SNPAnalyzer 2.0: A web-based integrated workbench for linkage disequilibrium analysis and association analysis

<p>Abstract</p> <p>Background</p> <p>Since the completion of the HapMap project, huge numbers of individual genotypes have been generated from many kinds of laboratories. The efforts of finding or interpreting genetic association between disease and SNPs/haplotypes have been on-going widely. So, the necessity of the capability to analyze huge data and diverse interpretation of the results are growing rapidly.</p> <p>Results</p> <p>We have developed an advanced tool to perform linkage disequilibrium analysis, and genetic association analysis between disease and SNPs/haplotypes in an integrated web interface. It comprises of four main analysis modules: (i) data import and preprocessing, (ii) haplotype estimation, (iii) LD blocking and (iv) association analysis. Hardy-Weinberg Equilibrium test is implemented for each SNPs in the data preprocessing. Haplotypes are reconstructed from unphased diploid genotype data, and linkage disequilibrium between pairwise SNPs is computed and represented by D', r²and LOD score. Tagging SNPs are determined by using the square of Pearson's correlation coefficient (r²). If genotypes from two different sample groups are available, diverse genetic association analyses are implemented using additive, codominant, dominant and recessive models. Multiple verified algorithms and statistics are implemented in parallel for the reliability of the analysis.</p> <p>Conclusion</p> <p>SNPAnalyzer 2.0 performs linkage disequilibrium analysis and genetic association analysis in an integrated web interface using multiple verified algorithms and statistics. Diverse analysis methods, capability of handling huge data and visual comparison of analysis results are very comprehensive and easy-to-use.</p

BitE : Accelerating Learned Query Optimization in a Mixed-Workload Environment

Although the many efforts to apply deep reinforcement learning to query optimization in recent years, there remains room for improvement as query optimizers are complex entities that require hand-designed tuning of workloads and datasets. Recent research present learned query optimizations results mostly in bulks of single workloads which focus on picking up the unique traits of the specific workload. This proves to be problematic in scenarios where the different characteristics of multiple workloads and datasets are to be mixed and learned together. Henceforth, in this paper, we propose BitE, a novel ensemble learning model using database statistics and metadata to tune a learned query optimizer for enhancing performance. On the way, we introduce multiple revisions to solve several challenges: we extend the search space for the optimal Abstract SQL Plan(represented as a JSON object called ASP) by expanding hintsets, we steer the model away from the default plans that may be biased by configuring the experience with all unique plans of queries, and we deviate from the traditional loss functions and choose an alternative method to cope with underestimation and overestimation of reward. Our model achieves 19.6% more improved queries and 15.8% less regressed queries compared to the existing traditional methods whilst using a comparable level of resources.Comment: This work was done when the first three author were interns in SAP Labs Korea and they have equal contributio

MicroRNA 139-5p coordinates APLNR-CXCR4 crosstalk during vascular maturation

G protein-coupled receptor (GPCR) signalling, including that involving apelin (APLN) and its receptor APLNR, is known to be important in vascular development. How this ligand–receptor pair regulates the downstream signalling cascades in this context remains poorly understood. Here, we show that mice with Apln, Aplnr or endothelial-specific Aplnr deletion develop profound retinal vascular defects, which are at least in part due to dysregulated increase in endothelial CXCR4 expression. Endothelial CXCR4 is negatively regulated by miR-139-5p, whose transcription is in turn induced by laminar flow and APLN/APLNR signalling. Inhibition of miR-139-5p in vivo partially phenocopies the retinal vascular defects of APLN/APLNR deficiency. Pharmacological inhibition of CXCR4 signalling or augmentation of the miR-139-5p-CXCR4 axis can ameliorate the vascular phenotype of APLN/APLNR deficient state. Overall, we identify an important microRNA-mediated GPCR crosstalk, which plays a key role in vascular development

DGU-HAO: A Dataset With Daily Life Objects for Comprehensive 3D Human Action Analysis

The importance of a high-quality dataset availability in 3D human action analysis research cannot be overstated. This paper introduces DGU-HAO (Human Action analysis dataset with daily life Objects). This novel 3D human action multi-modality dataset encompasses four distinct data modalities accompanied by annotation data, including motion capture, RGB video, image, and 3D object modeling data. It features 63 action classes involving interactions with 60 common furniture and electronic devices. Each action class comprises approximately 1,000 motion capture data representing 3D skeleton data and corresponding RGB video and 3D object modeling data, resulting in 67,505 motion capture data samples. It offers comprehensive 3D structural information of the human, RGB images and videos, and point cloud data for 60 objects, collected through the participation of 126 subjects to ensure inclusivity and account for diverse human body types. To validate our dataset, we leveraged MMNet, a 3D human action recognition model, achieving Top-1 accuracy of 91.51&#x0025; and 92.29&#x0025; using the skeleton joint and bone methods, respectively. Beyond human action recognition, our versatile dataset is valuable for various 3D human action analysis research endeavors

Identification of Eupatilin from Artemisia argyi as a Selective PPARα Agonist Using Affinity Selection Ultrafiltration LC-MS

Peroxisome proliferator-activated receptors (PPARs) are key nuclear receptors and therapeutic targets for the treatment of metabolic diseases through the regulation of insulin resistance, diabetes, and dyslipidemia. Although a few drugs that target PPARs have been approved, more diverse and novel PPAR ligands are necessary to improve the safety and efficacy of available drugs. To expedite the search for new natural agonists of PPARs, we developed a screening assay based on ultrafiltration liquid chromatography-mass spectrometry (LC-MS) that is compatible with complex samples such as dietary foods or botanical extracts. The known PPARα and/or PPARγ ligands resveratrol and rosiglitazone were used as positive controls to validate the developed method. When applied to the screening of an Artemisia argyi extract, eupatilin was identified as a selective PPARα ligand. A PPAR competitive binding assay based on FRET detection also confirmed eupatilin as a selective PPARα agonist exhibiting a binding affinity of 1.18 μM (IC50). Furthermore, eupatilin activation of the transcriptional activity of PPARα was confirmed using a cell-based transactivation assay. Thus, ultrafiltration LC-MS is a suitable assay for the identification of PPAR ligands in complex matrixes such as extracts of dietary foods and botanicals

Real-Time Longitudinal Evaluation of Tumor Blood Vessels Using a Compact Preclinical Fluorescence Imaging System

Tumor angiogenesis is enhanced in all types of tumors to supply oxygen and nutrients for their growth and metastasis. With the development of anti-angiogenic drugs, the importance of technology that closely monitors tumor angiogenesis has also been emerging. However, to date, the technology for observing blood vessels requires specialized skills with expensive equipment, thereby limiting its applicability only to the laboratory setting. Here, we used a preclinical optical imaging system for small animals and, for the first time, observed, in real time, the entire process of blood vessel development in tumor-bearing mice injected with indocyanine green. Time-lapse sequential imaging revealed blood vessel volume and blood flow dynamics on a microscopic scale. Upon analyzing fluorescence dynamics at each stage of tumor progression, vessel volume and blood flow were found to increase as the tumor developed. Conversely, these vascular parameters decreased when the mice were treated with angiogenesis inhibitors, which suggests that the effects of drugs targeting angiogenesis can be rapidly and easily screened. The results of this study may help evaluate the efficacy of angiogenesis-targeting drugs by facilitating the observation of tumor blood vessels easily in a laboratory unit without large and complex equipment

SNPAnalyzer 2.0: A web-based integrated workbench for linkage disequilibrium analysis and association analysis-5

Sis, (B) false discovery rate, (C) reconstructed haplotypes.<p><b>Copyright information:</b></p><p>Taken from "SNPAnalyzer 2.0: A web-based integrated workbench for linkage disequilibrium analysis and association analysis"</p><p>http://www.biomedcentral.com/1471-2105/9/290</p><p>BMC Bioinformatics 2008;9():290-290.</p><p>Published online 23 Jun 2008</p><p>PMCID:PMC2453143.</p><p></p

SNPAnalyzer 2.0: A web-based integrated workbench for linkage disequilibrium analysis and association analysis-3

<p><b>Copyright information:</b></p><p>Taken from "SNPAnalyzer 2.0: A web-based integrated workbench for linkage disequilibrium analysis and association analysis"</p><p>http://www.biomedcentral.com/1471-2105/9/290</p><p>BMC Bioinformatics 2008;9():290-290.</p><p>Published online 23 Jun 2008</p><p>PMCID:PMC2453143.</p><p></p