Identifying the risk of depression in a large sample of adolescents: An artificial neural network based on random forest.

BACKGROUND: This study aims to develop an artificial neural network (ANN) prediction model incorporating random forest (RF) screening ability for predicting the risk of depression in adolescents and identifies key risk factors to provide a new approach for primary care screening of depression among adolescents. METHODS: The data were from a large cross-sectional study conducted in China from July to September 2021, enrolling 8635 adolescents aged 10-17 with their parents. We used the Patient health questionnaire (PHQ-9) to rate adolescent depression symptoms, using scales and single-item questions to collect demographic information and other variables. Initial model variables screening used the RF importance assessment, followed by building prediction model using the screened variables through the ANN. RESULTS: The rate of depression symptoms in adolescents was 24.6%, and the depression risk prediction model was built based on 70% of the training set and 30% of the test set. Ten variables were included in the final prediction model with a model accuracy of 85.03%, AUC of 0.892, specificity of 89.79%, and sensitivity of 70.81%. The top 10 significant factors of depression risk were adolescent rumination, adolescent self-esteem, adolescent mobile phone addiction, peer victimization, care in parenting styles, overprotection in parenting styles, academic pressure, conflict in parent-child relationship, parental rumination, and relationship between parents. CONCLUSIONS: The ANN model based on the RF effectively identifies depression risk in adolescents and provides a methodological reference for large-scale primary screening. Cross-sectional studies and single-item scales limit further improvements in model accuracy.

Proton-Gradient-Driven Porphyrin-Based Liposome Remote-Loaded with Imiquimod as In Situ Nanoadjuvants for Synergistically Augmented Tumor Photoimmunotherapy.

Cancer immunotherapy is expected to achieve tumor treatment mainly by stimulating the patient's own immune system to kill tumor cells. However, the low immunogenicity of the tumor and the poor efficiency of tumor antigen presentation result in a variety of solid tumors that do not respond to immunotherapy. Herein, we designed a proton-gradient-driven porphyrin-based liposome (PBL) with highly efficient Toll-like receptor 7 (TLR7) agonist (imiquimod, R837) encapsulation (R837@PBL). R837@PBL rapidly released R837 in the acid microenvironment to activate the TLR in the endosome inner membrane to promote bone-marrow-derived dendritic cell maturation and enhance antigen presentation. R837@PBL upon laser irradiation triggered immunogenic cell death of tumor cells and tumor-associated antigen release after subcutaneous injection, activated TLR7, formed in situ tumor nanoadjuvants, and enhanced the antigen presentation efficiency. Photoimmunotherapy promoted the infiltration of cytotoxic T lymphocytes into tumor tissues, inhibited the growth of the treated and abscopal tumors, and exerted highly effective photoimmunotherapeutic effects. Hence, our designed in situ tumor nanoadjuvants are expected to be an effective treatment for treated and abscopal tumors, providing a novel approach for synergistic photoimmunotherapy of tumors.

Prostaglandin D2 is involved in the regulation of inflammatory response in Staphylococcus aureus-infected mice macrophages.

Staphylococcus aureus (S. aureus) is one of the most infamous and widespread bacterial pathogens, causing a hard-to-estimate number of uncomplicated skin infections and probably hundreds of thousands to millions of more severe, invasive infections globally per year. S. aureus may also be acquired from animals, especially in the livestock industry. The interaction mechanism of host and S. aureus has significance for finding ways to against S. aureus infection and control inflammatory response of host, while the molecular biological activities after S. aureus infection, particular in inflammatory and immune cells are not fully clear. The present study aimed to explore whether pattern recognition receptors (PRRs) mediate prostaglandin D2 (PGD2) synthesis and PGD2 participates in the regulation of inflammatory response in macrophages during S. aureus infection or synthetic bacterial lipopeptide (Pam2CSK4) stimulation. PGD2 secretion level was enhanced by mice peritoneal macrophages infected with the S. aureus. The results indicated that PGD2 secretion was impaired in S. aureus infected-macrophages from toll-like receptors 2 (TLR2)-deficient and NLR pyrin domain-containing 3 (NLRP3)-deficient mice. PGD2 synthetase (hematopoietic PGD synthase, HPGDS) inhibitors could reduce the activation of macrophage mitogen-activated protein kinase (MAPK)/nuclear factor-κ-gene binding (NF-κB) signaling pathways. HPGDS inhibition impaired cytokines (TNF-α, IL-1ß, IL-10 and RANTES) secretion and macrophage phagocytosis during S. aureus infection. In addition, inhibition of endogenous PGD2 synthesis was unable to affect the TLR2 and NLRP3 expression in S. aureus-infected macrophages. Taken together, macrophage PGD2 secretion after S. aureus infection depended on receptors TLR2 and NLRP3, and the induced PGD2 participated in the regulation of inflammatory response in S. aureus-infected macrophages. Interestingly, it was found that exogenous PGD2 down-regulated the cytokines secretion and had no effect on phagocytosis in the S. aureus-infected macrophages.

CCIBP: a comprehensive cosmetic ingredients bioinformatics platform.

SUMMARY: Cosmetics form an important part of our daily lives, and it is therefore important to understand the basic physicochemical properties, metabolic pathways, and toxicological and safe concentrations of these cosmetics molecules. Therefore, comprehensive cosmetic ingredients bioinformatics platform (CCIBP) was developed here, which is a unique comprehensive cosmetic database providing information on regulations, physicochemical properties, and human metabolic pathways for cosmetic molecules from major regions of the world, whilst also correlating plant information in natural products. CCIBP supports formulation analysis, efficacy component analysis, and also combines knowledge of synthetic biology to facilitate access to natural molecules and biosynthetic production. CCIBP, empowered with chemoinformatics, bioinformatics, and synthetic biology data and tools, presents a very helpful platform for cosmetic research and development of ingredients. AVAILABILITY AND IMPLEMENTATION: CCIBP is available at: http://design.rxnfinder.org/cosing/.

SynBioTools: a one-stop facility for searching and selecting synthetic biology tools.

BACKGROUND: The rapid development of synthetic biology relies heavily on the use of databases and computational tools, which are also developing rapidly. While many tool registries have been created to facilitate tool retrieval, sharing, and reuse, no relatively comprehensive tool registry or catalog addresses all aspects of synthetic biology. RESULTS: We constructed SynBioTools, a comprehensive collection of synthetic biology databases, computational tools, and experimental methods, as a one-stop facility for searching and selecting synthetic biology tools. SynBioTools includes databases, computational tools, and methods extracted from reviews via SCIentific Table Extraction, a scientific table-extraction tool that we built. Approximately 57% of the resources that we located and included in SynBioTools are not mentioned in bio.tools, the dominant tool registry. To improve users' understanding of the tools and to enable them to make better choices, the tools are grouped into nine modules (each with subdivisions) based on their potential biosynthetic applications. Detailed comparisons of similar tools in every classification are included. The URLs, descriptions, source references, and the number of citations of the tools are also integrated into the system. CONCLUSIONS: SynBioTools is freely available at https://synbiotools.lifesynther.com/ . It provides end-users and developers with a useful resource of categorized synthetic biology databases, tools, and methods to facilitate tool retrieval and selection.

Charge reversal yolk-shell liposome co-loaded JQ1 and doxorubicin with high drug loading and optimal ratio for synergistically enhanced tumor chemo-immunotherapy via blockade PD-L1 pathway.

Antitumor immunotherapy has become a powerful therapeutic modality to identify and kill various malignant tumors by harnessing the immune system. However, it is hampered by the immunosuppressive microenvironment and poor immunogenicity in malignant tumors. Herein, in order to achieve multi-loading of drugs with different pharmacokinetic properties and targets, a charge reversal yolk-shell liposome co-loaded with JQ1 and doxorubicin (DOX) into the poly (D,L-lactic-co-glycolic acid) (PLGA) yolk and the lumen of the liposome respectively was engineered to increase hydrophobic drug loading capacity and stability under physiological conditions and further enhance tumor chemotherapy via blockade programmed death ligand 1 (PD-L1) pathway. This nanoplatform could release less JQ1 compared to traditional liposomes to avoid drug leakage under physiological conditions due to the protection of liposomes on JQ1 loaded PLGA nanoparticles while the release of JQ1 increased in an acidic environment. In the tumor microenvironment, released DOX promoted immunogenic cell death (ICD), and JQ1 blocked the PD-L1 pathway to strengthen chemo-immunotherapy. The in vivo antitumor results demonstrated the collaborative treatment of DOX and JQ1 in B16-F10 tumor-bearing mice models with minimized systemic toxicity. Furthermore, the orchestrated yolk-shell nanoparticle system could enhance the ICD effect, caspase 3 activation, and cytotoxic T lymphocyte infiltration while inhibiting PD-L1 expression, provoking a strong antitumor effect, whereas yolk-shell liposomes encapsulating only JQ1 or DOX showed modest tumor therapeutic effects. Hence, the cooperative yolk-shell liposome strategy provides a potential candidate for enhancement of hydrophobic drug loading and stability, showing potential for clinic application and synergistic cancer chemo-immunotherapy.

Atypical development of social and nonsocial working memory capacity among preschoolers with autism spectrum disorders.

Individuals with autism spectrum disorders (ASD) have shown impaired performance in canonical and nonsocial working memory (WM). However, no study has investigated social WM and its early development. Using biological motion stimuli, our study assessed the development of social and nonsocial WM capacity among children with or without ASD across the age span between 4 and 6 (N = 150). While typically developing (TD) children show a rapid development from age 5 to 6, children with ASD showed a delayed development for both social and nonsocial WM capacity, reaching a significant group difference at age 6. Furthermore, we found a negative correlation between social (but not nonsocial) WM capacity and the severity of autistic symptoms among children with ASD. In contrast, there is a positive correlation between both types of WM capacity and intelligence among TD children but not among children with ASD. Our findings thus indicate that individuals with ASD miss the rapid development of WM capacity in early childhood and, particularly, their delayed social WM development might contribute to core symptoms that critically depend on social information processing.

The use of a technology-assisted and teacher-supervised online discussion platform to promote academic progress in blended embryology courses.

BACKGROUND: Students' engagement with learning materials and discussions with teachers and peers before and after lectures are among the keys to the successful implementation of blended programs. Mixed results have been reported by previous studies on blended learning. This study evaluated the effectiveness of embedding a teacher-supervised online discussion platform in a blended embryology course in terms of its impact on students' capabilities to handle difficult and cognitively challenging tasks. METHODS: Two forms of blended learning were investigated and compared in this study. Students in the control group (n = 85) learned online materials before each class, followed by classroom instruction and activities in which face-to-face discussion and communication between students were encouraged. Students in the experimental group (n = 83) followed a similar procedure with an additional teacher-supervised online discussion platform to guide, supervise and evaluate their learning progress. All participants were first-year medical students in clinical medicine at Dalian Medical University who had enrolled in 2017. All participants took the final exam to test their learning outcomes. RESULTS: The embryology grades of students in the experimental group were significantly higher than those of students in the control group (p = 0.001). Additionally, the scores of students in the experimental group on questions with a high difficulty level (p = 0.003) and questions assessing high-order cognitive skills (p = 0.003) were higher than those of students in the control group; the effect size was moderate (η2 > 0.05). CONCLUSIONS: In blended embryology courses, compared with learner-led and face-to-face discussion, the teacher-supervised online discussion platform has great potential to enable students to achieve higher grades and solve difficult and cognitively challenging tasks.

AddictedChem: A Data-Driven Integrated Platform for New Psychoactive Substance Identification.

The mechanisms underlying drug addiction remain nebulous. Furthermore, new psychoactive substances (NPS) are being developed to circumvent legal control; hence, rapid NPS identification is urgently needed. Here, we present the construction of the comprehensive database of controlled substances, AddictedChem. This database integrates the following information on controlled substances from the US Drug Enforcement Administration: physical and chemical characteristics; classified literature by Medical Subject Headings terms and target binding data; absorption, distribution, metabolism, excretion, and toxicity; and related genes, pathways, and bioassays. We created 29 predictive models for NPS identification using five machine learning algorithms and seven molecular descriptors. The best performing models achieved a balanced accuracy (BA) of 0.940 with an area under the curve (AUC) of 0.986 for the test set and a BA of 0.919 and an AUC of 0.968 for the external validation set, which were subsequently used to identify potential NPS with a consensus strategy. Concurrently, a chemical space that included the properties of vectorised addictive compounds was constructed and integrated with AddictedChem, illustrating the principle of diversely existing NPS from a macro perspective. Based on these potential applications, AddictedChem could be considered a highly promising tool for NPS identification and evaluation.

The NF-κB-Regulated miR-221/222/Syndecan-1 Axis and Intestinal Mucosal Barrier Function in Radiation Enteritis.

PURPOSE: Radiation enteritis (RE) is the most common complication of pelvic radiation therapy, but proven therapies are lacking. Barrier function defects are closely associated with numerous inflammatory disorders. In this study, we investigated whether barrier dysfunction contributes to RE and whether syndecan-1 (Sdc1) protects intestinal barrier function in RE. The mechanism was also elucidated. METHODS AND MATERIALS: Blood, urine, and tissue samples were collected from 21 patients with cervical cancer who experienced RE during radiation therapy. The samples were used to detect inflammatory responses and barrier function. The role of Sdc1 in barrier function was examined in cultured fetal human colon (FHC) cells exposed to radiation and an induced mouse RE model. Barrier function was determined by zonula occludens (ZO)-1 and occludin expression, transepithelial electrical resistance (TEER), and fluorescein isothiocyanate-dextran (FD4) flux. The role of the nuclear factor (NF)-κB-P65 pathway was detected by Western blotting and chromatin immunoprecipitation. The role of miR-221/222 was assessed by real-time polymerase chain reaction and luciferase reporter assays. RESULTS: Patients with RE exhibited obvious pathologic and ultramicrostructural inflammatory injury and barrier disruption in the intestinal mucosa, as well as higher serum lipopolysaccharide (LPS), LPS-binding protein, and cytokine levels and a higher urine lactulose-to-mannitol ratio. Overexpression of Sdc1 in irradiated FHC cells reversed TEER suppression, repressed FD4 flux, and upregulated ZO-1 and occludin expression. Exogenous low-molecular-weight heparin supplementation in RE mice ameliorated the activity of enteritis and barrier defects. Mechanistically, irradiation-activated P65 increased the transcription of miR-221/222 via direct binding to the promoter regions, and miR-221/222 then posttranscriptionally suppressed the Sdc1 gene by binding to its 3'-untranslated region. CONCLUSIONS: The findings suggest that Sdc1 protects barrier function and controls inflammation during RE under transcriptional regulation by the NF-κB pathway and miR-221/222. The network including NF-κB, miR-221/222, and Sdc1 is important in the pathogenesis of RE, and Sdc1 might represent a therapeutic target for novel anti-RE strategies.

ChemHub: a knowledgebase of functional chemicals for synthetic biology studies.

SUMMARY: The field of synthetic biology lacks a comprehensive knowledgebase for selecting synthetic target molecules according to their functions, economic applications and known biosynthetic pathways. We implemented ChemHub, a knowledgebase containing >90 000 chemicals and their functions, along with related biosynthesis information for these chemicals that was manually extracted from >600 000 published studies by more than 100 people over the past 10 years. AVAILABILITY AND IMPLEMENTATION: Multiple algorithms were implemented to enable biosynthetic pathway design and precursor discovery, which can support investigation of the biosynthetic potential of these functional chemicals. ChemHub is freely available at: http://www.rxnfinder.org/chemhub/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

SARS2020: an integrated platform for identification of novel coronavirus by a consensus sequence-function model.

MOTIVATION: The 2019 novel coronavirus outbreak has significantly affected global health and society. Thus, predicting biological function from pathogen sequence is crucial and urgently needed. However, little work has been conducted to identify viruses by the enzymes that they encode, and which are key to pathogen propagation. RESULTS: We built a comprehensive scientific resource, SARS2020, which integrates coronavirus-related research, genomic sequences and results of anti-viral drug trials. In addition, we built a consensus sequence-catalytic function model from which we identified the novel coronavirus as encoding the same proteinase as the severe acute respiratory syndrome virus. This data-driven sequence-based strategy will enable rapid identification of agents responsible for future epidemics. AVAILABILITYAND IMPLEMENTATION: SARS2020 is available at http://design.rxnfinder.org/sars2020/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Cell2Chem: mining explored and unexplored biosynthetic chemical spaces.

SUMMARY: Living cell strains have important applications in synthesizing their native compounds and potential for use in studies exploring the universal chemical space. Here, we present a web server named as Cell2Chem which accelerates the search for explored compounds in organisms, facilitating investigations of biosynthesis in unexplored chemical spaces. Cell2Chem uses co-occurrence networks and natural language processing to provide a systematic method for linking living organisms to biosynthesized compounds and the processes that produce these compounds. The Cell2Chem platform comprises 40 370 species and 125 212 compounds. Using reaction pathway and enzyme function in silico prediction methods, Cell2Chem reveals possible biosynthetic pathways of compounds and catalytic functions of proteins to expand unexplored biosynthetic chemical spaces. Cell2Chem can help improve biosynthesis research and enhance the efficiency of synthetic biology. AVAILABILITY AND IMPLEMENTATION: Cell2Chem is available at: http://www.rxnfinder.org/cell2chem/.

Abnormal Gait Patterns in Autism Spectrum Disorder and Their Correlations with Social Impairments.

Ground walking in humans is typically stable, symmetrical, characterized by smooth heel-to-toe ground contact. Previous studies on children with autism spectrum disorder (ASD) identified various gait abnormalities. However, they produced inconsistent findings, particularly for the occurrence of toe walking and gait symmetry between feet, owing to their reliance on retrospective reports, visual analysis of videos, or kinematic analysis of the gait. The present study examined gait functions in children with ASD using plantar pressure that quantified foot-ground interaction with high spatial and temporal resolutions. Fifty-eight 4-6-year-old children with ASD (12 low-functioning and 46 high-functioning autism) and 28 age-matched typically developed children walked straight 6 m at their preferred speed for 10 repetitions. We found that both ASD groups walked with more flat-footed contact pattern, more left-right asymmetry, and larger step-to-step variability than their controls. Furthermore, these abnormal gait characteristics were related to social impairments measured by the Autism Spectrum Quotient and Social Responsive Scale, supporting a close association between impaired motor coordination and core symptoms of autism. Autism Res 2020, 13: 1215-1226. © 2020 International Society for Autism Research, Wiley Periodicals, Inc. LAY SUMMARY: We examined gait functions among children with autism by measuring their foot plantar pressure during simple straight walking. Children with ASD walked with a characteristic foot-ground contact pattern with inappropriate contact forces and large step-to-step variability when compared with their age-matched controls. These walking abnormalities were dependent on their social impairments but independent from their intelligence, indicating a close relationship between atypical motor coordination and core symptoms of autism.

Erratum to: Smad4 mediates malignant behaviors of human ovarian carcinoma cell through the effect on expressions of E-cadherin, plasminogen activator inhibitor-1 and VEGF.

[Erratum to: BMB Reports 2010; 43(8): 554-560, PMID: 20797318] The authors apologize that due to our neglect when doing the picture layout of Fig. 1A, the wrong Western blot analysis image were pasted for the "ß-actin"group in the middle plot of Fig. 1A. The middle plot of Fig. 1A and its related statistics results (bottom plot in Fig.1A) have been corrected. However, the conclusions of the original article are not affected. The authors would like to apologize for any inconvenience caused.

In-situ mineral CO2 sequestration in a methane producing microbial electrolysis cell treating sludge hydrolysate.

Microbial electrolysis cell (MEC) has excellent CH4 production performance, however, CO2 still remains in the produced biogas at high content. For achieving in-situ CO2 sequestration and thus upgrading biogas, mineral carbonation was integrated into a MEC treating sludge hydrolysate. With 19 g/L wollastonite addition, in-situ mineral CO2 sequestration was achieved by formation of calcite precipitates. CH4 content in the biogas was increased by 5.1 % and reached 95.9 %, with CH4 production improved by 16.9 %. In addition, the removals of polysaccharide, protein, and chemical oxygen demand (COD) of the MEC were increased by 4.4 %, 6.7 %, and 8.4 %, respectively. The generated precipitates rarely accumulated on bio-cathode, and did not significantly affect the morphology of cathode biofilm. However, integrating mineral carbonation resulted in a higher relative abundance of Methanosarcina on anode and slightly decreased the ratio of Methanobacterium to Methanosaeta on cathode, which should be noticed. In conclusion, integrating mineral carbonation is an attractive way to improve the performance of MEC by achieving in-situ CO2 sequestration, accompanied with CH4 production enhancement.

FRCD: A comprehensive food risk component database with molecular scaffold, chemical diversity, toxicity, and biodegradability analysis.

The presence of natural toxins, pesticide residues, and illegal additives in food products has been associated with a range of potential health hazards. However, no systematic database exists that comprehensively includes and integrates all research information on these compounds, and valuable information remains scattered across numerous databases and extensive literature reports. Thus, using natural language processing technology, we curated 12,018 food risk components from 152,737 literature reports, 12 authoritative databases, and numerous related regulatory documents. Data on molecular structures, physicochemical properties, chemical taxonomy, absorption, distribution, metabolism, excretion, toxicity properties, and physiological targets within the human body were integrated to afford the comprehensive food risk component database (FRCD, http://www.rxnfinder.org/frcd/). We also analyzed the molecular scaffold and chemical diversity, in addition to evaluating the toxicity and biodegradability of the food risk components. The FRCD could be considered a highly promising tool for future food safety studies.

Clinical outcome for small cell lung cancer patients with bone metastases at the time of diagnosis.

OBJECTIVES: The characteristics and prognostic factors of small-cell lung cancer (SCLC) patients with bone metastases at first diagnosis have scarcely been reported. This study aimed to analyze the prognostic factors of these patients and to develop a scoring system for survival to provide evidence for clinical treatment decisions. MATERIALS AND METHODS: The records of 102 SCLC patients with bone metastasis at the time of diagnosis who were seen in our hospital between May 2010 and May 2015 were retrospectively reviewed. The log-rank test and multivariate Cox regression analysis were used to evaluate potential clinical predictors of survival. A scoring system was developed based on the hazard ratios of significant independent prognostic factors. RESULT: The most common site of bone metastases was the spine (64.7%), and 26 patients (25.6%) had a single bone metastasis. The median survival was 10.4 months, and the 2-year survival rate was 10.3%. Age, number of bone metastases, and occurrence of extraosseous distant metastases were significant independent prognostic factors for overall survival. Based on their scores, patients were divided into three groups. The median survival times of the three groups were 6.4 months, 8.5 months and 12.4 months, and the 2-year survival rates were 0%, 2.9%, and 19.3% (p=0.000). Twenty-six patients (25.5%) developed skeletal-related events (SREs), and the most common SREs were radiation to the bone (22.5%) and spinal cord compression (11.8%). CONCLUSION: This study includes preliminary clinical data of SCLC patients with bone metastases at the time of diagnosis, and more studies are needed.

Silicate mediated simultaneous in-situ CO2 sequestration and nutrients removal in anaerobic digestion.

This study investigated the reactions among CO32-, PO43-, NH4+, Mg2+, and Ca2+, under different CO32- concentration and Mg2+/Ca2+ ratio, and conducted sludge anaerobic digestion (AD) with silicate addition to achieve in-situ CO2 sequestration and nutrients removal. High CO32- concentration facilitated the formation of MgNH4PO4, and Mg2+/Ca2+ ratio of 1:1 achieved best CO32-, PO43-, and NH4+ removal in simulated anaerobic digestate. Supplementation of 40 g/L magnesium silicate combined with 20 g/L wollastonite decreased CO2 content in biogas from 28.2% to 19.0%, and removed PO43- and NH4+ by 61.8% and 21.2%, respectively, in AD. Simultaneous in-situ CO2 sequestration and nutrients removal was achieved by directed precipitation of PO43-, NH4+, and CO2 with silicate released Mg2+ and Ca2+, to form MgNH4PO4 and CaCO3. Meanwhile, methane production was improved by 51.2% with silicate supplementation. This study provides an attractive measure for CO2 and nutrients removal as well as methane production enhancement of sludge AD.