ATACgraph: Profiling genome-wide chromatin accessibility from ATAC-seq

Assay for transposase-accessible chromatin using sequencing data (ATAC-seq) is an efficient and precise method for revealing chromatin accessibility across the genome. Most of the current ATAC-seq tools follow chromatin immunoprecipitation sequencing (ChIP-seq) strategies that do not consider ATAC-seq-specific properties. To incorporate specific ATAC-seq quality control and the underlying biology of chromatin accessibility, we developed a bioinformatics software named ATACgraph for analyzing and visualizing ATAC-seq data. ATACgraph profiles accessible chromatin regions and provides ATAC-seq-specific information including definitions of nucleosome-free regions (NFRs) and nucleosome-occupied regions. ATACgraph also allows identification of differentially accessible regions between two ATAC-seq datasets. ATACgraph incorporates the docker image with the Galaxy platform to provide an intuitive user experience via the graphical interface. Without tedious installation processes on a local machine or cloud, users can analyze data through activated websites using pre-designed workflows or customized pipelines composed of ATACgraph modules. Overall, ATACgraph is an effective tool designed for ATAC-seq for biologists with minimal bioinformatics knowledge to analyze chromatin accessibility. ATACgraph can be run on any ATAC-seq data with no limit to specific genomes. As validation, we demonstrated ATACgraph on human genome to showcase its functions for ATAC-seq interpretation. This software is publicly accessible and can be downloaded at https://github.com/RitataLU/ATACgraph

3D-PL: Domain Adaptive Depth Estimation with 3D-aware Pseudo-Labeling

For monocular depth estimation, acquiring ground truths for real data is not easy, and thus domain adaptation methods are commonly adopted using the supervised synthetic data. However, this may still incur a large domain gap due to the lack of supervision from the real data. In this paper, we develop a domain adaptation framework via generating reliable pseudo ground truths of depth from real data to provide direct supervisions. Specifically, we propose two mechanisms for pseudo-labeling: 1) 2D-based pseudo-labels via measuring the consistency of depth predictions when images are with the same content but different styles; 2) 3D-aware pseudo-labels via a point cloud completion network that learns to complete the depth values in the 3D space, thus providing more structural information in a scene to refine and generate more reliable pseudo-labels. In experiments, we show that our pseudo-labeling methods improve depth estimation in various settings, including the usage of stereo pairs during training. Furthermore, the proposed method performs favorably against several state-of-the-art unsupervised domain adaptation approaches in real-world datasets.Comment: Accepted in ECCV 2022. Project page: https://ccc870206.github.io/3D-PL

Banner Advertisements Scheduling to Maximize Space Utilization

One of the commercial Internet applications is banner advertisement, which is also the major source of income for portal websites. Limited research works address the issues of efficiently scheduling advertisement requests into available advertisement banners in view of profitably. This paper proposes a new model for scheduling banner advertisements that more closely resembles the Internet business world. In the proposed model, we apply a feasible time window to each candidate order, and schedule advertisements into various predefined banner spaces on the webpage. This approach allows different pricing strategies according to banner types and is contrary to previous research models that schedule and price by banner space sharing. Each order for ad space will demand a certain frequency for each type of banner. The goal is to select and schedule requests to achieve the maximum ad capacity utilization. We first give a mathematical formulation to formally describe the problem. Due to the computational complexity of the studied problem, we seek to produce approximate solutions in a reasonable time. A three-phase heuristic is developed to cope with this problem. In addition, an upper bound on profits is developed. Computational experiments are designed to examine the performance of the heuristic. Statistics from the experiments reveal that the heuristic can successfully fill up to 97% of ad spaces

Inhibitors of SARS-CoV entry--identification using an internally-controlled dual envelope pseudovirion assay.

Severe acute respiratory syndrome-associated coronavirus (SARS-CoV) emerged as the causal agent of an endemic atypical pneumonia, infecting thousands of people worldwide. Although a number of promising potential vaccines and therapeutic agents for SARS-CoV have been described, no effective antiviral drug against SARS-CoV is currently available. The intricate, sequential nature of the viral entry process provides multiple valid targets for drug development. Here, we describe a rapid and safe cell-based high-throughput screening system, dual envelope pseudovirion (DEP) assay, for specifically screening inhibitors of viral entry. The assay system employs a novel dual envelope strategy, using lentiviral pseudovirions as targets whose entry is driven by the SARS-CoV Spike glycoprotein. A second, unrelated viral envelope is used as an internal control to reduce the number of false positives. As an example of the power of this assay a class of inhibitors is reported with the potential to inhibit SARS-CoV at two steps of the replication cycle, viral entry and particle assembly. This assay system can be easily adapted to screen entry inhibitors against other viruses with the careful selection of matching partner virus envelopes

Imaging of Renal Tuberculosis in Eastern Taiwan: Correlation with Clinical Course and Different Communities

Hualien, located in eastern Taiwan, is a relatively isolated district. The population is composed of different ethnic communities. Our hospital is the only medical center in eastern Taiwan, so is the most important referral hospital for epidemic diseases. After reviewing our collected cases of renal tuberculosis (TB), we observed a great diversity in staging and outcomes. The aim of this study was to classify different imaging presentations and clinical outcomes in the ethnic communities represented by these cases (non-aboriginal and aboriginal). We retrospectively reviewed 22 cases from 1991 to 2001. We reviewed laboratory data, radiologic reports, and clinical outcomes. Before TB was proved by biopsy or culture, patients were not treated with an anti-TB regimen. Roentgenography showed that 68% of patients had renal calcification, 59% had dilated calyces, 55% had lung involvement, and 41% had auto-nephrectomy. The proportion of mild and severe forms was significantly different between aboriginal and non-aboriginal groups (0.05 > p ≥ 0.00409). From this series, we recommend routine plain film roentgenography, including chest roentgenography and kidney, ureter, and bladder or abdominal roentgenography, followed by intravenous urography or computerized tomography as investigative tools for renal TB. Based on the significantly different outcomes of the disease between aboriginal and non-aboriginal groups, a stronger health education program for the isolated district in eastern Taiwan is necessary

Exploring the challenges of taiwanese nurses in the COVID-19 post-pandemic era

In the wake of the COVID-19 pandemic, the fluctuating nurse resignation rates highlighted an understudied area in healthcare: post-pandemic challenges in clinical settings. This study, conducted from May to November 2023, employed a qualitative inquiry using focus groups to delve into these challenges. Six focus group sessions, involving 33 nurse participants recruited through snowball sampling from various hospital settings were conducted to explore their clinical experiences during and after the pandemic. Thematic analysis revealed two primary themes: the 'Invisibility of Nurses' within the healthcare system and the 'Moral Duty of Nursing Practice'. These findings illuminate a tension between the overlooked role of nurses and their ethical obligations, underscoring a critical need for policy reassessment. The study advocates for systemic changes, particularly in the undervaluation of the nursing profession and the National Health Insurance system, to address the poor working environment and mitigate long-term nursing shortages. This research deepens understanding of post-pandemic nursing workforce challenges in Taiwan, highlighting the need for policy evolution to enhance recognition and support for the nursing industry. It is suggested to provide tangible compensation to acknowledge nurses' daily care and health education for patients. A healthier working environment can be enhanced by collaborative efforts between healthcare institutions and nurses

Clonal dissemination of invasive and colonizing clonal complex 1 of serotype VI group B Streptococcus in central Taiwan

Background/PurposeThe aim of this study was to investigate clinical presentation, serotype distribution and genetic correlation of group B streptococcus (GBS) diseases. Since serotype VI prevalence far exceeded that reported in prior studies, genetic relationship of isolates was further analyzed.MethodsGBS isolates obtaining from patients with invasive diseases and pregnant women with colonization between June 2007 and December 2010 were analyzed. All isolates were tested for serotypes by multiplex PCR assay and pulsed-field gel electrophoresis (PFGE). Serotype VI isolates were further analyzed by multilocus sequence typing (MLST).ResultsA total of 134 GBS isolates were recovered from blood of 126 patients with invasive disease (94.0%) and anogenital swabs of 8 pregnant women (6.0%). Most common serotype was Ib (21.6%), followed by V (20.1%), VI (18.7%), III (15.7%), II (11.9 %), Ia (11.2%), and IX (0.7%). Serotype VI was also the leading type in infants with early onset disease (EOD; 3/8, 37.5%) and colonizing pregnant women (3/8, 37.5%). PFGE distinguished 33 pulsotypes, reflecting genetic diversity among GBS isolates. Among 25 serotype VI isolates tested, 14 were ST-1, seven were ST-679, three were ST-678, one was ST-681, and distributed into four PFGE pulsotypes. ST-678, ST-679, and ST-681 were novel sequence types; ST-678 and ST-679 are single-locus variants of ST-1 that belongs to clonal complex (CC) 1.ConclusionCC1 dissemination of serotype VI GBS thus emerges as an important invasive pathogen in infants and nonpregnant adults in central Taiwan. Serotype prevalence of GBS must be continuously monitored geographically to guide prevention strategy of GBS vaccines