Ovoid foveal hyperreflective lesions as a sign of familial adenomatous polyposis: A case series and review.

Purpose: To report 2 cases of presumed retinal hamartoma (RH) in pediatric patients with genetically-confirmed familial adenomatous polyposis (FAP), both evaluated by optical coherence tomography (OCT) and one evaluated with optical coherence tomography angiography (OCTA).

Observations: A six-year-old girl presented with occasional blurry vision in the left eye. OCT showed a foveal hyperreflective lesion with disruption of photoreceptors and retinal pigment epithelium (RPE).

Where the Patterns Are: Repetition-Aware Compression for Colored de Bruijn Graphs.

We describe lossless compressed data structures for the de Bruijn graph (or c-dBG). Given a collection of reference sequences, a c-dBG can be essentially regarded as a map from -mers to their . The color set of a -mer is the set of all identifiers, or , of the references that contain the -mer.

Where the patterns are: repetition-aware compression for colored de Bruijn graphs .

Unlabelled: We describe lossless compressed data structures for the de Bruijn graph (or, c-dBG). Given a collection of reference sequences, a c-dBG can be essentially regarded as a map from -mers to their . The color set of a -mer is the set of all identifiers, or , of the references that contain the -mer.

Foveal photoreceptor atrophy, persistent fetal vasculature, congenital cataracts, and microphthalmia in a pediatric patient with -associated oculo-facio-cardio-dental (OFCD) syndrome.

Purpose: To report a case of oculo-facio-cardio-dental (OFCD) syndrome secondary to a novel variant in a pediatric patient with congenital cataracts, microphthalmia, persistent fetal vasculature (PFV), focal chorioretinal hyperpigmentation, peripheral retinal avascularity, and foveal photoreceptor atrophy.

Observations: A 3-month-old female patient was referred for bilateral congenital cataracts with microphthalmia. Her past medical history was significant for syndactyly of the toes, left bifid rib, atrial septal defect, patent ductus arteriosus, mitral regurgitation, pulmonary hypertension, anemia of prematurity, vesicoureteral reflux, and duodenal atresia.

Clinical Outcomes in Patients With Traumatic Dehiscence of Penetrating Keratoplasty Grafts.

Purpose: The purpose of this study was to report clinical characteristics and outcomes of surgical repair for patients with traumatic dehiscence of penetrating keratoplasty (PKP) grafts.

Methods: Retrospective, consecutive chart review of patients evaluated at Bascom Palmer Eye Institute between 2015 and 2020 with traumatic dehiscence of penetrating keratoplasty grafts.

Results: The study cohort consisted of 65 eyes of 65 patients.

Fulgor: a fast and compact k-mer index for large-scale matching and color queries.

The problem of sequence identification or matching-determining the subset of reference sequences from a given collection that are likely to contain a short, queried nucleotide sequence-is relevant for many important tasks in Computational Biology, such as metagenomics and pangenome analysis. Due to the complex nature of such analyses and the large scale of the reference collections a resource-efficient solution to this problem is of utmost importance. This poses the threefold challenge of representing the reference collection with a data structure that is efficient to query, has light memory usage, and scales well to large collections.

Tree-based differential testing using inferential uncertainty for RNA-Seq.

Identifying differentially expressed transcripts poses a crucial yet challenging problem in transcriptomics. Substantial uncertainty is associated with the abundance estimates of certain transcripts which, if ignored, can lead to the exaggeration of false positives and, if included, may lead to reduced power. For a given set of RNA-Seq samples, TreeTerminus arranges transcripts in a hierarchical tree structure that encodes different layers of resolution for interpretation of the abundance of transcriptional groups, with uncertainty generally decreasing as one ascends the tree from the leaves.

A patient with concurrent Axenfeld-Rieger and Stickler syndromes verified by molecular genetics.

Purpose: To report a case of Axenfeld-Rieger and Stickler Syndrome in a pediatric patient.

Observations: A 3-month-old male was referred to the glaucoma clinic after he was noted to have elevated intraocular pressures in both eyes. His family history was notable for infantile glaucoma on his maternal side and retinal detachment on his paternal side.

Meta-colored compacted de Bruijn graphs.

Motivation: The colored compacted de Bruijn graph (c-dBG) has become a fundamental tool used across several areas of genomics and pangenomics. For example, it has been widely adopted by methods that perform read mapping or alignment, abundance estimation, and subsequent downstream analyses. These applications essentially regard the c-dBG as a map from k-mers to the set of references in which they appear.

Fulgor: A fast and compact -mer index for large-scale matching and color queries.

The problem of sequence identification or matching - determining the subset of references from a given collection that are likely to contain a query nucleotide sequence - is relevant for many important tasks in Computational Biology, such as metagenomics and pan-genome analysis. Due to the complex nature of such analyses and the large scale of the reference collections a resourceefficient solution to this problem is of utmost importance. The reference collection should therefore be pre-processed into an for fast queries.

Peripheral Retinal Nonperfusion in Pediatric Patients with Optic Disc Hypoplasia.

Purpose: This study aims to report the association of optic nerve hypoplasia (ONH), peripheral retinal nonperfusion, and secondary complications in pediatric patients.

Design: Retrospective case series.

Methods: The study was conducted between January 2015 and January 2022 at the Bascom Palmer Eye Institute.

Evolving Use of Regional versus General Anesthesia for the Surgical Repair of Open Globe Injuries.

Purpose: The purpose of the current study is to report outcomes with the evolving use of regional anesthesia with monitored anesthesia care (RA-MAC) vs general anesthesia (GA) in the repair of open globe injuries.

Design: Retrospective, consecutive, comparative, nonrandomized clinical study.

Methods: The study includes 507 eyes of 507 patients with open globe injuries treated with either RA-MAC or GA at a tertiary referral center between 2015 and 2020.

ACUTE- AND DELAYED-ONSET ENDOPHTHALMITIS AFTER OPEN GLOBE INJURIES: Clinical Features and Visual Acuity Outcomes.

Purpose: The purpose of the study was to report the clinical features and best-corrected visual acuity outcomes in patients with acute- and delayed-onset endophthalmitis after open globe injuries.

Methods: The study included a retrospective, comparative, consecutive case series of patients with endophthalmitis after open globe injury between January 2016 and October 2020 at the Bascom Palmer Eye Institute.

Results: Acute-onset endophthalmitis accounted for 16 of 20 cases (80%), and all cases were diagnosed at the initial examination.

Outcomes in Patients with Suprachoroidal Hemorrhage After Anterior Segment Surgery.

Objective: The purpose of the current study is to report outcomes of suprachoroidal hemorrhage (SCH) after anterior segment surgery at a single institution, and to identify clinical features associated with visual prognosis.

Methods And Analysis: Retrospective consecutive case series of patients with SCH occurring after anterior segment surgery.

Results: The study includes 112 eyes of 112 patients between 2014 and 2020.

Chemical induction of gut β-like-cells by combined FoxO1/Notch inhibition as a glucose-lowering treatment for diabetes.

Objective: Lifelong insulin replacement remains the mainstay of type 1 diabetes treatment. Genetic FoxO1 ablation promotes enteroendocrine cell (EECs) conversion into glucose-responsive β-like cells. Here, we tested whether chemical FoxO1 inhibitors can generate β-like gut cells.

Pharmacological conversion of gut epithelial cells into insulin-producing cells lowers glycemia in diabetic animals.

As a highly regenerative organ, the intestine is a promising source for cellular reprogramming for replacing lost pancreatic β cells in diabetes. Gut enterochromaffin cells can be converted to insulin-producing cells by forkhead box O1 (FoxO1) ablation, but their numbers are limited. In this study, we report that insulin-immunoreactive cells with Paneth/goblet cell features are present in human fetal intestine.

Plasma-first: accelerating lung cancer diagnosis and molecular profiling through liquid biopsy.

Introduction: Molecular profiling of tumor tissue is the gold standard for treatment decision-making in advanced non-small cell lung cancer (NSCLC). Results may be delayed or unavailable due to insufficient tissue, prolonged wait times for biopsy, pathology assessment and testing. We piloted the use of plasma testing in the initial diagnostic workup for patients with suspected advanced lung cancer.

Recurrent, bilateral endogenous Candida endophthalmitis with multiple focal chorioretinal lesions: management with pars plana vitrectomy and focal endolaser.

Purpose: Bilateral endogenous Candida endophthalmitis (ECE) treatment usually involves administering systemic and intravitreal antifungal medications. In advanced cases with vitreous seeding, pars plana vitrectomy (PPV) is considered. The use of focal endolaser treatment to chorioretinal lesions has not been reported.