Utilizing quantitative phase microscopy to localize fluorescence in three dimensions via the transport of intensity equation.

We demonstrate the use of a novel, to the best of our knowledge, localization algorithm for digitally refocusing fluorescence images from a three-dimensional cell culture. Simultaneous phase and fluorescence intensity images are collected through a multimodal system that combines digital holography via quantitative phase microscopy (QPM) and fluorescence microscopy. Defocused fluorescence images are localized to a specific z-plane within the three-dimensional (3D) matrix using the transport of intensity equation (TIE) and depth-resolved information derived from the QPM measurements. This technique is applied to cells stained with different fluorescent tags suspended in 3D collagen hydrogel cultures. Experimental findings demonstrate the localization of defocused images, facilitating the analysis and comparison of cells within the hydrogel matrix. This method holds promise for comprehensive cellular imaging of fluorescence labeling in three-dimensional environments, enabling detailed investigations into cellular behavior and interactions.

Range-wide salamander densities reveal a key component of terrestrial vertebrate biomass in eastern North American forests.

Characterizing the population density of species is a central interest in ecology. Eastern North America is the global hotspot for biodiversity of plethodontid salamanders, an inconspicuous component of terrestrial vertebrate communities, and among the most widespread is the eastern red-backed salamander, Plethodon cinereus. Previous work suggests population densities are high with significant geographic variation, but comparisons among locations are challenged by lack of standardization of methods and failure to accommodate imperfect detection. We present results from a large-scale research network that accounts for detection uncertainty using systematic survey protocols and robust statistical models. We analysed mark-recapture data from 18 study areas across much of the species range. Estimated salamander densities ranged from 1950 to 34 300 salamanders ha-1, with a median of 9965 salamanders ha-1. We compared these results to previous estimates for P. cinereus and other abundant terrestrial vertebrates. We demonstrate that overall the biomass of P. cinereus, a secondary consumer, is of similar or greater magnitude to widespread primary consumers such as white-tailed deer (Odocoileus virginianus) and Peromyscus mice, and two to three orders of magnitude greater than common secondary consumer species. Our results add empirical evidence that P. cinereus, and amphibians in general, are an outsized component of terrestrial vertebrate communities in temperate ecosystems.

Hyperreflective Dots in Central Fovea Visualized by a Novel Application of Visible-Light Optical Coherence Tomography.

Visible-light optical coherence tomography (vis-OCT) is a novel noninvasive retinal imaging system that offers improved resolution compared to conventional near-infrared (NIR) OCT systems. Here, we utilized vis-OCT to produce fibergrams (vis-OCTF) for the first time in human patients, enabling en face visualization and precise quantification of hyperreflective dots in the central fovea in two patients. We also directly compare the imaging qualities of conventional vis-OCT and NIR-OCT. Vis-OCT generated a 3 × 3 mm2 en face image with an impressive axial resolution of 1.3 µm, whereas NIR-OCT produced an en face image with a larger field of view (FOV) (9 × 9 mm2) but a lower resolution of 7.0 µm. Moreover, vis-OCTF unveiled clear images of hyperreflective dots in the fovea of both patients, which were not discernible in the NIR-OCT en face images. Foveal dots have often been linked to several age-related and pathological conditions. The high-resolution images generated by vis-OCTF enable more precise characterization of changes in retinal sublayers within the central fovea.

Deep learning classification of ex vivo human colon tissues using spectroscopic optical coherence tomography.

Screening for colorectal cancer (CRC) with colonoscopy has improved patient outcomes; however, it remains the third leading cause of cancer-related mortality, novel strategies to improve screening are needed. Here, we propose an optical biopsy technique based on spectroscopic optical coherence tomography (OCT). Depth resolved OCT images are analyzed as a function of wavelength to measure optical tissue properties and used as input to machine learning algorithms. Previously, we used this approach to analyze mouse colon polyps. Here, we extend the approach to examine human biopsied colonic epithelial tissue samples ex vivo. Optical properties are used as input to a novel deep learning architecture, producing accuracy of up to 97.9% in discriminating tissue type. SOCT parameters are used to create false colored en face OCT images and deep learning classifications are used to enable visual classification by tissue type. This study advances SOCT toward clinical utility for analysis of colonic epithelium.

Recovery of angular scattering profiles through a flexible multimode fiber.

Endoscopic angle-resolved light scattering methods have been developed for early cancer detection but they typically require multi-element coherent fiber optic bundles to recover scattering distributions from tissues. Recent work has focused on using a single multimode fiber (MMF) to measure angle resolved scattering but this approach has practical limitations to overcome before clinical translation. Here we address these limitations by proposing an MMF-based endoscope capable of measuring angular scattering patterns suitable for determining structure. Significantly, this approach implements a spectrally resolved detection scheme to reduce speckle and leverages the azimuthal symmetry of the angular scattering patterns to enable measurements that are robust to fiber bending. This results in a unique method that does not require matrix inversion or machine learning to measure a transmitted scattering distribution. The MMF utilized here is 1000 mm in length with a 200 µm core and is demonstrated to recover angular scattering distributions even with bending displacements of up to 30 cm. This advance has a significant impact on the clinical translation of biomedical endoscopic diagnostic techniques that use angular scattering to determine the size of cell nuclei to detect early cancer.

Nimodipine-associated standard dose reductions and neurologic outcomes after aneurysmal subarachnoid hemorrhage: the era of pharmacogenomics.

Nimodipine, an L-type cerebroselective calcium channel antagonist, is the only drug approved by the US Food and Drug Administration for the neuroprotection of patients with aneurysmal subarachnoid hemorrhage (aSAH). Four randomized, placebo-controlled trials of nimodipine demonstrated clinical improvement over placebo; however, these occurred before precision medicine with pharmacogenomics was readily available. The standard enteral dose of nimodipine recommended after aSAH is 60 mg every 4 h. However, up to 78% of patients with aSAH develop systemic arterial hypotension after taking the drug at the recommended dose, which could theoretically limit its neuroprotective role and worsen cerebral perfusion pressure and cerebral blood flow, particularly when concomitant vasospasm is present. We investigated the association between nimodipine dose changes and clinical outcomes in a consecutive series of 150 patients (mean age, 56 years; 70.7% women) with acute aSAH. We describe the pharmacogenomic relationship of nimodipine dose reduction with clinical outcomes. These results have major implications for future individualized dosing of nimodipine in the era of precision medicine.

Updated range map of an endangered salamander and congeneric competitor reveals different niche preferences.

Estimating distributions for cryptic and highly range-restricted species induces unique challenges for species distribution modeling. In particular, bioclimatic covariates that are typically used to model species ranges at regional and continental scales may not show strong variation at scales of 100s and 10s of meters. This limits both the likelihood and usefulness of correlated occurrence to data typically used in distribution models. Here, we present analyses of species distributions, at 100 × 100 m resolution, for a highly range restricted salamander species (Shenandoah salamander, Plethodon shenandoah) and a closely related congener (red-backed salamander, Plethodon cinereus). We combined data across multiple survey types, account for seasonal variation in availability of our target species, and control for repeated surveys at locations- all typical challenges in range-scale monitoring datasets. We fit distribution models using generalized additive models that account for spatial covariates as well as unexplained spatial variation and spatial uncertainty. Our model accommodates different survey protocols using offsets and incorporates temporal variation in detection and availability resulting from survey-specific variation in temperature and precipitation. Our spatial random effect was crucial in identifying small-scale differences in the occurrence of each species and provides cell-specific estimates of uncertainty in the density of salamanders across the range. Counts of both species were seen to increase in the 3 days following a precipitation event. However, P. cinereus were observed even in extremely wet conditions, while surface activity of P. shenandoah was associated with a more narrow range. Our results demonstrate how a flexible analytical approach improves estimates of both distribution and uncertainty, and identify key abiotic relationships, even at small spatial scales and when scales of empirical data are mismatched. While our approach is especially valuable for species with small ranges, controlling for spatial autocorrelation, estimating spatial uncertainty, and incorporating survey-specific information in estimates can improve the reliability of distribution models in general.

Longitudinal imaging of vitreal hyperreflective foci in mice with acute optic nerve damage using visible-light optical coherence tomography.

Hyperreflective foci (HRFs) appear in optical coherence tomography (OCT) images of the retina and vitreous of patients with various ocular diseases. HRFs are hypothesized to be immune cells that appear in response to ischemia or tissue damage. To accurately identify HRFs and establish their clinical significance, it is necessary to replicate the detection of similar patterns in vivo in a small animal model. We combined visible-light OCT with temporal speckle averaging (TSA) to visualize and track vitreal HRFs (VHRFs) densities for three days after an optic nerve crush (ONC) injury. Resulting vis-OCT images revealed that VHRF density significantly increased approximately 10-fold at 12 h after ONC and returned to baseline three days after ONC. Additional immunohistochemistry results confirmed these VHRFs as inflammatory cells induced from optic nerve damage.

Comparative In Vivo Imaging of Retinal Structures in Tree Shrews, Humans, and Mice.

Rodent models, such as mice and rats, are commonly used to examine retinal ganglion cell damage in eye diseases. However, as nocturnal animals, rodent retinal structures differ from primates, imposing significant limitations in studying retinal pathology. Tree shrews (Tupaia belangeri) are small, diurnal paraprimates that exhibit superior visual acuity and color vision compared with mice. Like humans, tree shrews have a dense retinal nerve fiber layer (RNFL) and a thick ganglion cell layer (GCL), making them a valuable model for investigating optic neuropathies. In this study, we applied high-resolution visible-light optical coherence tomography to characterize the tree shrew retinal structure in vivo and compare it with that of humans and mice. We quantitatively characterize the tree shrew's retinal layer structure in vivo, specifically examining the sublayer structures within the inner plexiform layer (IPL) for the first time. Next, we conducted a comparative analysis of retinal layer structures among tree shrews, mice, and humans. We then validated our in vivo findings in the tree shrew inner retina using ex vivo confocal microscopy. The in vivo and ex vivo analyses of the shrew retina build the foundation for future work to accurately track and quantify the retinal structural changes in the IPL, GCL, and RNFL during the development and progression of human optic diseases.

Visible-Light Optical Coherence Tomography Fibergraphy of the Tree Shrew Retinal Ganglion Cell Axon Bundles.

We seek to develop techniques for high-resolution imaging of the tree shrew retina for visualizing and parameterizing retinal ganglion cell (RGC) axon bundles in vivo. We applied visible-light optical coherence tomography fibergraphy (vis-OCTF) and temporal speckle averaging (TSA) to visualize individual RGC axon bundles in the tree shrew retina. For the first time, we quantified individual RGC bundle width, height, and cross-sectional area and applied vis-OCT angiography (vis-OCTA) to visualize the retinal microvasculature in tree shrews. Throughout the retina, as the distance from the optic nerve head (ONH) increased from 0.5 mm to 2.5 mm, bundle width increased by 30%, height decreased by 67%, and cross-sectional area decreased by 36%. We also showed that axon bundles become vertically elongated as they converge toward the ONH. Ex vivo confocal microscopy of retinal flat-mounts immunostained with Tuj1 confirmed our in vivo vis-OCTF findings.

Long-Term Safety and Efficacy of Pipeline Embolization Device in Anterior and Posterior Circulation Aneurysms: A Systematic Review and Meta-Analysis.

BACKGROUND: Flow diversion using the pipeline embolization device (PED) has been a paradigm shift for anterior circulation (AC) aneurysms. However, only a few studies report the long-term (≥1 year) angiographic and clinical outcomes for posterior circulation (PC) aneurysms. This study aims to compare the long-term safety and efficacy of treatment of AC and PC aneurysms with PED. METHODS: The databases included Ovid MEDLINE, Ovid EMBASE, Ovid Cochrane, and Scopus. Studies with at least 10 patients and 1-year follow-up were included. Twenty-four studies met our inclusion criteria. A random effect meta-analysis was performed to estimate the ischemic and hemorrhagic complications. A meta-analysis of proportions was performed to estimate the pooled rates of long-term complete aneurysmal occlusion, symptomatic stroke, aneurysmal rupture, and intracranial hemorrhage. RESULTS: There were 1952 aneurysms, of which 1547 (79.25%) were in the AC and 405 (20.75%) in the PC. The 1-year occlusion rate was 78% in AC compared to 73% in PC aneurysms (P < 0.01). The symptomatic infarct rate was 5% in AC compared to 13% in PC (P < 0.01). While the rupture rate was 1% in AC compared to 4% in PC (P = 0.01), the rate of intracranial hemorrhage was 2% for both (P = 0.99). CONCLUSIONS: The long-term occlusion rate after PED was higher in AC aneurysms, and the cumulative incidence of stroke and aneurysm rupture was higher in PC aneurysms.

Broad-Scale Assessment of Methylmercury in Adult Amphibians.

Mercury (Hg) is a toxic contaminant that has been mobilized and distributed worldwide and is a threat to many wildlife species. Amphibians are facing unprecedented global declines due to many threats including contaminants. While the biphasic life history of many amphibians creates a potential nexus for methylmercury (MeHg) exposure in aquatic habitats and subsequent health effects, the broad-scale distribution of MeHg exposure in amphibians remains unknown. We used nonlethal sampling to assess MeHg bioaccumulation in 3,241 juvenile and adult amphibians during 2017-2021. We sampled 26 populations (14 species) across 11 states in the United States, including several imperiled species that could not have been sampled by traditional lethal methods. We examined whether life history traits of species and whether the concentration of total mercury in sediment or dragonflies could be used as indicators of MeHg bioaccumulation in amphibians. Methylmercury contamination was widespread, with a 33-fold difference in concentrations across sites. Variation among years and clustered subsites was less than variation across sites. Life history characteristics such as size, sex, and whether the amphibian was a frog, toad, newt, or other salamander were the factors most strongly associated with bioaccumulation. Total Hg in dragonflies was a reliable indicator of bioaccumulation of MeHg in amphibians (R2 ≥ 0.67), whereas total Hg in sediment was not (R2 ≤ 0.04). Our study, the largest broad-scale assessment of MeHg bioaccumulation in amphibians, highlights methodological advances that allow for nonlethal sampling of rare species and reveals immense variation among species, life histories, and sites. Our findings can help identify sensitive populations and provide environmentally relevant concentrations for future studies to better quantify the potential threats of MeHg to amphibians.

Adaptive balanced detection spectral domain optical coherence tomography.

Balanced detection optical coherence tomography (BD-OCT) enables near-shot noise-limited imaging by suppressing wavelength-dependent relative intensity noise (RIN) originating from the light source. In spectral-domain BD-OCT (SD-BD-OCT), the level of RIN suppression relies on the co-registration accuracy of the spectra simultaneously captured by two independent spectrometers. However, existing matching methods require careful pre-calibration using a RIN-dominated dataset or subjective post-processing using a signal-dominated dataset. We developed an adaptive subpixel matching approach, referred to as adaptive balance, that can be applied to any SD-BD-OCT dataset regardless of RIN or signal level without the need for pre-calibration. We showed that adaptive balance performed comparable to or better than reported methods by imaging phantoms with varying spectrometer camera gain, exposure time, and supercontinuum laser repetition rate. We further demonstrated the benefits of adaptive balance in human retinal imaging.

Malignant Carotid Paraganglioma: A Case Report.

Carotid body tumors (CBTs) are rare neoplasms of the neuroectoderm accounting for 0.6% of head and neck tumors, with a 2%-12.5% risk of malignancy. While surgical resection has been associated with a high rate of neurologic and vascular complications, it remains the mainstay of treatment for malignant CBTs. We present the case of a 40-year-old female with a 5-year history of progressively enlarging right-sided neck mass, with MRI and MRA showing a Shamblin grade III CBT encasement of the internal carotid artery (ICA). Blood flow was absent in the petrous segment of ICA, with great collateralization of brain blood supply, enabling en bloc resection of the tumor with a carotid bulb and ligation of the common carotid artery (CCA) without vascular reconstruction. Further, we describe the characteristics and current management for malignant CBTs, including surgical management, pre-surgical embolization, and adjuvant radiation therapy.

Alignment of Visible-Light Optical Coherence Tomography Fibergrams with Confocal Images of the Same Mouse Retina.

In recent years, in vivo retinal imaging, which provides non-invasive, real-time, and longitudinal information about biological systems and processes, has been increasingly applied to obtain an objective assessment of neural damage in eye diseases. Ex vivo confocal imaging of the same retina is often necessary to validate the in vivo findings especially in animal research. In this study, we demonstrated a method for aligning an ex vivo confocal image of the mouse retina with its in vivo images. A new clinical-ready imaging technology called visible light optical coherence tomography fibergraphy (vis-OCTF) was applied to acquire in vivo images of the mouse retina. We then performed the confocal imaging of the same retina as the "gold standard" to validate the in vivo vis-OCTF images. This study not only enables further investigation of the molecular and cellular mechanisms but also establishes a foundation for a sensitive and objective evaluation of neural damage in vivo.

Demographic consequences of phenological asynchrony for North American songbirds.

Changes in phenology in response to ongoing climate change have been observed in numerous taxa around the world. Differing rates of phenological shifts across trophic levels have led to concerns that ecological interactions may become increasingly decoupled in time, with potential negative consequences for populations. Despite widespread evidence of phenological change and a broad body of supporting theory, large-scale multitaxa evidence for demographic consequences of phenological asynchrony remains elusive. Using data from a continental-scale bird-banding program, we assess the impact of phenological dynamics on avian breeding productivity in 41 species of migratory and resident North American birds breeding in and around forested areas. We find strong evidence for a phenological optimum where breeding productivity decreases in years with both particularly early or late phenology and when breeding occurs early or late relative to local vegetation phenology. Moreover, we demonstrate that landbird breeding phenology did not keep pace with shifts in the timing of vegetation green-up over a recent 18-y period, even though avian breeding phenology has tracked green-up with greater sensitivity than arrival for migratory species. Species whose breeding phenology more closely tracked green-up tend to migrate shorter distances (or are resident over the entire year) and breed earlier in the season. These results showcase the broadest-scale evidence yet of the demographic impacts of phenological change. Future climate change-associated phenological shifts will likely result in a decrease in breeding productivity for most species, given that bird breeding phenology is failing to keep pace with climate change.

Visible-Light Optical Coherence Tomography Fibergraphy of the Tree Shrew Retinal Ganglion Cell Axon Bundles.

We seek to develop techniques for high-resolution imaging of the tree shrew retina for visualizing and parameterizing retinal ganglion cell (RGC) axon bundles in vivo. We applied visible-light optical coherence tomography fibergraphy (vis-OCTF) and temporal speckle averaging (TSA) to visualize individual RGC axon bundles in the tree shrew retina. For the first time, we quantified individual RGC bundle width, height, and cross-sectional area and applied vis-OCT angiography (vis-OCTA) to visualize the retinal microvasculature in tree shrews. Throughout the retina, as the distance from the optic nerve head (ONH) increased from 0.5 mm to 2.5 mm, bundle width increased by 30%, height decreased by 67%, and cross-sectional area decreased by 36%. We also showed that axon bundles become vertically elongated as they converge toward the ONH. Ex vivo confocal microscopy of retinal flat-mounts immunostained with Tuj1 confirmed our in vivo vis-OCTF findings.

Systematic Review on Magnetic Resonance Angiography with Vessel Wall Imaging for the Characterization of Symptomatic Carotid Artery Plaque.

BACKGROUND: To perform a systematic literature review to assess the usefulness of performing magnetic resonance angiography (MRA) with vessel wall imaging (VWI) sequences for the assessment of symptomatic carotid artery plaques and the identification of risky plaque features predisposing for stroke. METHODS: We performed a systematic review of the literature pertaining to MRA with VWI techniques in patients with carotid artery disease, focusing on symptomatic patients' plaque features and morphology. Independent reviewers screened and analyzed data extracted from eligible studies, and a modified Newcastle-Ottawa Scale was used to appraise the quality of the design and content of the selected manuscripts to achieve an accurate interpretation. RESULTS: This review included nineteen peer-reviewed manuscripts, all of them including MRA and VWI assessments of the symptomatic carotid artery plaque. We focused on patients' comorbidities and reviewed plaque features, including intraplaque hemorrhage, a lipid-rich necrotic core, a ruptured fibrous cap, and plaque ulceration. CONCLUSIONS: MRA with VWI is a useful tool in the evaluation of carotid artery plaques. This imaging technique allows clinicians to identify plaques at risk of causing a neurovascular event. The presence of intraplaque hemorrhage, plaque ulceration, a ruptured fibrous cap, and a lipid-rich necrotic core are associated with neurovascular symptoms. The timely identification of these features could have a positive impact on neurovascular event prevention.

Longitudinal Analysis of Retinal Ganglion Cell Damage at Individual Axon Bundle Level in Mice Using Visible-Light Optical Coherence Tomography Fibergraphy.

Purpose: We developed a new analytic tool based on visible-light optical coherence tomography fibergraphy (vis-OCTF) to longitudinally track individual axon bundle transformation as a new in vivo biomarker for retinal ganglion cell (RGC) damage. Methods: After acute optic nerve crush injury (ONC) in mice, we analyzed four parameters: lateral bundle width, axial bundle height, cross-sectional area, and the shape of individual bundles. We next correlated the morphological changes in RGC axon bundles with RGC soma loss. Results: We showed that axon bundles became wider and taller at three days post ONC (pONC), which correlated with about 15% RGC soma loss. At six days pONC, axon bundles showed a significant reduction in lateral width and cross-sectional area, followed by a reduction in bundle height at nine days pONC. Bundle shrinking at nine days pONC correlated with about 68% RGC soma loss. Both experimental and simulated results suggested that the cross-sectional area of individual RGC axon bundles is more sensitive than bundle width and height to indicate RGC soma loss. Conclusions: This study is the first to track and quantify individual RGC axon bundles in vivo after ONC injury. Translational Relevance: Recognizing RGC loss at its earliest stage is crucial for disease diagnosis and treatment. However, current clinical methods to detect the functional and structural changes in the inner retina are not sensitive enough to directly assess RGC health. In this study, we developed vis-OCTF-based parameters to track RGC damage, making possible to establishing a quantifiable biomarker for glaucoma.

Flow diversion using the Pipeline embolization device for intracranial and extracranial pseudoaneurysms: a systematic review and meta-analysis of the literature.

OBJECTIVE: Pseudoaneurysms (PSAs) are complex vascular lesions. Flow diversion has been proposed as an alternative treatment to parent artery occlusion that preserves laminar flow. The authors of the present study investigated the safety and short-term (< 1 year) and long-term (≥ 1 year) aneurysm occlusion rates following the treatment of intracranial and extracranial PSAs using the Pipeline embolization device (PED). METHODS: An electronic database search for full-text English-language articles in Ovid MEDLINE and Epub Ahead of Print, Ovid Embase, Ovid Cochrane Central Register of Controlled Trials, Ovid Cochrane Database of Systematic Reviews, and Scopus was conducted following the PRISMA guidelines. Studies of any design including at least 4 patients with intracranial or extracranial PSAs treated using a PED were included in this analysis. The primary outcome of interest was the rate of peri- and postprocedural complications. Secondarily, the authors analyzed the incidence of complete aneurysm occlusion. RESULTS: A total of 90 patients with 96 PSAs across 9 studies were included. The mean age was 38.2 (SD 15.14) years, and 37.8% of the patients were women. The mean PSA size was 4.9 mm. Most PSAs were unruptured, and the most common etiology was trauma (n = 32, 35.5%), followed by spontaneous formation (n = 21, 23.3%) and iatrogenic injury (n = 19, 21.1%). Among the 51 (53.1%) intracranial and 45 (46.9%) extracranial PSAs were 19 (19.8%) dissecting PSAs. Sixty-six (77.6%) PSAs were in the internal carotid artery and 10 (11.8%) in the vertebral artery. Thirty-three (34.4%) PSAs were treated with ≥ 2 devices, and 8 (8.3%) underwent adjunctive coiling. The mean clinical and angiographic follow-up durations were 10.7 and 12.9 months, respectively. The short-term (< 1 year) and long-term (≥ 1 year) complete occlusion rates were 79% (95% CI 66%-88%, p = 0.82) and 84% (95% CI 70%-92%, p = 0.95), respectively. Complication rates were 8% for iatrogenic dissection (95% CI 3%-16%, p = 0.94), 10% for silent thromboembolism (95% CI 5%-21%, p = 0.77), and 12% for symptomatic thromboembolism (95% CI 6%-23%, p = 0.48). No treatment-related hemorrhage was observed. The overall mortality rate at the last follow-up was 14%. CONCLUSIONS: The complete occlusion rate for PSAs treated with the PED was high and increased over time. Although postprocedural complications and mortality were not insignificant, flow diversion represents a reasonably safe option for managing these complex lesions.