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Diet–drug interactions (DDIs) are pivotal in drug discovery and pharmacovigilance. DDIs can modify the systemic bioavailability/pharmacokinetics of drugs, posing a threat to public health and patient safety. Therefore, it is crucial to establish a platform to reveal the correlation between diets and drugs. Accordingly, we have established a publicly accessible online platform, known as Diet-Drug Interactions Database (DDID, https://bddg.hznu.edu.cn/ddid/), to systematically detail the correlation and corresponding mechanisms of DDIs. The platform comprises 1338 foods/herbs, encompassing flora and fauna, alongside 1516 widely used drugs and 23 950 interaction records. All interactions are meticulously scrutinized and segmented into five categories, thereby resulting in evaluations (positive, negative, no effect, harmful and possible). Besides, cross-linkages between foods/herbs, drugs and other databases are furnished. In conclusion, DDID is a useful resource for comprehending the correlation between foods, herbs and drugs and holds a promise to enhance drug utilization and research on drug combinations. [ABSTRACT FROM AUTHOR]

Due to its promising capacity in improving drug efficacy, polypharmacology has emerged to be a new theme in the drug discovery of complex disease. In the process of novel multi-target drugs (MTDs) discovery, in silico strategies come to be quite essential for the advantage of high throughput and low cost. However, current researchers mostly aim at typical closely related target pairs. Because of the intricate pathogenesis networks of complex diseases, many distantly related targets are found to play crucial role in synergistic treatment. Therefore, an innovational method to develop drugs which could simultaneously target distantly related target pairs is of utmost importance. At the same time, reducing the false discovery rate in the design of MTDs remains to be the daunting technological difficulty. In this research, effective small molecule clustering in the positive dataset, together with a putative negative dataset generation strategy, was adopted in the process of model constructions. Through comprehensive assessment on 10 target pairs with hierarchical similarity-levels, the proposed strategy turned out to reduce the false discovery rate successfully. Constructed model types with much smaller numbers of inhibitor molecules gained considerable yields and showed better false-hit controllability than before. To further evaluate the generalization ability, an in-depth assessment of high-throughput virtual screening on ChEMBL database was conducted. As a result, this novel strategy could hierarchically improve the enrichment factors for each target pair (especially for those distantly related/unrelated target pairs), corresponding to target pair similarity-levels. [ABSTRACT FROM AUTHOR]

The type IV bacterial secretion system (SS) is reported to be one of the most ubiquitous SSs in nature and can induce serious conditions by secreting type IV SS effectors (T4SEs) into the host cells. Recent studies mainly focus on annotating new T4SE from the huge amount of sequencing data, and various computational tools are therefore developed to accelerate T4SE annotation. However, these tools are reported as heavily dependent on the selected methods and their annotation performance need to be further enhanced. Herein, a convolution neural network (CNN) technique was used to annotate T4SEs by integrating multiple protein encoding strategies. First, the annotation accuracies of nine encoding strategies integrated with CNN were assessed and compared with that of the popular T4SE annotation tools based on independent benchmark. Second, false discovery rates of various models were systematically evaluated by (1) scanning the genome of Legionella pneumophila subsp. ATCC 33152 and (2) predicting the real-world non-T4SEs validated using published experiments. Based on the above analyses, the encoding strategies, (a) position-specific scoring matrix (PSSM), (b) protein secondary structure & solvent accessibility (PSSSA) and (c) one-hot encoding scheme (Onehot), were identified as well-performing when integrated with CNN. Finally, a novel strategy that collectively considers the three well-performing models (CNN-PSSM, CNN-PSSSA and CNN-Onehot) was proposed, and a new tool (CNN-T4SE, https://idrblab.org/cnnt4se/) was constructed to facilitate T4SE annotation. All in all, this study conducted a comprehensive analysis on the performance of a collection of encoding strategies when integrated with CNN, which could facilitate the suppression of T4SS in infection and limit the spread of antimicrobial resistance. [ABSTRACT FROM AUTHOR]

Functional annotation of protein sequence with high accuracy has become one of the most important issues in modern biomedical studies, and computational approaches of significantly accelerated analysis process and enhanced accuracy are greatly desired. Although a variety of methods have been developed to elevate protein annotation accuracy, their ability in controlling false annotation rates remains either limited or not systematically evaluated. In this study, a protein encoding strategy, together with a deep learning algorithm, was proposed to control the false discovery rate in protein function annotation, and its performances were systematically compared with that of the traditional similarity-based and de novo approaches. Based on a comprehensive assessment from multiple perspectives, the proposed strategy and algorithm were found to perform better in both prediction stability and annotation accuracy compared with other de novo methods. Moreover, an in-depth assessment revealed that it possessed an improved capacity of controlling the false discovery rate compared with traditional methods. All in all, this study not only provided a comprehensive analysis on the performances of the newly proposed strategy but also provided a tool for the researcher in the fields of protein function annotation. [ABSTRACT FROM AUTHOR]

Background: No single pure enantiomeric pesticide residues was investigated and set regulations for tea quality safety and risk assessment. Objective: Due to lack of chiral pesticide analysis method and data, the Maximum residue limits (MRLs) about the chiral pesticides in tea was unknown. Method: An analytical method for the determination of chiral pesticide residues by QuEChERS combined chiral liquid chromatography quadruple/linear ion trap mass spectrometry (LC-MS/MS-Qtrap) was developed and applied to the analysis of various teas. Results: The mean recoveries for pesticides enantiomers ranged from 75.9% to 112.4%. Reproducibility represented by relative standard deviation percentage was 10% or less. Good linearity was achieved for all enantiomers with determination coefficients (r²) greater than 0.99. The detection of limit (CCa) and quantification of limit (CCb) were 0.2 ~1 mg/kg and 0.5~5 mg/kg, respectively. Conclusions: The method was suitable for monitoring the enantiomeric pesticide residues in various teas. Highlights: Enantioselective multiclass pesticide residues were determined in various teas by LC-MS/MS-Qtrap, additional Qtrap scan functions greatly enhance the performance of screening, confirmation, and identification of chiral pesticides. [ABSTRACT FROM AUTHOR]

The pathogenesis of multiple sclerosis (MS) is significantly regulated by long noncoding RNAs (lncRNAs), the expression of which is substantially influenced by a number of MS-associated risk single nucleotide polymorphisms (SNPs). It is thus hypothesized that the dysregulation of lncRNA induced by genomic variants may be one of the key molecular mechanisms for the pathology of MS. However, due to the lack of sufficient data on lncRNA expression and SNP genotypes of the same MS patients, such molecular mechanisms underlying the pathology of MS remain elusive. In this study, a bioinformatics strategy was applied to obtain lncRNA expression and SNP genotype data simultaneously from 142 samples (51 MS patients and 91 controls) based on RNA-seq data, and an expression quantitative trait loci (eQTL) analysis was conducted. In total, 2383 differentially expressed lncRNAs were identified as specifically expressing in brain-related tissues, and 517 of them were affected by SNPs. Then, the functional characterization, secondary structure changes and tissue and disease specificity of the cis -eQTL SNPs and lncRNA were assessed. The cis -eQTL SNPs were substantially and specifically enriched in neurological disease and intergenic region, and the secondary structure was altered in 17.6% of all lncRNAs in MS. Finally, the weighted gene coexpression network and gene set enrichment analyses were used to investigate how the influence of SNPs on lncRNAs contributed to the pathogenesis of MS. As a result, the regulation of lncRNAs by SNPs was found to mainly influence the antigen processing/presentation and mitogen-activated protein kinases (MAPK) signaling pathway in MS. These results revealed the effectiveness of the strategy proposed in this study and give insight into the mechanism (SNP-mediated modulation of lncRNAs) underlying the pathology of MS. [ABSTRACT FROM AUTHOR]

The effect of nine constant temperatures on developmental time of Oligota flavicornis (Boisduval and Lacordaire) preying on Tetranychus cinnabarinus (Boisduval) (Acari: Tetranychidae) eggs was determined under laboratory conditions of 75 ± 5% RH and a 16:8 (L:D) h photoperiod. O. flavicornis survival rates were highest between 18 and 30°C, although O. flavicornis eggs developed successfully to adults at 12–32°C, and the developmental durations to adult at the seven temperatures (12, 15, 18, 20, 25, 30, and 32°C) were 114.41, 51.66, 33.45, 23.21, 13.43, 11.54, and 17.18 d, respectively. Two linear and seven nonlinear models (Logan-6 and Logan-10, Taylor, Lactin-1 and Lactin-2, and Brière-1 and Brière-2) were fit to the developmental rates of the immature predatory stages to estimate the thermal constant (K) and critical temperatures. The lower temperature threshold (T0) and K for the immature stages using the common linear model were 9.96°C and 225.73 degree-days and Ikemoto–Takai linear model were 11.01°C and 167.14 degree-days, respectively. The upper temperature threshold values estimated by the Logan-6 and Lactin-1 models were both 34.86°C. The T0 values estimated by the Brière-1 and Brière-2 models were 10.67 and 9.32°C for all immature stages, respectively, and the estimated optimal temperature according to the Brière-2 model was 29.59°C. Therefore, the two linear models and Brière-2 model estimates approximated the actual relationship between the temperature and developmental rate of immature O. flavicornis. [ABSTRACT FROM AUTHOR]

OBJECTIVES: The management of non-small cell lung cancer (NSCLC) relies on the tumour-node-metastasis (TNM) stage, and the treatment regimen differs based on the N status. Positron emission tomography-computed tomography (PET-CT) has emerged as a powerful imaging tool for the detection of various cancers with a relatively low false-negative rate. We explored predictors to identify false-negative N2 disease in PET-CT. METHODS: A total of 284 consecutive cN0 patients with peripheral NSCLC who underwent PET-CT scans followed by curative intent resections were enrolled as a training set to identify predictors of occult N2 metastases by multivariable analysis. The accuracy and cut-off values for the predictors were calculated using a receiver operating characteristic curve. Clinical and pathological data were analysed retrospectively. An additional 151 patients were collected as a test set to validate the results, including the occult N2 rate and accuracy. RESULTS: In total, 8.5% (24/284) PET-CT-diagnosed N0 NSCLC cases had pathologically diagnosed N2 metastases. The SUVmax of the primary tumour was a unique independent risk factor for occult N2 NSCLC [P = 0.003, 95% confidence interval = 0.81-0.96, odds ratio (OR) = 0.88]. Occult N2 metastases occurred more frequently in the subcarinal (16/24) and right lower paratracheal lymph nodes (12/24). Accordingly, we divided the patients into two groups by SUVmax: the occult N2 rates in the SUVmaxof <2.6 and SUVmax of ≥2.6 groups were 1.0% (1/100) and 12.5% (23/184), respectively (P = 0.001). In the test set, the occult N2 incidence rate was 9.3% (14/151), with the highest rates occurring in the subcarinal (9/14) and right lower paratracheal lymph nodes (6/14). In the two groups defined by SUVmax, the occult N2 rates were 4% (2/50) and 11.9% (12/101), respectively. CONCLUSIONS: The SUVmax of the primary tumour was an independent risk factor for occult N2 metastases in NSCLC patients diagnosed as clinical N0 by PET-CT. SUVmax of ≥2.6 of the primary tumour may indicate the risk of N2 metastases, and invasive mediastinal staging techniques or comprehensive therapy should not be ignored in these patients. [ABSTRACT FROM AUTHOR]

An inactivated, alum-adjuvanted, whole-virion H5N1 vaccine had been evaluated previously. Hemagglutination inhibition (HI) assays showed that the antibody levels declined significantly, with 4.8%-20.8% and 0%-18.8% of participants retaining seroprotection (HI titer ⩾ 1:40) 6 and 12 months after the second dose, respectively. A third dose of the same vaccine given 12 months after the second dose significantly boosted immune responses. Thirty days after the third dose in the 1.25-, 2.5-, 5-, and 10-μg dose groups, 29.4%, 31.3%, 78.6%, and 90.0% of participants had HI titers ⩾1:40,and 52.9%, 81.2%, 92.9%, and 100% of participants had microneutralization titers ⩾1:40, respectively. Both the 5-μg and 10-μg doses met European Union criteria. (ClinicalTrials.gov identifier: NCT00660257.) [ABSTRACT FROM AUTHOR]

Cryptochromes are blue-light receptors that mediate blue-light inhibition of hypocotyl elongation and blue-light stimulation of floral initiation in Arabidopsis. In addition to their blue-light-dependent functions, cryptochromes are also involved in blue-light-independent regulation of the circadian clock, cotyledon unfolding, and hypocotyl inhibition. However, the molecular mechanism associated with the blue-light-independent function of cryptochromes remains unclear. We reported here a comparative proteomics study of the light regulation of protein expression. We showed that, as expected, the protein expression of many metabolic enzymes changed in response to both blue light and red light. Surprisingly, some light-regulated protein expression changes are impaired in the cry1cry2 mutant in both blue light and red light. This result suggests that, in addition to mediating blue-light-dependent regulation of protein expression, cryptochromes are also involved in the blue-light-independent regulation of gene expression. Consistent with this hypothesis, the cry1cry2 mutant exhibited reduced changes of mRNA expression in response to not only blue light, but also red light, although the cryptochrome effects on the red-light-dependent gene expression changes are generally less pronounced. These results support a hypothesis that, in addition to their blue-light-specific functions, cryptochromes also play roles in the control of gene expression mediated by the red/far-red-light receptor phytochromes. [ABSTRACT FROM PUBLISHER]

Introduction. Erectile dysfunction (ED) represents a common quality-of-life issue of any treatment used for prostate cancer, including high-intensity focused ultrasound (HIFU) and targeted cryoablation of the prostate (TCAP). There is a paucity of comparative studies regarding the difference in the erectile function and penile size of patients undergoing HIFU or TCAP. Aim. The aim of this study is to compare the erectile function and penile size of patients undergoing HIFU or TCAP. Methods. Patients with a preoperative erectile function domain of the International Index of Erectile Function (IIEF-EF) score ≥26 were prospectively included. All patients were preoperatively evaluated by IIEF-EF and penile color Doppler ultrasound. Penile length and circumference were measured in flaccidity and at maximum erection. At 6, 12, 18, 24, 36 months after surgery, patients were assessed with the same protocol. Main Outcome Measures. IIEF-EF score, penile color Doppler ultrasound, penile length, and circumference at different time points. Results. There were 55 patients in the HIFU group and 47 in the TCAP group. At each time point, there were significant differences in mean IIEF-EF scores and penile color Doppler results between the two groups. At 36 months, TCAP patients experienced lower erectile function recovery rate compared with HIFU patients (TCAP = 46.8%; HIFU = 65.5%; P = 0.021). No significant decreases in penile length and circumference were found in the two groups (all P values ≥0.05). Conclusions. Our data demonstrate TCAP caused significantly decreased erectile function than HIFU. We found no change in penile size after HIFU or TCAP. The option of HIFU may be more attractive to the patient who wants to avoid ED afterward, to maintain their quality of life. Li L-Y, Lin Z, Yang M, Gao X, Xia T-L, and Ding T. Comparison of penile size and erectile function after high-intensity focused ultrasound and targeted cryoablation for localized prostate cancer: A prospective pilot study. J Sex Med 2010;7:3135–3142. [ABSTRACT FROM AUTHOR]