Ribocentre-switch: a database of riboswitches.

Riboswitches are regulatory elements found in the untranslated regions (UTRs) of certain mRNA molecules. They typically comprise two distinct domains: an aptamer domain that can bind to specific small molecules, and an expression platform that controls gene expression. Riboswitches work by undergoing a conformational change upon binding to their specific ligand, thus activating or repressing the genes downstream. This mechanism allows gene expression regulation in response to metabolites or small molecules. To systematically summarise riboswitch structures and their related ligand binding functions, we present Ribocentre-switch, a comprehensive database of riboswitches, including the information as follows: sequences, structures, functions, ligand binding pockets and biological applications. It encompasses 56 riboswitches and 26 orphan riboswitches from over 430 references, with a total of 89 591 sequences. It serves as a good resource for comparing different riboswitches and facilitating the identification of potential riboswitch candidates. Therefore, it may facilitate the understanding of RNA structural conformational changes in response to ligand signaling. The database is publicly available at https://riboswitch.ribocentre.org.

Broadband Terahertz Detection by Laser Plasma with Balanced Optical Bias.

Using a controlled optical bias and balanced geometry, we propose a new scheme for broadband terahertz detection by laser-gas interaction without high-voltage manipulation. Compared to the conventional optical bias scheme, the common noise is reduced and the dynamic range as well as the signal-to-noise ratio are doubled. It provides a simple alternative for coherent broadband terahertz detection. The influence of optical bias on terahertz waveform is also investigated, and the evolution of the terahertz-induced second harmonic with probe delay is further revealed. This new detection scheme for broadband terahertz will boost the application of terahertz time-domain spectroscopy for its miniaturization and integrability.

Wind-Direction Estimation from Single X-Band Marine Radar Image Improvement by Utilizing the DWT and Azimuth-Scale Expansion Method.

In this study, a method based on the discrete wavelet transform (DWT) and azimuth-scale expansion is presented to retrieve the sea-surface wind direction from a single X-band marine radar image. The algorithm first distinguishes rain-free and rain-contaminated radar images based on the occlusion zero-pixel percentage and then discards the rain-contaminated images. The radar image whose occlusion areas have been removed is decomposed into different low-frequency sub-images by the 2D DWT, and the appropriate low-frequency sub-image is selected. Images collected with a standard marine HH-polarized X-band radar operating at grazing incidence display a single intensity peak in the upwind direction. To overcome the influence of the occlusion area, before determining the wind direction, the data near the ship bow are shifted to expand the azimuth scale of the data. Finally, a harmonic function is least-square-fitted to the range-averaged radar return of the low-frequency sub-image as a function of the antenna look azimuth to determine the wind direction. Different from the wind-direction retrieval algorithms previously presented, this method is more suitable for sailing ships, as it functions well even if the radar data are heavily blocked. The results show that compared with the single-curve fitting algorithm, the algorithm based on DWT and azimuth-scale expansion can improve the wind-direction results in sailing ships, showing a reduction of 7.84° in the root-mean-square error with respect to the reference.

Sea Clutter Suppression and Target Detection Algorithm of Marine Radar Image Sequence Based on Spatio-Temporal Domain Joint Filtering.

In marine radar target detection, sea clutter will cause a large number of missed alarms and false alarms, which will affect the accuracy of target detection. In order to suppress sea clutter effectively, a sea clutter suppression and target detection algorithm of marine radar image sequence based on spatio-temporal domain joint filtering is proposed in this paper. The proposed method is to add a sea clutter suppression link before detecting the target. Firstly, the marine radar image sequence is transformed into three-dimensional frequency wavenumber domain by three-dimensional fast Fourier transform (3D-FFT), and then the three-dimensional image spectrum is obtained. According to the fact that the sea clutter spectrum obtained from the image spectrum satisfies the dispersion relation of linear wave theory in the three-dimensional frequency wavenumber domain, a sea clutter model is established. Then, through the established sea clutter model, a spatio-temporal domain joint sea clutter suppressor is designed to filter the image spectrum. After that, the filtered image spectrum is transformed by three-dimensional inverse fast Fourier transform (3D-IFFT) to obtain the image sequence in which sea clutter is suppressed. Finally, target detection is carried out for sea clutter suppressed image sequence. The method is validated by using the real data of X-band marine radar. Compared with the classical Empirical mode decomposition (EMD) method, the improvement of signal-to-noise ratio (SNR) is more obvious, and SNR can be increased by 15.3 db at most. In addition, compared with target detection on original images directly, the proposed method has excellent detection rate and can increase detection rates by at least 8%.

Sparsity Adaptive Matching Pursuit Detection Algorithm Based on Compressed Sensing for Radar Signals.

In this paper, the application of the emerging compressed sensing (CS) theory and the geometric characteristics of the targets in radar images are investigated. Currently, the signal detection algorithms based on the CS theory require knowing the prior knowledge of the sparsity of target signals. However, in practice, it is often impossible to know the sparsity in advance. To solve this problem, a novel sparsity adaptive matching pursuit (SAMP) detection algorithm is proposed. This algorithm executes the detection task by updating the support set and gradually increasing the sparsity to approximate the original signal. To verify the effectiveness of the proposed algorithm, the data collected in 2010 at Pingtan, which located on the coast of the East China Sea, were applied. Experiment results illustrate that the proposed method adaptively completes the detection task without knowing the signal sparsity, and the similar detection performance is close to the matching pursuit (MP) and orthogonal matching pursuit (OMP) detection algorithms.

A diagnostic test: diagnostic value of gastrointestinal endoscopy narrow-band imaging (NBI) for colorectal laterally spreading tumor (LST) and submucosal invasion.

Background: Endoscopic ultrasonography is an effective endoscopic examination method for determining the depth of colorectal cancer invasion. Narrow-band imaging (NBI) techniques increase the contrast of vascular structures and more clearly highlight subtle structures on mucosal surfaces, thereby improving the accuracy of endoscopic assessment. This study investigated the diagnostic efficacy of NBI in colorectal laterally spreading tumor (LST) and its submucosal invasion. Methods: A total of 224 patients with colorectal LST admitted to the Affiliated Hospital of Putian University from January 2015 to December 2021 were enrolled in this study. The patients were divided into NBI and endoscopic ultrasonography groups according to the different examination methods they received. Subsequently, the clinicopathological characteristics of the patients were collected, and the rates of submucosal invasion of the four subtypes (LST-G-H, LST-G-NM, LST-NG-F, LST-NG-PD) were compared between the two groups. Also, the accuracy, sensitivity, specificity, positive predictive value, negative predictive value, and accuracy of judging the depth of LST lesions of the two examination methods were compared, taking the results of pathological tissue examination as the gold standard. Results: This study enrolled 224 patients with LST (mean onset age: 57.98±6.48 years), including 123 males and 101 females. In terms of tumor location, 21 cases were located in the cecum, 22 cases in the ascending colon, 38 cases in the transverse colon, 11 cases in the descending colon, 12 cases in the descending sigmoid junction, 23 cases in the sigmoid colon, and 97 cases in the rectum. The sizes of the tumors ranged from 18.81 to 52.88 mm. Moreover, there were 21 cases of lesion infiltration into the submucosa, and the infiltration rate was 9.38%. Furthermore, the accuracy of NBI in diagnosing colorectal LST was significantly higher than that of endoscopic ultrasonography (87.05% vs. 57.14%); NBI was more accurate than endoscopic ultrasonography in the preoperative diagnosis of LST lesion depth in the rectal, non-rectal, granular (LST-G), non-granular (LST-NG), <40, and ≥40 mm groups. Conclusions: Gastrointestinal NBI has a superior accuracy rate and value than endoscopic ultrasonography in diagnosing colorectal LST, tumor lesion depth, and submucosal invasion. Therefore, gastrointestinal NBI deserves to be promoted in clinical work.

[Increased expressions of programmed death 1 (PD-1) and its ligands in peripheral CD3(+) T cells and CD19(+) B cells in patients with hepatocellular carcinoma].

Objective To investigate the changes of programmed death 1 (PD-1) and ligands, as well as interferon-γ (IFN-γ) in peripheral blood mononuclear cells (PBMCs) of patients with hepatocellular carcinoma (HCC). Methods The peripheral blood was collected from 15 early HCC patients, 13 progressive HCC patients and 12 healthy volunteers. PBMCs was isolated from the peripheral blood. The expressions of PD-1, PD-L1 and PD-L2 in PBMCs were detected by flow cytometry; the serum level of IFN-γ was determined by ELISA; the correlation of PD-1 and IFN-γ was analyzed with Pearson's correlation and One-way ANOVA. Results The expression levels of PD-1, PD-L1 and PD-L2 in CD3(+) T cells and CD19(+) B cells and serum IFN-γ level in progressive HCC patients were significantly higher than those in the healthy group and early HCC patients. The expression levels of PD-1, PD-L1 and PD-L2 in the CD3(+) T cells and CD19(+) B cells of the HCC patients were positively correlated with IFN-γ. Conclusion The expression levels of PD-1, PD-L1 and PD-L2 increase in the PBMCs of HCC patients; PD-1 and PD-L1 are correlated with IFN-γ level.

Epigenetic silencing of miRNA-9 is correlated with promoter-proximal CpG island hypermethylation in gastric cancer in vitro and in vivo.

Silencing of protein-coding tumor suppressor genes (TSGs) by CpG island hypermethylation is a common occurrence in gastric cancer (GC). Here, we examine if tumor suppressor microRNAs (miRNAs) are silenced in a similar manner. Real-time quantitative PCR (RTQ-PCR) was employed to investigate the expression level of four candidate miRNAs in GC tissues (n=30) and cell lines. Basing on RTQ-PCR results and bioinformatics approach, miR-9 was chosen for further study on epigenetic regulation. Bisulfite genomic sequencing PCR (BSP) was performed to assess the methylation status of miR-9 in GC tissues. In both GC cell lines and animal models, demethylation was performed either by treatment with 5-aza-2'-deoxycytidine (5-AZA-CdR) or by siRNA targeting DNMT1. We also analyzed the relationship between miRNAs and several clinicopathological features. Candidate miRNAs (miR-9, miR-433, miR-19b, and miR-370) were found strongly downregulated in GC tissues and cell lines. Their expression was increased following 5-AZA-CdR treatment. CpG island methylation of miR-9 was significantly higher in GC tissues compared to normal controls. After two demethylation treatments, miR-9 methylation degree was significantly decreased and miR-9 expression was ob-viously restored in GC cells and animal models. Deregulation of miR-9 was positively correlated with tumor lesion size. Three other miRNAs, miR-19b, miR-433, and miR-370 were assοciated with lymph node metastasis, decreased curvature, and poorly differentiated carcinoma. miR-19b and miR-433 were positively correlated with male gender. Of four candidate miRNAs downregulated in GC, miR-9 is epigenetically regulated by DNA methylation both in vitro and in vivo.

[Study on technological characters of anaerobic-aerobic bioreactor landfill].

A technology of anaerobic-aerobic landfill bioreactor aimed at reusing landfill site is studied, and it's based on landfill bioreactor technology. A set of stimulating equipment is designed, and the technology characters are studied. In the anaerobic period, technological conditions are controlled by the means of leachate recirculation. The main experimental results are: pH, R1 rises to 6.7 - 7.8 in 6 weeks, and R2 is under 6.8 in 17 weeks; COD concentration of leachate, R1 declines to 10 617 mg/L in 13 weeks, while R2 rises to 60 000 mg/L in 5 weeks, and keeps stabilization in long time; the cumulating methane production, R1 reaches 44% in 8 weeks, while R2 almost cannot produce methane. The stabilization can be evaluated by pH of leachate, COD and BOD5/COD decreasing ratio, and cumulating methane production. They are main evidences to transform anaerobic period to aerobic period. In the aerobic period, odor and moisture are reduced by the means of aeration. The main experimental results are: ammonia concentration reduces to 1.16 mg/m3 in 19 days, and the odor concentration reduces to 19 in 23 days; the moisture of the wastes reduces to 26% in 14 days. The technological indexes to evaluate finishing of this period can be determined by the ultimately purpose of exploited wastes. Numerical modeling has been researched with the use of experimental data. The succession of microbes in the anaerobic-aerobic course is studied by RISA (ribosomal intergenic spacer analysis) analysis. There are 4 preponderant groups in this course, and some facultative anaerobes play important roles in the transition of anaerobic period to aerobic period.

[Studies of on-site night soil and kitchen garbage treatment].

The biological treatment technique of collection at source and disposition on-site of night soil and kitchen garbage were presented. By design project of overall technics, the lab-scale experiments were performed. It was revealed that water consumption of vacuum closestool was about 1 L/time. It consumed 0.4- 0.6L water to shred 1 kg kitchen garbage. Night soil covered 40%, kitchen garbage covered 60% in the influent. Water was controlled at about 93%, the C:N ratio was about 25:1, pH was between 6.2 and 7.3, the optical blend frequency was 6h/d and the overall solid retention time was 28 days in anaerobic digestion reactor. The COD removal rate of mixed supernatant was 91% in anaerobic baffled reactor. It was identified that these phosphorus strains and potassium strains were Bacillus. sp, and biological activated fertilizer was obtained by mixed these strains with digestion sludge which had been dehydrated and deodorized. These strains ability of forming phosphorus and potassium were determined, and the concentration of phosphorus increased 67.5%, potassium increased 33.4%.