Measurement method of tear meniscus height based on deep learning.

Tear meniscus height (TMH) is an important reference parameter in the diagnosis of dry eye disease. However, most traditional methods of measuring TMH are manual or semi-automatic, which causes the measurement of TMH to be prone to the influence of subjective factors, time consuming, and laborious. To solve these problems, a segmentation algorithm based on deep learning and image processing was proposed to realize the automatic measurement of TMH.

Comparisons of the short-term effectiveness and safety of surgical treatment for neovascular glaucoma: a systematic review and network meta-analysis.

Objective: To compare the effectiveness and safety of the six interventions for neovascular glaucoma.

Design: A systematic review and network meta-analysis.

Methods: Randomised controlled trials and cohort studies which compared the six interventions in neovascular glaucoma were identified using the following databases searched up to 1 September 2020: PubMed, Cochrane Library, Embase and Web of Science.

Visual-Text Reference Pretraining Model for Image Captioning.

People can accurately describe an image by constantly referring to the visual information and key text information of the image. Inspired by this idea, we propose the VTR-PTM (Visual-Text Reference Pretraining Model) for image captioning. First, based on the pretraining model (BERT/UNIML), we design the dual-stream input mode of image reference and text reference and use two different mask modes (bidirectional and sequence to sequence) to realize the VTR-PTM suitable for generating tasks.

Guided Punctures with Ultrasound Volume Navigation in Percutaneous Transforaminal Endoscopic Discectomy: A Technical Note.

Objective: Ultrasound volume navigation (UVN) has been widely used for accurate guidance and decreased radiation exposure. However, few studies have focused on the clinical significance of UVN in guiding percutaneous puncture in percutaneous transforaminal endoscopic discectomy (PTED). We evaluated UVN to guide percutaneous puncture in PTED.

Contrast-Enhanced Ultrasonography Versus Contrast-Enhanced Computed Tomography for Assessment of Residual Tumor From Hepatocellular Carcinoma Treated With Transarterial Chemoembolization: A Meta-analysis.

Objectives: This study reviewed the literature to directly evaluate the diagnostic performance of contrast-enhanced ultrasonography (CEUS) versus contrast-enhanced computed tomography (CECT) for assessing residual tumors of hepatocellular carcinoma treated with transarterial chemoembolization.

Methods: PubMed, Embase, the Cochrane Library, and the China National Knowledge Infrastructure were searched through April 30, 2017. The pooled sensitivity, specificity, positive predictive value, negative predictive value, positive likelihood ratio, negative likelihood ratio, diagnostic odds ratio, and summary receiver operating characteristic curve were calculated and compared to examine the diagnostic performance of CEUS versus CECT.

Discovery of cell-type specific DNA motif grammar in cis-regulatory elements using random Forest.

Background: It has been observed that many transcription factors (TFs) can bind to different genomic loci depending on the cell type in which a TF is expressed in, even though the individual TF usually binds to the same core motif in different cell types. How a TF can bind to the genome in such a highly cell-type specific manner, is a critical research question. One hypothesis is that a TF requires co-binding of different TFs in different cell types.

Impact of sequencing depth and read length on single cell RNA sequencing data of T cells.

Single cell RNA sequencing (scRNA-seq) provides great potential in measuring the gene expression profiles of heterogeneous cell populations. In immunology, scRNA-seq allowed the characterisation of transcript sequence diversity of functionally relevant T cell subsets, and the identification of the full length T cell receptor (TCRαβ), which defines the specificity against cognate antigens. Several factors, e.

CIDR: Ultrafast and accurate clustering through imputation for single-cell RNA-seq data.

Most existing dimensionality reduction and clustering packages for single-cell RNA-seq (scRNA-seq) data deal with dropouts by heavy modeling and computational machinery. Here, we introduce CIDR (Clustering through Imputation and Dimensionality Reduction), an ultrafast algorithm that uses a novel yet very simple implicit imputation approach to alleviate the impact of dropouts in scRNA-seq data in a principled manner. Using a range of simulated and real data, we show that CIDR improves the standard principal component analysis and outperforms the state-of-the-art methods, namely t-SNE, ZIFA, and RaceID, in terms of clustering accuracy.

Transcriptional response to mitochondrial protease IMMP2L knockdown in human primary astrocytes.

IMMP2L encodes the inner membrane peptidase subunit 2, a mitochondrial protease involved in cleaving the space-sorting signals of mitochondrial membrane proteins. IMMP2L has been implicated in Tourette syndrome, but how its dysfunction contributes to the neurodevelopmental phenotype remains unclear. Here we show that IMMP2L transcription requires Topoisomerase I in human primary astrocytes, and characterize the downstream effects of IMMP2L knockdown on gene expression.

Transcriptome analysis of human brain tissue identifies reduced expression of complement complex C1Q Genes in Rett syndrome.

Background: MECP2, the gene mutated in the majority of Rett syndrome cases, is a transcriptional regulator that can activate or repress transcription. Although the transcription regulatory function of MECP2 has been known for over a decade, it remains unclear how transcriptional dysregulation leads to the neurodevelopmental disorder. Notably, little convergence was previously observed between the genes abnormally expressed in the brain of Rett syndrome mouse models and those identified in human studies.

A clinical validation study for the feasibility and reliability of three-dimensional ultrasound-ultrasound automatic image registration.

Purpose: The purpose of our study was to assess the feasibility and reliability of 3D ultrasound-ultrasound (US-US) automatic registration-based analysis of the hepatic vessel tree (VT) (3D VT-based automatic registration) in clinical applications.

Materials And Methods: A total of 70 pairs of 3D ultrasound data were acquired from the livers of 10 healthy volunteers enrolled in the study. An automatic registration method was applied to the acquired volumetric data pairs, and anatomic landmarks were picked by an experienced sonographer as 'ground truth'.

Coexpression networks identify brain region-specific enhancer RNAs in the human brain.

Despite major progress in identifying enhancer regions on a genome-wide scale, the majority of available data are limited to model organisms and human transformed cell lines. We have identified a robust set of enhancer RNAs (eRNAs) expressed in the human brain and constructed networks assessing eRNA-gene coexpression interactions across human fetal brain and multiple adult brain regions. Our data identify brain region-specific eRNAs and show that enhancer regions expressing eRNAs are enriched for genetic variants associated with autism spectrum disorders.

Estimation of the methylation pattern distribution from deep sequencing data.

Background: Bisulphite sequencing enables the detection of cytosine methylation. The sequence of the methylation states of cytosines on any given read forms a methylation pattern that carries substantially more information than merely studying the average methylation level at individual positions. In order to understand better the complexity of DNA methylation landscapes in biological samples, it is important to study the diversity of these methylation patterns.

CD1d induction in solid tumor cells by histone deacetylase inhibitors through inhibition of HDAC1/2 and activation of Sp1.

CD1d is a MHC class-like molecule that presents glycolipids to natural killer T (NKT) cells, then regulates innate and adaptive immunity. The regulation of CD1d gene expression in solid tumors is still largely unknown. Gene expression can be epigenetically regulated by DNA methylation and histone acetylation.