Single-particle cryo-Electron Microscopy (EM) has become a popular technique for determining the structure of challenging biomolecules that are inaccessible to other technologies. Recent advances in automation, both i...
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We study a low-rank iterative solver for the unsteady Navier–Stokes equations for incompressible flows with a stochastic viscosity. The equations are discretized using the stochastic Galerkin method, and we consider ...
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Evidence suggests that brain network dynamics is a key determinant of brain function and dysfunction. Here we propose a new framework to assess the dynamics of brain networks based on recurrence analysis. Our framewor...
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Dimension reduction approach is one of the main data reduction approaches in order to reduce the storage and processing time while maintaining the integrity of the original data. A wide range of dimension reduction ap...
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Systems biology involves the integration of multiple data types (across different data sources) to offer a more complete picture of the biological system being studied. While many existing biological databases are imp...
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ISBN:
(纸本)9781728118680
Systems biology involves the integration of multiple data types (across different data sources) to offer a more complete picture of the biological system being studied. While many existing biological databases are implemented using the traditional SQL (Structured Query Language) database technology, NoSQL database technologies have been explored as a more relationship-based, flexible and scalable method of data integration. In this paper, we describe how to use the Neo4J graph database to integrate a variety of types of data sets in the context of systems vaccinology. Specifically, we have converted into a common graph model diverse types of vaccine response measurement data from the NIH/NIAID ImmPort data repository, pathway data from Reactome, influenza virus strains from WHO, and taxonomic data from NCBI Taxon. While Neo4J provides a graph-based query language (Cypher) for data retrieval, we develop a web-based dashboard for users to easily browse and visualize data without the need to learn Cypher. In addition, we have prototyped a natural language query interface for users to interact with our system. In conclusion, we demonstrate the feasibility of using a graph-based database for storing and querying immunological data with complex biological relationships. Querying a graph database through such relationships has the potential to reveal novel relationships among heterogeneous biological data.
In this paper we present the Markov variation, a smoothness measure which offers a probabilistic interpretation of graph signal smoothness. This measure is then used to develop an optimization framework for graph sign...
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KAGRA, the underground and cryogenic gravitational-wave detector, was operated for its solo observation from February 25 to March 10, 2020, and its first joint observation with the GEO 600 detector from April 7 to Apr...
KAGRA, the underground and cryogenic gravitational-wave detector, was operated for its solo observation from February 25 to March 10, 2020, and its first joint observation with the GEO 600 detector from April 7 to April 21, 2020 (O3GK). This study presents an overview of the input optics systems of the KAGRA detector, which consist of various optical systems, such as a laser source, its intensity and frequency stabilization systems, modulators, a Faraday isolator, mode-matching telescopes, and a high-power beam dump. These optics were successfully delivered to the KAGRA interferometer and operated stably during the observations. The laser frequency noise was observed to limit the detector sensitivity above a few kilohertz, whereas the laser intensity did not significantly limit the detector sensitivity.
Background: Network propagation has been widely used for nearly 20 years to predict gene functions and phenotypes. Despite the popularity of this approach, little attention has been paid to the question of provenance ...
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Diffusion maps are a commonly used kernel-based method for manifold learning, which can reveal intrinsic structures in data and embed them in low dimensions. However, as with most kernel methods, its implementation re...
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