SiteFinding-PCR: a simple and efficient PCR method for chromosome walking

In this paper, we present a novel PCR method, termed SiteFinding-PCR, for gene or chromosome walking. The PCR was primed by a SiteFinder at a low temperature, and then the target molecules were amplified exponentially with gene-specific and SiteFinder primers, and screened out by another gene-specific primer and a vector primer. However, non-target molecules could not be amplified exponentially owing to the suppression effect of stem–loop structure and could not be screened out. This simple method proved to be efficient, reliable, inexpensive and time-saving, and may be suitable for the molecules for which gene-specific primers are available. More importantly, large DNA fragments can be obtained easily using this method. To demonstrate the feasibility and efficiency of SiteFinding-PCR, we employed this method to do chromosome walking and obtained 16 positive results from 17 samples

A heterogeneous graph-based semi-supervised learning framework for access control decision-making

For modern information systems, robust access control mechanisms are vital in safeguarding data integrity and ensuring the entire system’s security. This paper proposes a novel semi-supervised learning framework that leverages heterogeneous graph neural network-based embedding to encapsulate both the intricate relationships within the organizational structure and interactions between users and resources. Unlike existing methods focusing solely on individual user and resource attributes, our approach embeds organizational and operational interrelationships into the hidden layer node embeddings. These embeddings are learned from a self-supervised link prediction task based on a constructed access control heterogeneous graph via a heterogeneous graph neural network. Subsequently, the learned node embeddings, along with the original node features, serve as inputs for a supervised access control decision-making task, facilitating the construction of a machine-learning access control model. Experimental results on the open-sourced Amazon access control dataset demonstrate that our proposed framework outperforms models using original or manually extracted graph-based features from previous works. The prepossessed data and codes are available on GitHub,facilitating reproducibility and further research endeavors

Genome-Wide Linkage Mapping Reveals QTLs for Seed Vigor-Related Traits Under Artificial Aging in Common Wheat (Triticum aestivum)

Long-term storage of seeds leads to lose seed vigor with slow and non-uniform germination. Time, rate, homogeneity, and synchrony are important aspects during the dynamic germination process to assess seed viability after storage. The aim of this study is to identify quantitative trait loci (QTLs) using a high-density genetic linkage map of common wheat (Triticum aestivum) for seed vigor-related traits under artificial aging. Two hundred and forty-six recombinant inbred lines derived from the cross between Zhou 8425B and Chinese Spring were evaluated for seed storability. Ninety-six QTLs were detected on all wheat chromosomes except 2B, 4D, 6D, and 7D, explaining 2.9–19.4% of the phenotypic variance. These QTLs were clustered into 17 QTL-rich regions on chromosomes 1AL, 2DS, 3AS (3), 3BS, 3BL (2), 3DL, 4AS, 4AL (3), 5AS, 5DS, 6BL, and 7AL, exhibiting pleiotropic effects. Moreover, 10 stable QTLs were identified on chromosomes 2D, 3D, 4A, and 6B (QaMGT.cas-2DS.2, QaMGR.cas-2DS.2, QaFCGR.cas-2DS.2, QaGI.cas-3DL, QaGR.cas-3DL, QaFCGR.cas-3DL, QaMGT.cas-4AS, QaMGR.cas-4AS, QaZ.cas-4AS, and QaGR.cas-6BL.2). Our results indicate that one of the stable QTL-rich regions on chromosome 2D flanked by IWB21991 and IWB11197 in the position from 46 to 51 cM, presenting as a pleiotropic locus strongly impacting seed vigor-related traits under artificial aging. These new QTLs and tightly linked SNP markers may provide new valuable information and could serve as targets for fine mapping or markers assisted breeding

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

DUXAP8 Promotes LPS-Induced Cell Injury in Pulpitis by Regulating miR-18b-5p/HIF3A

ABSTRACT: Background: The dysregulated long noncoding RNAs (lncRNAs) are implicated in progression of various diseases, including pulpitis. Double homeobox A pseudogene 8 (DUXAP8) has been found to be upregulated in pulpitis. Herein, the functional mechanism of DUXAP8 in lipopolysaccharide (LPS)-induced pulpitis was explored. Material and methods: DUXAP8, microRNA-18b-5p (miR-18b-5p), or hypoxia-inducible factor 3A (HIF3A) levels were examined through reverse transcription-quantitative polymerase chain reaction assay. Cell behaviours were determined by Cell Counting Kit-8 assay for cell viability, Ethynyl-2′-deoxyuridine (EdU) assay for cell proliferation, and flow cytometry for cell apoptosis. Protein levels were measured using western blot. Inflammatory reaction was analysed via enzyme-linked immunosorbent assay. Oxidative stress was assessed by commercial kits. Dual-luciferase reporter assay, RNA immunoprecipitation assay, and pull-down assay were used for validation of interaction between targets. Results: Cell apoptosis, inflammatory reaction, and oxidative stress were induced by LPS in human dental pulp cells (HDPCs). DUXAP8 upregulation and miR-18b-5p downregulation were found in pulpitis. LPS-induced cell injury was relieved after downregulation of DUXAP8. DUXAP8 interacted with miR-18b-5p. The regulation of DUXAP8 was related to miR-18b-5p sponging function in LPS-treated HDPCs. HIF3A served as a target of miR-18b-5p. MiR-18b-5p protected against LPS-induced cell injury through targeting HIF3A. DUXAP8 targeted miR-18b-5p to regulate HIF3A level. Conclusions: Results demonstrated that LPS-induced cell injury in pulpitis was promoted by DUXAP8 through mediating miR-18b-5p/HIF3A axis