Sensitive Discrete Frequency Mid-Infrared Absorption Spectroscopy Using Digitally Referenced Detection.

Broadly tunable mid-infrared (IR) lasers, including quantum cascade lasers (QCL), are an asset for vibrational spectroscopy wherein high-intensity, coherent illumination can target specific spectral bands for rapid, direct chemical detection with microscopic localization. These emerging spectrometers are capable of high measurement throughputs with large detector signals from the high-intensity lasers and fast detection speeds as short as a single laser pulse, challenging the decades old benchmarks of Fourier transform infrared spectroscopy. However, noise in QCL emissions limits the feasible acquisition time for high signal-to-noise ratio (SNR) data. Here, we present an implementation that is broadly compatible with many laser-based spectrometer and microscope designs to address these limitations by leveraging high-speed digitizers and dual detectors to digitally reference each pulse individually. Digitally referenced detection (DRD) is shown to improve measurement sensitivity, with broad spectral indifference, regardless of imbalance due to dissimilarities among system designs or component manufacturers. We incorporated DRD into existing instruments and demonstrated its generalizability: a spectrometer with a 10-fold reduction in spectral noise, a microscope with reduced pixel dwell times to as low as 1 pulse while maintaining SNR normally achieved when operating 8-fold slower, and finally, a spectrometer to measure vibrational circular dichroism (VCD) with a ∼ 4-fold reduction in scan times. The approach not only proves versatile and effective but can also be tailored for specific applications with minimal hardware changes, positioning it as a simple and promising module for spectrometer designs using lasers.

Rapid and Label-Free Histopathology of Oral Lesions Using Deep Learning Applied to Optical and Infrared Spectroscopic Imaging Data.

Oral potentially malignant disorders (OPMDs) are precursors to over 80% of oral cancers. Hematoxylin and eosin (H&E) staining, followed by pathologist interpretation of tissue and cellular morphology, is the current gold standard for diagnosis. However, this method is qualitative, can result in errors during the multi-step diagnostic process, and results may have significant inter-observer variability. Chemical imaging (CI) offers a promising alternative, wherein label-free imaging is used to record both the morphology and the composition of tissue and artificial intelligence (AI) is used to objectively assign histologic information. Here, we employ quantum cascade laser (QCL)-based discrete frequency infrared (DFIR) chemical imaging to record data from oral tissues. In this proof-of-concept study, we focused on achieving tissue segmentation into three classes (connective tissue, dysplastic epithelium, and normal epithelium) using a convolutional neural network (CNN) applied to three bands of label-free DFIR data with paired darkfield visible imaging. Using pathologist-annotated H&E images as the ground truth, we demonstrate results that are 94.5% accurate with the ground truth using combined information from IR and darkfield microscopy in a deep learning framework. This chemical-imaging-based workflow for OPMD classification has the potential to enhance the efficiency and accuracy of clinical oral precancer diagnosis.

Gender- and age-related differences in foveal pit morphology.

AIMS: To measure the foveal pit morphology parameters and evaluate their correlations with age and sex. SETTINGS AND DESIGN: A retrospective cross-sectional matched comparison study in a tertiary center. METHODS AND MATERIALS: Forty men and 40 age-matched women who had normal macular structures and foveal contours were enrolled. Foveal pit parameters including top width, base width, nasal width, temporal width, minimal thickness, nasal thickness, temporal thickness, nasal height, temporal height, nasal slope, and temporal slope were measured on horizontal B-scan macular optical coherence tomography and compared between men and women. STATISTICAL ANALYSIS USED: Paired t-tests and Pearson's correlation analysis. RESULTS: The average patient age was 51.4 ± 17.5 (21-84) years. Women had a wider base width (313.1 ± 68.0 µm vs 266.8 ± 70.9 µm, P = 0.006), wider temporal width (1043.1 ± 245.6 µm vs 968.9 ± 261.0 µm, P = 0.006), thinner nasal thickness (345.6 ± 36.2 µm vs 359.7 ± 35.8 µm, P = 0.048), and flatter temporal slope (11.60 ± 2.52° vs 12.98 ± 2.68°, P = 0.016) than men. With age, the base width (r = 0.35, P = 0.025) and temporal width (r = 0.54, P = 0.0003) tended to be wider and the temporal slope was flatter (r = -0.45, P = 0.003) in women but not men. The minimal thickness tended to be thinner in the elderly group (r = 0.038, P = 0.015). CONCLUSIONS: Women had a significantly wider base width, wider temporal width, thinner nasal thickness, and flatter temporal slope of the foveal pit than age-matched men. The base width and temporal width were wider and the temporal slope was flatter with age in women but not men.

Infrared spectroscopic laser scanning confocal microscopy for whole-slide chemical imaging.

Chemical imaging, especially mid-infrared spectroscopic microscopy, enables label-free biomedical analyses while achieving expansive molecular sensitivity. However, its slow speed and poor image quality impede widespread adoption. We present a microscope that provides high-throughput recording, low noise, and high spatial resolution where the bottom-up design of its optical train facilitates dual-axis galvo laser scanning of a diffraction-limited focal point over large areas using custom, compound, infinity-corrected refractive objectives. We demonstrate whole-slide, speckle-free imaging in ~3 min per discrete wavelength at 10× magnification (2 µm/pixel) and high-resolution capability with its 20× counterpart (1 µm/pixel), both offering spatial quality at theoretical limits while maintaining high signal-to-noise ratios (>100:1). The data quality enables applications of modern machine learning and capabilities not previously feasible - 3D reconstructions using serial sections, comprehensive assessments of whole model organisms, and histological assessments of disease in time comparable to clinical workflows. Distinct from conventional approaches that focus on morphological investigations or immunostaining techniques, this development makes label-free imaging of minimally processed tissue practical.

Ossification of posterior atlantoaxial membrane causing spinal stenosis - A case report.

Background: Ossification of the posterior atlantoaxial membrane (PAAM) is a rare cause of spinal cord compression. Case presentation: A 46-year-old woman with rheumatoid arthritis (RA) and a 2-year history of slowly progressive gait disturbance underwent surgery for right knee stiffness and right lower limb mild weakness. A neurologic examination revealed brisk deep tendon reflexes (DTR) and spasticity in her four limbs. A computed tomography (CT) scan revealed spinal stenosis caused by ossification of the PAAM, a rare cause of spinal cord compression. The patient's lower limbs weakness and walking capability were ameliorated post-surgery. Conclusions: Although the exact mechanism of ossification of PAAM remains unclear, chronic mechanical stress as well as persistent atlantoaxial instability may promote the development of the ossification.

Methyltransferase Inhibition Enables Tgfß Driven Induction of CDKN2A and B in Cancer Cells.

CDKN2A/B deletion or silencing is common across human cancer, reinforcing the general importance of bypassing its tumor suppression in cancer formation or progression. In rhabdomyosarcoma (RMS) and neuroblastoma, two common childhood cancers, the three CDKN2A/B transcripts are independently expressed to varying degrees, but one, ARF, is uniformly silenced. Although TGFß induces certain CDKN2A/B transcripts in HeLa cells, it was unable to do so in five tested RMS lines unless the cells were pretreated with a broadly acting methyltransferase inhibitor, DZNep, or one targeting EZH2. CDKN2A/B induction by TGFß correlated with de novo appearance of three H3K27Ac peaks within a 20 kb cis element ∼150 kb proximal to CDKN2A/B. Deleting that segment prevented their induction by TGFß but not a basal increase driven by methyltransferase inhibition alone. Expression of two CDKN2A/B transcripts was enhanced by dCas9/CRISPR activation targeting either the relevant promoter or the 20 kb cis elements, and this "precise" manipulation diminished RMS cell propagation in vitro. Our findings show crosstalk between methyltransferase inhibition and TGFß-dependent activation of a remote enhancer to reverse CDKN2A/B silencing. Though focused on CDKN2A/B here, such crosstalk may apply to other TGFß-responsive genes and perhaps govern this signaling protein's complex effects promoting or blocking cancer.

Revealing the nanometric structural changes in myocardial infarction models by time-lapse intravital imaging.

In the development of bioinspired nanomaterials for therapeutic applications, it is very important to validate the design of nanomaterials in the disease models. Therefore, it is desirable to visualize the change of the cells in the diseased site at the nanoscale. Heart diseases often start with structural, morphological, and functional alterations of cardiomyocyte components at the subcellular level. Here, we developed straightforward technique for long-term real-time intravital imaging of contracting hearts without the need of cardiac pacing and complex post processing images to understand the subcellular structural and dynamic changes in the myocardial infarction model. A two-photon microscope synchronized with electrocardiogram signals was used for long-term in vivo imaging of a contracting heart with subcellular resolution. We found that the structural and dynamic behaviors of organelles in cardiomyocytes closely correlated with heart function. In the myocardial infarction model, sarcomere shortening decreased from ∼15% (healthy) to ∼8% (diseased) as a result of impaired cardiac function, whereas the distances between sarcomeres increased by 100 nm (from 2.11 to 2.21 µm) in the diastolic state. In addition, T-tubule system regularity analysis revealed that T-tubule structures that were initially highly organized underwent significant remodeling. Morphological remodeling and changes in dynamic activity at the subcellular level are essential to maintain heart function after infarction in a heart disease model.

Superior gait performance and balance ability in Latin dancers.

Background: Latin dance consists of various fast and stability-challenging movements that require constant body adjustments to maintain proper posture and balance. Although human gaits are assumed to be symmetrical, several factors can contribute to asymmetrical behavior of the lower extremities in healthy adults. These include lower limb dominance, ground reaction forces, lower limb muscle power, foot placement angle, and range of joint motion. Gait impairment can lead to a high risk of falling, diminished mobility, and even cognition impairment. We hypothesized that Latin dancers might have a more symmetric gait pattern and better balance ability than healthy non-dancer controls. Methods: We investigated the impact of Latin dance training on gait behaviors and body balance. We recruited twenty Latin dancers and 22 normal healthy subjects to conduct walking experiments and one-leg stance tests, and we measured their kinematic data by inertial measurement units. We then defined four performance indexes to assess gait performance and body stability to quantify the potential advantages of dance training. Results: We found that the two gait asymmetric indexes during the walking test and the two performance indexes during the one-leg stance tests were better in Latin dancers compared with the healthy control group. The results confirmed the superiority of Latin dancers over the healthy control group in gait symmetry and balance stability. Our results suggest that Latin dancing training could effectively strengthen lower limb muscles and core muscle groups, thereby improving coordination and enhancing gait performance and balance. Conclusion: Latin dance training can benefit gait performance and body balance. Further studies are needed to investigate the effect of Latin dance training on gait and balance outcomes in healthy subjects and patients with gait disorders.

Optogenetic manipulation of cell migration with high spatiotemporal resolution using lattice lightsheet microscopy.

Lattice lightsheet microscopy (LLSM) featuring three-dimensional recording is improved to manipulate cellular behavior with subcellular resolution through optogenetic activation (optoLLSM). A position-controllable Bessel beam as a stimulation source is integrated into the LLSM to achieve spatiotemporal photoactivation by changing the spatial light modulator (SLM) patterns. Unlike the point-scanning in a confocal microscope, the lattice beams are capable of wide-field optical sectioning for optogenetic activation along the Bessel beam path.We show that the energy power required for optogenetic activations is lower than 1 nW (or 24 mWcm-2) for time-lapses of CRY2olig clustering proteins, and membrane ruffling can be induced at different locations within a cell with subcellular resolution through light-triggered recruitment of phosphoinositide 3-kinase. Moreover, with the epidermal growth factor receptor (EGFR) fused with CRY2olig, we are able to demonstrate guided cell migration using optogenetic stimulation for up to 6 h, where 463 imaging volumes are collected, without noticeable cellular damages.

ASC-J9 Blocks Cell Proliferation and Extracellular Matrix Production of Keloid Fibroblasts through Inhibiting STAT3 Signaling.

Keloids are a fibrotic skin disorder caused by abnormal wound healing and featuring the activation and expansion of fibroblasts beyond the original wound margin. Signal transducer and activator of transcription 3 (STAT3) has been found to mediate the biological functions of keloid fibroblasts (KFs). Therefore, we aimed to demonstrate whether ASC-J9, an inhibitor of STAT3 phosphorylation, can suppress the activation of KFs. Western blotting results showed that ASC-J9 inhibited the levels of COL1A1 and FN1 proteins, which were upregulated in KFs, by decreasing the expression of pSTAT3 and STAT3. RNA sequencing and in vitro studies further demonstrated that ASC-J9 treatment of KFs reduced cell division, inflammation, and ROS generation, as well as extracellular matrix (ECM) synthesis. ELISA assays verified that ASC-J9 treatment significantly mitigated IL-6 protein secretion in KFs. Transmission electron microscopy images revealed that ASC-J9 induced the formation of multilamellar bodies in KFs, which is associated with autophagy-related signaling. These results suggested that inhibiting a vicious cycle of the ROS/STAT3/IL-6 axis by ASC-J9 may represent a potential therapeutic approach to suppress cell proliferation and ECM production in KFs.

Quantifying molecular- to cellular-level forces in living cells.

Mechanical cues have been suggested to play an important role in cell functions and cell fate determination, however, such physical quantities are challenging to directly measure in living cells with single molecule sensitivity and resolution. In this review, we focus on two main technologies that are promising in probing forces at the single molecule level. We review their theoretical fundamentals, recent technical advancements, and future directions, tailored specifically for interrogating mechanosensitive molecules in live cells.

Effects of orthopedic insoles on postural balance in patients with chronic stroke: A randomized crossover study.

BACKGROUND: Orthopedic insoles (OIs) with medial arch support and heel cushion are widely used to manage lower extremity injuries, but their effects on postural balance in patients with chronic stroke have not been adequately explored. METHODS: Design: Double-blinded, sham-controlled, randomized crossover trial. PARTICIPANTS: A total of 32 ambulatory patients (20 men and 12 women, aged between 30 and 76 years) with more than 6 months since stroke onset. INTERVENTIONS: All participants received one assessment session wearing OIs and one session wearing sham insole (SI) in a random order with a 1-day interval. OUTCOMES: Our primary outcome was the Berg Balance Scale score. Secondary outcomes included the Functional Reach Test, Timed Up and Go test, and computerized posturography. All were performed in both sessions. Subgroup analyses regarding demographic and functional variables were conducted to identify potential responders. RESULTS: Significant between-insole differences favoring OIs were seen in all clinical tests (P < 0.05), but were seen only in the static medial-lateral sway in computerized posturography assessment (P = 0.04). An approximate 2-point difference in the BBS score favoring OIs was observed in all subgroups, not reaching the minimal clinically important difference. CONCLUSION: The use of OIs generated small but significant positive effects on improving postural balance among patients with chronic stroke. Additional biomechanical and clinical studies are required to evaluate their potential for routine clinical use. TRIAL REGISTRATION: NCT03194282.

Microfluidic channel integrated with a lattice lightsheet microscopic system for continuous cell imaging.

In this study, a continuous cell-imaging system with subcellular resolution was developed by integrating a microfluidic platform with lattice lightsheet microscopy (LLSM). To reduce aberrations of the lightsheet propagating into the device, a microfluidic channel sealed with a water refractive index-matched thin film was fabricated. When the lightsheet emerged from the water-immersed objectives and penetrated through the water refractive-matched thin film into the microfluidic channel at an incident angle, less light scattering and fewer aberrations were found. Suspended cells flowed across the lattice lightsheet, and an imaging system with the image plane perpendicular to the lightsheet was used to sequentially acquire cell images. By applying a thinner lattice lightsheet, higher-resolution, higher-contrast images were obtained. Furthermore, three-dimensional cell images could be achieved by reconstructing sequential two-dimensional cell images.

Calcium Silicate-Activated Gelatin Methacrylate Hydrogel for Accelerating Human Dermal Fibroblast Proliferation and Differentiation.

Wound healing is a complex process that requires specific interactions between multiple cells such as fibroblasts, mesenchymal, endothelial, and neural stem cells. Recent studies have shown that calcium silicate (CS)-based biomaterials can enhance the secretion of growth factors from fibroblasts, which further increased wound healing and skin regeneration. In addition, gelatin methacrylate (GelMa) is a compatible biomaterial that is commonly used in tissue engineering. However, it has low mechanical properties, thus restricting its fullest potential for clinical applications. In this study, we infused Si ions into GelMa hydrogel and assessed for its feasibility for skin regeneration applications by observing for its influences on human dermal fibroblasts (hDF). Initial studies showed that Si could be successfully incorporated into GelMa, and printability was not affected. The degradability of Si-GelMa was approximately 20% slower than GelMa hydrogels, thus allowing for better wound healing and regeneration. Furthermore, Si-GelMa enhanced cellular adhesion and proliferation, therefore leading to the increased secretion of collagen I other important extracellular matrix (ECM) remodeling-related proteins including Ki67, MMP9, and decorin. This study showed that the Si-GelMa hydrogels were able to enhance the activity of hDF due to the gradual release of Si ions, thus making it a potential candidate for future skin regeneration clinical applications.

Graphite Felt Modified by Atomic Layer Deposition with TiO2 Nanocoating Exhibits Super-Hydrophilicity, Low Charge-Transform Resistance, and High Electrochemical Activity.

Graphite felt (GF) is a multi-functional material and is widely used as electrodes of electrochemical devices for energy and environmental applications. However, due to the inherent hydrophobicity of graphite felt, it must be hydrophilically pretreated to obtain good electrochemical activity. Metal oxides coating is one of the feasible methods to modify the surface of GF, and in order to ensure that the metal oxides have a better conductivity for obtaining higher electrochemical activity, a subsequent H2 heat-treatment process is usually adopted. In this study, atomic layer deposition (ALD) is used to deposit TiO2 nanocoating on graphite felt (GF) for surface modification without any H2 thermal post-treatment. The results show that the ALD-TiO2-modified GF (ALD-TiO2/GF) owns excellent hydrophilicity. Moreover, the ALD-TiO2/GF exhibits excellent electrochemical properties of low equivalent series resistance (Rs), low charge-transfer resistance (Rct), and high electrochemical activity. It demonstrates that ALD is an applicable technique for modifying the GF surface. In addition, it can be reasonably imagined that not only TiO2 film can effectively modify the GF surface, but also other metal oxides grown by ALD with nanoscale-thickness can also obtain the same benefits. We anticipate this work to be a starting point for modifying GF surface by using ALD with metal oxides nanocoating.

ATACgraph: Profiling Genome-Wide Chromatin Accessibility From ATAC-seq.

Assay for transposase-accessible chromatin using sequencing data (ATAC-seq) is an efficient and precise method for revealing chromatin accessibility across the genome. Most of the current ATAC-seq tools follow chromatin immunoprecipitation sequencing (ChIP-seq) strategies that do not consider ATAC-seq-specific properties. To incorporate specific ATAC-seq quality control and the underlying biology of chromatin accessibility, we developed a bioinformatics software named ATACgraph for analyzing and visualizing ATAC-seq data. ATACgraph profiles accessible chromatin regions and provides ATAC-seq-specific information including definitions of nucleosome-free regions (NFRs) and nucleosome-occupied regions. ATACgraph also allows identification of differentially accessible regions between two ATAC-seq datasets. ATACgraph incorporates the docker image with the Galaxy platform to provide an intuitive user experience via the graphical interface. Without tedious installation processes on a local machine or cloud, users can analyze data through activated websites using pre-designed workflows or customized pipelines composed of ATACgraph modules. Overall, ATACgraph is an effective tool designed for ATAC-seq for biologists with minimal bioinformatics knowledge to analyze chromatin accessibility. ATACgraph can be run on any ATAC-seq data with no limit to specific genomes. As validation, we demonstrated ATACgraph on human genome to showcase its functions for ATAC-seq interpretation. This software is publicly accessible and can be downloaded at https://github.com/RitataLU/ATACgraph.

Rapid high resolution 3D imaging of expanded biological specimens with lattice light sheet microscopy.

Expansion microscopy was invented to surpass the optical diffraction limit by physically expanding biological specimens with swellable polymers. Due to the large sizes of expanded specimens, 3D imaging techniques that are capable to acquire large volumetric data rapidly at high spatial resolution are therefore required for expansion microscopy. Lattice light sheet microscopy (LLSM) was developed to image biological specimens rapidly at high 3D spatial resolution by using a thin lattice light sheet for sample illumination. However, due to the current limitations of LLSM mechanism and the optical design of LLS microscopes, it is challenging to image large expanded specimens at isotropic high spatial resolution using LLSM. To address the problem, we first optimized the sample preparation and expansion procedure for LLSM. Then, we implement a tiling lattice light sheet method to minimize sample translation during imaging and achieve much faster 3D imaging speed at high spatial resolution with more isotropic performance. Taken together, we report a general and improved 3D super-resolution imaging method for expanded samples.

Liquid Biopsy Detects Relapse Five Months Earlier than Regular Clinical Follow-Up and Guides Targeted Treatment in Breast Cancer.

Genetic alterations in circulating tumor DNA (ctDNA) are an emerging biomarker for the early detection of relapse and have the potential to guide targeted treatment. ctDNA analysis is often performed by droplet digital PCR; however, next-generation sequencing (NGS) allows multigene testing without having to access a tumor sample to identify target alterations. Here, we report the case of a stage III hormone receptor-positive breast cancer patient who remained symptomless after receiving surgery and adjuvant chemotherapy. Liquid biopsy analysis by NGS revealed the presence of a ctDNA PIK3CA N345K mutation five months before the detection of relapse with multiple liver metastases by regular clinical follow-up. To date, clinical implications of the PIK3CA N345K variant remain insufficiently investigated; however, everolimus treatment resulted in the shrinkage of tumor lesions and decreased the levels of tumor markers. Four months after treatment initiation, a second ctDNA analysis suggested a relapse, and the patient clinically progressed after five months of everolimus therapy. This case report demonstrates the value of ctDNA analysis by NGS for the early detection of relapse in breast cancer patients. The study further indicates its usefulness for the choice of targeted treatments, suggesting that the variant PIK3CA N345K might be associated with everolimus sensitivity.

Testis-specific Arf promoter expression in a transposase-aided BAC transgenic mouse model.

CDKN2A is an evolutionarily conserved gene encoding proteins implicated in tumor suppression, ocular development, aging, and metabolic diseases. Like the human form, mouse Cdkn2a encodes two distinct proteins-p16Ink4a, which blocks cyclin-dependent kinase activity, and p19Arf, which is best known as a positive regulator of the p53 tumor suppressor-and their functions have been well-studied in genetically engineered mouse models. Relatively little is known about how expression of the two transcripts is controlled in normal development and in certain disease states. To better understand their coordinate and transcript-specific expression in situ, we used a transposase-aided approach to generate a new BAC transgenic mouse model in which the first exons encoding Arf and Ink4a are replaced by fluorescent reporters. We show that mouse embryo fibroblasts generated from the transgenic lines faithfully display induction of each transgenic reporter in cell culture models, and we demonstrate the expected expression of the Arf reporter in the normal testis, one of the few places where that promoter is normally expressed. Interestingly, the TGFß-2-dependent induction of the Arf reporter in the eye-a process essential for normal eye development-does not occur. Our findings illustrate the value of BAC transgenesis in mapping key regulatory elements in the mouse by revealing the genomic DNA required for Cdkn2a induction in cultured cells and the developing testis, and the apparent lack of elements driving expression in the developing eye.

Rapid single-wavelength lightsheet localization microscopy for clarified tissue.

Optical super-resolution microscopy allows nanoscale imaging of protein molecules in intact biological tissues. However, it is still challenging to perform large volume super-resolution imaging for entire animal organs. Here we develop a single-wavelength Bessel lightsheet method, optimized for refractive-index matching with clarified specimens to overcome the aberrations encountered in imaging thick tissues. Using spontaneous blinking fluorophores to label proteins of interest, we resolve the morphology of most, if not all, dopaminergic neurons in the whole adult brain (3.64 × 107 µm3) of Drosophila melanogaster at the nanometer scale with high imaging speed (436 µm3 per second) for localization. Quantitative single-molecule localization reveals the subcellular distribution of a monoamine transporter protein in the axons of a single, identified serotonergic Dorsal Paired Medial (DPM) neuron. Large datasets are obtained from imaging one brain per day to provide a robust statistical analysis of these imaging data.