A Bayesian Hierarchical Model to Derive Novel Gene Networks from Gene Ontology Fingerprints

We developed a Bayesian hierarchical model to identify gene networks based on the similarity score generated from comparing the gene ontology fingerprints of gene pairs. Genes in this network were assumed to have similar biological functions that can be indicated by their ontology fingerprints. Our results indicate that different pathways show consistent score threshold that allow us to distinguish biological relevant gene—gene connections in the network

Study on Hypertext Reading in Students’ Autonomous Learning

The study was conducted on 100 non-English major sophomores for one semester in a University of Shanxi Province in China with the purpose to explore the variation of sophomore’s learning achievements through hypertext English reading based on Schematic Theory and Constructionist Theory. The results show that hypertext reading is beneficial to improve students’ learning, which is consistent with the conclusion that hypertext reading model is relatively a feasible and efficient way to improve students’ autonomous learning and achievement

A genome-wide MeSH-based literature mining system predicts implicit gene-to-gene relationships and networks

Abstract Background The large amount of literature in the post-genomics era enables the study of gene interactions and networks using all available articles published for a specific organism. MeSH is a controlled vocabulary of medical and scientific terms that is used by biomedical scientists to manually index articles in the PubMed literature database. We hypothesized that genome-wide gene-MeSH term associations from the PubMed literature database could be used to predict implicit gene-to-gene relationships and networks. While the gene-MeSH associations have been used to detect gene-gene interactions in some studies, different methods have not been well compared, and such a strategy has not been evaluated for a genome-wide literature analysis. Genome-wide literature mining of gene-to-gene interactions allows ranking of the best gene interactions and investigation of comprehensive biological networks at a genome level. Results The genome-wide GenoMesh literature mining algorithm was developed by sequentially generating a gene-article matrix, a normalized gene-MeSH term matrix, and a gene-gene matrix. The gene-gene matrix relies on the calculation of pairwise gene dissimilarities based on gene-MeSH relationships. An optimized dissimilarity score was identified from six well-studied functions based on a receiver operating characteristic (ROC) analysis. Based on the studies with well-studied Escherichia coli and less-studied Brucella spp., GenoMesh was found to accurately identify gene functions using weighted MeSH terms, predict gene-gene interactions not reported in the literature, and cluster all the genes studied from an organism using the MeSH-based gene-gene matrix. A web-based GenoMesh literature mining program is also available at: http://genomesh.hegroup.org. GenoMesh also predicts gene interactions and networks among genes associated with specific MeSH terms or user-selected gene lists. Conclusions The GenoMesh algorithm and web program provide the first genome-wide, MeSH-based literature mining system that effectively predicts implicit gene-gene interaction relationships and networks in a genome-wide scope.http://deepblue.lib.umich.edu/bitstream/2027.42/112478/1/12918_2013_Article_1166.pd

High-efficient optical frequency mixing in all-dielectric metasurface empowered by multiple bound states in the continuum

We present nonlinear optical four-wave mixing in a silicon nanodisk dimer metasurface. Under the oblique incident plane waves, the designed metasurface exhibits a multi-resonant feature with simultaneous excitations of three quasi-bound states in the continuum (BIC). Through employing these quasi-BIC with maximizing electric field energy at the input bump wavelengths, significant enhancements of third-order nonlinear processes including third-harmonic generation, degenerate and non-degenerate four-wave mixing are demonstrated, giving rise to ten new frequencies in the visible wavelengths. This work may lead to a new frontier of ultracompact optical mixer for applications in optical circuitry, ultrasensitive sensing, and quantum nanophotonics

Longitudinal survey of microbiome associated with particulate matter in a megacity.

BackgroundWhile the physical and chemical properties of airborne particulate matter (PM) have been extensively studied, their associated microbiome remains largely unexplored. Here, we performed a longitudinal metagenomic survey of 106 samples of airborne PM2.5 and PM10 in Beijing over a period of 6 months in 2012 and 2013, including those from several historically severe smog events.ResultsWe observed that the microbiome composition and functional potential were conserved between PM2.5 and PM10, although considerable temporal variations existed. Among the airborne microorganisms, Propionibacterium acnes, Escherichia coli, Acinetobacter lwoffii, Lactobacillus amylovorus, and Lactobacillus reuteri dominated, along with several viral species. We further identified an extensive repertoire of genes involved in antibiotic resistance and detoxification, including transporters, transpeptidases, and thioredoxins. Sample stratification based on Air Quality Index (AQI) demonstrated that many microbial species, including those associated with human, dog, and mouse feces, exhibit AQI-dependent incidence dynamics. The phylogenetic and functional diversity of air microbiome is comparable to those of soil and water environments, as its composition likely derives from a wide variety of sources.ConclusionsAirborne particulate matter accommodates rich and dynamic microbial communities, including a range of microbial elements that are associated with potential health consequences

The impact of mouth breathing on dentofacial development: A concise review

Mouth breathing is one of the most common deleterious oral habits in children. It often results from upper airway obstruction, making the air enter completely or partially through oral cavity. In addition to nasal obstruction caused by various kinds of nasal diseases, the pathological hypertrophy of adenoids and/or tonsils is often the main etiologic factor of mouth breathing in children. Uncorrected mouth breathing can result in abnormal dental and maxillofacial development and affect the health of dentofacial system. Mouth breathers may present various types of growth patterns and malocclusion, depending on the exact etiology of mouth breathing. Furthermore, breathing through the oral cavity can negatively affect oral health, increasing the risk of caries and periodontal diseases. This review aims to provide a summary of recent publications with regard to the impact of mouth breathing on dentofacial development, describe their consistencies and differences, and briefly discuss potential reasons behind inconsistent findings

Leveraging Architectural Approaches in Web3 Applications -- A DAO Perspective Focused

Architectural design contexts contain a set of factors that influence software application development. Among them, \textit{\textbf{organizational}} design contexts consist of high-level company concerns and how it is structured, for example, stakeholders and development schedule, heavily impacting design considerations. Decentralized Autonomous Organization (DAO), as a vital concept in the Web3 space, is an organization constructed by automatically executed rules such as via smart contracts, holding features of the permissionless committee, transparent proposals, and fair contribution by stakeholders. In this work, we conduct a systematic literature review to summarize how DAO is structured as well as explore its benefits\&challenges in Web3 applications