Low-rank latent matrix-factor prediction modeling for generalized high-dimensional matrix-variate regression.

Motivated by diagnosing the COVID-19 disease using two-dimensional (2D) image biomarkers from computed tomography (CT) scans, we propose a novel latent matrix-factor regression model to predict responses that may come from an exponential distribution family, where covariates include high-dimensional matrix-variate biomarkers. A latent generalized matrix regression (LaGMaR) is formulated, where the latent predictor is a low-dimensional matrix factor score extracted from the low-rank signal of the matrix variate through a cutting-edge matrix factor model. Unlike the general spirit of penalizing vectorization plus the necessity of tuning parameters in the literature, instead, our prediction modeling in LaGMaR conducts dimension reduction that respects the geometric characteristic of intrinsic 2D structure of the matrix covariate and thus avoids iteration.

Structural insights into the evolution of the RAG recombinase.

Adaptive immunity in jawed vertebrates relies on the assembly of antigen receptor genes by the recombination activating gene 1 (RAG1)-RAG2 (collectively RAG) recombinase in a reaction known as V(D)J recombination. Extensive biochemical and structural evidence indicates that RAG and V(D)J recombination evolved from the components of a RAG-like (RAGL) transposable element through a process known as transposon molecular domestication. This Review describes recent advances in our understanding of the functional and structural transitions that occurred during RAG evolution.

Mammalian retrovirus-like protein PEG10 packages its own mRNA and can be pseudotyped for mRNA delivery.

Eukaryotic genomes contain domesticated genes from integrating viruses and mobile genetic elements. Among these are homologs of the capsid protein (known as Gag) of long terminal repeat (LTR) retrotransposons and retroviruses. We identified several mammalian Gag homologs that form virus-like particles and one LTR retrotransposon homolog, PEG10, that preferentially binds and facilitates vesicular secretion of its own messenger RNA (mRNA).

Sarco/endoplasmic reticulum Ca2+-ATPase (SERCA) activity is required for V(D)J recombination.

A whole-genome CRISPR/Cas9 screen identified ATP2A2, the gene encoding the Sarco/endoplasmic reticulum Ca2+-ATPase (SERCA) 2 protein, as being important for V(D)J recombination. SERCAs are ER transmembrane proteins that pump Ca2+ from the cytosol into the ER lumen to maintain the ER Ca2+ reservoir and regulate cytosolic Ca2+-dependent processes. In preB cells, loss of SERCA2 leads to reduced V(D)J recombination kinetics due to diminished RAG-mediated DNA cleavage.

Randomized Control Trial on the Effectiveness of Collagen Cross-linking on Bullous Keratopathy.

Purpose: To investigate the long-term effect and safety of collagen cross-linking (CXL) on patients with bullous keratopathy (BK) in a randomized control manner. It is, to our knowledge, the first randomized control study on the effect of CXL on BK.

Methods: Subjects were randomized to receive CXL as in the standard protocol for treating keratoconus or a placebo treatment.

Nucleolar localization of RAG1 modulates V(D)J recombination activity.

V(D)J recombination assembles and diversifies Ig and T cell receptor genes in developing B and T lymphocytes. The reaction is initiated by the RAG1-RAG2 protein complex which binds and cleaves at discrete gene segments in the antigen receptor loci. To identify mechanisms that regulate V(D)J recombination, we used proximity-dependent biotin identification to analyze the interactomes of full-length and truncated forms of RAG1 in pre-B cells.

Incidence and Risk Factors of Retinopathy of Prematurity From 2 Neonatal Intensive Care Units in a Hong Kong Chinese Population.

Purpose: To determine the incidence and risk factors of retinopathy of prematurity (ROP) in very low birth weight (VLBW) preterm Chinese infants.

Design: Retrospective review.

Methods: Medical records were reviewed for all neonates screened for ROP between January 2007 and December 2012 in Hong Kong.

Optimal selective laser trabeculoplasty energy for maximal intraocular pressure reduction in open-angle glaucoma.

Purpose: To identify the optimal energy level to be used in selective laser trabeculoplasty (SLT) for maximal intraocular pressure (IOP) reduction in open-angle glaucoma (OAG) patients.

Patients And Methods: This cohort sequentially recruited OAG subjects in Hong Kong, China during 2011 to 2012. All subjects received a single session of SLT with near confluent spots to 360 degrees of the trabecular meshwork.

Differences in risk factors for retinopathy of prematurity development in paired twins: a Chinese population study.

Purpose: To determine the differences in risk factors for retinopathy of prematurity (ROP) in paired twins.

Methods: A retrospective medical record review was performed for all paired twins screened for ROP between 2007 and 2012. Screening was offered to very low birth weight (≤ 1500 grams) and preterm (≤ 32 weeks) neonates.

Predictors of success in selective laser trabeculoplasty for primary open angle glaucoma in Chinese.

Purpose: To determine the predictors of success for adjuvant selective laser trabeculoplasty (SLT) in Chinese primary open angle glaucoma (POAG) patients.

Methods: This prospective study recruited Chinese subjects with unilateral or bilateral POAG currently taking medication to reduce intraocular pressure (IOP). All subjects received a single session of 360° SLT treatment and continued their medications for 1 month.

Incidence and risk factors for retinopathy of prematurity in extreme low birth weight Chinese infants.

The objective of this study is to determine the incidence and risk factors of retinopathy of prematurity (ROP) in extremely low birth weight (ELBW) Chinese infants. A retrospective medical record review of all ELBW (≤1,000 g) neonates screened for ROP from 2007 to 2012 was performed in Hong Kong. ROP screening was conducted at 2 neonatal intensive care units by 3 pediatric ophthalmologists using the Royal College of Ophthalmologists ROP guideline and the International Classification of ROP.

Predictors of success in selective laser trabeculoplasty for chinese open-angle glaucoma.

Aim: To investigate the determinants of success of selective laser trabeculoplasty (SLT) in Chinese open-angle glaucoma patients.

Methods: This prospective cohort study sequentially recruited Chinese subjects with unilateral or bilateral primary open-angle glaucoma (POAG) or normal tension glaucoma (NTG). All subjects received a single session of 360-degree SLT treatment.

Combining markers with and without the limit of detection.

In this paper, we consider the combination of markers with and without the limit of detection (LOD). LOD is often encountered when measuring proteomic markers. Because of the limited detecting ability of an equipment or instrument, it is difficult to measure markers at a relatively low level.

Homogeneity tests of clustered diagnostic markers with applications to the BioCycle Study.

Diagnostic trials often require the use of a homogeneity test among several markers. Such a test may be necessary to determine the power both during the design phase and in the initial analysis stage. However, no formal method is available for the power and sample size calculation when the number of markers is greater than two and marker measurements are clustered in subjects.