A Computational Method Based on the Integration of Heterogeneous Networks for Predicting Disease-Gene Associations

The identification of disease-causing genes is a fundamental challenge in human health and of great importance in improving medical care, and provides a better understanding of gene functions. Recent computational approaches based on the interactions among human proteins and disease similarities have shown their power in tackling the issue. In this paper, a novel systematic and global method that integrates two heterogeneous networks for prioritizing candidate disease-causing genes is provided, based on the observation that genes causing the same or similar diseases tend to lie close to one another in a network of protein-protein interactions. In this method, the association score function between a query disease and a candidate gene is defined as the weighted sum of all the association scores between similar diseases and neighbouring genes. Moreover, the topological correlation of these two heterogeneous networks can be incorporated into the definition of the score function, and finally an iterative algorithm is designed for this issue. This method was tested with 10-fold cross-validation on all 1,126 diseases that have at least a known causal gene, and it ranked the correct gene as one of the top ten in 622 of all the 1,428 cases, significantly outperforming a state-of-the-art method called PRINCE. The results brought about by this method were applied to study three multi-factorial disorders: breast cancer, Alzheimer disease and diabetes mellitus type 2, and some suggestions of novel causal genes and candidate disease-causing subnetworks were provided for further investigation

Potential of Core-Collapse Supernova Neutrino Detection at JUNO

JUNO is an underground neutrino observatory under construction in Jiangmen, China. It uses 20kton liquid scintillator as target, which enables it to detect supernova burst neutrinos of a large statistics for the next galactic core-collapse supernova (CCSN) and also pre-supernova neutrinos from the nearby CCSN progenitors. All flavors of supernova burst neutrinos can be detected by JUNO via several interaction channels, including inverse beta decay, elastic scattering on electron and proton, interactions on C12 nuclei, etc. This retains the possibility for JUNO to reconstruct the energy spectra of supernova burst neutrinos of all flavors. The real time monitoring systems based on FPGA and DAQ are under development in JUNO, which allow prompt alert and trigger-less data acquisition of CCSN events. The alert performances of both monitoring systems have been thoroughly studied using simulations. Moreover, once a CCSN is tagged, the system can give fast characterizations, such as directionality and light curve

Detection of the Diffuse Supernova Neutrino Background with JUNO

As an underground multi-purpose neutrino detector with 20 kton liquid scintillator, Jiangmen Underground Neutrino Observatory (JUNO) is competitive with and complementary to the water-Cherenkov detectors on the search for the diffuse supernova neutrino background (DSNB). Typical supernova models predict 2-4 events per year within the optimal observation window in the JUNO detector. The dominant background is from the neutral-current (NC) interaction of atmospheric neutrinos with 12C nuclei, which surpasses the DSNB by more than one order of magnitude. We evaluated the systematic uncertainty of NC background from the spread of a variety of data-driven models and further developed a method to determine NC background within 15\% with {\it{in}} {\it{situ}} measurements after ten years of running. Besides, the NC-like backgrounds can be effectively suppressed by the intrinsic pulse-shape discrimination (PSD) capabilities of liquid scintillators. In this talk, I will present in detail the improvements on NC background uncertainty evaluation, PSD discriminator development, and finally, the potential of DSNB sensitivity in JUNO

Real-time Monitoring for the Next Core-Collapse Supernova in JUNO

Core-collapse supernova (CCSN) is one of the most energetic astrophysical events in the Universe. The early and prompt detection of neutrinos before (pre-SN) and during the SN burst is a unique opportunity to realize the multi-messenger observation of the CCSN events. In this work, we describe the monitoring concept and present the sensitivity of the system to the pre-SN and SN neutrinos at the Jiangmen Underground Neutrino Observatory (JUNO), which is a 20 kton liquid scintillator detector under construction in South China. The real-time monitoring system is designed with both the prompt monitors on the electronic board and online monitors at the data acquisition stage, in order to ensure both the alert speed and alert coverage of progenitor stars. By assuming a false alert rate of 1 per year, this monitoring system can be sensitive to the pre-SN neutrinos up to the distance of about 1.6 (0.9) kpc and SN neutrinos up to about 370 (360) kpc for a progenitor mass of 30$M_{\odot}$ for the case of normal (inverted) mass ordering. The pointing ability of the CCSN is evaluated by using the accumulated event anisotropy of the inverse beta decay interactions from pre-SN or SN neutrinos, which, along with the early alert, can play important roles for the followup multi-messenger observations of the next Galactic or nearby extragalactic CCSN.Comment: 24 pages, 9 figure

Multiple whole genome comparison in bluejay

Bibliography: p. 168-173Some pages are in colour

A Meta-Analysis of Randomized Controlled Trials on Acupuncture for Amblyopia

Objective. To assess the evidence of efficacy and safety of acupuncture for amblyopia and analyze the current situation of its clinical setting. Methods. We systemically searched Wanfang, Chongqing Weipu Database for Chinese Technical Periodicals (VIP), China National Knowledge Infrastructure (CNKI), and PubMed. Published randomized controlled trials (RCT) and controlled clinical trials (CCT) that evaluated the effect of acupuncture for amblyopia compared with conventional treatment were identified. The methodological quality of the included trials was assessed based on the Jadad scale. Data synthesis was facilitated using RevMan 5.1. Results. Fourteen trials involving 2662 participants satisfied the minimum criteria for meta-analysis. The evidence showed that the total effective rate of treatment within the group receiving acupuncture was higher than that in conventional group; there were statistically significant differences between groups (polled random effects model (RR) = 1.17, 95% confidence interval (1.11, 1.24), Z=5.56, P<0.00001). Conclusion. The total effective rate of acupuncture for amblyopia was significantly superior to conventional treatment, indicating that acupuncture was a promising treatment for amblyopia. However, due to the limited number of CCTs and RCTs, especially those of large sample size and multicenter randomized controlled studies that were quantitatively insufficient, we could not reach a completely affirmative conclusion until further studies of high quality are available

Syntax-Guided Domain Adaptation for Aspect-based Sentiment Analysis

Aspect-based sentiment analysis (ABSA) aims at extracting opinionated aspect terms in review texts and determining their sentiment polarities, which is widely studied in both academia and industry. As a fine-grained classification task, the annotation cost is extremely high. Domain adaptation is a popular solution to alleviate the data deficiency issue in new domains by transferring common knowledge across domains. Most cross-domain ABSA studies are based on structure correspondence learning (SCL), and use pivot features to construct auxiliary tasks for narrowing down the gap between domains. However, their pivot-based auxiliary tasks can only transfer knowledge of aspect terms but not sentiment, limiting the performance of existing models. In this work, we propose a novel Syntax-guided Domain Adaptation Model, named SDAM, for more effective cross-domain ABSA. SDAM exploits syntactic structure similarities for building pseudo training instances, during which aspect terms of target domain are explicitly related to sentiment polarities. Besides, we propose a syntax-based BERT mask language model for further capturing domain-invariant features. Finally, to alleviate the sentiment inconsistency issue in multi-gram aspect terms, we introduce a span-based joint aspect term and sentiment analysis module into the cross-domain End2End ABSA. Experiments on five benchmark datasets show that our model consistently outperforms the state-of-the-art baselines with respect to Micro-F1 metric for the cross-domain End2End ABSA task.Comment: I want to withdraw this article due to personal reaso

The ranks of known disease-causing or susceptibility genes for three cases on the whole genome.

<p>In <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0024171#pone-0024171-t001" target="_blank">Table 1</a>, both the known disease-causing genes and the susceptibility genes for three cases of Breast Cancer, Alzheimer Disease and Diabetes Mellitus Type 2 are listed, altogether with the corresponding rank in the whole genome.</p

The ranks of genes in candidate disease subnetworks.

<p>In <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0024171#pone-0024171-t002" target="_blank">Table 2</a>, the genes in the candidate disease subnetworks (in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0024171#pone-0024171-g005" target="_blank">Fig. 5</a>) and their ranks are listed.</p