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.

Dual Photoreactive Ternary Ruthenium(II) Terpyridyl Complexes: A Comparative Study on Visible-Light-Induced Single-Step Dissociation of Bidentate Ligands and Generation of Singlet Oxygen.

The versatile and tunable ligand-exchange dynamics in ruthenium(II)-polypyridyl complexes imposed by the modulation of the steric and electronic effects of the coordinated ligands provide an unlimited scope for developing phototherapeutic agents. The photorelease of a bidentate ligand from the Ru-center is better suited for potent Ru(II)-based photocytotoxic agents with two available labile sites for cross-linking with biological targets augmented with possible phototriggered 1O2 generation. Herein, we introduced a phenyl-terpyridine (ptpy) ligand in the octahedral Ru(II) core of [Ru(ptpy)(L-L)Cl]+ to induce structural distortion for the possible photorelease of electronically distinct bidentate ligands (L-L). For a systematic study, we designed four Ru(II) polypyridyl complexes: [Ru(ptpy)(L-L)Cl](PF6), ([1]-[4]), where L-L = 1,2-bis(phenylthio)ethane (SPH) [1], N,N,N',N'-tetramethylethylenediamine (TMEN) [2], N1,N2-diphenylethane-1,2-diimine (BPEDI) [3], and bis[2-(diphenylphosphino)phenyl]ether (DPE-Phos) [4]. The detailed photochemical studies suggest a single-step dissociation of L-L from the bis-thioether (SPH) complex [1] and diamine (TMEN) complex [2], while no photosubstitution was observed for [3] and [4]. Complex [1] and [2] demonstrated a dual role, involving both photosubstitution and 1O2 generation, while [3] and [4] solely exhibited poor to moderate 1O2 production. The interplay of excited states leading to these behaviors was rationalized from the lifetimes of the 3MLCT excited states by using transient absorption spectroscopy, suggesting intricate relaxation dynamics and 1O2 generation upon excitation. Therefore, the photolabile complexes [1] and [2] could potentially act as dual photoreactive agents via the phototriggered release of L-L (PACT) and/or 1O2-mediated PDT mechanisms, while [4] primarily can be utilized as a PDT agent.

On the nature of initial solvation in bulk polar liquids: Gaussian or exponential?

Measurement of time evolution of fluorescence of a probe solute has been a quintessential technique to quantify how dipolar solvent molecules dynamically minimize the free energy of an electronically excited probe. During such solvation dynamics in bulk liquids, a substantial part of relaxation was shown to complete within sub-100 fs from time-gated fluorescence measurements, as also predicted by molecular dynamics simulation studies. However, equivalent quantification of solvation timescales by femtosecond pump-probe and broadband fluorescence measurements revealed an exponential nature of this initial relaxation having quite different timescales. Here, we set out to unveil the reason behind these puzzling contradictions. We introduce a method for estimating probe wavelength-dependent instrument response and demonstrate that the observation of the Gaussian vs exponential nature of initial relaxation is indeed dependent on the method of data analysis. These findings call for further experimental investigation and parallel development of theoretical models to elucidate the molecular-level mechanism accounting for different types of early time solvation.

Beyond profit margins: Orchestrating social, economic, and environmental sustainability within the Norwegian Salmon Food Supply Chain.

Food Supply Chains (FSCs) have become increasingly complex with the average distance between producers and consumers rising considerably in the past two decades. Consequently, FSCs are a major source of carbon emissions and reducing transportation costs a major challenge for businesses. To address this, we present a mathematical model to promote the three core dimensions of sustainability (economic, environmental, and social), based on the Mixed-Integer Linear Programming (MILP) method. The model addresses the environmental dimension by intending to decrease the carbon emissions of different transport modes involved in the logistics network. Several supply chain network characteristics are incorporated and evaluated, with a consideration of social sustainability (job generation from operating various facilities). The mathematical model's robustness is demonstrated by testing and deploying it to a variety of problem instances. A real-life case study (Norwegian salmon supply chain) helps to comprehend the model's applicability. To understand the importance of optimizing food supply networks holistically, the paper investigates the impact of multiple supply chain permutations on total cost, demand fluctuations and carbon emissions. To address fluctuations in retail demand, we undertook sensitivity analysis for variations in demand, enabling the proposed model to revamp Norway's salmon supply chain network. Subsequently, the results are thoroughly examined to identify managerial implications.

One-Pot Multienzyme Cascades for Stereodivergent Synthesis of Tetrahydroquinolines.

The tetrahydroquinoline (THQ) framework is commonly found in natural products and pharmaceutically relevant molecules. Apart from the use of transition metal catalysts and chiral phosphoric acids, the chiral 2-substituted 1,2,3,4-THQs are synthesized using amine oxidase biocatalysts. However, the use of imine reductases (IREDs) in their asymmetric synthesis remained unexplored. In the current work, IREDs are employed in telescopic multienzyme cascades to catalyze the intramolecular reductive amination leading to chiral 2-alkyl and 2-aryl substituted-1,2,3,4-tetrahydroquinolines starting from inexpensive nitroalkenones. The cascades containing NtDBR (an ene reductase), NfsB (a nitro reductase) with either Na2S2O4 or V2O5, various IREDs, and glucose dehydrogenase (for NADPH regeneration) are used to synthesize a broad range of (R)/(S)-2-alkyl-substituted (THQs) (26 examples) with high yield (up to 93%) and excellent ee (up to 99%) in one-pot. The method further facilitates the one-pot biocatalytic synthesis of chiral 2-aryl substituted THQs (26 examples) from amino chalcones. Lastly, the asymmetric synthesis of several (R)- and (S)-THQ based intermediates of Hancock alkaloids showed the practical application of the newly developed biocatalytic cascades.

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.

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.

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.

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 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.

Unravelling the Role of Water in Ultrafast Excited-State Relaxation Dynamics within Nano-Architectures of Chlorophyll a.

Water plays a pivotal role in structural stability of supramolecular pigment assemblies designed for natural light harvesting (for example, chlorosome antenna complex) as well as their artificial analogs. However, the dynamic role of water in the context of excite-state relaxation has not been explored till date, which we report here. Using femtosecond transient absorption spectroscopy, we investigate the excited-state dynamics of two types of nano-scale assemblies of chlorophyll a with different structural motifs, rod-shaped and micellar assemblies, that depend on the water content. We show how water participates in excess energy dissipation by vibrational cooling of the non-thermally populated Qy band at different rates in different types of clusters but exhibits no polar solvation dynamics. For the micelles, we observe a bifurcation of stimulated emission line shape, whereas a positive-to-negative switching of differential absorption is observed for the rods; both these observations are correlated with their specific structural aspects. Density functional theory calculations reveal two possible stable ground state geometries of dimers, accounting for the bifurcation of line shape in micelles. Thus, our study elucidates water-mediated structure-function relationship within these pigment assemblies.

Early Time Solvation Dynamics Probed by Spectrally Resolved Degenerate Pump-Probe Spectroscopy.

The dynamic role of solvent in influencing the rates of physico-chemical processes (for example, polar solvation and electron transfer) has been extensively studied using time-resolved fluorescence spectroscopy. Here we study ultrafast excited state relaxation dynamics of three different fluorescent probes (DNTTCI, IR-140 and IR-144) in two polar solvents, ethanol and ethylene glycol, using spectrally resolved degenerate pump-probe spectroscopy. We discuss how time-resolved emission spectra can be directly used for constructing relaxation correlation function, obviating spectral reconstruction and estimation of time-zero spectrum in non-polar solvents. We show that depending on the specific probe used, the relaxation dynamics is governed either by intramolecular vibrational relaxation (for IR140) or by intermolecular solvation (for DNTTCI) or by both (for IR144). We further show (using DNTTCI as a probe) that major differences in solvation by ethanol and ethylene glycol is contributed by early time (<1 ps) dynamics.

Theoretical Estimation of Optimal Parameters for Maximum Fluorescence under Pulsed Excitation.

We present a detailed theoretical study on choosing optimum excitation parameters for maximizing the fluorescence yield. Using a model system, we show how the time-averaged emission (fluorescence) is modulated as the excitation conditions are changed from continuous wave excitation to pulsed excitation with various combinations of pulse widths and pulse repetition-rates for the same time-averaged excitation intensity. We conclude that depending on the excitation intensity, different pulse parameters are required for generating maximum fluorescence output. Our method can be implemented for other more sophisticated models without much difficulty.

Probing the excited state dynamics of Venus: origin of dual-emission in fluorescent proteins.

Fluorescent proteins exhibit interesting excited state photochemistry, leading to bright fluorescence emission that renders their versatile biological role and wide use as biomarkers. A molecular-level mechanism of the excited state dynamics is desirable to pinpoint the origin of the bright fluorescence of these proteins. Here we present studies on a yellow fluorescent protein variant, Venus, and investigate the photophysics behind the dual fluorescence emission upon UV excitation. Based on our studies, we propose that the unique nature of the potential energy surface is responsible for the observation of minor fluorescence in Venus which is not seen in wild type GFP.

Theoretical investigation on nonlinear optical effects in laser trapping of dielectric nanoparticles with ultrafast pulsed excitation.

The use of low-power high-repetition-rate ultrafast pulsed excitation in stable optical trapping of dielectric nanoparticles has been demonstrated in the recent past; the high peak power of each pulse leads to instantaneous trapping of a nanoparticle with fast inertial response and the high repetition-rate ensures repetitive trapping by successive pulses However, with such high peak power pulsed excitation under a tight focusing condition, nonlinear optical effects on trapping efficiency also become significant and cannot be ignored. Thus, in addition to the above mentioned repetitive instantaneous trapping, trapping efficiency under pulsed excitation is also influenced by the optical Kerr effect, which we theoretically investigate here. Using dipole approximation we show that with an increase in laser power the radial component of the trapping potential becomes progressively more stable but the axial component is dramatically modulated due to increased Kerr nonlinearity. We justify that the relevant parameter to quantify the trapping efficiency is not the absolute depth of the highly asymmetric axial trapping potential but the height of the potential barrier along the beam propagation direction. We also discuss the optimal excitation parameters leading to the most stable dipole trap. Our results show excellent agreement with previous experiments.

Exploring the physics of efficient optical trapping of dielectric nanoparticles with ultrafast pulsed excitation.

Stable optical trapping of dielectric nanoparticles with low power high-repetition-rate ultrafast pulsed excitation has received considerable attention in recent years. However, the exact role of such excitation has been quite illusive so far since, for dielectric micron-sized particles, the trapping efficiency turns out to be similar to that of continuous-wave excitation and independent of pulse chirping. In order to provide a coherent explanation of this apparently puzzling phenomenon, we justify the superior role of high-repetition-rate pulsed excitation in dielectric nanoparticle trapping which is otherwise not possible with continuous-wave excitation at a similar average power level. We quantitatively estimate the optimal combination of pulse peak power and pulse repetition rate leading to a stable trap and discuss the role of inertial response on the dependence of trapping efficiency on pulse width. In addition, we report gradual trapping of individual quantum dots detected by a stepwise rise in a two-photon fluorescence signal from the trapped quantum dots which conclusively proves individual particle trapping.

Two-dimensional fluorescence-detected coherent spectroscopy with absolute phasing by confocal imaging of a dynamic grating and 27-step phase-cycling.

We present a novel experimental scheme for two-dimensional fluorescence-detected coherent spectroscopy (2D-FDCS) using a non-collinear beam geometry with the aid of "confocal imaging" of dynamic (population) grating and 27-step phase-cycling to extract the signal. This arrangement obviates the need for distinct experimental designs for previously developed transmission detected non-collinear two-dimensional coherent spectroscopy (2D-CS) and collinear 2D-FDCS. We also describe a novel method for absolute phasing of the 2D spectrum. We apply this method to record 2D spectra of a fluorescent dye in solution at room temperature and observe "spectral diffusion."

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.