Indefinite and bidirectional near-infrared nanocrystal photoswitching.

Materials whose luminescence can be switched by optical stimulation drive technologies ranging from superresolution imaging1-4, nanophotonics5, and optical data storage6,7, to targeted pharmacology, optogenetics, and chemical reactivity8. These photoswitchable probes, including organic fluorophores and proteins, can be prone to photodegradation and often operate in the ultraviolet or visible spectral regions. Colloidal inorganic nanoparticles6,9 can offer improved stability, but the ability to switch emission bidirectionally, particularly with near-infrared (NIR) light, has not, to our knowledge, been reported in such systems. Here, we present two-way, NIR photoswitching of avalanching nanoparticles (ANPs), showing full optical control of upconverted emission using phototriggers in the NIR-I and NIR-II spectral regions useful for subsurface imaging. Employing single-step photodarkening10-13 and photobrightening12,14-16, we demonstrate indefinite photoswitching of individual nanoparticles (more than 1,000 cycles over 7 h) in ambient or aqueous conditions without measurable photodegradation. Critical steps of the photoswitching mechanism are elucidated by modelling and by measuring the photon avalanche properties of single ANPs in both bright and dark states. Unlimited, reversible photoswitching of ANPs enables indefinitely rewritable two-dimensional and three-dimensional multilevel optical patterning of ANPs, as well as optical nanoscopy with sub-Å localization superresolution that allows us to distinguish individual ANPs within tightly packed clusters.

Giant nonlinear optical responses from photon-avalanching nanoparticles.

Avalanche phenomena use steeply nonlinear dynamics to generate disproportionately large responses from small perturbations, and are found in a multitude of events and materials1. Photon avalanching enables technologies such as optical phase-conjugate imaging2, infrared quantum counting3 and efficient upconverted lasing4-6. However, the photon-avalanching mechanism underlying these optical applications has been observed only in bulk materials and aggregates6,7, limiting its utility and impact. Here we report the realization of photon avalanching at room temperature in single nanostructures-small, Tm3+-doped upconverting nanocrystals-and demonstrate their use in super-resolution imaging in near-infrared spectral windows of maximal biological transparency. Avalanching nanoparticles (ANPs) can be pumped by continuous-wave lasers, and exhibit all of the defining features of photon avalanching, including clear excitation-power thresholds, exceptionally long rise time at threshold, and a dominant excited-state absorption that is more than 10,000 times larger than ground-state absorption. Beyond the avalanching threshold, ANP emission scales nonlinearly with the 26th power of the pump intensity, owing to induced positive optical feedback in each nanocrystal. This enables the experimental realization of photon-avalanche single-beam super-resolution imaging7 with sub-70-nanometre spatial resolution, achieved by using only simple scanning confocal microscopy and without any computational analysis. Pairing their steep nonlinearity with existing super-resolution techniques and computational methods8-10, ANPs enable imaging with higher resolution and at excitation intensities about 100 times lower than other probes. The low photon-avalanching threshold and excellent photostability of ANPs also suggest their utility in a diverse array of applications, including sub-wavelength imaging7,11,12 and optical and environmental sensing13-15.

Notch-dependent DNA cis-regulatory elements and their dose-dependent control of C. elegans stem cell self-renewal.

A long-standing biological question is how DNA cis-regulatory elements shape transcriptional patterns during metazoan development. Reporter constructs, cell culture assays and computational modeling have made major contributions to answering this question, but analysis of elements in their natural context is an important complement. Here, we mutate Notch-dependent LAG-1 binding sites (LBSs) in the endogenous Caenorhabditis elegans sygl-1 gene, which encodes a key stem cell regulator, and analyze the consequences on sygl-1 expression (nascent transcripts, mRNA, protein) and stem cell maintenance. Mutation of one LBS in a three-element cluster approximately halved both expression and stem cell pool size, whereas mutation of two LBSs essentially abolished them. Heterozygous LBS mutant clusters provided intermediate values. Our results lead to two major conclusions. First, both LBS number and configuration impact cluster activity: LBSs act additively in trans and synergistically in cis. Second, the SYGL-1 gradient promotes self-renewal above its functional threshold and triggers differentiation below the threshold. Our approach of coupling CRISPR/Cas9 LBS mutations with effects on both molecular and biological readouts establishes a powerful model for in vivo analyses of DNA cis-regulatory elements.

Short-Wave Infrared Upconverting Nanoparticles.

Optical technologies enable real-time, noninvasive analysis of complex systems but are limited to discrete regions of the optical spectrum. While wavelengths in the short-wave infrared (SWIR) window (typically, 1700-3000 nm) should enable deep subsurface penetration and reduced photodamage, there are few luminescent probes that can be excited in this region. Here, we report the discovery of lanthanide-based upconverting nanoparticles (UCNPs) that efficiently convert 1740 or 1950 nm excitation to wavelengths compatible with conventional silicon detectors. Screening of Ln3+ ion combinations by differential rate equation modeling identifies Ho3+/Tm3+ or Tm3+ dopants with strong visible or NIR-I emission following SWIR excitation. Experimental upconverted photoluminescence excitation (U-PLE) spectra find that 10% Tm3+-doped NaYF4 core/shell UCNPs have the strongest 800 nm emission from SWIR wavelengths, while UCNPs with an added 2% or 10% Ho3+ show the strongest red emission when excited at 1740 or 1950 nm. Mechanistic modeling shows that addition of a low percentage of Ho3+ to Tm3+-doped UCNPs shifts their emission from 800 to 652 nm by acting as a hub of efficient SWIR energy acceptance and redistribution up to visible emission manifolds. Parallel experimental and computational analysis shows rate equation models are able to predict compositions for specific wavelengths of both excitation and emission. These SWIR-responsive probes open a new IR bioimaging window, and are responsive at wavelengths important for vision technologies.

Ligand-Assisted Direct Lithography of Upconverting and Avalanching Nanoparticles for Nonlinear Photonics.

Upconverting nanoparticles (UCNPs) exhibit unique nonlinear optical properties that can be harnessed in microscopy, sensing, and photonics. However, forming high-resolution nano- and micropatterns of UCNPs with large packing fractions is still challenging. Additionally, there is limited understanding of how nanoparticle patterning chemistries are affected by the particle size. Here, we explore direct patterning chemistries for 6-18 nm Tm3+-, Yb3+/Tm3+-, and Yb3+/Er3+-based UCNPs using ligands that form either new ionic linkages or covalent bonds between UCNPs under ultraviolet (UV), electron-beam (e-beam), and near-infrared (NIR) exposure. We study the effect of UCNP size on these patterning approaches and find that 6 nm UCNPs can be patterned with compact ionic-based ligands. In contrast, patterning larger UCNPs requires long-chain, cross-linkable ligands that provide sufficient interparticle spacing to prevent irreversible aggregation upon film casting. Compared to approaches that use a cross-linkable liquid monomer, our patterning method limits the cross-linking reaction to the ligands bound on UCNPs deposited as a thin film. This highly localized photo-/electron-initiated chemistry enables the fabrication of densely packed UCNP patterns with high resolutions (∼1 µm with UV and NIR exposure; <100 nm with e-beam). Our upconversion NIR lithography approach demonstrates the potential to use inexpensive continuous-wave lasers for high-resolution 2D and 3D lithography of colloidal materials. The deposited UCNP patterns retain their upconverting, avalanching, and photoswitching behaviors, which can be exploited in patterned optical devices for next-generation UCNP applications.

Photodarkening, Photobrightening, and the Role of Color Centers in Emerging Applications of Lanthanide-Based Upconverting Nanomaterials.

Upconverting nanoparticles (UCNPs) compose a class of luminescent materials that utilize the unique wavelength-converting properties of lanthanide (Ln) ions for light-harvesting applications, photonics technologies, and biological imaging and sensing experiments. Recent advances in UCNP design have shed light on the properties of local color centers, both intrinsic and controllably induced, within these materials and their potential influence on UCNP photophysics. In this review, we describe fundamental studies of color centers in Ln-based materials, including research into their origins and their roles in observed photodarkening and photobrightening mechanisms. We place particular focus on the new functionalities that are enabled by harnessing the properties of color centers within Ln-doped nanocrystals, illustrated through applications in afterglow-based bioimaging, X-ray detection, all-inorganic nanocrystal photoswitching, and fully rewritable optical patterning and memory.

A Generalized Approach to Photon Avalanche Upconversion in Luminescent Nanocrystals.

Photon avalanching nanoparticles (ANPs) exhibit extremely nonlinear upconverted emission valuable for subdiffraction imaging, nanoscale sensing, and optical computing. Avalanching has been demonstrated with Tm3+-, Pr3+-, or Nd3+-doped nanocrystals, but their emission is limited to a few wavelengths and materials. Here, we utilize Gd3+-assisted energy migration to tune the emission wavelengths of Tm3+-sensitized ANPs and generate highly nonlinear emission from Eu3+, Tb3+, Ho3+, and Er3+ ions. The upconversion intensities of these spectrally discrete ANPs scale with nonlinearity factor s = 10-17 under 1064 nm excitation at power densities as low as 7 kW cm-2. This strategy for imprinting avalanche behavior on remote emitters can be extended to fluorophores adjacent to ANPs, as we demonstrate with CdS/CdSe/CdS core/shell/shell quantum dots. ANPs with rationally designed energy transfer networks provide the means to transform conventional linear emitters into a highly nonlinear ones, expanding the use of photon avalanching in biological, chemical, and photonic applications.

The examination of the visual-perceptual locus in hemispheric laterality of the word length effect using Korean visual word.

Greater word length effects have been reported when a word was presented in the left visual field (LVF) than when presented in the right visual field (RVF). The current study employed 2 experiments to examine the visual-perceptual loci of asymmetric word length effect while testing the physical and linguistic length effects and the effect of visual angle increase at the RVF. Experiment 1 showed significant effects on the number of strokes in both VHFs (visual half fields) with the added significance of the number of syllables in the LVF, suggesting both parafoveal fields were affected by the physical length factors in contrast with the linguistic length factors, inducing asymmetric word length effects in the symmetrically presented word recognition in parafoveal vision. Experiment 2 widened the visual angle of the RVF presentation to test the differential effects of the visual-perceptual difficulty across the VHFs. It showed successful interruption at the RVF word recognition and comparable word length effects between the LVF and RVF. Therefore, this study suggests that the asymmetric word length effects in the parafoveal word recognition are attributable to the greater visual-perceptual difficulty at the LVF than at the RVF.

Manipulation of hot electron flow on plasmonic nanodiodes fabricated by nanosphere lithography.

Energy conversion to generate hot electrons through the excitation of localized surface plasmon resonance (LSPR) in metallic nanostructures is an emerging strategy in photovoltaics and photocatalytic devices. Important factors for surface plasmon and hot electron generation are the size, shape, and materials of plasmonic metal nanostructures, which affect LSPR excitation, absorbance, and hot electron collection. Here, we fabricated the ordered structure of metal-semiconductor plasmonic nanodiodes using nanosphere lithography and reactive ion etching. Two types of hole-shaped plasmonic nanostructures with the hole diameter of 280 and 115 nm were fabricated on Au/TiO2Schottky diodes. We show that hot electron flow can be manipulated by changing the size of plasmonic nanostructures on the Schottky diode. We show that the short-circuit photocurrent changes and the incident photon-to-electron conversion efficiency results exhibit the peak shift depending on the structures. These phenomena are explicitly observed with finite difference time domain simulations. The capability of tuning the morphology of plasmonic nanostructure on the Schottky diode can give rise to new possibilities in controlling hot electron generation and developing novel hot-electron-based energy conversion devices.

Elongated Lifetime and Enhanced Flux of Hot Electrons on a Perovskite Plasmonic Nanodiode.

A fundamental understanding of hot electron transport is critical for developing efficient hot-carrier-based solar cells. There have been significant efforts to enhance hot electron flux, and it has been found that a key factor affecting the hot electron flux is the lifetime of the hot electrons. Here, we report a combined study of hot electron flux and the lifetime of hot carriers using a perovskite-modified plasmonic nanodiode. We found that perovskite deposition on a plasmonic nanodiode can considerably improve hot electron generation induced by photon absorption. The perovskite plasmonic nanodiode consists of MAPbI3 layers covering a plasmonic-Au/TiO2 Schottky junction that is composed of randomly connected Au nanoislands deposited on a TiO2 layer. The measured incident photon-to-electron conversion efficiency and the short-circuit photocurrent show a significantly improved solar-to-electrical conversion performance of this nanodiode. Such an improvement is ascribed to the improved hot electron flux in MAPbI3 caused by effective light absorption from near-field enhancement of plasmonic Au and the efficient capture of hot electrons from Au nanoislands via the formation of a three-dimensional Schottky interface. The relation between the lifetime and flux of hot electrons was confirmed by femtosecond transient absorption spectroscopy that showed considerably longer hot electron lifetimes in MAPbI3 combined with the plasmonic Au structure. These findings can provide a fundamental understanding of hot electron generation and transport in perovskite, which can provide helpful guidance to designing efficient hot carrier photovoltaics.

Automatic Disease Annotation From Radiology Reports Using Artificial Intelligence Implemented by a Recurrent Neural Network.

OBJECTIVE: Radiology reports are rich resources for biomedical researchers. Before utilization of radiology reports, experts must manually review these reports to identify the categories. In fact, automatically categorizing electronic medical record (EMR) text with key annotation is difficult because it has a free-text format. To address these problems, we developed an automated system for disease annotation. MATERIALS AND METHODS: Reports of musculoskeletal radiography examinations performed from January 1, 2016, through December 31, 2016, were exported from the database of Hanyang University Medical Center. After sentences not written in English and sentences containing typos were excluded, 3032 sentences were included. We built a system that uses a recurrent neural network (RNN) to automatically identify fracture and nonfracture cases as a preliminary study. We trained and tested the system using orthopedic surgeon-classified reports. We evaluated the system for the number of layers in the following two ways: the word error rate of the output sentences and performance as a binary classifier using standard evaluation metrics including accuracy, precision, recall, and F1 score. RESULTS: The word error rate using Levenshtein distance showed the best performance in the three-layer model at 1.03%. The three-layer model also showed the highest overall performance with the highest precision (0.967), recall (0.967), accuracy (0.982), and F1 score (0.967). CONCLUSION: Our results indicate that the RNN-based system has the ability to classify important findings in radiology reports with a high F1 score. We expect that our system can be used in cohort construction such as for retrospective studies because it is efficient for analyzing a large amount of data.

Biological Significance of Photoreceptor Photocycle Length: VIVID Photocycle Governs the Dynamic VIVID-White Collar Complex Pool Mediating Photo-adaptation and Response to Changes in Light Intensity.

Most organisms on earth sense light through the use of chromophore-bearing photoreceptive proteins with distinct and characteristic photocycle lengths, yet the biological significance of this adduct decay length is neither understood nor has been tested. In the filamentous fungus Neurospora crassa VIVID (VVD) is a critical player in the process of photoadaptation, the attenuation of light-induced responses and the ability to maintain photosensitivity in response to changing light intensities. Detailed in vitro analysis of the photochemistry of the blue light sensing, FAD binding, LOV domain of VVD has revealed residues around the site of photo-adduct formation that influence the stability of the adduct state (light state), that is, altering the photocycle length. We have examined the biological significance of VVD photocycle length to photoadaptation and report that a double substitution mutant (vvdI74VI85V), previously shown to have a very fast light to dark state reversion in vitro, shows significantly reduced interaction with the White Collar Complex (WCC) resulting in a substantial photoadaptation defect. This reduced interaction impacts photoreceptor transcription factor WHITE COLLAR-1 (WC-1) protein stability when N. crassa is exposed to light: The fast-reverting mutant VVD is unable to form a dynamic VVD-WCC pool of the size required for photoadaptation as assayed both by attenuation of gene expression and the ability to respond to increasing light intensity. Additionally, transcription of the clock gene frequency (frq) is sensitive to changing light intensity in a wild-type strain but not in the fast photo-reversion mutant indicating that the establishment of this dynamic VVD-WCC pool is essential in general photobiology and circadian biology. Thus, VVD photocycle length appears sculpted to establish a VVD-WCC reservoir of sufficient size to sustain photoadaptation while maintaining sensitivity to changing light intensity. The great diversity in photocycle kinetics among photoreceptors may be viewed as reflecting adaptive responses to specific and salient tasks required by organisms to respond to different photic environments.

Early Effect of Phonological Information in Korean Visual Word Recognition: An ERP Investigation with Transposed Letters.

The purpose of this study was to examine the role of phonological information on visual word recognition by using letter transposition effects. The Korean writing system gives a unique opportunity to investigate such phenomenon since the transposition of the beginning consonant (onset) and the end consonant (coda) of a certain syllable allows one to keep the coda phonology constant while changing the written alphabetic characters. In this study, 23 participants' ERPs to such transposition cases were compared with the ERPs to cases that do not maintain coda phonology while the participants were performing a go/no-go lexical decision task for visually presented letter strings. The results of the current study showed that transposed materials with original phonological information produce less N250 than both the baseline condition and the transposed materials with different phonological information condition. The results suggest that phonological information is used early in the lexical process in Korean and early orthographic processing is influenced by the characteristics of the grapheme to phoneme conversion process.

Risk factors for transmission of Middle East respiratory syndrome coronavirus infection during the 2015 outbreak in South Korea.

Background: Transmission heterogeneity was observed during the 2015 South Korean outbreak of Middle East respiratory syndrome coronavirus (MERS-CoV) infection. Only 22 of 186 cases transmitted the infection, and 5 super-spreading events caused 150 transmissions. We investigated the risk factors for MERS-CoV transmission. Methods: Epidemiological reports were used to classify patients as non-spreaders, spreaders (1-4 transmission), or those associated with super-spreading event (≥4 transmissions). Logistic regression analyses were used to evaluate the factors that influenced MERS-CoV transmission. Results: Compared to non-spreaders, spreaders exhibited a longer interval from symptom onset to isolation (7 days vs. 3 days) and more frequent pre-isolation pneumonia diagnoses (68.2% vs. 17.1%). Spreaders also exhibited higher values for pre-isolation contacts (149 vs. 17.5), pre-isolation hospitalization (68.2% vs. 16.5%), and emergency room visits (50% vs. 7.3%). Spreaders exhibited lower cycle thresholds for the upE and ORF1a genes (22.7 vs. 27.2 and 23.7 vs. 27.9, respectively). Transmission was independently associated with the cycle threshold (odds ratio [OR]: 0.84, 95% confidence interval [CI]: 0.75-0.96) and pre-isolation hospitalization or emergency room visits (OR: 6.82, 95% CI: 2.06-22.84). The spreaders with ≥4 transmissions exhibited higher values for pre-isolation contacts (777 vs. 78), pre-isolation emergency room visits (100% vs. 35.3%), and doctor-shopping (100% vs. 47.1%), compared to other spreaders. Conclusions: These findings indicate that transmission is determined by host infectivity and the number of contacts, whereas super-spreading events were determined by the number of contacts and hospital visits. These relationships highlight the importance of rapidly enforcing infection control measures to prevent outbreaks.

Quantitative spatial analysis of transcripts in multinucleate cells using single-molecule FISH.

mRNA positioning in the cell is important for diverse cellular functions and proper development of multicellular organisms. Single-molecule RNA FISH (smFISH) enables quantitative investigation of mRNA localization and abundance at the level of individual molecules in the context of cellular features. Details about spatial mRNA patterning at various times, in different genetic backgrounds, at different developmental stages, and under varied environmental conditions provide invaluable insights into the mechanisms and functions of spatial regulation. Here, we describe detailed methods for performing smFISH along with immunofluorescence for two large, multinucleate cell types: the fungus Ashbya gossypii and cultured mouse myotubes. We also put forward a semi-automated image processing tool that systematically detects mRNAs from smFISH data and statistically analyzes the spatial pattern of mRNAs using a customized MATLAB code. These protocols and image analysis tools can be adapted to a wide variety of transcripts and cell types for systematically and quantitatively analyzing mRNA distribution in three-dimensional space.

Graphene-Semiconductor Catalytic Nanodiodes for Quantitative Detection of Hot Electrons Induced by a Chemical Reaction.

Direct detection of hot electrons generated by exothermic surface reactions on nanocatalysts is an effective strategy to obtain insight into electronic excitation during chemical reactions. For this purpose, we fabricated a novel catalytic nanodiode based on a Schottky junction between a single layer of graphene and an n-type TiO2 layer that enables the detection of hot electron flows produced by hydrogen oxidation on Pt nanoparticles. By making a comparative analysis of data obtained from measuring the hot electron current (chemicurrent) and turnover frequency, we demonstrate that graphene's unique electronic structure and extraordinary material properties, including its atomically thin nature and ballistic electron transport, allow improved conductivity at the interface between the catalytic Pt nanoparticles and the support. Thereby, graphene-based nanodiodes offer an effective and facile way to approach the study of chemical energy conversion mechanisms in composite catalysts with carbon-based supports.

Hot Electrons at Solid-Liquid Interfaces: A Large Chemoelectric Effect during the Catalytic Decomposition of Hydrogen Peroxide.

The study of energy and charge transfer during chemical reactions on metals is of great importance for understanding the phenomena involved in heterogeneous catalysis. Despite extensive studies, very little is known about the nature of hot electrons generated at solid-liquid interfaces. Herein, we report remarkable results showing the detection of hot electrons as a chemicurrent generated at the solid-liquid interface during decomposition of hydrogen peroxide (H2 O2 ) catalyzed on Schottky nanodiodes. The chemicurrent reflects the activity of the catalytic reaction and the state of the catalyst in real time. We show that the chemicurrent yield can reach values up to 10(-1) electrons/O2 molecule, which is notably higher than that for solid-gas reactions on similar nanodiodes.

Amplification of hot electron flow by the surface plasmon effect on metal-insulator-metal nanodiodes.

Au-TiO2-Ti nanodiodes with a metal-insulator-metal structure were used to probe hot electron flows generated upon photon absorption. Hot electrons, generated when light is absorbed in the Au electrode of the nanodiode, can travel across the TiO2, leading to a photocurrent. Here, we demonstrate amplification of the hot electron flow by (1) localized surface plasmon resonance on plasmonic nanostructures fabricated by annealing the Au-TiO2-Ti nanodiodes, and (2) reducing the thickness of the TiO2. We show a correlation between changes in the morphology of the Au electrodes caused by annealing and amplification of the photocurrent. Based on the exponential dependence of the photocurrent on TiO2 thickness, the transport mechanism for the hot electrons across the nanodiodes is proposed.

Chemical-reaction-induced hot electron flows on platinum colloid nanoparticles under hydrogen oxidation: impact of nanoparticle size.

Generation of hot electron flows and the catalytic activity of Pt nanoparticles (NPs) with different sizes were investigated using catalytic nanodiodes. We show that smaller Pt NPs lead to higher chemicurrent yield, which is associated with the shorter travel length for the hot electrons, compared with their inelastic mean free path. We also show the impact of capping on charge carrier transfer between Pt NPs and their support.

Lateralized displays reveal the perceptual locus of the syllable transposition effect in Korean.

Studies of letter transposition effects in alphabetic scripts provide compelling evidence that letter position is encoded flexibly during reading, potentially during an early, perceptual stage of visual word recognition. Recent studies additionally suggest similar flexibility in the spatial encoding of syllabic information in the Korean Hangul script. With the present research, we conducted two experiments to investigate the locus of this syllabic transposition effect. In Experiment 1, lexical decisions for foveal stimulus presentations were less accurate and slower for four-syllable nonwords created by transposing two syllables in a base word as compared to control nonwords, replicating prior evidence for a transposed syllable effect in Korean word recognition. In Experiment 2, the same stimuli were presented to the right and left visual hemifields (i.e., RVF and LVF), which project both unilaterally and contralaterally to each participant's left and right cerebral hemisphere (i.e., LH and RH) respectively, using lateralized stimulus displays. Lexical decisions revealed a syllable transposition effect in the accuracy and latency of lexical decisions for both RVF and LVF presentations. However, response times for correct responses were longer in the LVF, and therefore the RH, as compared to the RVF/LH. As the LVF/RH appears to be selectively sensitive to the visual-perceptual attributes of words, the findings suggest that this syllable transposition effect partly finds its locus within a perceptual stage of processing. We discuss these findings in relation to current models of the spatial encoding of orthographic information during visual word recognition and accounts of visual word recognition in Korean.