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

Clinical Features of Ehlers-Danlos Syndrome

Background/PurposeEhlers-Danlos syndrome (EDS) is a clinically and genetically heterogeneous connective tissue disorder characterized by hyperextensibility of the skin, hypermobility of joints, and tissue fragility. This retrospective study analyzed the characteristics of patients with EDS.MethodsReview of medical records identified 16 cases of EDS during the study period from November 1997 to October 2002. Data on these patients, including clinical presentation, physical examinations, Beighton score, echocardiogram, bone mineral density findings and clinical classification, were analyzed.ResultsThe age of the patients ranged from 13 months to 36 years. All patients had skin hyperextensibility, joint hypermobility (Beighton score > 5 points), and tissue fragility. Complete bone mineral density study was performed in 11 patients and revealed that all had osteoporosis. Echocardiographic study was performed in 14 patients and showed aortic root dilatation/valve prolapse in 6/14 (43%). Other common features of EDS had the following prevalence: premature rupture of membranes in 3/16 (19%); prematurity in 3/16 (19%); neonatal hypotonia in 5/16 (31%); congenital hip dislocation in 3/16 (19%); unstable gait in 7/16 (44%); bone fracture(s) in 3/16 (19%); motor delay in 3/16 (19%); scoliosis in 3/16 (19%); short stature in 7/16 (44%); and positive family history in 8/16 (50%). All patients had a Beighton score of more than 5 points.ConclusionThe results of this study emphasize the importance of echocardiographic monitoring of aortic size and valvular condition, and assessment of bone mineral density in patients with EDS. Clinical evaluation and counseling should be undertaken prior to pregnancy in patients with EDS because of the risk from labor and vaginal delivery in patients with type IV and the inability to distinguish EDS subtypes in Taiwan due to the unavailability of biochemical assay or molecular mutation analysis as part of standard care

Distributed Training Large-Scale Deep Architectures

Scale of data and scale of computation infrastructures together enable the current deep learning renaissance. However, training large-scale deep architectures demands both algorithmic improvement and careful system configuration. In this paper, we focus on employing the system approach to speed up large-scale training. Via lessons learned from our routine benchmarking effort, we first identify bottlenecks and overheads that hinter data parallelism. We then devise guidelines that help practitioners to configure an effective system and fine-tune parameters to achieve desired speedup. Specifically, we develop a procedure for setting minibatch size and choosing computation algorithms. We also derive lemmas for determining the quantity of key components such as the number of GPUs and parameter servers. Experiments and examples show that these guidelines help effectively speed up large-scale deep learning training

IGF-1/IGFBP-1 increases blastocyst formation and total blastocyst cell number in mouse embryo culture and facilitates the establishment of a stem-cell line

BACKGROUND: Apoptosis occurs frequently for blastocysts cultured in vitro, where conditions are suboptimal to those found in the natural environment. Insulin-like growth factor-1 (IGF-1) plays an important role in preventing apoptosis in the early development of the embryo, as well as in the progressive regulation of organ development. We hypothesize that IGF-1 and its dephosphorylated binding protein (IGFBP-1) may be able to improve embryo culture with an associated reduced cell death, and that the resultant increase in the total cell number of the embryo could increase the chances of establishing an embryonic stem-cell line. RESULTS: In vivo fertilized zygotes were cultured in medium containing supplementary IGF-1, or IGFBP-1/IGF-1. The stages of the resultant embryos were evaluated at noon on day five post-hCG injection. The extent of apoptosis and necrosis was evaluated using Annexin V and propidium iodine staining under fluorescent microscopy. The establishment of embryonic stem-cell lines was performed using the hatching blastocysts that were cultured in the presence of IGF-1 or IGFBP-1/IGF-1. The results show that the rate of blastocyst formation in a tissue-culture system in the presence of IGF-1 was 88.7% and IGFBP-1/IGF-1 it was 94.6%, respectively, and that it was significantly greater than the figure for the control group (81.9%). IGFBP-1/IGF-1 also resulted in a higher hatching rate than was the case for the control group (68.8% vs. 48.6% respectively). IGF-1 also increased the number of Annexin V-free and propidium iodine-free blastocysts in culture (86.8% vs. 75.9% respectively). Total cell number of blastocyst in culture was increased by 18.9% for those examples cultured with dephosphorylated IGFBP-1/IGF-1. For subsequent stem-cell culture, the chances of the successful establishment of a stem-cell line was increased for the IGF-1 and IGFBP-1/IGF-1 groups (IGF-1 vs. IGFBP-1/IGF-1 vs. control: 45.8% vs. 59.6% vs. 27.3% respectively). CONCLUSION: IGF-1 or dephosphorylated IGFBP-1/IGF-1 supplement does result in an anti-apoptotic effect for early embryo development in culture, with a subsequent increased total cell number resulting from cell culture. The effect is beneficial for the later establishment of a stem-cell line

MethylC-analyzer: A comprehensive downstream pipeline for the analysis of genome-wide DNA methylation

DNA methylation is a crucial epigenetic modification involved in multiple biological processes and diseases. Current approaches for measuring genome-wide DNA methylation via bisulfite sequencing (BS-seq) include whole-genome bisulfite sequencing (WGBS), reduced representation bisulfite sequencing (RRBS), and enzymatic methyl-seq (EM-seq). The computational analysis tools available for BS-seq data include customized aligners for mapping bisulfite-converted reads and computational pipelines for downstream data analysis. Current post-alignment methylation tools are specialized for the interpretation of CG methylation, which is known to dominate mammalian genomes, however, non-CG methylation (CHG and CHH, where H refers to A, C, or T) is commonly observed in plants and fungi and is closely associated with gene regulation, transposon silencing, and plant development. Thus, we have developed a MethylC-analyzer to analyze and visualize post-alignment WGBS, RRBS, and EM-seq data focusing on CG. The tool is able to also analyze non-CG sites to enhance deciphering genomes of plants and fungi. By processing aligned data and gene location files, MethylC-analyzer generates a genome-wide view of methylation levels and methylation in user-specified genomic regions. The meta-plot, for example, allows the investigation of DNA methylation within specific genomic elements. Moreover, our tool identifies differentially methylated regions (DMRs) and investigates the enrichment of genomic features associated with variable methylation. MethylC-analyzer functionality is not limited to specific genomes, and we demonstrated its performance on both plant and human BS-seq data. MethylC-analyzer is a Python- and R-based program designed to perform comprehensive downstream analyses of methylation data, providing an intuitive analysis platform for scientists unfamiliar with DNA methylation analysis. It is available as either a standalone version for command-line uses or a graphical user interface (GUI) and is publicly accessible at https://github.com/RitataLU/MethylC-analyzer

QoS routing with link stability in mobile ad hoc networks

Abstract. In this paper, in accordance with requirements of different users and supplying effective usage of limited network resources, we propose a stable QoS routing mechanism to determine a guaranteed route suited for mobile ad hoc wireless networks. The manner exploits the received signal strength (RSS) techniques to estimate the distance and the signal change of the velocity to evaluate the breakaway. To ensure the QoS it chooses a steady path from the source to the destination and tries to reserve the bandwidth. Ultimately, it is clear to find that the performance never decrease even the growth of the overhead and the movement of users via the simulated by ns-2. Introduction Mobile Ad Hoc Wireless Networks (MANET), also called the Ad hoc network, is lots of moving nodes (mobile hosts) communicating with their adjacent mobile node by radio wave. Every node can contact each other without existence infrastructural network. In the Ad hoc network, it differs from cellular wireless networks that need base stations to deliver and receive the packets. Each node plays the role as a router. When one of them wants to deliver packets to destination out of its coverage, intermediate nodes will forward this packet to the next node till the destination node receive it. In traditional cellular wireless networks, generally we need to establish base stations in advance. Fixed nodes far and near connect to the backbone and become a wireless network environment. In this network the customer who wants to communicate with another must locate in the base station coverage. If user moved out of base station's service scope, he can't take the communication. Consequently, we need to establish enough base stations to achieve the objective. Ad hoc networks do not demand fixed network infrastructures and centralized management mechanisms, as well as can be built anytime, anywhere rapidly. Ad hoc networks also have the feature of self-creating, self-organization and elf-management as well as deploy and remove network easily. Ad hoc network has above advantages. However, the Ad hoc network environment has the following restricts [1], including of Network topology instable, Limited energy constrained and Limited network bandwidth-constrained QoS Routing with Link Stability in Mobile A

Traditional Chinese Medicine Diagnosis “ Yang-Xu Zheng

Pathogenesis of sepsis includes complex interaction between pathogen activities and host response, manifesting highly variable signs and symptoms, possibly delaying diagnosis and timely life-saving interventions. This study applies traditional Chinese medicine (TCM) Zheng diagnosis in patients with severe sepsis and septic shock to evaluate its adaptability and use as an early predictor of sepsis mortality. Three-year prospective observational study enrolled 126 septic patients. TCM Zheng diagnosis, Acute Physiology and Chronic Health Evaluation (APACHE) II score, and blood samples for host response cytokines measurement (tumor necrosis factor-α, Interleukin-6, Interleukin-8, Interleukin-10, Interleukin-18) were collected within 24 hours after admission to Intensive Care Unit. Main outcome was 28-day mortality; multivariate logistic regression analysis served to determine predictive variables of the sepsis mortality. APACHE II score, frequency of Nutrient-phase heat, and Qi-Xu and Yang-Xu Zhengs were significantly higher in nonsurvivors. The multivariate logistic regression analysis identified Yang-Xu Zheng as the outcome predictor. APACHE II score and levels of five host response cytokines between patients with and without Yang-Xu Zheng revealed significant differences. Furthermore, cool extremities and weak pulse, both diagnostic signs of Yang-Xu Zheng, were also proven independent predictors of sepsis mortality. TCM diagnosis “Yang-Xu Zheng” may provide a new mortality predictor for septic patients

Ludwigia octovalvis extract improves glycemic control and memory performance in diabetic mice

Ethnopharmacological relevance Ludwigia octovalvis (Jacq.) P.H. Raven (Onagraceae) extracts have historically been consumed as a healthful drink for treating various conditions, including edema, nephritis, hypotension and diabetes. Aim of the study We have previously shown that Ludwigia octovalvis extract (LOE) can significantly extend lifespan and improve age-related memory deficits in Drosophila melanogaster through activating AMP-activated protein kinase (AMPK). Since AMPK has become a critical target for treating diabetes, we herein investigate the anti-hyperglycemic potential of LOE. Materials and methods Differentiated C2C12 muscle cells, HepG2 hepatocellular cells, streptozotocin (STZ)-induced diabetic mice and high fat diet (HFD)-induced diabetic mice were used to investigate the anti-hyperglycemic potential of LOE. The open field test and novel object recognition test were used to evaluate spontaneous motor activity and memory performance of HFD-induced diabetic mice. Results In differentiated C2C12 muscle cells and HepG2 hepatocellular cells, treatments with LOE and its active component (β-sitosterol) induced significant AMPK phosphorylation. LOE also enhanced uptake of a fluorescent glucose derivative (2-NBDG) and inhibited glucose production in these cells. The beneficial effects of LOE were completely abolished when an AMPK inhibitor, dorsomorphin, was added to the culture system, suggesting that LOE requires AMPK activation for its action in vitro. In streptozotocin (STZ)-induced diabetic mice, we found that both LOE and β-sitosterol induced an anti-hyperglycemic effect comparable to that of metformin, a drug that is commonly prescribed to treat diabetes. Moreover, LOE also improved glycemic control and memory performance of mice fed a HFD. Conclusions These results indicate that LOE is a potent anti-diabetic intervention that may have potential for future clinical applications