Fundamentals of DNA methylation in development.

DNA methyation is critical to regulation of gene expression especially during developmentally dynamic changes. A large proportion occurs at CpG (a cytosine followed by a guanine nucleotide) sites and impacts gene expression based on location, timing and level of DNA methylation. The spectrum of effects produced by DNA methylation ranges from inhibition to enhancement of gene expression.

A Simple and Fast Optical Clearing Method for Whole-Mount Fluorescence In Situ Hybridization (FISH) Imaging.

We report a single-step optical clearing method that is compatible with RNA fluorescence in situ hybridization (FISH) imaging. We previously demonstrated microscopy imaging with immunohistochemistry and genetic reporters using a technique called lipid-preserving refractive index matching for prolonged imaging depth (LIMPID). Our protocol reliably produces high-resolution three-dimensional (3D) images with minimal aberrations using high magnification objectives, captures large field-of-view images of whole-mount tissues, and supports co-labeling with antibody and FISH probes.

Stratospheric air intrusions promote global-scale new particle formation.

New particle formation in the free troposphere is a major source of cloud condensation nuclei globally. The prevailing view is that in the free troposphere, new particles are formed predominantly in convective cloud outflows. We present another mechanism using global observations.

Considering intentional stratospheric dehydration for climate benefits.

We introduce a climate intervention strategy focused on decreasing water vapor (WV) concentrations near the tropopause and in the stratosphere to increase outbound longwave radiation. The mechanism is the targeted injection of ice-nucleating particles (INP) in air supersaturated with respect to ice at high altitudes in the tropical entryway to the stratosphere. Ice formation in this region is a critical control of stratospheric WV.

Image harmonization and deep learning automated classification of plus disease in retinopathy of prematurity.

Purpose: Retinopathy of prematurity (ROP) is a retinal vascular disease affecting premature infants that can culminate in blindness within days if not monitored and treated. A disease stage for scrutiny and administration of treatment within ROP is "plus disease" characterized by increased tortuosity and dilation of posterior retinal blood vessels. The monitoring of ROP occurs via routine imaging, typically using expensive instruments ($50 to $140 K) that are unavailable in low-resource settings at the point of care.

Segmentation of beating embryonic heart structures from 4-D OCT images using deep learning.

Optical coherence tomography (OCT) has been used to investigate heart development because of its capability to image both structure and function of beating embryonic hearts. Cardiac structure segmentation is a prerequisite for the quantification of embryonic heart motion and function using OCT. Since manual segmentation is time-consuming and labor-intensive, an automatic method is needed to facilitate high-throughput studies.

Experiences of medical device innovators as they navigate the regulatory system in Uganda.

Objective: A medical device must undergo rigorous regulatory processes to verify its safety and effectiveness while in use. In low-and middle-income countries like Uganda however, medical device innovators and designers face challenges around bringing a device from ideation to being market-ready. This is mainly attributed to a lack of clear regulatory procedures among other factors.

Phase-Decorrelation Optical Coherence Tomography Measurement of Cold-Induced Nuclear Cataract.

Purpose: The purpose of this work is to determine the sensitivity of phase-decorrelation optical coherence tomography (OCT) to protein aggregation associated with cataracts in the ocular lens, as compared to OCT signal intensity.

Methods: Six fresh porcine globes were held at 4°C until cold cataracts developed. As the globes were re-warmed to ambient temperature, reversing the cold cataract, each lens was imaged repeatedly using a conventional OCT system.

Automated analysis framework for cardiac ablation therapy monitoring with optical coherence tomography.

Radiofrequency ablation (RFA) is a minimally invasive procedure that is commonly used for the treatment of atrial fibrillation. However, it is associated with a significant risk of arrhythmia recurrence and complications owing to the lack of direct visualization of cardiac substrates and real-time feedback on ablation lesion transmurality. Within this manuscript, we present an automated deep learning framework for intracardiac optical coherence tomography (OCT) analysis of swine left atria.

Influence of Wildfire on Urban Ozone: An Observationally Constrained Box Modeling Study at a Site in the Colorado Front Range.

Increasing trends in biomass burning emissions significantly impact air quality in North America. Enhanced mixing ratios of ozone (O) in urban areas during smoke-impacted periods occur through transport of O produced within the smoke or through mixing of pyrogenic volatile organic compounds (PVOCs) with urban nitrogen oxides (NO = NO + NO) to enhance local O production. Here, we analyze a set of detailed chemical measurements, including carbon monoxide (CO), NO, and speciated volatile organic compounds (VOCs), to evaluate the effects of smoke transported from relatively local and long-range fires on O measured at a site in Boulder, Colorado, during summer 2020.

Polarization-sensitive optical coherence tomography monitoring of percutaneous radiofrequency ablation in left atrium of living swine.

Radiofrequency ablation (RFA) is commonly used to treat atrial fibrillation (AF). However, the outcome is often compromised due to the lack of direct real-time feedback to assess lesion transmurality. In this work, we evaluated the ability of polarization-sensitive optical coherence tomography (PSOCT) to measure cardiac wall thickness and assess RF lesion transmurality during left atrium (LA) RFA procedures.

Ozone chemistry in western U.S. wildfire plumes.

Wildfires are a substantial but poorly quantified source of tropospheric ozone (O). Here, to investigate the highly variable O chemistry in wildfire plumes, we exploit the in situ chemical characterization of western wildfires during the FIREX-AQ flight campaign and show that O production can be predicted as a function of experimentally constrained OH exposure, volatile organic compound (VOC) reactivity, and the fate of peroxy radicals. The O chemistry exhibits rapid transition in chemical regimes.

CompassLSM: axially swept light-sheet microscopy made simple.

Axially swept light-sheet microscopy (ASLM) is an effective method of generating a uniform light sheet across a large field of view (FOV). However, current ASLM designs are more complicated than conventional light-sheet systems, limiting their adaptation in less experienced labs. By eliminating difficult-to-align components and reducing the total number of components, we show that high-performance ASLM can be accomplished much simpler than existing designs, requiring less expertise and effort to construct, align, and operate.

Biomechanics of Ophthalmic Crosslinking.

Crosslinking involves the formation of bonds between polymer chains, such as proteins. In biological tissues, these bonds tend to stiffen the tissue, making it more resistant to mechanical degradation and deformation. In ophthalmology, the crosslinking phenomenon is being increasingly harnessed and explored as a treatment strategy for treating corneal ectasias, keratitis, degenerative myopia, and glaucoma.

Prenatal ethanol exposure impairs the conduction delay at the atrioventricular junction in the looping heart.

The etiology of ethanol-related congenital heart defects has been the focus of much study, but most research has concentrated on cellular and molecular mechanisms. We have shown with optical coherence tomography (OCT) that ethanol exposure led to increased retrograde flow and smaller atrioventricular (AV) cushions compared with controls. Since AV cushions play a role in patterning the conduction delay at the atrioventricular junction (AVJ), this study aims to investigate whether ethanol exposure alters the AVJ conduction in early looping hearts and whether this alteration is related to the decreased cushion size.

Pocket MUSE: an affordable, versatile and high-performance fluorescence microscope using a smartphone.

Smartphone microscopes can be useful tools for a broad range of imaging applications. This manuscript demonstrates the first practical implementation of Microscopy with Ultraviolet Surface Excitation (MUSE) in a compact smartphone microscope called Pocket MUSE, resulting in a remarkably effective design. Fabricated with parts from consumer electronics that are readily available at low cost, the small optical module attaches directly over the rear lens in a smartphone.

Glutathione Protects the Developing Heart from Defects and Global DNA Hypomethylation Induced by Prenatal Alcohol Exposure.

Background: Fetal alcohol spectrum disorder (FASD) is caused by prenatal alcohol exposure (PAE), the intake of ethanol (C H OH) during pregnancy. Features of FASD cover a range of structural and functional defects including congenital heart defects (CHDs). Folic acid and choline, contributors of methyl groups to one-carbon metabolism (OCM), prevent CHDs in humans.

Genetically Encoded Calcium Indicators for In Situ Functional Studies of Corneal Nerves.

Purpose: Millions of people suffer from diseases that involve corneal nerve dysfunction, caused by various conditions, including dry eye syndrome, neurotrophic keratopathy, diabetes, herpes simplex, glaucoma, and Alzheimer's disease. The morphology of corneal nerves has been studied extensively. However, corneal nerve function has only been studied in a limited fashion owing to a lack of tools.

Semi-automated shear stress measurements in developing embryonic hearts.

Blood-induced shear stress influences gene expression. Abnormal shear stress patterns on the endocardium of the early-stage heart tube can lead to congenital heart defects. To have a better understanding of these mechanisms, it is essential to include shear stress measurements in longitudinal cohort studies of cardiac development.

Imaging of Atrioventricular Nodal Conduction Tissue in Porcine Hearts Using Optical Coherence Tomography.

Optical coherence tomography (OCT) employs near-infrared light to image the microstructure of different tissues. Clinically, it has been used to image the walls of coronary arteries. In research settings, one of the applications for OCT is visualizing endocardial and subendocardial structures.