Quantitative model for genome-wide cyclic AMP receptor protein binding site identification and characteristic analysis.

Cyclic AMP receptor proteins (CRPs) are important transcription regulators in many species. The prediction of CRP-binding sites was mainly based on position-weighted matrixes (PWMs). Traditional prediction methods only considered known binding motifs, and their ability to discover inflexible binding patterns was limited. Thus, a novel CRP-binding site prediction model called CRPBSFinder was developed in this research, which combined the hidden Markov model, knowledge-based PWMs and structure-based binding affinity matrixes. We trained this model using validated CRP-binding data from Escherichia coli and evaluated it with computational and experimental methods. The result shows that the model not only can provide higher prediction performance than a classic method but also quantitatively indicates the binding affinity of transcription factor binding sites by prediction scores. The prediction result included not only the most knowns regulated genes but also 1089 novel CRP-regulated genes. The major regulatory roles of CRPs were divided into four classes: carbohydrate metabolism, organic acid metabolism, nitrogen compound metabolism and cellular transport. Several novel functions were also discovered, including heterocycle metabolic and response to stimulus. Based on the functional similarity of homologous CRPs, we applied the model to 35 other species. The prediction tool and the prediction results are online and are available at: https://awi.cuhk.edu.cn/∼CRPBSFinder.

Bimekizumab for the treatment of moderate-to-severe plaque psoriasis: a meta-analysis of randomized clinical trials.

Background: Bimekizumab is a monoclonal IgG1 antibody that selectively inhibits both interleukin (IL)-17A and IL-17F, and is a promising drug for patients with moderate-to-severe plaque psoriasis. Objectives: This study aimed to assess the efficacy and safety of bimekizumab in treating patients with psoriasis and to determine the optimal maintenance dosing schedules of bimekizumab. Methods and design: Eligible trials were identified from PubMed, Cochrane Controlled Register of Trials, Embase, ClinicalTrials.gov, and Chinese medical databases. Only double-blind, randomized, active comparator, or placebo-controlled trials of bimekizumab treatment on patients with psoriasis were included in this study. Results: Five studies were identified, which included 2473 patients with moderate-to-severe plaque psoriasis. The results indicated that bimekizumab had better efficacy than placebo or active comparator for Psoriasis Area and Severity Index (PASI) 90 [risk ratio (RR) = 29.29, 1.52; 95% confidence interval (CI) = 10.30-83.30, 1.06-2.19], PASI 100 (RR = 59.87, 2.06; 95% CI = 15.06-237.99, 1.12-3.79), and Investigator's Global Assessment scores of 0 or 1 (IGA 0/1) (RR = 21.55, 1.36; 95% CI = 9.25-50.19, 1.02-1.81). Faster onset of clinically meaningful responses was observed with bimekizumab compared with both active comparators (RR = 2.59; 95% CI = 1.32-5.10) and placebo (RR = 40.46; 95% CI = 13.19-124.13), with PASI 75 response observed at week 4 after one dose. Subgroup analysis showed no significant difference in the reduction of PASI scores between 320 mg q4w dosage and q8w dosage (RR = 1.00; 95% CI = 0.96-1.03). Rates of patients with adverse events (AEs) were comparable in the bimekizumab and active comparator groups (RR = 1.13; 95% CI = 1.01-1.26), and oral candidiasis was one of the most common treatment-emergent AEs. Conclusion: The results of this meta-analysis suggest that bimekizumab is more efficacious and has a rapid onset of action than active comparators and placebo in the treatment of moderate-to-severe plaque psoriasis. After 16 weeks of initial maintenance treatment, both bimekizumab maintenance dosing schedules (320 mg every 4 and 8 weeks) had similar efficacy.

Risk factors of cardiovascular involvement in patients with Behcet's disease.

Objectives: Behcet's disease (BD) is a multi-systemic inflammatory vasculitis which may be life-threatening if combined with cardiovascular problems. The aim of the study was to identify potential risk factors associated with cardiovascular involvement in BD. Methods: We reviewed the medical databases of a single center. All BD patients identified as fulfilling the 1990 International Study Group criteria or the International Criteria for Behcet's Disease criteria. Cardiovascular involvement, clinical manifestations, laboratory features, and treatments were recorded. The relationship between parameters and cardiovascular involvement was analyzed. Results: 111 BD patients were included: 21 (18.9%) had documented cardiovascular involvement (CV BD group) and 99 (81.1%) had no cardiovascular involvement (non-CV BD group). Compared with non-CV BD, the proportion of males and smokers were significantly increased in CV BD (p = 0.024 and p < 0.001, respectively). Levels of activated partial thromboplastin time (APTT), cardiac troponin I and C-reactive protein were significantly higher (p = 0.001, p = 0.031, and p = 0.034, respectively) in the CV BD group. Cardiovascular involvement was associated with smoking state, the presence of papulopustular lesions, and higher APTT in multivariate analyzed (p = 0.029, p = 0.021, and p = 0.006, respectively). The ROC curve showed that APTT predicts the risk of cardiovascular involvement (p < 0.01) at a cut-off value of 33.15 s with a sensitivity of 57.1% and specificity of 82.2%. Conclusion: Cardiovascular involvement in BD patients was associated with gender, smoking state, the presence of papulopustular lesions, and higher APTT. All patients newly diagnosed with BD should be systematically screened for cardiovascular involvement.

Enzyme Activity of Natural Products on Cytochrome P450.

Drug-metabolizing enzymes, particularly the cytochrome P450 (CYP450) monooxygenases, play a pivotal role in pharmacokinetics. CYP450 enzymes can be affected by various xenobiotic substrates, which will eventually be responsible for most metabolism-based herb-herb or herb-drug interactions, usually involving competition with another drug for the same enzyme binding site. Compounds from herbal or natural products are involved in many scenarios in the context of such interactions. These interactions are decisive both in drug discovery regarding the synergistic effects, and drug application regarding unwanted side effects. Herein, this review was conducted as a comprehensive compilation of the effects of herbal ingredients on CYP450 enzymes. Nearly 500 publications reporting botanicals' effects on CYP450s were collected and analyzed. The countries focusing on this topic were summarized, the identified herbal ingredients affecting enzyme activity of CYP450s, as well as methods identifying the inhibitory/inducing effects were reviewed. Inhibitory effects of botanicals on CYP450 enzymes may contribute to synergistic effects, such as herbal formulae/prescriptions, or lead to therapeutic failure, or even increase concentrations of conventional medicines causing serious adverse events. Conducting this review may help in metabolism-based drug combination discovery, and in the evaluation of the safety profile of natural products used therapeutically.

CircNet 2.0: an updated database for exploring circular RNA regulatory networks in cancers.

Circular RNAs (circRNAs), which are single-stranded RNA molecules that have individually formed into a covalently closed continuous loop, act as sponges of microRNAs to regulate transcription and translation. CircRNAs are important molecules in the field of cancer diagnosis, as growing evidence suggests that they are closely related to pathological cancer features. Therefore, they have high potential for clinical use as novel cancer biomarkers. In this article, we present our updates to CircNet (version 2.0), into which circRNAs from circAtlas and MiOncoCirc, and novel circRNAs from The Cancer Genome Atlas database have been integrated. In total, 2732 samples from 37 types of cancers were integrated into CircNet 2.0 and analyzed using several of the most reliable circRNA detection algorithms. Furthermore, target miRNAs were predicted from the full-length circRNA sequence using three reliable tools (PITA, miRanda and TargetScan). Additionally, 384 897 experimentally verified miRNA-target interactions from miRTarBase were integrated into our database to facilitate the construction of high-quality circRNA-miRNA-gene regulatory networks. These improvements, along with the user-friendly interactive web interface for data presentation, search, and visualization, showcase the updated CircNet database as a powerful, experimentally validated resource, for providing strong data support in the biomedical fields. CircNet 2.0 is currently accessible at https://awi.cuhk.edu.cn/∼CircNet.

miRTarBase update 2022: an informative resource for experimentally validated miRNA-target interactions.

MicroRNAs (miRNAs) are noncoding RNAs with 18-26 nucleotides; they pair with target mRNAs to regulate gene expression and produce significant changes in various physiological and pathological processes. In recent years, the interaction between miRNAs and their target genes has become one of the mainstream directions for drug development. As a large-scale biological database that mainly provides miRNA-target interactions (MTIs) verified by biological experiments, miRTarBase has undergone five revisions and enhancements. The database has accumulated >2 200 449 verified MTIs from 13 389 manually curated articles and CLIP-seq data. An optimized scoring system is adopted to enhance this update's critical recognition of MTI-related articles and corresponding disease information. In addition, single-nucleotide polymorphisms and disease-related variants related to the binding efficiency of miRNA and target were characterized in miRNAs and gene 3' untranslated regions. miRNA expression profiles across extracellular vesicles, blood and different tissues, including exosomal miRNAs and tissue-specific miRNAs, were integrated to explore miRNA functions and biomarkers. For the user interface, we have classified attributes, including RNA expression, specific interaction, protein expression and biological function, for various validation experiments related to the role of miRNA. We also used seed sequence information to evaluate the binding sites of miRNA. In summary, these enhancements render miRTarBase as one of the most research-amicable MTI databases that contain comprehensive and experimentally verified annotations. The newly updated version of miRTarBase is now available at https://miRTarBase.cuhk.edu.cn/.

Identification of causal intervention effects under contagion.

Defining and identifying causal intervention effects for transmissible infectious disease outcomes is challenging because a treatment - such as a vaccine - given to one individual may affect the infection outcomes of others. Epidemiologists have proposed causal estimands to quantify effects of interventions under contagion using a two-person partnership model. These simple conceptual models have helped researchers develop causal estimands relevant to clinical evaluation of vaccine effects. However, many of these partnership models are formulated under structural assumptions that preclude realistic infectious disease transmission dynamics, limiting their conceptual usefulness in defining and identifying causal treatment effects in empirical intervention trials. In this paper, we propose causal intervention effects in two-person partnerships under arbitrary infectious disease transmission dynamics, and give nonparametric identification results showing how effects can be estimated in empirical trials using time-to-infection or binary outcome data. The key insight is that contagion is a causal phenomenon that induces conditional independencies on infection outcomes that can be exploited for the identification of clinically meaningful causal estimands. These new estimands are compared to existing quantities, and results are illustrated using a realistic simulation of an HIV vaccine trial.

miRTarBase 2020: updates to the experimentally validated microRNA-target interaction database.

MicroRNAs (miRNAs) are small non-coding RNAs (typically consisting of 18-25 nucleotides) that negatively control expression of target genes at the post-transcriptional level. Owing to the biological significance of miRNAs, miRTarBase was developed to provide comprehensive information on experimentally validated miRNA-target interactions (MTIs). To date, the database has accumulated >13,404 validated MTIs from 11,021 articles from manual curations. In this update, a text-mining system was incorporated to enhance the recognition of MTI-related articles by adopting a scoring system. In addition, a variety of biological databases were integrated to provide information on the regulatory network of miRNAs and its expression in blood. Not only targets of miRNAs but also regulators of miRNAs are provided to users for investigating the up- and downstream regulations of miRNAs. Moreover, the number of MTIs with high-throughput experimental evidence increased remarkably (validated by CLIP-seq technology). In conclusion, these improvements promote the miRTarBase as one of the most comprehensively annotated and experimentally validated miRNA-target interaction databases. The updated version of miRTarBase is now available at http://miRTarBase.cuhk.edu.cn/.

Selective elimination of chromophoric and fluorescent dissolved organic matter in a full-scale municipal wastewater treatment plant.

Effluent organic matter (EfOM) from municipal wastewater treatment plants potentially has a detrimental effect on both aquatic organisms and humans. This study evaluated the removal and transformation of chromophoric dissolved organic matter (CDOM) and fluorescent dissolved organic matter (FDOM) in a full-scale wastewater treatment plant under different seasons. The results showed that bio-treatment was found to be more efficient in removing bulk DOM (in term of dissolved organic carbon, DOC) than CDOM and FDOM, which was contrary to the disinfection process. CDOM and FDOM were selectively removed at various stages during the treatment. Typically, the low molecular weight fractions of CDOM and protein-like FDOM were more efficiently removed during bio-treatment process, whereas the humic-like FDOM exhibited comparable decreases in both bio-treatment and disinfection processes. Overall, the performance of the WWTP was weak in terms of CDOM and FDOM removal, resulting in enrichment of CDOM and FDOM in effluent. Moreover, the total removal of the bulk DOM (P<0.05) and the protein-like FDOM (P<0.05) displayed a significant seasonal variation, with higher removal efficiencies in summer, whereas removal of CDOM and the humic-like FDOM showed little differences between summer and winter. In all, the results provide useful information for understanding the fate and transformation of DOM, illustrating that sub-fractions of DOM could be selectively removed depending on treatment processes and seasonality.