Development of interactive biological web applications with R/Shiny.

Development of interactive web applications to deposit, visualize and analyze biological datasets is a major subject of bioinformatics. R is a programming language for data science, which is also one of the most popular languages used in biological data analysis and bioinformatics. However, building interactive web applications was a great challenge for R users before the Shiny package was developed by the RStudio company in 2012. By compiling R code into HTML, CSS and JavaScript code, Shiny has made it incredibly easy to build web applications for the large R community in bioinformatics and for even non-programmers. Over 470 biological web applications have been developed with R/Shiny up to now. To further promote the utilization of R/Shiny, we reviewed the development of biological web applications with R/Shiny, including eminent biological web applications built with R/Shiny, basic steps to build an R/Shiny application, commonly used R packages to build the interface and server of R/Shiny applications, deployment of R/Shiny applications in the cloud and online resources for R/Shiny.

LILRB4 signalling in leukaemia cells mediates T cell suppression and tumour infiltration.

Immune checkpoint blockade therapy has been successful in treating some types of cancer but has not shown clinical benefits for treating leukaemia1. This result suggests that leukaemia uses unique mechanisms to evade this therapy. Certain immune inhibitory receptors that are expressed by normal immune cells are also present on leukaemia cells. Whether these receptors can initiate immune-related primary signalling in tumour cells remains unknown. Here we use mouse models and human cells to show that LILRB4, an immunoreceptor tyrosine-based inhibition motif-containing receptor and a marker of monocytic leukaemia, supports tumour cell infiltration into tissues and suppresses T cell activity via a signalling pathway that involves APOE, LILRB4, SHP-2, uPAR and ARG1 in acute myeloid leukaemia (AML) cells. Deletion of LILRB4 or the use of antibodies to block LILRB4 signalling impeded AML development. Thus, LILRB4 orchestrates tumour invasion pathways in monocytic leukaemia cells by creating an immunosuppressive microenvironment. LILRB4 represents a compelling target for the treatment of monocytic AML.

LIRBase: a comprehensive database of long inverted repeats in eukaryotic genomes.

Small RNAs (sRNAs) constitute a large portion of functional elements in eukaryotic genomes. Long inverted repeats (LIRs) can be transcribed into long hairpin RNAs (hpRNAs), which can further be processed into small interfering RNAs (siRNAs) with vital biological roles. In this study, we systematically identified a total of 6 619 473 LIRs in 424 eukaryotic genomes and developed LIRBase (https://venyao.xyz/lirbase/), a specialized database of LIRs across different eukaryotic genomes aiming to facilitate the annotation and identification of LIRs encoding long hpRNAs and siRNAs. LIRBase houses a comprehensive collection of LIRs identified in a wide range of eukaryotic genomes. In addition, LIRBase not only allows users to browse and search the identified LIRs in any eukaryotic genome(s) of interest available in GenBank, but also provides friendly web functionalities to facilitate users to identify LIRs in user-uploaded sequences, align sRNA sequencing data to LIRs, perform differential expression analysis of LIRs, predict mRNA targets for LIR-derived siRNAs, and visualize the secondary structure of candidate long hpRNAs encoded by LIRs. As demonstrated by two case studies, collectively, LIRBase bears the great utility for systematic investigation and characterization of LIRs and functional exploration of potential roles of LIRs and their derived siRNAs in diverse species.

The combination of machine learning and untargeted metabolomics identifies the lipid metabolism -related gene CH25H as a potential biomarker in asthma.

BACKGROUND: Lipids, significant signaling molecules, regulate a multitude of cellular responses and biological pathways in asthma which are closely associated with disease onset and progression. However, the characteristic lipid genes and metabolites in asthma remain to be explored. It is also necessary to further investigate the role of lipid molecules in asthma based on high-throughput data. OBJECTIVE: To explore the biomarkers and molecular mechanisms associated with lipid metabolism in asthma. METHODS: In this study, we selected three mouse-derived datasets and one human dataset (GSE41665, GSE41667, GSE3184 and GSE67472) from the GEO database. Five machine learning algorithms, LASSO, SVM-RFE, Boruta, XGBoost and RF, were used to identify core gene. Additionally, we used non-negative matrix breakdown (NMF) clustering to identify two lipid molecular subgroups and constructed a lipid metabolism score by principal component analysis (PCA) to differentiate the subtypes. Finally, Western blot confirmed the altered expression levels of core genes in OVA (ovalbumin) and HDM+LPS (house dust mite+lipopolysaccharide) stimulated and challenged BALB/c mice, respectively. Results of non-targeted metabolomics revealed multiple differentially expressed metabolites in the plasma of OVA-induced asthmatic mice. RESULTS: Cholesterol 25-hydroxylase (CH25H) was finally localized as a core lipid metabolism gene in asthma and was verified to be highly expressed in two mouse models of asthma. Five-gene lipid metabolism constructed from CYP2E1, CH25H, PTGES, ALOX15 and ME1 was able to distinguish the subtypes effectively. The results of non-targeted metabolomics showed that most of the aberrantly expressed metabolites in the plasma of asthmatic mice were lipids, such as LPC 16:0, LPC 18:1 and LPA 18:1. CONCLUSION: Our findings imply that the lipid-related gene CH25H may be a useful biomarker in the diagnosis of asthma.

Functional and structural MRI based obsessive-compulsive disorder diagnosis using machine learning methods.

BACKGROUND: The success of neuroimaging in revealing neural correlates of obsessive-compulsive disorder (OCD) has raised hopes of using magnetic resonance imaging (MRI) indices to discriminate patients with OCD and the healthy. The aim of this study was to explore MRI based OCD diagnosis using machine learning methods. METHODS: Fifty patients with OCD and fifty healthy subjects were allocated into training and testing set by eight to two. Functional MRI (fMRI) indices, including amplitude of low-frequency fluctuation (ALFF), fractional ALFF (fALFF), regional homogeneity (ReHo), degree of centrality (DC), and structural MRI (sMRI) indices, including volume of gray matter, cortical thickness and sulcal depth, were extracted in each brain region as features. The features were reduced using least absolute shrinkage and selection operator regression on training set. Diagnosis models based on single MRI index / combined MRI indices were established on training set using support vector machine (SVM), logistic regression and random forest, and validated on testing set. RESULTS: SVM model based on combined fMRI indices, including ALFF, fALFF, ReHo and DC, achieved the optimal performance, with a cross-validation accuracy of 94%; on testing set, the area under the receiver operating characteristic curve was 0.90 and the validation accuracy was 85%. The selected features were located both within and outside the cortico-striato-thalamo-cortical (CSTC) circuit of OCD. Models based on single MRI index / combined fMRI and sMRI indices underperformed on the classification, with a largest validation accuracy of 75% from SVM model of ALFF on testing set. CONCLUSION: SVM model of combined fMRI indices has the greatest potential to discriminate patients with OCD and the healthy, suggesting a complementary effect of fMRI indices on the classification; the features were located within and outside the CSTC circuit, indicating an importance of including various brain regions in the model.

Clinical characteristics, risk factors and outcomes of Klebsiella pneumoniae pneumonia developing secondary Klebsiella pneumoniae bloodstream infection.

PURPOSE: The clinical characteristics of Klebsiella pneumoniae (KP) pneumonia and KP bloodstream infection (KP-BSI) are often reported, while the risk factors for KP pneumonia developing into secondary KP-BSI (KP-pneumonia/KP-BSI) are largely unknown. Therefore, this study attempted to investigate the clinical characteristics, risk factors and outcomes of KP-pneumonia/KP-BSI. METHODS: A retrospective observational study was conducted at a tertiary hospital between January 1, 2018, and December 31, 2020. The patients were divided into groups of KP pneumonia alone and KP pneumonia/KP-BSI, and the clinical information were collected from medical records electronic system. RESULTS: A total of 409 patients were finally recruited. According to the multivariate logistic regression analysis, male sex (adjusted odds ratio [aOR] 3.7; 95% CI, 1.44-9.5), immunosuppression (aOR, 13.52; 95% CI, 2.53,72.22), APACHE II score higher than 21 (aOR, 3.39; 95% CI, 1.41-8.12), serum procalcitonin (PCT) levels above 1.8 ng/ml (aOR, 6.37; 95% CI, 2.67-15.27), ICU stay of more than 2.5 days before pneumonia onset (aOR, 1.09; 95% CI, 1.02,1.17), mechanical ventilation (aOR, 4.96; 95% CI, 1.2,20.5), Klebsiella pneumoniae isolates producing extended spectrum ß-lactamase (ESBL-positive KP) (aOR, 12.93; 95% CI, 5.26-31.76), and inappropriate antibacterial therapy (aOR, 12.38; 95% CI, 5.36-28.58) were independent factors of KP pneumonia/KP BSI. In comparison with the patients with KP pneumonia alone, the patients with KP pneumonia/KP BSI showed an almost 3 times higher incidence of septic shock (64.4% vs. 20.1%, p < 0.01), a longer duration of mechanical ventilation, and longer lengths of ICU stay and total hospital stay (median days, 15 vs. 4,19 vs. 6, 34 vs. 17, respectively, both p < 0.01). Additionally, the overall in-hospital crude mortality rate in the patients with KP-pneumonia/KP-BSI was more than two times higher than that in those with KP pneumonia alone (61.5% vs. 27.4%, p < 0.01). CONCLUSION: Factors including male sex, immunosuppression, APACHE II score higher than 21, serum PCT levels above 1.8 ng/ml, ICU stay of more than 2.5 days before pneumonia onset, mechanical ventilation, ESBL-positive KP, and inappropriate antibacterial therapy are independent risk factors for KP pneumonia/KP-BSI. Of note, the outcomes in patients with KP pneumonia worsen once they develop secondary KP-BSI, which merits more attention.

Preparation of Enzyme-Soluble Swim Bladder Collagen from Sea Eel (Muraenesox cinereus) and Evaluation Its Wound Healing Capacity.

In the present research, the enzyme-facilitated collagen from sea eel (Muraenesox cinereus) swim bladder was isolated, and the collagen characteristics were analyzed. Then, the collagen sponge was prepared and its potential mechanism in promoting skin wound healing in mice was further investigated. Collagen was obtained from the swim bladder of sea eels employing the pepsin extraction technique. Single-factor experiments served as the basis for the response surface method (RSM) to optimize pepsin concentration, solid-liquid ratio, and hydrolysis period. With a pepsin concentration of 2067 U/g, a solid-liquid ratio of 1:83 g/mL, and a hydrolysis period of 10 h, collagen extraction achieved a yield of 93.76%. The physicochemical analysis revealed that the extracted collagen belonged to type I collagen, and the collagen sponge displayed a fibrous structure under electron microscopy. Furthermore, in comparison to the control group, mice treated with collagen sponge dressing exhibited elevated activities of superoxide dismutase (SOD), catalase (CAT), total antioxidant capacity (T-AOC), and glutathione peroxidase (GSH-Px), and decreased levels of malondialdehyde (MDA), interleukin (IL)-1ß, interleukin (IL)-6, and tumor necrosis factor (TNF)-α. The collagen sponge dressing effectively alleviated inflammation in the wound area, facilitating efficient repair and rapid healing of the skin tissue. During the initial phase of wound healing, the group treated with collagen sponge dressing exhibited an enhancement in the expressions of cluster of differentiation (CD)31, epidermal growth factor (EGF), transforming growth factor (TGF)-ß1, and type I collagen, leading to an accelerated rate of wound healing. In addition, this collagen sponge dressing could also downregulate the expressions of CD31, EGF, and type I collagen to prevent scar formation in the later stage. Moreover, this collagen treatment minimized oxidative damage and inflammation during skin wound healing and facilitated blood vessel formation in the wound. Consequently, it exhibits significant potential as an ideal material for the development of a skin wound dressing.

The pathophysiological and molecular mechanisms of atmospheric PM2.5 affecting cardiovascular health: A review.

BACKGROUND: Exposure to ambient fine particulate matter (PM2.5, with aerodynamic diameter less than 2.5 µm) is a leading environmental risk factor for global cardiovascular health concern. OBJECTIVE: To provide a roadmap for those new to this field, we reviewed the new insights into the pathophysiological and cellular/molecular mechanisms of PM2.5 responsible for cardiovascular health. MAIN FINDINGS: PM2.5 is able to disrupt multiple physiological barriers integrity and translocate into the systemic circulation and get access to a range of secondary target organs. An ever-growing body of epidemiological and controlled exposure studies has evidenced a causal relationship between PM2.5 exposure and cardiovascular morbidity and mortality. A variety of cellular and molecular biology mechanisms responsible for the detrimental cardiovascular outcomes attributable to PM2.5 exposure have been described, including metabolic activation, oxidative stress, genotoxicity, inflammation, dysregulation of Ca2+ signaling, disturbance of autophagy, and induction of apoptosis, by which PM2.5 exposure impacts the functions and fates of multiple target cells in cardiovascular system or related organs and further alters a series of pathophysiological processes, such as cardiac autonomic nervous system imbalance, increasing blood pressure, metabolic disorder, accelerated atherosclerosis and plaque vulnerability, platelet aggregation and thrombosis, and disruption in cardiac structure and function, ultimately leading to cardiovascular events and death. Therein, oxidative stress and inflammation were suggested to play pivotal roles in those pathophysiological processes. CONCLUSION: Those biology mechanisms have deepen insights into the etiology, course, prevention and treatment of this public health concern, although the underlying mechanisms have not yet been entirely clarified.

A comparison of 'not just right experiences' in obsessive-compulsive disorder, anxiety and depressive disorders and non-clinical controls in China.

OBJECTIVE: The aim of this study is to investigate the characteristics of 'not just right experiences' (NJREs) in patients with obsessive-compulsive disorder (OCD), anxiety disorders (ADs) or major depressive disorder (MDD), compared with those of healthy controls (HCs). METHOD: One hundred adults with OCD, 86 adults with ADs, 57 adults with MDD and 60 HCs were enrolled in the study. The Not Just Right Experiences Questionnaire Revised (NJRE-QR), Yale-Brown Obsessive-Compulsive Scale (Y-BOCS), Beck Depression Inventory (BDI) and Beck Anxiety Inventory (BAI) were used to evaluate clinical symptoms in patients with OCD, ADs or MDD. The Obsessive Belief Questionnaire-44 (OBQ-44) was used to evaluate OC beliefs in the OCD patients. The HCs only received assessment using the NJRE-QR. Analysis of variance (ANOVA) and covariance (ANCOVA) were performed to compare the NJREs scores across the groups, while Pearson correlation and partial correlation analyses were used to examine the association between NJREs and other clinical features. The contribution of NJREs to predict OC symptoms was determined by multiple stratified linear regression. RESULTS: Individuals with OCD had significantly higher scores for the number of NJREs than ADs, but not MDD. The severity of NJREs was also significantly higher in patients with OCD than those with MDD or ADs (F = 5.23 and F = 19.79, respectively, P < 0.01). All the clinical scores in the NJRE-QR were significantly higher than those in the HC group. The number and severity of NJREs correlated significantly with the Y-BOCS total score (r = 0.29 and r = 0.39, respectively, P < 0.01). NJREs showed an independent contribution to OC symptoms, which alone explained 8% of the variation (F = 16.49, ΔR2 = 0.08; P < 0.01). CONCLUSION: NJREs are related closely to OC symptoms, with their severity discriminating between OCD patients and those with ADs or MDD. NJREs were more specific for OCD in the Chinese population and are therefore worthy of further study in the future.

Propeller vs Quasi-Planar 6-Cantilever Small Molecular Platforms with Extremely Two-Dimensional Conjugated Extension.

Two exotic 6-cantilever small molecular platforms, characteristic of quite different molecular configurations of propeller and quasi-plane, are established by extremely two-dimensional conjugated extension. When applied in small molecular acceptors, the only two cases of CH25 and CH26 that could contain six terminals and such broad conjugated backbones have been afforded thus far, rendering featured absorptions, small reorganization and exciton binding energies. Moreover, their distinctive but completely different molecular geometries result in sharply contrasting nanoscale film morphologies. Finally, CH26 contributes to the best device efficiency of 15.41 % among acceptors with six terminals, demonstrating two pioneered yet highly promising 6-cantilever molecular innovation platforms.

Genome-wide association study reveals the genetic architecture for calcium accumulation in grains of hexaploid wheat (Triticum aestivum L.).

BACKGROUND: Hexaploid wheat (Triticum aestivum L.) is a leading cereal crop worldwide. Understanding the mechanism of calcium (Ca) accumulation in wheat is important to reduce the risk of human micronutrient deficiencies. However, the mechanisms of Ca accumulation in wheat grain are only partly understood. RESULTS: Here, a genome-wide association study (GWAS) was performed to dissect the genetic basis of Ca accumulation in wheat grain using an association population consisting of 207 varieties, with phenotypic data from three locations. In total, 11 non-redundant genetic loci associated with Ca concentration were identified and they explained, on average, 9.61-26.93% of the phenotypic variation. Cultivars containing more superior alleles had increased grain Ca concentrations. Notably, four non-redundant loci were mutually verified by different statistical models in at least two environments, indicating their stability across different environments. Four putative candidate genes linked to Ca accumulation were revealed from the stable genetic loci. Among them, two genes, associated with the stable genetic loci on chromosomes 4A (AX-108912427) and 3B (AX-110922471), encode the subunits of V-type Proton ATPase (TraesCS4A02G428900 and TraesCS3B02G241000), which annotated as the typical generators of a proton gradient that might be involved in Ca homeostasis in wheat grain. CONCLUSION: To identify genetic loci associated with Ca accumulation, we conducted GWAS on Ca concentrations and detected 11 genetic loci; whereas four genetic loci were stable across different environments. A genetic loci hot spot exists at the end of chromosome 4A and associated with the putative candidate gene TraesCS4A02G428900. The candidate gene TraesCS4A02G428900 encodes V-type proton ATPase subunit e and highly expressed in wheat grains, and it possibly involved in Ca accumulation. This study increases our understanding of the genetic architecture of Ca accumulation in wheat grains, which is potentially helpful for wheat Ca biofortification pyramid breeding.

Fucoxanthin Attenuates Free Fatty Acid-Induced Nonalcoholic Fatty Liver Disease by Regulating Lipid Metabolism/Oxidative Stress/Inflammation via the AMPK/Nrf2/TLR4 Signaling Pathway.

Fucoxanthin, a xanthophyll carotenoid abundant in brown algae, is reported to have several biological functions, such as antioxidant, anti-inflammatory, and anti-tumor activities, in mice. We investigated the effects and mechanisms of fucoxanthin in the mixture oleate/palmitate = 2/1(FFA)-induced nonalcoholic fatty liver disease (NAFLD) cell model in this study. The results showed that the content of superoxide dismutase in the FFA group was 9.8 ± 1.0 U/mgprot, while that in the fucoxanthin high-dose (H-Fx) group (2 µg/mL) increased to 22.9 ± 0.6 U/mgprot. The content of interleukin-1ß in the FFA group was 89.3 ± 3.6 ng/mL, while that in the H-Fx group was reduced to 53.8 ± 2.8 ng/mL. The above results indicate that fucoxanthin could alleviate the FFA-induced oxidative stress and inflammatory levels in the liver cells. Oil red-O staining revealed visible protrusions and a significant decrease in the number of lipid droplets in the cytoplasm of cells in the fucoxanthin group. These findings on the mechanisms of action suggest that fucoxanthin can repair FFA-induced NAFLD via the adenosine monophosphate-activated protein kinase (AMPK) signaling pathway and nuclear factor erythroid-2-related factor 2-mediated (Nrf2) signaling pathway, as well as by downregulating the expression of the Toll-like receptor 4-mediated (TLR4) signaling pathway. Fucoxanthin exhibited alleviating effects in the FFA-induced NAFLD model and could be explored as a potential anti-NAFLD substance.

Azaphilones from the Endophyte Diaporthe sp. and Their Toxicity.

Chemotherapy and targeted therapies are increasingly used as conventional means to control tumor growth and prolong survival. Patient treated with anti-neoplastic agents experience severe side effects, especially those cytotoxic chemotherapies. Exploring chemo agents with less side effects is the hot spot of anticancer research. In this study, three azaphilone derivatives (chaetoviridin A (1), chaetoviridin E (2) and chaetomugilin D (3)) were isolated from the endophyte of the plant Anoectochilus roxburghii (Wall.) Lindl, their structures were elucidated by NMR. The toxicity of these compounds was evaluated by zebrafish model. The results show that these compounds had no toxicity against zebrafish. These compounds may act as safe anticancer drug leads according to this result. These three azaphilone derivatives were first time reported isolated from Diaporthe species which mainly used to isolate from Chaetomium species.

[Accelerated rehabilitation nursing in improving the symptoms of prostate cancer patients after surgery].

OBJECTIVE: To study the clinical value of accelerated rehabilitation nursing (ARN) in improving the symptoms of PCa patients after surgery. METHODS: This study included 80 cases of PCa treated surgically in our hospital from October 2020 to October 2021. We randomly divided the patients into two groups of an equal number to receive ARN and routine nursing care (the control group), respectively. We obtained the scores of the patients on IPSS, TCM syndromes, quality of life (QOL) and pain, incidence of postoperative complications, satisfaction with nursing care and Gleason scores, and compared them between the two groups. RESULTS: The IPSS and TCM syndrome scores were significantly lower (P < 0.05 ), and the physical and psychological function score remarkably higher in the ARN than in the control group (P < 0.05), but there was no statistically significant difference in the social function scores between the two groups (P > 0.05). The postoperative pain score was also significantly lower in the ARN than in the control group (P < 0.05), and so was the incidence rate of postoperative complications (10% vs 37.5%, P < 0.05). The patients' satisfaction with nursing care was markedly higher in the former than in the latter group (90% vs 80%, P < 0.05). No statistically significant difference was observed in the Gleason scores between the two groups of patients. CONCLUSION: Accelerated rehabilitation nursing can effectively improve the symptoms of PCa patients after surgery and therefore deserves clinical application.

Ferroptosis-related gene AKR1C1 predicts the prognosis of non-small cell lung cancer.

BACKGROUND: Ferroptosis is a newly discovered mode of cell death distinct from apoptosis and necrosis, and its activation contributes to anticancer therapy in a variety of cancers. However, the prognostic value of ferroptosis-related genes in non-small cell lung cancer (NSCLC) remains to be further investigated. METHODS: NSCLC transcriptome mRNA-seq data set and corresponding clinical data set were downloaded from the Cancer Genome Atlas (TCGA). Then, bioinformatics approaches were subsequently employed to identify potential prognostic markers. Finally, the effects of candidate markers on NSCLC cell proliferation, migration, and ferroptosis were assessed by CCK8, colony formation, wound-healing assay, and functional assays related to ferroptosis. RESULTS: A total of 37 common differentially expressed genes were screened based TCGA database. Six overall survival associated genes (ENPP2, ULK1, CP, LURAP1L, HIC1, AKR1C1) were selected to build survival model, of which hub gene AKR1C1 was with high expression and low ferroptosis level in NSCLC tumor. Further research showed that AKR1C1 was related with many pathways involved in the process of ferroptosis and associated with diverse cancer-infiltrating immune cells. Moreover, the results of in vitro experiments indicated that the expression of AKR1C1 was upregulated in NSCLC cell lines, and silencing AKR1C1 can inhibit the proliferation and migration of NSCLC cells and promote the occurrence of ferroptosis. CONCLUSIONS: Our study revealed the potential role of ferroptosis-related gene AKR1C1 in NSCLC, which can be used for prognostic prediction in NSCLC.

Targeting effect of berberine on type I fimbriae of Salmonella Typhimurium and its effective inhibition of biofilm.

As a primary cause of food contamination and human diseases, Salmonella Typhimurium can easily form a biofilm that is difficult to remove from food surfaces, and often causes significant invisible threats to food safety. Although berberine has been widely used as an anti-infective drug in traditional medicine, some basic principles underlying its mechanism, especially the interaction between berberine and type I fimbriae genes, has not been verified yet. In this study, two strains of major fimbrial gene mutants (ΔfimA and ΔfimH) were constructed to demonstrate the possible action of berberine on type I fimbriae genes. The broth microdilution method was used to determine the antibacterial activity of berberine against selected strains (WT, ΔfimA, and ΔfimH). Cell agglutination experiments revealed that the number of S. Typhimurium type I fimbriae reduced after berberine treatment, which was consistent with transmission electron microscopy results. Quantitative real-time PCR experiments also confirmed that berberine reduced fimA gene expression, indicating a certain interaction between berberine and fimA gene. Furthermore, confocal laser scanning microscopy imaging of biofilm clearly revealed that berberine prevents biofilm formation by reducing the number of type I fimbriae. Overall, it is well speculated for us that berberine could be an excellent combating-biofilm drug in clinical microbiology and food preservation. KEY POINTS: • Reduce the number of fimbriae. • Berberine targeting fimA. • Effective biofilm inhibitor.

Effectiveness of acupuncture on anxiety disorder: a systematic review and meta-analysis of randomised controlled trials.

BACKGROUND: A number of studies have shown the positive effects of acupuncture on state anxiety. However, the efficacy of acupuncture in treating anxiety disorder remains unclear. This review and meta-analysis aimed to explore whether acupuncture has a positive effect on anxiety disorder. METHODS: Randomised controlled trials (RCTs) published in English and Chinese were found through various electronic databases, including PubMed, Scopus, the Cochrane Central Register of Controlled Trials, Embase, and the Chinese databases WanFang data, VIP Chinese Sci tech periodical database, and China National Knowledge Infrastructure. The primary outcome variable was extent of anxiety symptoms. The secondary outcomes included side effects and dropout rate. Effect sizes were pooled by random-effects modelling using Rev Man 5.3. RESULTS: Twenty RCTs were included in this systematic review and meta-analysis. All included studies were designed for patients with generalised anxiety disorder (GAD), and 18 studies were published in Chinese. Egger's test showed that the asymmetry of the funnel plot in all studies was not significant (t = - 0.34, p = 0.74). The meta-analysis of anxiety symptoms showed that acupuncture was more effective than the control condition, with a standard mean effect size of - 0.41 (95% CI - 0.50 to - 0.31; p < 0.001), and that acupuncture intervention showed good tolerance and safety in the treatment of anxiety disorder. CONCLUSION: Our findings suggest that acupuncture therapy aimed at reducing anxiety in patients with GAD has certain beneficial effects compared to controls. More RCTs with high quality should be conducted to fully understand the role of acupuncture in the treatment of various types of anxiety disorder. The protocol of this review was registered at the Prospero International Prospective Register of Systematic Reviews (Registration ID: PROSPERO 2020CRD42020148536).

ECOGEMS: efficient compression and retrieve of SNP data of 2058 rice accessions with integer sparse matrices.

SUMMARY: We proposed to store large-scale genotype data as integer sparse matrices, which consumed much fewer computing resources for storage and analysis than traditional approaches. In addition, the raw genotype data could be readily recovered from integer sparse matrices. Utilizing this approach, we stored the genotype data of 1612 Asian cultivated rice accessions and 446 Asian wild rice accessions across 8 584 244 SNP sites in the ECOGEMS database with 310 MB of disk usage. Graphical interface for visualization, analysis and download of SNP data were implemented in ECOGEMS, which made it a valuable resource for rice functional genomic studies. AVAILABILITY AND IMPLEMENTATION: The code and data of ECOGEMS are freely available at https://github.com/venyao/ECOGEMS. ECOGEMS is deployed at http://ecogems.ncpgr.cn and http://150.109.59.144: 3838/ECOGEMS/ for online use. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

A review of therapeutic agents and Chinese herbal medicines against SARS-COV-2 (COVID-19).

The epidemic of pneumonia (COVID-19) caused by novel coronavirus (SARS-CoV-2) infection has been listed as a public health emergency of international concern by the World Health Organization (WHO), and its harm degree is defined as a global "pandemic". At present, the efforts of various countries focus on the rapid diagnosis and isolation of patients, as well as to find a treatment that can combat the most serious impact of the disease. The number of reported COVID-19 virus infections is still increasing. Unfortunately, no drugs or vaccines have been approved for the treatment of human coronaviruses, but there is an urgent need for in-depth research on emerging human infectious coronaviruses. Clarification transmission routes and pathogenic mechanisms, and identification of potential drug treatment targets will promote the development of effective prevention and treatment measures. In the absence of confirmed effective treatments, due to public health emergencies, it is essential to study the possible effects of existing approved antivirals drugs or Chinese herbal medicines for SARS-CoV-2. This review summarizes the epidemiological characteristics, pathogenesis, virus structure and targeting strategies of COVID-19. Meanwhile, this review also focus on the re-purposing of clinically approved drugs and Chinese herbal medicines that may be used to treat COVID-19 and provide new ideas for the discovery of small molecular compounds with potential therapeutic effects on novel COVID-19.

G-quadruplex-based assay combined with aptamer and gold nanoparticles for Escherichia coli K88 determination.

A colorimetric method was developed using G-quadruplex and gold nanoparticles (AuNPs) for determination of Escherichia coli K88 (ETEC K88). It was composed of two modules: (1) an aptamer as biorecognizing element and (2) a capturing DNA (modified with AuNPs at 5') as a transducer. In the absence of target bacteria, the aptamer can form stable double strands with capturing DNA, preventing the binding of capturing DNA to the G-quadruplex. However, the double strands of capturing DNA and aptamer are untied due to the stronger binding of aptamers to bacteria in the presence of target bacteria. As a result, the G-quadruplex binds to capture DNA and leads to the aggregation and color change of AuNPs, which can be monitored by a spectrophotometer or visualization. The quantitative determination was achieved by monitoring the optical density change of AuNPs solution at 524 nm after target addition. Under optimal conditions, the method has a low detection limit (1.35 × 102 CFU mL-1) and a linear response in the range 102 to 106 CFU mL-1. Graphical abstract The manuscripts describe a colorimetric method for the detection of ETEC K88 by using intermolecular G-quadruplex to induce the agglomeration of gold nanoparticles, which can be directly used to determine the presence of bacteria with our naked eyes.