Identification of Protein Pupylation Sites Using Bi-Profile Bayes Feature Extraction and Ensemble Learning

Pupylation, one of the most important posttranslational modifications of proteins, typically takes place when prokaryotic ubiquitin-like protein (Pup) is attached to specific lysine residues on a target protein. Identification of pupylation substrates and their corresponding sites will facilitate the understanding of the molecular mechanism of pupylation. Comparing with the labor-intensive and time-consuming experiment approaches, computational prediction of pupylation sites is much desirable for their convenience and fast speed. In this study, a new bioinformatics tool named EnsemblePup was developed that used an ensemble of support vector machine classifiers to predict pupylation sites. The highlight of EnsemblePup was to utilize the Bi-profile Bayes feature extraction as the encoding scheme. The performance of EnsemblePup was measured with a sensitivity of 79.49%, a specificity of 82.35%, an accuracy of 85.43%, and a Matthews correlation coefficient of 0.617 using the 5-fold cross validation on the training dataset. When compared with other existing methods on a benchmark dataset, the EnsemblePup provided better predictive performance, with a sensitivity of 80.00%, a specificity of 83.33%, an accuracy of 82.00%, and a Matthews correlation coefficient of 0.629. The experimental results suggested that EnsemblePup presented here might be useful to identify and annotate potential pupylation sites in proteins of interest. A web server for predicting pupylation sites was developed

An indoor UWB 3D positioning method for coplanar base stations

As an indispensable type of information, location data are used in various industries. Ultrawideband (UWB) technology has been used for indoor location estimation due to its excellent ranging performance. However, the accuracy of the location estimation results is heavily affected by the deployment of base stations; in particular, the base station deployment space is limited in certain scenarios. In underground mines, base stations must be placed on the roof to ensure signal coverage, which is almost coplanar in nature. Existing indoor positioning solutions suffer from both difficulties in the correct convergence of results and poor positioning accuracy under coplanar base-station conditions. To correctly estimate position in coplanar base-station scenarios, this paper proposes a novel iterative method. Based on the Newton iteration method, a selection range for the initial value and iterative convergence control conditions were derived to improve the convergence performance of the algorithm. In this paper, we mathematically analyze the impact of the localization solution for coplanar base stations and derive the expression for the localization accuracy performance. The proposed method demonstrated a positioning accuracy of 5 cm in the experimental campaign for the comparative analysis, with the multi-epoch observation results being stable within 10 cm. Furthermore, it was found that, when base stations are coplanar, the test point accuracy can be improved by an average of 63.54% compared to the conventional positioning algorithm. In the base-station coplanar deployment scenario, the upper bound of the CDF convergence in the proposed method outperformed the conventional positioning algorithm by about 30%

Unique post-translational oxime formation in the biosynthesis of the azolemycin complex of novel ribosomal peptides from Streptomyces sp. FXJ1.264

Streptomycetes are a rich source of bioactive specialized metabolites, including several examples of the rapidly growing class of ribosomally-biosynthesized and post-translationally-modified peptide (RiPP) natural products. Here we report the discovery from Streptomyces sp. FXJ1.264 of azolemycins A–D, a complex of novel linear azole-containing peptides incorporating a unique oxime functional group. Bioinformatics analysis of the Streptomyces sp. FXJ1.264 draft genome sequence identified a cluster of genes that was hypothesized to be responsible for elaboration of the azolemycins from a ribosomally-biosynthesized precursor. Inactivation of genes within this cluster abolished azolemycin production, consistent with this hypothesis. Moreover, mutants lacking the azmE and azmF genes accumulated azolemycin derivatives lacking the O-methyl groups and an amino group in place of the N-terminal oxime (as well as proteolysed derivatives), respectively. Thus AzmE, a putative S-adenosyl methionine-dependent methyl transferase, is responsible for late-stage O-methylation reactions in azolemycin biosynthesis and AzmF, a putative flavin-dependent monooxygenase, catalyzes oxidation of the N-terminal amino group in an azolemycin precursor to the corresponding oxime. To the best of our knowledge, oxime formation is a hitherto unknown posttranslational modification in RiPP biosynthesis

Gigahertz-rate-switchable wavefront shaping through integration of metasurfaces with photonic integrated circuit

Achieving spatiotemporal control of light at high-speeds presents immense possibilities for various applications in communication, computation, metrology, and sensing. The integration of subwavelength metasurfaces and optical waveguides offers a promising approach to manipulate light across multiple degrees of freedom at high-speed in compact photonic integrated circuit (PICs) devices. Here, we demonstrate a gigahertz-rate-switchable wavefront shaping by integrating metasurface, lithium niobite on insulator (LNOI) photonic waveguide and electrodes within a PIC device. As proofs of concept, we showcase the generation of a focus beam with reconfigurable arbitrary polarizations, switchable focusing with lateral focal positions and focal length, orbital angular momentum light beams (OAMs) as well as Bessel beams. Our measurements indicate modulation speeds of up to gigahertz rate. This integrated platform offers a versatile and efficient means of controlling light field at high-speed within a compact system, paving the way for potential applications in optical communication, computation, sensing, and imaging

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

Study of Topography and Distribution State of the Nanoscale Passivation Film on a Rough Tinplate Surface

Topography observation of the nanoscale passivation film on tinplate using a scanning electron microscope and an electro-optical surface profilometer showed that it was difficult to observe the true topography because of the high surface roughness of the tinplate. Topography observation using a profilometer on bright tin plating with low surface roughness and work function measurement on tinplate surface using a Scanning Kelvin Probe Microscope (SKPM) were then carried out to solve the problem. The results indicated that there was a thin chemical passivation film distributed uniformly in different areas of microscopic bulges and valleys on the tinplate surface, and the film became more uniform with longer passivation time. In comparison, the electrolytic passivation film was thick, and the distribution uniformity was poorer. Specifically, the film was thicker on microscopic bulges and thinner in microscopic valleys, and this was worse with longer passivation time. Thus, the difference in performances of the corrosion and paint adhesion of the tinplate treated with different passivation processes can be explained in terms of the topography and distribution state of the passivation film

A Hybrid Indoor Altimetry Based on Barometer and UWB

Accurate altimetry is essential for location-based services in commercial and industrial applications. However, current altimetry methods only provide low-accuracy measurements, particularly in multistorey buildings with irregular structures, such as hollow areas found in various industrial and commercial sites. This paper innovatively proposes a tightly coupled indoor altimetry system that utilizes floor identification to improve height measurement accuracy. The system includes two optimized algorithms that improve floor identification accuracy through activity detection and address the problem of difficult convergence of z-axis coordinates due to indoor coplanarity by applying constraints to iterative least squares (ILS). Two experiments were conducted in a teaching building and a laboratory, including an irregular environment with a hollow area. The results show that our proposed method for identifying floors based on activity detection outperforms other methods. In dynamic experiments, our method effectively eliminates repeated transformations during the up- and downstairs process, and in static experiments, it minimizes the impact of barometric drift. Furthermore, our proposed altimetry method based on constrained ILS achieves significantly improved positioning accuracy compared to ILS, 1D-CNN, and WC. Specifically, in the teaching building, our method achieves improvements of 0.84 m, 0.288 m, and 0.248 m, respectively, while in the laboratory, the improvements are 2.607 m, 0.696 m, and 0.625 m

Identification and Characterization of Mycemycin Biosynthetic Gene Clusters in Streptomyces olivaceus FXJ8.012 and Streptomyces sp. FXJ1.235

Mycemycins A–E are new members of the dibenzoxazepinone (DBP) family, derived from the gntR gene-disrupted deep sea strain Streptomyces olivaceus FXJ8.012Δ1741 and the soil strain Streptomyces sp. FXJ1.235. In this paper, we report the identification of the gene clusters and pathways’ inference for mycemycin biosynthesis in the two strains. Bioinformatics analyses of the genome sequences of S. olivaceus FXJ8.012Δ1741 and S. sp. FXJ1.235 predicted two divergent mycemycin gene clusters, mym and mye, respectively. Heterologous expression of the key enzyme genes of mym and genetic manipulation of mye as well as a feeding study in S. sp. FXJ1.235 confirmed the gene clusters and led to the proposed biosynthetic pathways for mycemycins. To the best of our knowledge, this is the first report on DBP biosynthetic gene clusters and pathways