Direct observation of DNA target searching and cleavage by CRISPR-Cas12a

Cas12a (also called Cpf1) is a representative type V-A CRISPR effector RNA-guided DNA endonuclease, which provides an alternative to type II CRISPR-Cas9 for genome editing. Previous studies have revealed that Cas12a has unique features distinct from Cas9, but the detailed mechanisms of target searching and DNA cleavage by Cas12a are still unclear. Here, we directly observe this entire process by using single-molecule fluorescence assays to study Cas12a from Acidaminococcus sp. (AsCas12a). We determine that AsCas12a ribonucleoproteins search for their on-target site by a one-dimensional diffusion along elongated DNA molecules and induce cleavage in the two DNA strands in a well-defined order, beginning with the non-target strand. Furthermore, the protospacer-adjacent motif (PAM) for AsCas12a makes only a limited contribution of DNA unwinding during R-loop formation and shows a negligible role in the process of DNA cleavage, in contrast to the Cas9 PAM.

Korea HIV/AIDS Cohort Study: study design and baseline characteristics

The number of persons infected by HIV/AIDS has consistently increased in Korea since the first case of HIV/AIDS infection in 1985 and reached 15,208 by 2016. About 1,100 new patients with HIV/ AIDS infections have emerged every year since 2013. In Korea, the Korea HIV/AIDS Cohort Study was established for the evidenced-based prevention, treatment, and effective management of patients infected with human immunodeficiency virus (HIV) in December 2006. This study monitored 1,438 patients, who accounted for about 10% of all patients with HIV/AIDS in Korea, for 10 years with the following aims: (1) to develop an administrative system for the establishment of a HIV/AIDS cohort-based study; (2) to standardize methodologies and the case report forms; and (3) to standardize multi-cohort data and develop a data cleaning method. This study aims to monitor at least 1,000 patients (excluding those for whom investigation had been completed) per year (estimated number of patients who can be monitored by January 2018: 939). By December 2016, the sex distribution was 93.3% for men, and 6.7% for women (gender ratio, 13.9:1.0), and 98.9% of all participants were Korean. More than 50.0% of the participants were confirmed as HIV positive after 2006. This study reports competitive, long-term research that aimed to develop policies for the prevention of chronic infectious diseases for patients with HIV. The data collected over the last decade will be used to develop indices for HIV treatment and health promotion

Subspace clustering of data streams: new algorithms and effective evaluation measures

Nowadays, most streaming data sources are becoming high dimensional. Accordingly, subspace stream clustering, which aims at finding evolving clusters within subgroups of dimensions, has gained a significant importance. However, in spite of the rich literature of subspace and projected clustering algorithms on static data, only three stream projected algorithms are available. Additionally, existing subspace clustering evaluation measures are mainly designed for static data, and cannot reflect the quality of the evolving nature of data streams. On the other hand, available stream clustering evaluation measures care only about the errors of the full-space clustering but not the quality of subspace clustering. In this article we present a method for designing new stream subspace and projected algorithms. We propose also, to the first of our knowledge, the first subspace clustering measure that is designed for streaming data, called SubCMM: Subspace Cluster Mapping Measure. SubCMM is an effective evaluation measure for stream subspace clustering that is able to handle errors caused by emerging, moving, or splitting subspace clusters. Additionally, we propose a novel method for using available offline subspace clustering measures for data streams over the suggested new algorithms within the Subspace MOA framework

Sensor Fusion of Cameras and a Laser for City-Scale 3D Reconstruction

This paper presents a sensor fusion system of cameras and a 2D laser sensorfor large-scale 3D reconstruction. The proposed system is designed to capture data on afast-moving ground vehicle. The system consists of six cameras and one 2D laser sensor,and they are synchronized by a hardware trigger. Reconstruction of 3D structures is doneby estimating frame-by-frame motion and accumulating vertical laser scans, as in previousworks. However, our approach does not assume near 2D motion, but estimates free motion(including absolute scale) in 3D space using both laser data and image features. In orderto avoid the degeneration associated with typical three-point algorithms, we present a newalgorithm that selects 3D points from two frames captured by multiple cameras. The problemof error accumulation is solved by loop closing, not by GPS. The experimental resultsshow that the estimated path is successfully overlaid on the satellite images, such that thereconstruction result is very accurate

Mucoadhesive Phenolic Pectin Hydrogels for Saliva Substitute and Oral Patch

Oral disease is one of the most common conditions worldwide, negatively affecting general health, reducing the quality of life, and often developing into systemic illness. However, the design of therapeutic agents for oral diseases is challenging due to various unique features of the oral cavity, including its wet and dynamic environment and curved shape. Herein, the development of highly biocompatible mucoadhesive functional hydrogels for oral applications is reported, generated by introducing bio-inspired phenolic moieties into a pectin polymer. Pyrogallol-functionalized pectin (Pec-PG) can be crosslinked in situ via autoxidation without chemical agents and readily fabricated as various formulations. Sprayable Pec-PG hydrogel exhibits strong mucoadhesion and outstanding hydration ability ex vivo and in vivo, thus displaying significant potential as a novel saliva substitute for dry mouth. The authors further show that topical application of mucoadhesive Pec-PG patches pre-loaded with corticosteroid significantly promotes the repair of diabetic oral ulcer tissue via prolonged drug release, free radical scavenging, and physical barrier effects. Moreover, similar applications for oral ulcer treatment using a pectin hydrogel modified with catechol (Pec-CA), another phenolic moiety are demonstrated. Together, these findings suggest that mucoadhesive phenolic pectin derivatives can provide highly biocompatible, convenient, and effective hydrogel platforms for treating oral diseases. © 2023 Wiley-VCH GmbH.11Nsciescopu

Smoothed quantile residual life regression analysis with application to the Korea HIV/AIDS cohort study

Abstract Background The residual life of a patient with human immunodeficiency virus (HIV) is of major interest to patients and their physicians. While existing analyses of HIV patient survival focus mostly on data collected at baseline, residual life analysis allows for dynamic analysis based on additional data collected over a period of time. As survival times typically exhibit a right-skewed distribution, the median provides a more useful summary of the underlying distribution than the mean. In this paper, we propose an efficient inference procedure that fits a semiparametric quantile regression model assessing the effect of longitudinal biomarkers on the residual life of HIV patients until the development of dyslipidemia, a disease becoming more prevalent among those with HIV. Methods For estimation of model parameters, we propose an induced smoothing method that smooths nonsmooth estimating functions based on check functions. For variance estimation, we propose an efficient resampling-based estimator. The proposed estimators are theoretically justified. Simulation studies are used to evaluate their finite sample performances, including their prediction accuracy. We analyze the Korea HIV/AIDS cohort study data to examine the effects of CD4 (cluster of differentiation 4) cell count on the residual life of HIV patients to the onset of dyslipidemia. Results The proposed estimator is shown to be consistent and normally distributed asymptotically. Under various simulation settings, our estimates are approximately unbiased. Their variances estimates are close to the empirical variances and their computational efficiency is superior to that of the nonsmooth counterparts. Two measures of prediction performance indicate that our method adequately reflects the dynamic character of longitudinal biomarkers and residual life. The analysis of the Korea HIV/AIDS cohort study data shows that CD4 cell count is positively associated with residual life to the onset of dyslipidemia but the effect is not statistically significant. Conclusions Our method enables direct prediction of residual lifetimes with a dynamic feature that accommodates data accumulated at different times. Our estimator significantly improves computational efficiency in variance estimation compared to the existing nonsmooth estimator. Analysis of the HIV/AIDS cohort study data reveals dynamic effects of CD4 cell count on the residual life to the onset of dyslipidemia

Structure-From-Motion in 3D Space Using 2D Lidars

This paper presents a novel structure-from-motion methodology using 2D lidars (Light Detection And Ranging). In 3D space, 2D lidars do not provide sufficient information for pose estimation. For this reason, additional sensors have been used along with the lidar measurement. In this paper, we use a sensor system that consists of only 2D lidars, without any additional sensors. We propose a new method of estimating both the 6D pose of the system and the surrounding 3D structures. We compute the pose of the system using line segments of scan data and their corresponding planes. After discarding the outliers, both the pose and the 3D structures are refined via nonlinear optimization. Experiments with both synthetic and real data show the accuracy and robustness of the proposed method

Autonomous homing based on laser-camera fusion system

Building maps of unknown environments is a critical factor for autonomous navigation and homing, and this problem is especially challenging in large-scale environments. Recently, sensor fusion systems such as combinations of cameras and laser sensors have become popular in the effort to ensure a general level of performance in this task. In this paper, we present a new homing method in a large-scale environment using a laser-camera fusion system. Instead of fusing data to form a single map builder, we adaptively select sensor data to handle environments which contain ambiguity. For autonomous homing, we propose a new mapping strategy for building a hybrid map and a return strategy for selecting the next target waypoints efficiently. The experimental results demonstrate that the proposed algorithm enables the autonomous homing of a robot in a large-scale indoor environments in real time. © 2012 IEEE.1

Additional file 1 of Smoothed quantile residual life regression analysis with application to the Korea HIV/AIDS cohort study

Additional file 1. Additional results of simulation studies

Direct observation of DNA target searching and cleavage by CRISPR-Cas12a

Cas12a (also called Cpf1) is a representative type V-A CRISPR effector RNA-guided DNA endonuclease, which provides an alternative to type II CRISPR-Cas9 for genome editing. Previous studies have revealed that Cas12a has unique features distinct from Cas9, but the detailed mechanisms of target searching and DNA cleavage by Cas12a are still unclear. Here, we directly observe this entire process by using single-molecule fluorescence assays to study Cas12a from Acidaminococcus sp. (AsCas12a). We determine that AsCas12a ribonucleoproteins search for their on-target site by a one-dimensional diffusion along elongated DNA molecules and induce cleavage in the two DNA strands in a well-defined order, beginning with the non-target strand. Furthermore, the protospacer-adjacent motif (PAM) for AsCas12a makes only a limited contribution of DNA unwinding during R-loop formation and shows a negligible role in the process of DNA cleavage, in contrast to the Cas9 PAM. © 2018 The Author(s