcus's theory, respectively. This work is an in-depth study of the effect of mutual orientation of PMIs and regioisomerism in determining sustainable guidelines for using SB-CS.

Elucidating photocycle in large Stokes shift red fluorescent proteins: Focus on mKeima.

Large Stokes shift red fluorescent proteins (LSS-RFPs) are genetically encoded and exhibit a significant difference of a few hundreds of nanometers between their excitation and emission peak maxima (i.e., the Stokes shift). These LSS-RFPs (absorbing blue light and emitting red light) feature a unique photocycle responsible for their significant Stokes shift. The photocycle associated with this LSS characteristic in certain RFPs is quite perplexing, hinting at the complex nature of excited-state photophysics. This article provides a brief review on the fundamental mechanisms governing the photocycle of various LSS-RFPs, followed by a discussion on experimental results on mKeima emphasizing its relaxation pathways which garnered attention due to its >200 nm Stokes shift. Corroborating steady-state spectroscopy with computational studies, four different forms of chromophore of mKeima contributing to the cis-trans conformers of the neutral and anionic forms were identified in a recent study. Furthering these findings, in this account a detailed discussion on the photocycle of mKeima, which encompasses sequential excited-state isomerization, proton transfer, and subsequent structural reorganization involving three isomers, leading to an intriguing temperature and pH-dependent dual fluorescence, is explored using broadband femtosecond transient absorption spectroscopy.

Spectral characteristics of the flavones and anthocyanins present in passionflower (Passiflora incarnata).

Rich in antioxidants with a variety of flavones and anthocyanins, passionflower/fruit has been extensively used in food, beverage, medicinal, and natural dyes industries. The individual components present in passionflower are identified by extracting them in methanol, partitioning them between ethyl acetate and aqueous layers, and recording their ESI mass spectrometric data. The steady-state absorption and fluorescence spectra of the extract in methanol and dimethyl sulfoxide are recorded and the lifetime of the fluorescing species is reported. The pH dependence of the absorption spectrum confirms the presence of the anthocyanins.

Separating Vibrational Coherences in Ground/Excited Electronic States of Solvent/Solute Following Non-Resonant/Resonant Impulsive Excitation.

In a quest to track down the origin of coherent vibrational motions observed in femtosecond pump-probe transients, whether they arise from ground/excited electronic state of solute or are contributed by the solvent, we demonstrate a method for extricating vibrations under resonant and non-resonant impulsive excitations using a diatomic solute in condensed phase (iodine in carbon tetrachloride) with aid of spectral dispersion of the chirped broadband probe. Most importantly, we show how a sum over intensities for a select region of detection wavelengths and Fourier transform of data over select temporal window untwine contributions from vibrational modes of different origins. Thus, in a single pump-probe experiment, vibrational features specific to solute as well as solvent are disentangled that are otherwise spectrally overlapping and are non-separable in conventional (spontaneous/stimulated) Raman spectroscopy employing narrowband excitation. We envision wide-ranging applications of this method to unveil vibrational features in complex molecular systems.

Unveiling the Role of Hidden Isomers in Large Stokes Shift in mKeima: Harnessing pH-Sensitive Dual-Emission in Bioimaging.

Elucidating the origin of large Stokes shift (LSS) in certain fluorescent proteins absorbing in blue/blue-green and emitting in red/far-red has been quite illusive. Using a combination of spectroscopic measurements, corroborated by theoretical calculations, the presence of four distinct forms of the chromophore of the red fluorescent protein mKeima is confirmed, two of which are found to be emissive: a feeble bluish-green fluorescence (∼520 nm), which is enhanced appreciably in a low pH or deuterated medium but significantly at cryogenic temperatures, and a strong emission in red (∼615 nm). Using femtosecond transient absorption spectroscopy, the trans-protonated form is found to isomerize within hundreds of femtoseconds to the cis-protonated form, which further yields the cis-deprotonated form within picoseconds followed by structural reorganization of the local environment of the chromophore. Thus, the mechanism of LSS is substantiated to proceed via stepwise excited-state isomerization followed by proton transfer involving three isomers, leaving the fourth one (trans-deprotonated) as a bystander. The exquisite pH sensitivity of the dual emission is further exploited in fluorescence microscopy.

Complementing two-photon fluorescence detection with backscatter detection to decipher multiparticle dynamics inside a nonlinear laser trap.

Using wide-field and point detection modalities, we show how optical trapping dynamics under femtosecond pulsed excitation can be explored by complementing detection of two-photon fluorescence with backscatter. Radial trajectories of trapped particles are mapped from correlated/anti-correlated fluctuations in backscatter pattern whereas temporal evolution of two-photon fluorescence is used to mark the onset of trapping involving multiple particles. Simultaneous confocal detection of backscatter and two-photon fluorescence estimates axial trap stiffness, delineating short-time trapping dynamics. When a second particle is being trapped an oscillatory signal is observed which is due to interference of backscatter amplitudes, revealing inter-particle interactions within the trap. These findings are crucial steps forward to achieve controlled manipulation by harnessing optical nonlinearity under femtosecond pulsed excitation.

Inter-Network Charge-Transfer Excited State Formation Within a Two-fold Catenated Metal-Organic Framework.

Charge-transfer excited state (CTES) defines the ability to split photon energy into work producing redox equivalents suitable for photocatalysis. Here, we report inter-net CTES formation within a two-fold catenated crystalline metal-organic framework (MOF), constructed with two linkers, N,N'-di(4-pyridyl)-1,4,5,8-naphthalenetetracarboxydiimide (DPNDI) and 2,6-dicarboxynaphthalene (NDC). The structural flexibility puts two complementary linkers from two nets in a proximal position to interact strongly. Supported by the electrochemical and steady-state electronic spectroscopic data, this ground-state interaction facilitates forming CTES that can be populated by direct excitation. We map the dynamics of the CTES which persists over a few nanoseconds and highlight the utilities of such relatively long-lived CTES as enhanced conductivity of the MOF under light over that measured in dark and as a proof-of-the-principle test, photo-reduction of methyl viologen under white light.

Electron-Phonon Coupling Mediated Self-Trapped-Exciton Emission and Internal Quantum Confinement in Highly Luminescent Zero-Dimensional (Guanidinium)6Mn3X12 (X = Cl and Br).

We report a large Stokes shift and broad emission band in a Mn-based organic-inorganic hybrid halide, (Guanidinium)6Mn3Br12 [GuMBr], consisting of trimeric units of distorted MnBr6 octahedra representing a zero-dimensional compound with a liquid like crystalline lattice. Analysis of the photoluminescence (PL) line width and Raman spectra reveals the effects of electron-phonon coupling, suggestive of the formation of Frenkel-like bound excitons. These bound excitons, regarded as the self-trapped excitons (STEs), account for the large Stokes shift and broad emission band. The excited-state dynamics was studied using femtosecond transient absorption spectroscopy, which confirms the STE emission. Further, this compound is highly emissive with a PL quantum yield of ∼50%. With chloride ion incorporation, we observe enhancement of the emissive properties and attribute it to the effects of intrinsic quantum confinement. Localized electronic states in flat bands lining the gap and their strong coupling with phonons are confirmed with first-principles calculations.

Asymmetric synthesis of (+)-teratosphaerone B, its non-natural analogue and (+)-xylarenone using an ene- and naphthol reductase cascade.

Herein, a one-pot bienzymatic cascade containing an ene and a naphthol reductase is developed. It is applied for the synthesis of (+)-(3R,4R)-teratosphaerone B, its non-natural regioisomer in both cis- and trans-forms and (+)-xylarenone by the reduction of chemically synthesized naphthoquinone precursors in high yields (76-92%) and excellent ee (>99%). This work implies similar biosynthetic steps in the formation of the synthesized natural products.

A Deep Graph Cut Model For 3D Brain Tumor Segmentation.

Brain tumor segmentation plays a key role in tumor diagnosis and surgical planning. In this paper, we propose a solution to the 3D brain tumor segmentation problem using deep learning and graph cut from the MRI data. In particular, the probability maps of a voxel to belong to the object (tumor) and background classes from the UNet are used to improve the energy function of the graph cut. We derive new expressions for the data term, the region term and the weight factor balancing the data term and the region term for individual voxels in our proposed model. We validate the performance of our model on the publicly available BRATS 2018 dataset. Our segmentation accuracy with a dice similarity score of 0.92 is found to be higher than that of the graph cut and the UNet applied in isolation as well as over a number of state of the art approaches.

Enhanced optical force on multilayered dielectric nanoparticles by tuning material properties and nature of excitation: a theoretical investigation.

Using dipole approximation, a comparative study of trapping force/potential on different types of dielectric nanoparticles is presented. The trapping force for multilayered nanoparticles, i.e. core-shell-shell type nanoparticles, is found to be enhanced compared with both core-only type and core-shell type nanoparticles. It is shown that an appropriate choice of material and thickness of the middle layer results in tuning the polarizability, thereby playing a vital role in determining the trapping efficiency for core-shell-shell type nanoparticles. Further, the effect of optical nonlinearity under femtosecond pulsed excitation is investigated and it is elucidated that depending on the specific need (i.e. high force versus long confinement time), the nature of excitation (i.e. pulsed excitation or continuous-wave excitation) can be judiciously chosen. These findings are promised to open up new prospects for controlled nanoscale trapping and manipulation across different fields of nanoscience and nanotechnology.

Effect of Nanoscale Confinement on Ultrafast Dynamics of Singlet Fission in TIPS-Pentacene.

Singlet fission (SF) is a phenomenon for the generation of a pair of triplet excitons from anexcited molecule in singlet electronic state interacting with another adjacent molecule in its ground electronic state. By increasing the effective number of charge carriers and reducing thermal dissipation of excess energy, SF is promised to enhance light-harvesting efficiency for photovoltaic applications. While SF has been extensively studied in thin films and crystals, the same has not been explored much within a confined medium. Here, we report the ultrafast SF dynamics of triisopropylsilylethynyl pentacene (TIPS-Pn) in micellar nanocavity of varying sizes (prepared from TX-100, CTAB, and SDS surfactants). The nanoparticles with a smaller size contain weakly coupled chromophores which are shown to be more efficient for SF followed by triplet generation as compared to the nanoparticles of larger size which contain strongly coupled chromophores which are less efficient due to the presence of singlet exciton traps. Through these studies, we delineate how a subtle interplay between short-range and long-range interaction among chromophores confined within nanoparticles, fine-tuned by the curvature of the micellar interface but irrespective of the nature of the micelle (cationic or anionic or neutral), play a crucial role in SF through and generation of triplets.

Deciphering single- and multi-particle trapping dynamics under femtosecond pulsed excitation with simultaneous spatial and temporal resolution.

Recent theoretical and experimental studies have shed light on how laser trapping dynamics under femtosecond pulsed excitation are fine-tuned by optical and thermal nonlinearities. Here, we present experimental results of trapping of single and multiple polystyrene beads (of 1 µm diameter). We show how integration and synchronization of bright-field video microscopy with confocal detection of backscatter provide both spatial and temporal resolution required to capture intricate details of nonlinear trapping dynamics. Such spatiotemporal detection is promising to have far-reaching applications in exploring controlled laser trapping and manipulations harnessed by optical and thermal nonlinearities.

A Revisit on Impulsive Stimulated Raman Spectroscopy: Importance of Spectral Dispersion of Chirped Broadband Probe.

The usefulness of a chirped broadband probe and spectral dispersion to obtain Raman spectra under nonresonant/resonant impulsive excitation is revisited. A general methodology is presented that inherently takes care of phasing the time-domain low-frequency oscillations without probe pulse compression and retrieves the absolute phase of the oscillations. As test beds, neat solvents (CCl4, CHCl3, and CH2Cl2) are used. Observation of periodic intensity modulation along detection wavelengths for particular modes is explained using a simple electric field interaction picture. This method is extended to diatomic molecule (iodine) and polyatomic molecules (Nile blue and methylene blue) to assign vibrational frequencies in ground/excited electronic state that are supported by density functional theory calculations. A comparison between frequency-domain and time-domain counterparts, i.e., stimulated Raman scattering and impulsive stimulated Raman scattering using degenerate pump-probe pairs is presented, and most importantly, it is shown how impulsive stimulated Raman scattering using chirped broadband probe retains unique advantages offered by both.

Planar hexaphyrin-like macrocycles turning into bis-BODIPYs with box-shaped structures exhibiting excitonic coupling.

Planar carbazole based hexaphyrin-like macrocycles with bis-coordinating cores and box-shaped cyclic BODIPYs were synthesized. Solution and solid-state structure analysis of the free macrocycles indicates an inversion of two pyrrole rings, resulting in a two-dipyrrin-like environment. The BF2 complexes show large Stokes shifts and exhibit excitonic coupling, fine-tuned by the meso-substituents.

Elucidating Contributions from Multiple Species during Photoconversion of Enhanced Green Fluorescent Protein (EGFP) under Ultraviolet Illumination.

Photocycle in wild-type green fluorescent protein (wt-GFP) involves generation of a bright fluorescent deprotonated chromophore from feebly fluorescent protonated form via excited-state proton transfer. In addition to this usual photocycle, wt-GFP is also known to exhibit irreversible photoconversion upon illumination with ultraviolet and visible radiation. However, a detailed understanding of photoconversion in enhanced GFP (EGFP: S65T/F64L mutant of wt-GFP), which predominantly exists in deprotonated form, is yet to be explored. Using 254 nm irradiation, we study how photoconversion proceeds in EGFP. The key findings are observation of spreading out of an isosbestic point and existence of an initial lag phase in spectral kinetics of absorbance, indicative of sequential photoconversion through an intermediate. Fluorescence kinetics of EGFP and its photoproduct are estimated by assigning two unique fluorescence lifetimes which is further complicated by the fact that their fluorescence are spectrally inseparable, as evident from global analysis of fluorescence lifetime. Time-resolved fluorescence anisotropy studies further suggest minimal structural changes in protein scaffold upon photoconversion. Based on these findings, an analytic model is developed to account for the overall decay in fluorescence (as photoconversion proceeds) that inherently incorporates the initial lag phase and a summary of energetics and processes involved is provided.

Controlling optical trapping of metal-dielectric hybrid nanoparticles under ultrafast pulsed excitation: a theoretical investigation.

Crucial to effective optical trapping is the ability to precisely control the nature of force/potential to be attractive or repulsive. The nature of particles being trapped is as important as the role of laser parameters in determining the stability of the optical trap. In this context, hybrid particles comprising of both dielectric and metallic materials offer a wide range of new possibilities due to their tunable optical properties. On the other hand, femtosecond pulsed excitation is shown to provide additional advantages in tuning of trap stiffness through harnessing optical and thermal nonlinearity. Here we demonstrate that (metal/dielectric hybrid) core/shell type and hollow-core type nanoparticles experience more force than conventional core-type nanoparticles under both continuous-wave and, in particular, ultrafast pulsed excitation. Thus, for the first time, we show how tuning both materials properties as well as the nature of excitation can impart unprecedented control over nanoscale optical trapping and manipulation leading to a wide range of applications.

Synthesis of (-)-Flavoskyrins by Catalyst-Free Oxidation of (R)-Configured Dihydroanthracenones in Aqueous Media and Its (Bio)synthetic Implications.

A catalyst-free method for the synthesis of dimeric (-)-flavoskyrins has been developed. It involves the autoxidation of chemoenzymatically synthesized (R)-configured dihydroanthracenones in the presence of molecular oxygen in buffer of pH 6.0 followed by spontaneous [4 + 2] cycloaddition in stereocontrolled exo-anti fashion to form (-)-flavoskyrins. The method is applied to obtain several homo- as well as heterodimerized flavoskyrins (nine examples) in 27-72% yield and implies the involvement of a similar pathway in the (bio)synthesis of modified bisanthraquinones and their analogues.

Ultrafast Excited-State Dynamics of Tricarbocyanine Dyes Probed by Two-Dimensional Electronic Spectroscopy: Polar Solvation vs Photoisomerization.

Photophysical properties of tricarbocyanine dyes in various solvents have been widely investigated using a variety of spectroscopic tools. However, the presence of several ground-state isomers and interconversion between these isomers on an ultrafast timescale upon photoexcitation render unambiguous assignment of spectral features quite difficult. In this work, ultrafast excited-state dynamics of two tricarbocyanine dyes in two solvents, DNTTCI and IR140, in ethanol and ethylene glycol, are studied by two-dimensional electronic spectroscopy (2DES). We present a detailed discussion on design and calibration of the 2DES apparatus and on the method for data processing by phase-cycling. For DNTTCI we report a method to obtain solvation correlation function, the nature of which is found to be strongly dependent on the excitation frequencies; a blue-shifted spectrum at early time is observed and explained based on preferential emission from a subset among various isomers having overlapping spectral features. For IR140 in ethanol, four isomers with distinct spectral features are identified, and most importantly, three of these isomers were found to interconvert upon photoexcitation which completes within 100 fs and is explained based on a kinetic model of consecutive chemical reaction. Density functional theory calculations show the presence of several ground-state isomers for both these dyes. Through this work we demonstrate how 2DES can help us to decipher distinct excited-state photophysics in two carbocyanine dyes, polar solvation and photoisomerization, by resolving spectral congestion without sacrificing time resolution.