Single-cell transcriptomics of the ocular anterior segment: a comprehensive review.

Elucidating the cellular and genetic composition of ocular tissues is essential for uncovering the pathophysiology of ocular diseases. Since the introduction of single-cell RNA sequencing (scRNA-seq) in 2009, vision researchers have performed extensive single-cell analyses to better understand transcriptome complexity and heterogeneity of ocular structures. This technology has revolutionized our ability to identify rare cell populations and to make cross-species comparisons of gene expression in both steady state and disease conditions. Importantly, single-cell transcriptomic analyses have enabled the identification of cell-type specific gene markers and signalling pathways between ocular cell populations. While most scRNA-seq studies have been conducted on retinal tissues, large-scale transcriptomic atlases pertaining to the ocular anterior segment have also been constructed in the past three years. This timely review provides vision researchers with an overview of scRNA-seq experimental design, technical limitations, and clinical applications in a variety of anterior segment-related ocular pathologies. We review open-access anterior segment-related scRNA-seq datasets and illustrate how scRNA-seq can be an indispensable tool for the development of targeted therapeutics.

3-D OCT imaging of hyalocytes in partial posterior vitreous detachment and vaso-occlusive retinal disease.

Purpose: To describe the spatial distribution and morphologic characteristics of macrophage-like cells called hyalocytes in the posterior vitreous cortex of a patient with unilateral partial posterior vitreous detachment (PVD) using coronal plane en face optical coherence tomography (OCT). Observations: A 54-year-old male with sickle cell disease (HbSC genotype) presented with a partial PVD in one eye. Rendered volumes of a slab extending from 600 µm to 3 µm anterior to the inner limiting membrane (ILM) revealed hyperreflective foci in the detached posterior vitreous cortex suspended anterior to the macula, likely representing hyalocytes. In the fellow eye without PVD, hyperreflective foci were located 3 µm anterior to the ILM. The morphology of the cells in the eye with PVD varied between a ramified state with multiple elongated processes and a more activated state characterized by a plump cell body with fewer retracted processes. In the same anatomical location, the hyperreflective foci were 10-fold more numerous in the patient with vaso-occlusive disease than in an unaffected, age-matched control. Conclusions and Importance: Direct, non-invasive, and label-free techniques of imaging cells at the vitreoretinal interface and within the vitreous body is an emerging field. The findings from this case report suggest that coronal plane en face OCT can be used to provide a detailed and quantitative characterization of cells at the human vitreo-retinal interface in vivo. Importantly, this case report demonstrates that 3D-OCT renderings can enhance visualization of these cells in relation to the ILM, which may provide clues concerning the identity and contribution of these cells to the pathogenesis of vitreo-retinal diseases.

Posterior vitreous cortex hyalocytes visualization in asymmetric pigmented paravenous chorioretinal atrophy (PPCRA) using en face OCT.

Purpose: Pigmented paravenous chorioretinal atrophy (PPCRA) is a rare retinal disease with inflammatory or infectious associations affecting the retinal pigment epithelium (RPE) and choriocapillaris. While the clinical manifestations and imaging findings are well-documented in the literature, no reports exist describing potential biomarkers of intraocular inflammation or ischemia in this condition, such as the presence of posterior vitreous cortex hyalocytes. Observations: We report a case of a 26-year-old female who presented with progressive peripheral vision loss in both eyes over one year. Dilated fundus examination revealed bilateral, asymmetric bone-spicule pigmentary changes along the retinal veins, which appeared more advanced in the left eye. Optical coherence tomography (OCT) revealed the presence of numerous hyalocytes in both eyes 3 µm anterior to the inner limiting membrane (ILM). The morphology of the hyalocytes differed between the two eyes, suggesting different levels of activation related to the stage of the disease. Specifically, the left eye, with more advanced disease, exhibited hyalocytes with multiple elongated processes consistent with a quiescent state, whereas the right eye, with the less advanced disease state, exhibited amoeboid-appearing hyalocytes suggestive of more active inflammation. Conclusions: This case illustrates how hyalocyte morphology may reflect the underlying activity of an indolent retinal degeneration and provide a useful biomarker of disease progression.

Imaging vitreous cortex hyalocyte response to paracentral acute middle maculopathy (PAMM) using En Face OCT.

INTRODUCTION: Vitreous cortex hyalocytes (VCH) are resident macrophage cells that provide immunosurveillance, respond to tissue injury and inflammation, and help maintain the transparency of the media. In this case report we demonstrate the use of en face optical coherence tomography (OCT) to image VCH in vivo in a patient presenting with PAMM secondary to antiphospholipid syndrome. CASE DESCRIPTION: A 38-year-old female with no known medical history presented with complaints of visual disturbances in the right eye. OCT revealed hyperreflective bands in the IPL and INL nasal to the fovea. A diagnosis of PAMM was made. Work-up revealed elevated titers of antiphospholipid antibodies. En face OCT revealed a decline in the inflammatory activation over a seven-month period as evidenced by changes in VCH distribution and morphology. CONCLUSIONS: Our findings suggest that monitoring changes in the distribution and morphology of VCH could have a potential clinical utility for assessing disease severity, predicting recovery, and early recognition of treatment response in various inflammatory ocular pathologies such as PAMM.

Recent Advances in Nasoalveolar Molding Therapy Using 3D Technology.

Presurgical Nasoalveolar Molding (NAM) is an adjunctive treatment modality designed to reorient misaligned tissue structures and nasal cartilage in cleft lip and/or palate (CL/P) patients. Recent advances in NAM therapy focus on modifications to the intraoral molding plate or nasal stent intended to improve treatment outcomes, ease of use, compliance, and cost-effectiveness. Notably, 3D technological advancements have been employed to design NAM devices more efficiently and create objective, standardized means of measuring progressive morphological changes during therapy. These advances are designed to incorporate 3D technology in the treatment of cleft lip and/or palate to render it more precise, accurate, and time-efficient.

Surgical Scheduling Impacts Hospital Length of Stay and Associated Healthcare Costs for Patients Undergoing Total Hip and Knee Arthroplasty.

Background: Surgical scheduling, specifically the day of the week on which surgery is performed, has been associated with various postoperative outcomes in patients undergoing lower extremity joint arthroplasty. Purpose: We sought to investigate surgical scheduling as a potential modifiable factor for patient quality metrics and related costs. Methods: In a retrospective prognostic study, all total knee and total hip arthroplasty (TKA/THA) cases that took place in 2017 to 2018 at a multihospital academic health system were queried. Patients were separated by the day of the week the surgery was performed, with Monday/Tuesday compared to Thursday/Friday. Outcomes included length of stay (LOS) (extended LOS defined as 3 days or longer), cost, and complications. Multivariable regression models measured associations between scheduling of surgery and outcomes; odds ratios (OR) and 95% confidence intervals (CIs) are reported. Results: Overall, 1,571 TKA and 992 THA patients were included (65% and 35%, respectively, performed on Monday/Tuesday and 70% and 30%, respectively, performed on Thursday/Friday). Patients undergoing TKA on Monday/Tuesday versus Thursday/Friday had higher American Society of Anesthesiologists scores (42% vs 33% with score of 3 or higher) but less often an extended LOS (31% vs 54%; adjusted OR: 2.76, 95% CI: 2.22-3.46), lower skilled nursing facility costs (unadjusted mean, $12,515 vs $14,154) and lower home health aide costs (unadjusted mean, $3,793 vs $4,192). Similar patterns were observed in THA patients. Conclusion: These results from institutional data suggest that surgical scheduling is a modifiable factor possibly associated with postoperative outcomes. Furthermore, more rigorous study is warranted.

"When to Nuss? patient age as a risk factor for complications of minimally invasive repair of pectus excavatum: a systematic review and meta-analysis".

PURPOSE: The optimal age for minimally invasive repair of pectus excavatum (MIRPE) is unclear; this study investigates the differences in complication rates among different age groups undergoing repair. METHODS: PubMed and Embase databases were searched from inception to October 2020. To assess age as a risk factor for complications, odds ratios from relevant studies were analyzed using the Mantel-Haenszel method with a random-effects model for younger vs older patients. Specific complication rates were compared between the two cohorts using a chi-squared test. RESULTS: Of the 4448 studies retrieved, 25 studies stratified complication data by age groups. From these studies, ten studies compared groups at ages < 18 and ≥ 18 and four studies compared ages < 20 and ≥ 20, and one study compared ages < 19 and ≥ 19. These fifteen studies reported on 5978 patients, with 1188 complications, for a complication rate of 19.87%. Older patients were more likely to have complications in a pooled analysis of studies comparing older vs younger patients (OR = 1.66, 95% CI = 1.28-2.14, heterogeneity I2 = 49%). Specifically, older patients were significantly more likely to experience pneumothorax, pleural effusion, wound infection, bar displacement, and reoperations. CONCLUSION: Increased age is a risk factor for complications of MIRPE. This supports repair of pectus excavatum prior to late adolescence.

A Case of Multisystem Inflammatory Syndrome in a Pediatric Patient With Acute Appendicitis.

This case report details the clinical course of a 7-year-old patient with an initial presentation of acute appendicitis, who developed symptoms highly concerning multisystem inflammatory syndrome in children (MIS-C) after appendectomy. Despite appropriate management, the patient went on to develop left main coronary artery dilatation. Given the spectrum of clinical presentations and absence of pathognomonic findings or diagnostic tests for MIS-C, it is essential to maintain a high index of suspicion for MIS-C when pediatric patients first present with nonspecific gastrointestinal symptoms and recent exposure to coronavirus disease 2019 (COVID-19). Importantly, this case illustrates that the diagnosis of MIS-C can be missed in three different ways: 1) if the patient has an absence of classic symptoms such as rash, conjunctivitis, edema, or evidence of mucocutaneous involvement on initial presentation; 2) if the patient initially has leukocytosis, instead of leukopenia (which is more prevalent in MIS-C cases), and a normal platelet count early on in the disease course; and 3) if providers confuse MIS-C for other more common postoperative causes of fever, such as atelectasis. Finally, MIS-C should still be considered part of the differential even if abdominal computer tomography (CT) findings are unremarkable for systemic inflammation. Given the potential for a rapid clinical decline in patients with MIS-C, appropriate workup should be completed in a timely manner.

A global metagenomic map of urban microbiomes and antimicrobial resistance.

We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities.

The impact of cross-kingdom molecular forensics on genetic privacy.

Recent advances in metagenomic technology and computational prediction may inadvertently weaken an individual's reasonable expectation of privacy. Through cross-kingdom genetic and metagenomic forensics, we can already predict at least a dozen human phenotypes with varying degrees of accuracy. There is also growing potential to detect a "molecular echo" of an individual's microbiome from cells deposited on public surfaces. At present, host genetic data from somatic or germ cells provide more reliable information than microbiome samples. However, the emerging ability to infer personal details from different microscopic biological materials left behind on surfaces requires in-depth ethical and legal scrutiny. There is potential to identify and track individuals, along with new, surreptitious means of genetic discrimination. This commentary underscores the need to update legal and policy frameworks for genetic privacy with additional considerations for the information that could be acquired from microbiome-derived data. The article also aims to stimulate ubiquitous discourse to ensure the protection of genetic rights and liberties in the post-genomic era. Video abstract.

Considerations for Payment Bundling in Cleft Care.

SUMMARY: Since the introduction of the Bundled Payments for Care Improvement initiative, progress has been made in piloting bundled payment models to improve care coordination and curtail health care expenditures. In light of improvements in patient outcomes and the concomitant reduction in health care spending for certain high-volume and high-cost procedures, such as total joint arthroplasty and breast reconstruction, the authors discuss theoretical considerations for bundling payments for the care of patients with orofacial clefts. The reasons for and against adopting such a payment model to consolidate cleft care, as well as the challenges to implementation, are discussed. The authors purport that bundled payments can centralize components of cleft care and offer financial incentives to reduce costs and improve the value of care provided, but that risk adjustment based on the longitudinal nature of care, disease severity, etiologic heterogeneity, variations in outcomes reporting, and varying definitions of the episode of care remain significant barriers to implementation.

Fabrication of Nasoalveolar Molding Devices for the Treatment of Cleft Lip and Palate, Using Stereolithography Additive Manufacturing Processes and Computer-Aided Design Manipulation Software.

INTRODUCTION: Nasoalveolar molding (NAM) is a presurgical orthopedic treatment modality that attempts to reorient misaligned bony and soft tissue structures in patients with clefting of the lip and palate. The NAM devices are implemented prior to surgical intervention in order to minimize the gap across the cleft and thereby reduce tension across the eventual repair. Currently, NAM devices are fabricated in a laboratory and then refined chairside by the provider. The present article describes the potential of three-dimensional (3D) printing and computer-aided design (CAD) software for the fabrication of NAM devices. MATERIAL AND METHODS: A workflow was developed to demonstrate the use of 3D printing and CAD software to design NAM devices. This workflow encompasses scanning an impression into CAD software, performing a series of manipulations, and then printing the digital model. RESULTS: To test the workflow, a cleft palate plaster model was scanned into CAD software. Through a series of linear and angular freeform manipulations of the body, the model was modified to display a cleft with a reduced alveolar gap. Sequential molding devices were produced which would gradually apply pressure to targeted areas of hard and soft tissue until the cleft is minimized. The resulting devices are printed using a stereolithography printer. CONCLUSIONS: The use of 3D printing and CAD software shows promise in improving the accuracy, speed, and cost-effectiveness of designing NAM devices. The accuracy and flexibility from digitally visualizing the manipulations made to an appliance before its creation can result in a more personalized device for the patient.

Correction to: Comprehensive benchmarking and ensemble approaches for metagenomic classifiers.

Following publication of the original article [1], the authors would like to highlight the following two corrections.

Comprehensive benchmarking and ensemble approaches for metagenomic classifiers.

BACKGROUND: One of the main challenges in metagenomics is the identification of microorganisms in clinical and environmental samples. While an extensive and heterogeneous set of computational tools is available to classify microorganisms using whole-genome shotgun sequencing data, comprehensive comparisons of these methods are limited. RESULTS: In this study, we use the largest-to-date set of laboratory-generated and simulated controls across 846 species to evaluate the performance of 11 metagenomic classifiers. Tools were characterized on the basis of their ability to identify taxa at the genus, species, and strain levels, quantify relative abundances of taxa, and classify individual reads to the species level. Strikingly, the number of species identified by the 11 tools can differ by over three orders of magnitude on the same datasets. Various strategies can ameliorate taxonomic misclassification, including abundance filtering, ensemble approaches, and tool intersection. Nevertheless, these strategies were often insufficient to completely eliminate false positives from environmental samples, which are especially important where they concern medically relevant species. Overall, pairing tools with different classification strategies (k-mer, alignment, marker) can combine their respective advantages. CONCLUSIONS: This study provides positive and negative controls, titrated standards, and a guide for selecting tools for metagenomic analyses by comparing ranges of precision, accuracy, and recall. We show that proper experimental design and analysis parameters can reduce false positives, provide greater resolution of species in complex metagenomic samples, and improve the interpretation of results.

Genomic Methods and Microbiological Technologies for Profiling Novel and Extreme Environments for the Extreme Microbiome Project (XMP).

The Extreme Microbiome Project (XMP) is a project launched by the Association of Biomolecular Resource Facilities Metagenomics Research Group (ABRF MGRG) that focuses on whole genome shotgun sequencing of extreme and unique environments using a wide variety of biomolecular techniques. The goals are multifaceted, including development and refinement of new techniques for the following: 1) the detection and characterization of novel microbes, 2) the evaluation of nucleic acid techniques for extremophilic samples, and 3) the identification and implementation of the appropriate bioinformatics pipelines. Here, we highlight the different ongoing projects that we have been working on, as well as details on the various methods we use to characterize the microbiome and metagenome of these complex samples. In particular, we present data of a novel multienzyme extraction protocol that we developed, called Polyzyme or MetaPolyZyme. Presently, the XMP is characterizing sample sites around the world with the intent of discovering new species, genes, and gene clusters. Once a project site is complete, the resulting data will be publically available. Sites include Lake Hillier in Western Australia, the "Door to Hell" crater in Turkmenistan, deep ocean brine lakes of the Gulf of Mexico, deep ocean sediments from Greenland, permafrost tunnels in Alaska, ancient microbial biofilms from Antarctica, Blue Lagoon Iceland, Ethiopian toxic hot springs, and the acidic hypersaline ponds in Western Australia.

Precision Metagenomics: Rapid Metagenomic Analyses for Infectious Disease Diagnostics and Public Health Surveillance.

Next-generation sequencing (NGS) technologies have ushered in the era of precision medicine, transforming the way we treat cancer patients and diagnose disease. Concomitantly, the advent of these technologies has created a surge of microbiome and metagenomic studies over the last decade, many of which are focused on investigating the host-gene-microbial interactions responsible for the development and spread of infectious diseases, as well as delineating their key role in maintaining health. As we continue to discover more information about the etiology of infectious diseases, the translational potential of metagenomic NGS methods for treatment and rapid diagnosis is becoming abundantly clear. Here, we present a robust protocol for the implementation and application of "precision metagenomics" across various sequencing platforms for clinical samples. Such a pipeline integrates DNA/RNA extraction, library preparation, sequencing, and bioinformatics analyses for taxonomic classification, antimicrobial resistance (AMR) marker screening, and functional analysis (biochemical and metabolic pathway abundance). Moreover, the pipeline has 3 tracks: STAT for results within 24 h; Comprehensive that affords a more in-depth analysis and takes between 5 and 7 d, but offers antimicrobial resistance information; and Targeted, which also requires 5-7 d, but with more sensitive analysis for specific pathogens. Finally, we discuss the challenges that need to be addressed before full integration in the clinical setting.

Assessment of REPLI-g Multiple Displacement Whole Genome Amplification (WGA) Techniques for Metagenomic Applications.

Amplification of minute quantities of DNA is a fundamental challenge in low-biomass metagenomic and microbiome studies because of potential biases in coverage, guanine-cytosine (GC) content, and altered species abundances. Whole genome amplification (WGA), although widely used, is notorious for introducing artifact sequences, either by amplifying laboratory contaminants or by nonrandom amplification of a sample's DNA. In this study, we investigate the effect of REPLI-g multiple displacement amplification (MDA; Qiagen, Valencia, CA, USA) on sequencing data quality and species abundance detection in 8 paired metagenomic samples and 1 titrated, mixed control sample. We extracted and sequenced genomic DNA (gDNA) from 8 environmental samples and compared the quality of the sequencing data for the MDA and their corresponding non-MDA samples. The degree of REPLI-g MDA bias was evaluated by sequence metrics, species composition, and cross-validating observed species abundance and species diversity estimates using the One Codex and MetaPhlAn taxonomic classification tools. Here, we provide evidence of the overall efficacy of REPLI-g MDA on retaining sequencing data quality and species abundance measurements while providing increased yields of high-fidelity DNA. We find that species abundance estimates are largely consistent across samples, even with REPLI-g amplification, as demonstrated by the Spearman's rank order coefficient (R2 > 0.8). However, REPLI-g MDA often produced fewer classified reads at the species, genera, and family level, resulting in decreased species diversity. We also observed some areas with the PCR "jackpot effect," with varying input DNA values for the Metagenomics Research Group (MGRG) controls at specific genomic loci. We visualize this effect in whole genome coverage plots and with sequence composition analyses and note these caveats of the MDA method. Despite overall concordance of species abundance between the amplified and unamplified samples, these results demonstrate that amplification of DNA using the REPLI-g method has some limitations. These concerns could be addressed by future improvements in the enzymes or methods for REPLI-g to be considered a >99% robust method for increasing the amount of high-fidelity DNA from low-biomass samples or at the very least, accounted for during computational analysis of MDA samples.

Globalizing and crowdsourcing biomedical research.

INTRODUCTION OR BACKGROUND: Crowdfunding and crowdsourcing of medical research has emerged as a novel paradigm for many biomedical disciplines to rapidly collect, process and interpret data from high-throughput and high-dimensional experiments. The novelty and promise of these approaches have led to fundamental discoveries about RNA mechanisms, microbiome dynamics and even patient interpretation of test results. However, these methods require robust training protocols, uniform sampling methods and experimental rigor in order to be useful for subsequent research efforts. Executed correctly, crowdfunding and crowdsourcing can leverage public resources and engagement to generate support for scientific endeavors that would otherwise be impossible due to funding constraints and or the large number of participants needed for data collection. SOURCES OF DATA: We conducted a comprehensive literature review of scientific studies that utilized crowdsourcing and crowdfunding to generate data. We also discuss our own experiences conducting citizen-science research initiatives (MetaSUB and PathoMap) in ensuring data robustness, educational outreach and public engagement. AREAS OF AGREEMENT: We demonstrate the efficacy of crowdsourcing mechanisms for revolutionizing microbiome and metagenomic research to better elucidate the microbial and genetic dynamics of cities around the world (as well as non-urban areas). Crowdsourced studies have been able to create an improved and unprecedented ability to monitor, design and measure changes at the microbial and macroscopic scale. Thus, the use of crowdsourcing strategies has dramatically altered certain genomics research to create global citizen-science initiatives that reveal new discoveries about the world's genetic dynamics. AREAS OF CONTROVERSY: The effectiveness of crowdfunding and crowdsourcing is largely dependent on the study design and methodology. One point of contention for the present discussion is the validity and scientific rigor of data that are generated by non-scientists. Selection bias, limited sample sizes and limitations for scientists in enforcing standardized protocols are all challenges for those who engage in citizen-science initiatives. GROWING POINTS: Despite the aforementioned concerns, crowdsourced data allow for greater inroads into the field of personalized medicine, whereby community members take an active role in generating data about their personal and environmental health. AREAS TIMELY FOR DEVELOPING RESEARCH: Crowdsourced viral and metagenomic studies are the next step in elucidating the genomic and epigenomic characterization of urban population health.

Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics.

The panoply of microorganisms and other species present in our environment influence human health and disease, especially in cities, but have not been profiled with metagenomics at a city-wide scale. We sequenced DNA from surfaces across the entire New York City (NYC) subway system, the Gowanus Canal, and public parks. Nearly half of the DNA (48%) does not match any known organism; identified organisms spanned 1,688 bacterial, viral, archaeal, and eukaryotic taxa, which were enriched for harmless genera associated with skin (e.g., Acinetobacter). Predicted ancestry of human DNA left on subway surfaces can recapitulate U.S. Census demographic data, and bacterial signatures can reveal a station's history, such as marine-associated bacteria in a hurricane-flooded station. Some evidence of pathogens was found (Bacillus anthracis), but a lack of reported cases in NYC suggests that the pathogens represent a normal, urban microbiome. This baseline metagenomic map of NYC could help long-term disease surveillance, bioterrorism threat mitigation, and health management in the built environment of cities.