Nanoparticulate Photoluminescent Probes for Bioimaging: Small Molecules and Polymers.

Recent interest in research on photoluminescent molecules due to their unique properties has played an important role in advancing the bioimaging field. In particular, small molecules and organic dots as probes have great potential for the achievement of bioimaging because of their desirable properties. In this review, we provide an introduction of probes consisting of fluorescent small molecules and polymers that emit light across the ultraviolet and near-infrared wavelength ranges, along with a brief summary of the most recent techniques for bioimaging. Since photoluminescence probes emitting light in different ranges have different goals and targets, their respective strategies also differ. Diverse and novel strategies using photoluminescence probes against targets have gradually been introduced in the related literature. Among recent papers (published within the last 5 years) on the topic, we here concentrate on the photophysical properties and strategies for the design of molecular probes, with key examples of in vivo photoluminescence research for practical applications. More in-depth studies on these probes will provide key insights into how to control the molecular structure and size/shape of organic probes for expanded bioimaging research and applications.

Surfactant-in-Polymer Templating for Fabrication of Carbon Nanofibers with Controlled Interior Substructures: Designing Versatile Materials for Energy Applications.

A simple, scalable, surfactant-in-polymer templating approach is demonstrated to create controlled long-range secondary substructures in a primary structure. A metal bis(2-ethylhexyl) sulfosuccinate (MAOT) as the surfactant is shown to be capable of serving as a sacrificial template and metal precursor in carbon nanofibers. The low interfacial tension and controllable dimensions of the MAOT are maintained in the solid-phase polymer, even during electrospinning and heat-treatment processes, allowing for the long-range uniform formation of substructures in the nanofibers. The MAOT content is found to be a critical parameter for tailoring the diameter of the nanofibers and their textural properties, such as size and volume of interior pores. The metal counterion species in the MAOT determine the introduction of metallic phases in the nanofiber interior. The incorporation of MAOT with Na as the counterion into the polymer phase leads to the formation of a built-in pore structure in the nanofibers. In contrast, MAOT with Fe as a counterion generates unique iron-in-pore substructures in the nanofibers (FeCNFs). The FeCNFs exhibit outstanding charge storage and water splitting performances. As a result, the MAOT-in-polymer templating approach can be extended to combinations of various metal precursors and thus create desirable functionalities for different target applications.

Synthesis and biological evaluation of kresoxim-methyl analogues as novel inhibitors of hypoxia-inducible factor (HIF)-1 accumulation in cancer cells.

We designed and synthesized strobilurin analogues as hypoxia-inducible factor (HIF) inhibitors based on the molecular structure of kresoxim-methyl. Biological evaluation in human colorectal cancer HCT116 cells showed that most of the synthesized kresoxim-methyl analogues possessed moderate to potent inhibitory activity against hypoxia-induced HIF-1 transcriptional activation. Three candidates, compounds 11b, 11c, and 11d were identified as potent inhibitors against HIF-1 activation with IC50 values of 0.60-0.94µM. Under hypoxic condition, compounds 11b, 11c, and 11d increased the intracellular oxygen contents, thereby attenuating the hypoxia-induced accumulation of HIF-1α protein.

Immune signatures and disorder-specific patterns in a cross-disorder gene expression analysis.

BACKGROUND: Recent studies point to overlap between neuropsychiatric disorders in symptomatology and genetic aetiology. AIMS: To systematically investigate genomics overlap between childhood and adult attention-deficit hyperactivity disorder (ADHD), autism spectrum disorder (ASD) and major depressive disorder (MDD). METHOD: Analysis of whole-genome blood gene expression and genetic risk scores of 318 individuals. Participants included individuals affected with adult ADHD (n = 93), childhood ADHD (n = 17), MDD (n = 63), ASD (n = 51), childhood dual diagnosis of ADHD-ASD (n = 16) and healthy controls (n = 78). RESULTS: Weighted gene co-expression analysis results reveal disorder-specific signatures for childhood ADHD and MDD, and also highlight two immune-related gene co-expression modules correlating inversely with MDD and adult ADHD disease status. We find no significant relationship between polygenic risk scores and gene expression signatures. CONCLUSIONS: Our results reveal disorder overlap and specificity at the genetic and gene expression level. They suggest new pathways contributing to distinct pathophysiology in psychiatric disorders and shed light on potential shared genomic risk factors.

Effective encoder-decoder neural network for segmentation of orbital tissue in computed tomography images of Graves' orbitopathy patients.

PURPOSE: To propose a neural network (NN) that can effectively segment orbital tissue in computed tomography (CT) images of Graves' orbitopathy (GO) patients. METHODS: We analyzed orbital CT scans from 701 GO patients diagnosed between 2010 and 2019 and devised an effective NN specializing in semantic orbital tissue segmentation in GO patients' CT images. After four conventional (Attention U-Net, DeepLab V3+, SegNet, and HarDNet-MSEG) and the proposed NN train the various manual orbital tissue segmentations, we calculated the Dice coefficient and Intersection over Union for comparison. RESULTS: CT images of the eyeball, four rectus muscles, the optic nerve, and the lacrimal gland tissues from all 701 patients were analyzed in this study. In the axial image with the largest eyeball area, the proposed NN achieved the best performance, with Dice coefficients of 98.2% for the eyeball, 94.1% for the optic nerve, 93.0% for the medial rectus muscle, and 91.1% for the lateral rectus muscle. The proposed NN also gave the best performance for the coronal image. Our qualitative analysis demonstrated that the proposed NN outputs provided more sophisticated orbital tissue segmentations for GO patients than the conventional NNs. CONCLUSION: We concluded that our proposed NN exhibited an improved CT image segmentation for GO patients over conventional NNs designed for semantic segmentation tasks.

Neural network application for assessing thyroid-associated orbitopathy activity using orbital computed tomography.

This study aimed to propose a neural network (NN)-based method to evaluate thyroid-associated orbitopathy (TAO) patient activity using orbital computed tomography (CT). Orbital CT scans were obtained from 144 active and 288 inactive TAO patients. These CT scans were preprocessed by selecting eleven slices from axial, coronal, and sagittal planes and segmenting the region of interest. We devised an NN employing information extracted from 13 pipelines to assess these slices and clinical patient age and sex data for TAO activity evaluation. The proposed NN's performance in evaluating active and inactive TAO patients achieved a 0.871 area under the receiver operating curve (AUROC), 0.786 sensitivity, and 0.779 specificity values. In contrast, the comparison models CSPDenseNet and ConvNeXt were significantly inferior to the proposed model, with 0.819 (p = 0.029) and 0.774 (p = 0.04) AUROC values, respectively. Ablation studies based on the Sequential Forward Selection algorithm identified vital information for optimal performance and evidenced that NNs performed best with three to five active pipelines. This study establishes a promising TAO activity diagnosing tool with further validation.

Recent Developments and Implementations of Conductive Polymer-Based Flexible Devices in Sensing Applications.

Flexible sensing devices have attracted significant attention for various applications, such as medical devices, environmental monitoring, and healthcare. Numerous materials have been used to fabricate flexible sensing devices and improve their sensing performance in terms of their electrical and mechanical properties. Among the studied materials, conductive polymers are promising candidates for next-generation flexible, stretchable, and wearable electronic devices because of their outstanding characteristics, such as flexibility, light weight, and non-toxicity. Understanding the interesting properties of conductive polymers and the solution-based deposition processes and patterning technologies used for conductive polymer device fabrication is necessary to develop appropriate and highly effective flexible sensors. The present review provides scientific evidence for promising strategies for fabricating conductive polymer-based flexible sensors. Specifically, the outstanding nature of the structures, conductivity, and synthesis methods of some of the main conductive polymers are discussed. Furthermore, conventional and innovative technologies for preparing conductive polymer thin films in flexible sensors are identified and evaluated, as are the potential applications of these sensors in environmental and human health monitoring.

The COPILOT Raw Illumina Genotyping QC Protocol.

The Illumina genotyping microarrays generate data in image format, which is processed by the platform-specific software GenomeStudio, followed by an array of complex bioinformatics analyses that rely on various software, different programming languages, and numerous dependencies to be installed and configured correctly. The entire process can be time-consuming, can lead to reproducibility errors, and can be a daunting task for bioinformaticians. To address this, we introduce the COPILOT protocol, which has been successfully used to transform raw Illumina genotype intensity data into high-quality analysis-ready data on tens of thousands of human patient samples that have been genotyped on a variety of Illumina genotyping arrays. This includes processing both mainstream and custom content genotyping chips with over 4 million markers per sample. The COPILOT QC protocol consists of two distinct tandem procedures to process raw Illumina genotyping data. The first protocol is an up-to-date process to systematically QC raw Illumina microarray genotyping data using the Illumina-specific GenomeStudio software. The second protocol takes the output from the first protocol and further processes the data through the COPILOT (Containerised wOrkflow for Processing ILlumina genOtyping daTa) containerized QC pipeline, to automate an array of complex bioinformatics analyses to improve data quality through a secondary clustering algorithm and to automatically identify typical Genome-Wide Association Study (GWAS) data issues, including gender discrepancies, heterozygosity outliers, related individuals, and population outliers, through ancestry estimation. The data is returned to the user in analysis-ready PLINK binary format and is accompanied by a comprehensive and interactive HTML summary report file which quickly helps the user understand the data and guides the user for further data analyses. The COPILOT protocol and containerized pipeline are also available at https://khp-informatics.github.io/COPILOT/index.html. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Processing raw Illumina genotyping data using GenomeStudio Basic Protocol 2: COPILOT: A containerised workflow for processing Illumina genotyping data.

10-mer and 9-mer WALK Peptides with Both Antibacterial and Anti-Inflammatory Activities.

Natural antimicrobial peptides (AMPs) are multifunctional host defense peptides (HDPs) that are valuable for various therapeutic applications. In particular, natural and artificial AMPs with dual antibacterial immunomodulatory functions emerged as promising candidates for the development of therapeutic agents to treat infectious inflammation. In an effort to develop useful AMP variants with short lengths and simple amino acid composition, we devised a de novo design strategy to generate a series of model peptide isomer sequences, named WALK peptides, i.e., tryptophan (W)-containing amphipathic-helical (A) leucine (L)/lysine (K) peptides. Here, we generated two groups of WALK peptide isomers: W2L4K4 (WALK244.01~WALK244.10) and W2L4K3 (WALK243.01~WALK243.09). Most showed apparent antibacterial activities against both Gram-positive and Gram-negative bacteria at a concentration of approximately 4 µg/mL along with varied hemolytic activities against human red blood cells. In addition, some exhibited significant anti-inflammatory activities without any significant cytotoxicity in macrophages. Collectively, these results suggest that the two selected peptides, WALK244.04 and WALK243.04, showed promise for the development of antibacterial and anti-inflammatory agents.

Increasing the storage density of a page-based holographic data storage system by image upscaling using the PSF of the Nyquist aperture.

We introduce an image upscaling method that reduces bit errors caused by Nyquist apertures. Nyquist apertures used for higher storage densities generate optical aberrations and degrade the quality of the image that is recorded on the medium. Here, to correct the bit errors caused by the Nyquist aperture, an image upscaling method is used to restore the degraded image in the enhanced spatial frequency domain using its point spread function (PSF) as a restoration filter. The proposed method reduces the bit error rate (BER) significantly and hence allows higher storage densities.

Fire-Safe Polymer Composites: Flame-Retardant Effect of Nanofillers.

Currently, polymers are competing with metals and ceramics to realize various material characteristics, including mechanical and electrical properties. However, most polymers consist of organic matter, making them vulnerable to flames and high-temperature conditions. In addition, the combustion of polymers consisting of different types of organic matter results in various gaseous hazards. Therefore, to minimize the fire damage, there has been a significant demand for developing polymers that are fire resistant or flame retardant. From this viewpoint, it is crucial to design and synthesize thermally stable polymers that are less likely to decompose into combustible gaseous species under high-temperature conditions. Flame retardants can also be introduced to further reinforce the fire performance of polymers. In this review, the combustion process of organic matter, types of flame retardants, and common flammability testing methods are reviewed. Furthermore, the latest research trends in the use of versatile nanofillers to enhance the fire performance of polymeric materials are discussed with an emphasis on their underlying action, advantages, and disadvantages.

Morphology-Dependent Ambient-Condition Growth of Perovskite Nanocrystals for Enhanced Stability in Photoconversion Device.

CsPbBr3 perovskite nanocrystals with two different dimensionalities were synthesized at different temperatures and then integrated as optoelectronic transducers into transistor-type photoconversion devices. Postsynthesis transformation was observed for two-dimensional (2D) nanoplatelets, while the transformation was rarely found in 3D nanocubes. At ambient temperature and pressure, neighboring nanoplatelets made facet-to-facet contact and then fused into larger 2D nanoplatelets (2-5 times) without defects. The coalescence of 2D nanoplatelets at the ambient condition lowered the density of defects at the surface of the nanocrystals and thus could facilitate effective and stable photoconversion behavior in the nanocrystal film integrated into the device. Consequently, the ambient-condition aging of 2D nanoplatelets on device substrate led to 3 times higher retention in photoconversion performance. Importantly, these results provide a new concept of how perovskite nanocrystals can be integrated into a device for enhanced stability in device performance.

Upscaling image resolution of compact imaging systems using wavefront coding and a property of the point-spread function.

We propose an image-resolution upscaling method for compact imaging systems. The image resolution is calculated using the resolving power of the optics and the pixel size of a digital image sensor. The resolution limit of the compact imaging system comes from its size and the number of allowed lenses. To upscale the image resolution but maintain the small size, we apply wavefront coding and image restoration. Conventional image restoration could not enhance the image resolution of the sensor. Here, we use the upscaled image of a wavefront-coded optical system and apply an image-restoration algorithm using a more precisely calculated point-spread function (PSF) as the deconvolution filter. An example of a wavefront-coded optical system with a 5-megapixel image sensor is given. The final image had a resolution equivalent to that of a 10-megapixel image using only four plastic lenses. Moreover, image degradation caused by hand motion could also be reduced using the proposed method.

Moisture Effect on Particulate Matter Filtration Performance using Electro-Spun Nanofibers including Density Functional Theory Analysis.

In this study, we use density functional theory (DFT) calculations to investigate the effect of moisture on the performance of three types of nanofiber (NF)-based air-filter media prepared by electrospinning polyvinyl alcohol, polyvinylidene fluoride, and polyacrylonitrile (PAN). Based on the DFT calculations of the intermolecular interactions between the NF-based filter media and water molecules, the PAN-NF filter is expected to exhibit the best performance in the wet state. Experiment studies also successfully demonstrate that the PAN-NF filter medium has better performance in the filtration of particulate matter (PM) than a commercial semi-high efficiency particulate air filter under wet conditions, and these results are in good agreement with the DFT calculation. The PAN-NF filter shows better performance because of its hydrophilic nature and the relatively low thickness the filter medium that allowed fast recovery of its PM-filtration performance.

A genome-wide association meta-analysis of prognostic outcomes following cognitive behavioural therapy in individuals with anxiety and depressive disorders.

Major depressive disorder and the anxiety disorders are highly prevalent, disabling and moderately heritable. Depression and anxiety are also highly comorbid and have a strong genetic correlation (rg ≈ 1). Cognitive behavioural therapy is a leading evidence-based treatment but has variable outcomes. Currently, there are no strong predictors of outcome. Therapygenetics research aims to identify genetic predictors of prognosis following therapy. We performed genome-wide association meta-analyses of symptoms following cognitive behavioural therapy in adults with anxiety disorders (n = 972), adults with major depressive disorder (n = 832) and children with anxiety disorders (n = 920; meta-analysis n = 2724). We estimated the variance in therapy outcomes that could be explained by common genetic variants (h2SNP) and polygenic scoring was used to examine genetic associations between therapy outcomes and psychopathology, personality and learning. No single nucleotide polymorphisms were strongly associated with treatment outcomes. No significant estimate of h2SNP could be obtained, suggesting the heritability of therapy outcome is smaller than our analysis was powered to detect. Polygenic scoring failed to detect genetic overlap between therapy outcome and psychopathology, personality or learning. This study is the largest therapygenetics study to date. Results are consistent with previous, similarly powered genome-wide association studies of complex traits.

Breaking diffraction limit of a small f-number compact camera using wavefront coding.

We propose a resolution enhancement method for mobile small f-number compact imaging systems based on wavefront coding and superresolution image processing. Wavefront coding increases the focus depth of an optical system and produces point spread functions (PSFs) with similar characteristics at different field and defocus positions. The designed target wavefront is realized as a combination of wavefront errors of each rotationally symmetric lens, without including an additional phase plate. Finally, using one deconvolution filter containing all the characteristics of the PSFs, we achieve high resolution, breaking the diffraction limit of small f-number and the resolution limit of the image sensor by super-resolution image processing.

Adaptive-optics SLO imaging combined with widefield OCT and SLO enables precise 3D localization of fluorescent cells in the mouse retina.

Adaptive optics scanning laser ophthalmoscopy (AO-SLO) has recently been used to achieve exquisite subcellular resolution imaging of the mouse retina. Wavefront sensing-based AO typically restricts the field of view to a few degrees of visual angle. As a consequence the relationship between AO-SLO data and larger scale retinal structures and cellular patterns can be difficult to assess. The retinal vasculature affords a large-scale 3D map on which cells and structures can be located during in vivo imaging. Phase-variance OCT (pv-OCT) can efficiently image the vasculature with near-infrared light in a label-free manner, allowing 3D vascular reconstruction with high precision. We combined widefield pv-OCT and SLO imaging with AO-SLO reflection and fluorescence imaging to localize two types of fluorescent cells within the retinal layers: GFP-expressing microglia, the resident macrophages of the retina, and GFP-expressing cone photoreceptor cells. We describe in detail a reflective afocal AO-SLO retinal imaging system designed for high resolution retinal imaging in mice. The optical performance of this instrument is compared to other state-of-the-art AO-based mouse retinal imaging systems. The spatial and temporal resolution of the new AO instrumentation was characterized with angiography of retinal capillaries, including blood-flow velocity analysis. Depth-resolved AO-SLO fluorescent images of microglia and cone photoreceptors are visualized in parallel with 469 nm and 663 nm reflectance images of the microvasculature and other structures. Additional applications of the new instrumentation are discussed.

The cellular origins of the outer retinal bands in optical coherence tomography images.

PURPOSE: To test the recently proposed hypothesis that the second outer retinal band, observed in clinical OCT images, originates from the inner segment ellipsoid, by measuring: (1) the thickness of this band within single cone photoreceptors, and (2) its respective distance from the putative external limiting membrane (band 1) and cone outer segment tips (band 3). METHODS: Adaptive optics-optical coherence tomography images were acquired from four subjects without known retinal disease. Images were obtained at foveal (2°) and perifoveal (5°) locations. Cone photoreceptors (n = 9593) were identified and segmented in three dimensions using custom software. Features corresponding to bands 1, 2, and 3 were automatically identified. The thickness of band 2 was assessed in each cell by fitting the longitudinal reflectance profile of the band with a Gaussian function. Distances between bands 1 and 2, and between 2 and 3, respectively, were also measured in each cell. Two independent calibration techniques were employed to determine the depth scale (physical length per pixel) of the imaging system. RESULTS: When resolved within single cells, the thickness of band 2 is a factor of three to four times narrower than in corresponding clinical OCT images. The distribution of band 2 thickness across subjects and eccentricities had a modal value of 4.7 µm, with 48% of the cones falling between 4.1 and 5.2 µm. No significant differences were found between cells in the fovea and perifovea. The distance separating bands 1 and 2 was found to be larger than the distance between bands 2 and 3, across subjects and eccentricities, with a significantly larger difference at 5° than 2°. CONCLUSIONS: On the basis of these findings, we suggest that ascription of the outer retinal band 2 to the inner segment ellipsoid is unjustified, because the ellipsoid is both too thick and proximally located to produce the band.

Improved visualization of outer retinal morphology with aberration cancelling reflective optical design for adaptive optics - optical coherence tomography.

We present an aberration cancelling optical design for a reflective adaptive optics - optical coherence tomography (AO-OCT) retinal imaging system. The optical performance of this instrument is compared to our previous multimodal AO-OCT/AO-SLO retinal imaging system. The feasibility of new instrumentation for improved visualization of microscopic retinal structures is discussed. Examples of images acquired with this new AO-OCT instrument are presented.