A statistical simulation model to guide the choices of analytical methods in arrayed CRISPR screen experiments.

An arrayed CRISPR screen is a high-throughput functional genomic screening method, which typically uses 384 well plates and has different gene knockouts in different wells. Despite various computational workflows, there is currently no systematic way to find what is a good workflow for arrayed CRISPR screening data analysis. To guide this choice, we developed a statistical simulation model that mimics the data generating process of arrayed CRISPR screening experiments.

Comparison of Vision-related Quality of Life Between Normal Tension Glaucoma and Primary Open-angle Glaucoma.

Prcis: Although there was little difference in overall vision-related quality of life (VRQOL) between patients with normal tension glaucoma (NTG) and primary open-angle glaucoma (POAG) after controlling for confounding factors, POAG tended to have poorer VRQOL, especially in social functioning and dependency, than NTG.

Purpose: The fundamental goal of treatment of patients with glaucoma is to preserve their VRQOL. The aim of this study was to compare VRQOL between patients with NTG and those with POAG.

Major concerns regarding food services based on news media reports during the COVID-19 outbreak using the topic modeling approach.

Background/objectives: Coronavirus disease 2019 (COVID-19) cases were first reported in December 2019, in China, and an increasing number of cases have since been detected all over the world. The purpose of this study was to collect significant news media reports on food services during the COVID-19 crisis and identify public communication and significant concerns regarding COVID-19 for suggesting future directions for the food industry and services.

Subjects/methods: News articles pertaining to food services were extracted from the home pages of major news media websites such as BBC, CNN, and Fox News between March 2020 and February 2021.

Validation of the EuroClonality-NGS DNA capture panel as an integrated genomic tool for lymphoproliferative disorders.

Current diagnostic standards for lymphoproliferative disorders include multiple tests for detection of clonal immunoglobulin (IG) and/or T-cell receptor (TCR) rearrangements, translocations, copy-number alterations (CNAs), and somatic mutations. The EuroClonality-NGS DNA Capture (EuroClonality-NDC) assay was designed as an integrated tool to characterize these alterations by capturing IGH switch regions along with variable, diversity, and joining genes of all IG and TCR loci in addition to clinically relevant genes for CNA and mutation analysis. Diagnostic performance against standard-of-care clinical testing was assessed in a cohort of 280 B- and T-cell malignancies from 10 European laboratories, including 88 formalin-fixed paraffin-embedded samples and 21 reactive lesions.

Effects of Miosis on Anterior Chamber Structure in Glaucoma Implant Surgery.

We investigated changes in anterior chamber (AC) structure after miosis in phakic eyes and pseudophakic eyes with glaucoma. In this prospective study, patients scheduled for glaucoma implant surgery were examined using anterior segment optical coherence tomography before and after miosis. Four AC parameters (AC angle, peripheral anterior chamber (PAC) depth, central anterior chamber (CAC) depth, and AC area) were analyzed before and after miosis, and then compared between phakic and pseudophakic eyes.

Clinical outcomes of Ahmed glaucoma valve implantation without fixation of a plate: The free plate technique.

Objective: This study compared surgical outcomes between free plate Ahmed glaucoma valve (FPAGV) implantation without plate fixation and conventional Ahmed glaucoma valve (CAGV) implantation with plate fixation.

Methods: A retrospective, comparative case series study. Patients with refractory glaucoma who underwent FPAGV or CAGV implantation and were followed >1 year were enrolled consecutively.

Profiles and Clinical Characteristics of Newly Diagnosed Glaucoma in Urban Korea: A Multicenter Study.

Purpose: To explore the clinical characteristics and profiles of newly diagnosed glaucoma subtypes in urban Korea.

Methods: All newly diagnosed glaucoma patients enrolled in the participating ophthalmology outpatient clinics were included. A review of medical history including family history of glaucoma was conducted.

Using the Thickness Map from Macular Ganglion Cell Analysis to Differentiate Retinal Vein Occlusion from Glaucoma.

Purpose: We hypothesized that the thickness map from macular ganglion cell analysis (GCA) acquired from spectral-domain optical coherence tomography can be used to differentiate retinal vein occlusion (RVO) from glaucoma.

Methods: In this retrospective case control study, 37 patients with resolved RVO and 74 patients with primary open-angle glaucoma (POAG) were enrolled. Two independent examiners diagnosed patients with RVO or POAG based on the topographic pattern in the GCA thickness map.

Relationship between Tube Parameters and Corneal Endothelial Cell Damage after Ahmed Glaucoma Valve Implantation: A Comparative Study.

Purpose: We compared the clinical factors, including anterior chamber tube parameters, in patients with and without corneal endothelial cell damage after Ahmed glaucoma valve (AGV) implantation.

Methods: In this retrospective and comparative case series, patients who underwent AGV implantation were enrolled consecutively. Serial specular microscopy was performed before and after AGV implantation.

Comparison of college students' behavior toward nutrition information communication between Korea and the US.

Background/objectives: The expansion of menu labeling to restaurants has created a need to study customers' behavior toward nutrition information. Therefore, the purpose of this research was to compare college students' behavior toward nutrition information communication between Korea and the US. This study consisted of three objectives: 1) to compare the frequency of usage as well as degree of trust regarding smartphone-based communication channels in the acquisition of nutrition information among college students between Korea and the US, 2) to compare knowledge-sharing behavior related to nutrition information among college students between Korea and the US, and 3) to identify the role of country in the process of knowledge-sharing behavior.

Publisher Correction: Pulmonary venous circulating tumor cell dissemination before tumor resection and disease relapse.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Influence of Epiretinal Membranes on the Retinal Nerve Fiber Layer Thickness Measured by Spectral Domain Optical Coherence Tomography in Glaucoma.

Purpose: We investigated changes in the thickness of the peripapillary retinal nerve fiber layer (RNFL) following the onset of an epiretinal membrane (ERM) in glaucoma patients.

Methods: Among regularly monitored glaucoma patients, patients with a newly diagnosed ERM were consecutively enrolled. Before and after the onset of ERM, the RNFL thickness was measured using spectral domain optical coherence tomography, and a visual field examination was performed using a Humphrey field analyzer.

Pulmonary venous circulating tumor cell dissemination before tumor resection and disease relapse.

Approximately 50% of patients with early-stage non-small-cell lung cancer (NSCLC) who undergo surgery with curative intent will relapse within 5 years. Detection of circulating tumor cells (CTCs) at the time of surgery may represent a tool to identify patients at higher risk of recurrence for whom more frequent monitoring is advised. Here we asked whether CellSearch-detected pulmonary venous CTCs (PV-CTCs) at surgical resection of early-stage NSCLC represent subclones responsible for subsequent disease relapse.

Relationship between preoperative high intraocular pressure and retinal nerve fibre layer thinning after glaucoma surgery.

Recent reports show varying results regarding peripapillary retinal nerve fibre layer (RNFL) thickness after intraocular pressure (IOP)-lowering glaucoma surgery. We hypothesised that different levels of the preoperative IOP influence RNFL thickness. A total of 60 patients (60 eyes) with glaucoma, who underwent glaucoma surgery and had a stable postoperative mean IOP < 22 mmHg, were enrolled.

Effect of Preoperative Factor on Intraocular Pressure after Phacoemulsification in Primary Open-angle Glaucoma and Primary Angle-closure Glaucoma.

Purpose: To compare the effects of cataract surgery on intraocular pressure (IOP) according to preoperative factor in primary open-angle glaucoma (POAG) and primary angle-closure glaucoma (PACG).

Methods: The medical records of 75 POAG and 95 PACG patients who underwent cataract surgery were reviewed. We classified POAG patients with a preoperative peak IOP of less than 31 mmHg and less than three medications used before surgery and PACG patients with a peak IOP of less than 42 mmHg, less than three medications used, and peripheral anterior synechiae of less than four clock hours into group 1.

Encapsulated Bleb Excision with Collagen Matrix Implantation Following Failed Ahmed Glaucoma Valve Implantation.

Purpose: To investigate the clinical features and surgical outcomes of encapsulated bleb excision with collagen matrix implantation performed in patients with failed Ahmed glaucoma valve (AGV) implantation.

Methods: Eighteen eyes of 18 patients underwent encapsulated bleb excision and collagen matrix implantation. Patients were divided into two groups by reference to intraocular pressure (IOP) after preoperative ocular massage: group 1, patients who exhibited substantial IOP reductions; and group 2, patients who did not show substantial changes in IOP.

Effect of combined goniotomy and phacoemulsification on intraocular pressure in open-angle glaucoma patients.

Importance: Although goniotomy is known to be successful in treating congenital glaucoma, its effect in adult glaucoma patients remains unclear.

Background: To evaluate the efficacy and safety of goniotomy performed simultaneously with cataract surgery in treatment of open-angle glaucoma (OAG).

Design: Retrospective comparative study.

Vision-related quality of life according to location of visual field loss in patients with glaucoma.

Purpose: To assess influence of the location of visual field (VF) loss on vision-related quality of life (VRQOL) in patients with glaucoma.

Methods: We included 826 patients with primary open-angle glaucoma (POAG) enrolled in the prospectively designed Life Quality of Glaucoma Patients Who Underwent Treatment (LIGHT) study organized by the Korean Glaucoma Society. We divided the integrated binocular visual field (IVF) into four regions and evaluated the associations between Rasch-analysed 25-item National Eye Institute Visual Function Questionnaire (NEI VFQ-25) and location of the IVF using univariate and hierarchical multivariable linear regression.

In silico error correction improves cfDNA mutation calling.

Motivation: Circulating-free DNA (cfDNA) profiling by sequencing is an important minimally invasive protocol for monitoring the mutation profile of solid tumours in cancer patients. Since the concentration of available cfDNA is limited, sample library generation relies on multiple rounds of PCR amplification, during which the accumulation of errors results in reduced sensitivity and lower accuracy.

Results: We present PCR Error Correction (PEC), an algorithm to identify and correct errors in short read sequencing data.

Factors influencing vision-related quality of life according to glaucoma severity.

Purpose: To identify factors influencing vision-related quality of life (VRQOL) according to glaucoma severity.

Methods: A total of 901 patients with varying stages of glaucoma were recruited from the prospectively designed LIGHT (Life Quality of Glaucoma Patients Who Underwent Treatment) study organized by the Korean Glaucoma Society. Participants completed a basic questionnaire collecting socioeconomic status and clinical information, in addition to the 25-item National Eye Institute Visual Function Questionnaire (NEI VFQ-25).

K-mer clustering algorithm using a MapReduce framework: application to the parallelization of the Inchworm module of Trinity.

Background: De novo transcriptome assembly is an important technique for understanding gene expression in non-model organisms. Many de novo assemblers using the de Bruijn graph of a set of the RNA sequences rely on in-memory representation of this graph. However, current methods analyse the complete set of read-derived k-mer sequence at once, resulting in the need for computer hardware with large shared memory.

Difference in patterns of retinal ganglion cell damage between primary open-angle glaucoma and non-arteritic anterior ischaemic optic neuropathy.

Purpose: To compare the patterns of retinal ganglion cell damage between primary open-angle glaucoma (POAG) and non-arteritic anterior ischaemic optic neuropathy (NAION).

Methods: In total, 35 eyes with unilateral NAION, and 70 age- and average peripapillary retinal nerve fibre layer (RNFL) thickness-matched eyes with POAG, were enrolled as disease groups; 35 unaffected fellow eyes of the NAION, and 70 age- and refractive error-matched normal subjects for the POAG, were enrolled as their control groups, respectively. The peripapillary RNFL thickness and macular ganglion cell plus inner plexiform layer (GCIPL) thickness were compared between the disease groups and their controls, and between the two disease groups.

Properties of pattern standard deviation in open-angle glaucoma patients with hemi-optic neuropathy and bi-optic neuropathy.

Purpose: To evaluate the properties of pattern standard deviation (PSD) according to localization of the glaucomatous optic neuropathy.

Methods: We enrolled 242 eyes of 242 patients with primary open-angle glaucoma, with a best-corrected visual acuity ≥ 20/25, and no media opacity. Patients were examined via dilated fundus photography, spectral-domain optical coherence tomography, and Humphrey visual field examination, and divided into those with hemi-optic neuropathy (superior or inferior) and bi-optic neuropathy (both superior and inferior).

Safety and Efficacy of a Membrane-Tube-Type Glaucoma Shunt Device: An Animal Trial.

Purpose: To evaluate the safety and efficacy of a membrane-tube-type glaucoma shunt device (MT-device), which was developed to control intraocular pressure (IOP) with a lower chance of complications than conventional glaucoma surgery, in a rabbit model.

Materials And Methods: The MT-device consists of an expanded polytetrafluoroethylene membrane (thickness 0.2 mm, area 2.