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The dynamics of the RNA polymerase II (Pol II) backtracking process is poorly understood. We built a Markov State Model from extensive molecular dynamics simulations to identify metastable intermediate states and the dynamics of backtracking at atomistic detail. Our results reveal that Pol II backtracking occurs in a stepwise mode where two intermediate states are involved. We find that the continuous bending motion of the Bridge helix (BH) serves as a critical checkpoint, using the highly conserved BH residue T831 as a sensing probe for the 3'-terminal base paring of RNA:DNA hybrid. If the base pair is mismatched, BH bending can promote the RNA 3'-end nucleotide into a frayed state that further leads to the backtracked state. These computational observations are validated by site-directed mutagenesis and transcript cleavage assays, and provide insights into the key factors that regulate the preferences of the backward translocation.

The capacitors and inductors in actual circuits often fail to exhibit the ideal integer-order characteristics, so as the circuits containing these types of electronic components. The errors can be compensated by introducing the concept of fractional calculus. The Caputo–Fabrizio​ fractional derivative, which fixes the defect of the singularity problem in Caputo derivative, has been proposed in recent years. This work uses Caputo–Fabrizio fractional derivative to model the fractional Buck converter working in continuous conduction mode and to deduce its analytical solutions by Laplace transformation and its inverse transformation. The analytical solution of the output voltage is obtained and the waveform of the output voltage is simulated. The correctness of the model is verified and the impact of the fractional order on the dynamic performance of the Buck converter is analyzed. The steady-state average output voltage of the open-loop fractional Buck converter is also calculated.

ABSTRACT: Wake separation is crucial to aircraft landing safety and is an important factor in airport operational efficiency. The near-ground evolution characteristics of wake vortices form the foundation of the wake separation system design. In this study, we analysed the near-ground evolution of vortices in the wake of a domestic aircraft ARJ21 initialised by the lift-drag model using large eddy simulations based on an adaptive mesh. Evolution of wake vortices formed by the main wing, flap and horizontal tail was discussed in detail. The horizontal tail vortices are the weakest and dissipate rapidly, whereas the flap vortices are the strongest and induce the tip vortex to merge with them. The horizontal tail and flap of an ARJ21 do not significantly influence the circulation evolution, height change and movement trajectory of the wake vortices. The far-field evolution of wake vortices can therefore be analysed using the conventional wake vortex model.

Abstract Background The transplantation of bone marrow mesenchymal stem cells (BMSCs) is a promising therapeutic strategy for wound healing. However, the poor migration capacity and low survival rate of transplanted BMSCs in wounds weaken their potential application. Objective To identify the optimal protocol for BMSCs preconditioned with H2O2 and improve the therapeutic efficacy using H2O2-preconditioned BMSCs in wound healing. Methods Mouse BMSCs were exposed to various concentrations of H2O2, and the key cellular functional properties were assessed to determine the optimal precondition with H2O2. The H2O2-preconditioned BMSCs were transplanted into mice with full-thickness excisional wounds to evaluate their healing capacity and tissue engraftment. Results Treatment BMSCs with 50 μM H2O2 for 12 h could significantly enhance their proliferation, migration, and survival by maximizing the upregulation of cyclin D1, SDF-1, and its receptors CXCR4/7 expressions, and activating the PI3K/Akt/mTOR pathway, but inhibiting the expression of p16 and GSK-3β. Meanwhile, oxidative stress-induced BMSC apoptosis was also significantly attenuated by the same protocol pretreatment with a decreased ratio of Bax/Bcl-2 and cleaved caspase-9/3 expression. Moreover, after the identification of the optimal protocol of H2O2 precondition in vitro, the migration and tissue engraftment of transfused BMSCs with H2O2 preconditioning were dramatically increased into the wound site as compared to the un-preconditioned BMSCs. The increased microvessel density and the speedy closure of the wounds were observed after the transfusion of H2O2-preconditioned BMSCs. Conclusions The findings suggested that 50 μM H2O2 pretreated for 12 h is the optimal precondition for the transplantation of BMSCs, which gives a considerable insight that this protocol may be served as a promising candidate for improving the therapeutic potential of BMSCs for wound healing.

Abstract Background Maize ears and tassels are two separate types of inflorescence which are initiated by similar developmental processes but gradually develop distinct architectures. However, coordinated trans and cis regulation of differentially expressed genes determining ear and tassel architecture within the 3D genome context is largely unknown. Results We identify 56,055 and 52,633 open chromatin regions (OCRs) in developing maize ear and tassel primordia using ATAC-seq and characterize combinatorial epigenome features around these OCRs using ChIP-seq, Bisulfite-seq, and RNA-seq datasets. Our integrative analysis of coordinated epigenetic modification and transcription factor binding to OCRs highlights the cis and trans regulation of differentially expressed genes in ear and tassel controlling inflorescence architecture. We further systematically map chromatin interactions at high-resolution in corresponding tissues using in situ digestion-ligation-only Hi-C (DLO Hi-C). The extensive chromatin loops connecting OCRs and genes provide a 3D view on cis- and trans-regulatory modules responsible for ear- and tassel-specific gene expression. We find that intergenic SNPs tend to locate in distal OCRs, and our chromatin interaction maps provide a potential mechanism for trait-associated intergenic SNPs that may contribute to phenotypic variation by influencing target gene expression through chromatin loops. Conclusions Our comprehensive epigenome annotations and 3D genome maps serve as valuable resource and provide a deep understanding of the complex regulatory mechanisms of genes underlying developmental and morphological diversities between maize ear and tassel.

Abstract Background The application of n-3 Polyunsaturated Fatty Acids (n-3 PUFAs) supplementation for major depressive disorder (MDD) has been widely discussed in recent years, but its efficacy and application are still controversial. This network meta-analysis was conducted to compare the efficacy of different dosages of n-3 PUFAs on MDD patients in the early period of treatment. Methods Randomized controlled trials (RCTs) exploring the efficacy of n-3 PUFA supplementation for patients with MDD were retrieved from the databases of Pubmed, Embase and the Cochrane Library. RCTs comparing the efficacy of n-3 PUFA for adult (≥18 years) MDD patients without comorbidity were eligible for our study. The score of depressive symptoms in early therapy period of the treatment (≤9 weeks) was extracted. Standardized mean deviations (SMDs) of all the sores from the eligible RCTs were synthesized in a pairwise meta-analysis in frequentist framework and a random-effects network meta-analysis in Bayesian framework for the overall and subgroups (high- and low-dose) efficacy of n-3 PUFAs. Results A total of 910 MDD patients in 10 trials with 3 adjuvant therapy strategies (high-dose n-3 PUFAs, low-dose n-3 PUFAs and placebo) were included. Results of pairwise meta-analysis showed that n-3 PUFAs were superior to placebo (SMD: 1.243 ± 0.596; 95% CI: 0.060 ~ 2.414). Results of the network meta-analysis showed that both the high (SMD: 0.908 ± 0.331; 95% CI: 0.262 ~ 1.581) and the low-dose (SMD: 0.601 ± 0.286; 95% CI: 0.034 ~ 1.18) n-3 PUFAs were superior to placebo, and the efficacy of high-dose n-3 PUFAs is superior to that of low-dose. Conclusions High-dose n-3 PUFAs supplementation might be more superior than low-dose in the early therapy period for MDD. More head-to-head clinical trials need to be carried out to provide more direct comparison and enhance the evidence of the efficacy of n-3PUFAs for MDD.

Objectives To evaluate the status of conflict of interest and economic evidence in Chinese clinical practice guidelines published in 2018, and compare with the relevant content guidelines published in 2017. In order to find the changes in guidelines development and also provide implications for guidelines in China.Methods The CNKI, WanFang Data and CBM were searched to collect clinical practice guidelines published in China in 2018 from January 1st to December 31st. Two researchers independently selected literature, extracted relevant information such as statements of conflict of interest and economic evidences; then, the analysis was performed by using the Microsoft Excel 2019 software.Results A total of 92 clinical practice guidelines were included, in which 23 (25.00%) disclosed conflict of interest, 25 (27.17%) stated sources of funding, and 22 (23.91%) reported economic evidence, and half of the reported guidelines were supported by the National Key Research and Development Plan or Science and Technology Major Project of China (50.00%). However, of the 53 clinical practice guide released in 2017, 26.42% disclosed conflict of interest, 18.87% stated sources of funding, and 11.32% referred to economic evidence.Conclusion Comparative analysis of conflict of interest and economic evidence in Chinese clinical practice guidelines published in 2017-2018, with the increase of financial investment in the development of clinical practice guidelines in China, the attention to economic evidence has also increased, while, we found that the disclosed conflict of interest in the guidelines and the exact economic evidence are still very low. Therefore, we should further promote the report of conflict of interest statement and the generation of economic evidence in our clinical practice guidelines, which will make our guidelines more objective, transparent and independent.

Craniopharyngioma is a benign tumor, and the predominant treatment methods are surgical resection and radiotherapy. However, both treatments may lead to complex complications, seriously affecting patients’ survival rate and quality of life. Adamantinomatous craniopharyngioma (ACP), as one of the histological subtypes of craniopharyngioma, is associated with a high incidence and poor prognosis, and there is a gap in the targeted therapy of immune-related genes for ACP. In this study, two gene expression profiles of ACP, namely GSE68015 and GSE94349, were downloaded from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were identified by the Limma package, and 271 differentially expressed immune-related genes (DEIRGs) were obtained from the Immport database. The gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA) were performed for annotation, visualization, and integrated discovery. Five hub genes, including CXCL6, CXCL10, CXCL11, CXCL13, and SAA1, were screened out through protein-protein interaction (PPI) network interaction construction. Two diagnostic markers, namely S100A2 and SDC1 (both of which have the Area Under Curve value of 1), were screened by the machine learning algorithm. CIBERSORT analysis showed that M2 macrophages, activated NK cells, and gamma delta T cells had higher abundance in ACP infiltration, while CD8+ T cells, regulatory T cells, and Neutrophils had less abundance in ACP infiltration. The expression of gamma delta T cells was positively correlated with CXCL6, S100A2, SDC1, and SAA1, while CD8+ T cells expression was negatively correlated with CXCL6, S100A2, SDC1, and CXCL10. ACP with high CXCL6 showed remarkable drug sensitivity to Pentostatin and Wortmannin via CellMiner database analysis. Our results deepened the understanding of the molecular immune mechanism in ACP and provided potential biomarkers for the precisely targeted therapy for ACP.

Globalization has resulted in increases in air transportation demand and air passenger traffic. With the increases in air traffic, airports face challenges related to infrastructure, air services, and future development. Air traffic forecasting is essential to ensuring appropriate investment in airports. In this study, we combined fuzzy theory with support vector regression (SVR) to develop a fuzzy SVR (FSVR) model for forecasting international airport traffic. This model was used to predict the air traffic volumes at the world’s 10 busiest airports in terms of air traffic in 2018. The predictions were made for the period from August 2014 to December 2019. For fuzzy time series, the developed FSVR model can consider historical air traffic changes. The FSVR model can suitably divide air traffic changes into appropriate fuzzy sets, generate membership function values, and establish fuzzy relations to produce fuzzy interpolated values with minimal errors. Thus, in the prediction of continuous data, the fuzzy data with the smallest errors can be subjected to SVR to find the optimal hyperplane model with the minimum distance to the appropriate support vector sample points. The performance of the proposed model was compared with those of five other models. Of the compared models, the FSVR model exhibited the lowest mean absolute percentage error (MAPE), mean absolute error, and root mean square error for all types of traffic at all of the airports analyzed; all of the MAPE values were below 2.5. The FSVR model can predict future growth trends in air traffic, air passenger flows, aircraft flows, and logistics. An airport authority can use this model to analyze the existing operational facilities and service capacity, find bottlenecks in airport operations, and create a blueprint for future development. The findings revealed that implementing a hybrid modeling approach, specifically the FSVR model, can significantly enhance the performance of the SVR model. The FSVR model allows airlines to predict traffic growth patterns, identify viable new destinations, optimize their schedules or fleet, make accurate marketing decisions, and plan traffic effectively. The FSVR model can guide the timely construction of appropriate airport facilities with accurate predictions. Rapid, cost-effective, efficient, and balanced transportation planning enables the provision of fast, cost-effective, comfortable, safe, and convenient passenger and cargo services while ensuring the proper planning of the airport’s capacity for land-side transportation connections.

Background. Glioblastoma (GBM) is a highly prevalent brain tumor characterized by high rates of morbidity, recurrence, and mortality. While temozolomide (TMZ) is commonly used as a first-line treatment for this cancer, the emergence of TMZ resistance limits its utility. The long noncoding RNA HOXA-AS2 reportedly drives GBM progression, but whether it can influence therapeutic resistance to TMZ has yet to be established. Methods. HOXA-AS2 expression was analyzed in TMZ-resistant and sensitive GBM tissue samples and cell lines by qPCR. A siRNA-based approach was used to knock down HOXA-AS2 in GBM cells, after which TMZ resistance was tested. Bioinformatics approaches were used to predict miRNA binding targets of HOXA-AS2, after which a series of luciferase reporter assay and rescue experiments with appropriate miRNA inhibitor/mimic constructs were performed to validate these predictions and to clarify the ability of HOXA-AS2 to regulate chemoresistant activity. Results. TMZ-resistant GBM patients and cell lines exhibited increased HOXA-AS2 expression that was correlated with worse overall survival. Knocking down HOXA-AS2 increased the sensitivity of resistant GBM cells to TMZ. miR-302a-3p was identified as a HOXA-AS2 target confirmed through luciferase reporter assays and rescue experiments, and IGF1 was further identified as a confirmed miR-302a-3p target. In addition, HOXA-AS2 knockdown resulted in a corresponding drop in IGF1 expression consistent with indirect regulation mediated by miR-302a-3p. Conclusion. In summary, these results highlight the role of HOXA-AS2 as a driver of TMZ resistance in GBM through its ability to regulate the miR-302a-3p/IGF1 signaling axis, highlighting this pathway as a promising target for the diagnosis, therapeutic sensitization, and/or treatment of affected patients.

Increasing the efficiency of coal preparation is the key link of mine production. This study proposed a framework of coal preparation for life cycle based on Building Information Modeling (BIM), in which the data resources can be retransmitted, and the integration of BIM application links has a high level. In this paper, the kappa big data processing architecture is used to realize the integration and unification of stream data and batch data processing process. By using deep learning method and multimodal data fusion method, the multimodal data association fusion is realized, and Bentley software is adopted for verification and integration. Taking a coal preparation plant as an engineering case study, the proposed framework is applied to build a big data subplatform of three-dimensional visual management. The following is suggested: (1) the three-dimensional visual review of the coal preparation online is realized, and the efficiency of the design results is improved; (2) the production and operation management of the coal preparation are carried out through the established platform, which indicated that the proportion of clean coal increased by 1.97%, and the average increase percentage for the total output is about 5.6%. Results from the case study show that the framework proposed in this study can provide efficient reference for coal washing in the coal preparation.

Pyrophosphate ion (PPi) release during transcription elongation is a signature step in each nucleotide addition cycle. The kinetics and energetics of the process as well as how it proceeds with substantial conformational changes of the polymerase complex determine the mechano-chemical coupling mechanism of the transcription elongation. Here we investigated detailed dynamics of the PPi release process in a single-subunit RNA polymerase (RNAP) from bacteriophage T7, implementing all-atom molecular dynamics (MD) simulations. We obtained a jump-from-cavity kinetic model of the PPi release utilizing extensive nanosecond MD simulations. We found that the PPi release in T7 RNAP is initiated by the PPi dissociation from two catalytic aspartic acids, followed by a comparatively slow jump-from-cavity activation process. Combining with a number of microsecond long MD simulations, we also found that the activation process is hindered by charged residue associations as well as by local steric and hydrogen bond interactions. On the other hand, the activation is greatly assisted by a highly flexible lysine residue Lys472 that swings its side chain to pull PPi out. The mechanism can apply in general to single subunit RNA and DNA polymerases with similar molecular structures and conserved key residues. Remarkably, the flexible lysine or arginine residue appears to be a universal module that assists the PPi release even in multi-subunit RNAPs with charge facilitated hopping mechanisms. We also noticed that the PPi release is not tightly coupled to opening motions of an O-helix on the fingers domain of T7 RNAP according to the microsecond MD simulations. Our study thus supports the Brownian ratchet scenario of the mechano-chemical coupling in the transcription elongation of the single-subunit polymerase.

Objective Deep vein thrombosis (DVT) is one of the severe complications after total knee arthroplasty (TKA). Gender has been considered to influence the incidence of the thrombosis formation in TKA patients. However, it remains controversial which gender would be more prone to form thrombosis. The aim of this study was to assess the effects of gender differences on coagulation status after TKA via the thromboelastography (TEG). Methods A total of 57 male patients who underwent primary TKA from September 2015 to January 2021 were included in this study. According to the matching principle of age, body mass index (BMI), and anticoagulation treatment, 60 female patients were selected. The conventional coagulation tests, routine blood tests, and thromboelastography were conducted before the operation, 1 day and 7 days after the operation. In addition, Doppler ultrasound was also performed 1 day before the operation and at the 7 days after the operation. The parameters of conventional coagulation tests, routine blood tests, and thromboelastography were compared between the two groups. Results There were no significant differences in the blood transfusion rate, the incidence of DVT during the perioperative period, D-dimer (D-D), fibrin degradation products (FDP), hemoglobin (HB), hematocrit (HCT), prothrombin time (PT), activated partial thromboplastin time (APTT), and C-reactive protein (CRP) at any corresponding time point between the male group and the female group ( P > .05). There were no significant differences in neutrophil-to-lymphocyte ratio (NLR) preoperatively; however, there were significant differences in NLR 1 day after the surgery and 7 days after the surgery between the two groups ( P .05). Binary logistic regression analysis demonstrated that gender, age , BMI, tourniquet application time were not independent predictors ( P > .05). Conclusion Gender differences have no significant influence in TKA patients with regard to conventional coagulation tests and thromboelastography.

The RNA polymerase II elongation is central in eukaryotic transcription. Although multiple intermediates of the elongation complex have been identified, the dynamical mechanisms remain elusive or controversial. Here we build a structure-based kinetic model of a full elongation cycle of polymerase II, taking into account transition rates and conformational changes characterized from both single molecule experimental studies and computational simulations at atomistic scale. Our model suggests a force-dependent slow transition detected in the single molecule experiments corresponds to an essential conformational change of a trigger loop (TL) opening prior to the polymerase translocation. The analyses on mutant study of E1103G and on potential sequence effects of the translocation substantiate this proposal. Our model also investigates another slow transition detected in the transcription elongation cycle which is independent of mechanical force. If this force-independent slow transition happens as the TL gradually closes upon NTP binding, the analyses indicate that the binding affinity of NTP to the polymerase has to be sufficiently high. Otherwise, one infers that the slow transition happens pre-catalytically but after the TL closing. Accordingly, accurate determination of intrinsic properties of NTP binding is demanded for an improved characterization of the polymerase elongation. Overall, the study provides a working model of the polymerase II elongation under a generic Brownian ratchet mechanism, with most essential structural transition and functional kinetics elucidated.

Objective To evaluate the value of combined detection of serum C-reactive protein (CRP) and procalcitonin (PCT) for early warning of traumatic sepsis. Methods Two hundred and thirty five patients with severe trauma were included, including 110 patients with sepsis and 125 patients with non-sepsis.Blood samples were collected in 24 hours of admission and serum CRP and PCT were measured. The ROC curve was used to compare the early warning value of CRP and PCT for post-traumatic sepsis, and the improvement ability after combined use of NRI and IDI was analyzed. Results The results showed that CRP and PCT in patients with post-traumatic sepsis were significantly higher than those in non-sepsis patients (P＜0.001). ROC analysis revealed that the AUC of serum CRP and PCT were 0.766 (0.707-0.819) and 0.744 (0.684-0.799), respectively; The AUC of CRP and PCT combined with single-label early warning trauma sepsis was increased by 5.1%, 7.3%.Meanwhile, the results of NRI and IDI analysis also suggested the combination of CRP and PCT was sensitive to identify the patients with high risk of sepsis (P＜ 0.001). Conclusions CRP and PCT have early prediction effects on the risk of sepsis in major trauma patients. Combination of CPR and PCT can significantly improve early prediction ability.

Nucleotide selection is essential for fidelity control in gene replication and transcription. Recent work on T7 RNA polymerase suggested that a small posttranslocation free energy bias stabilizes Tyr(639) in the active site to aid nucleotide selection. However, it was not clear exactly how Tyr(639) assists the selection. Here we report a molecular-dynamics simulation study revealing atomistic detail of this critical selectivity. The study shows first that Tyr(639) blocks the active site at posttranslocation by marginally stacking to the end basepair of the DNA-RNA hybrid. The study then demonstrates that at the nucleotide preinsertion state, a cognate RNA nucleotide does not affect the local Tyr(639) stabilization, whereas a noncognate nucleotide substantially stabilizes Tyr(639) so that Tyr(639) keeps blocking the active site. As a result, further nucleotide insertion into the active site, which requires moving Tyr(639) out of the site, would be hindered for the noncognate nucleotide, but not for the cognate nucleotide. In particular, we note that water molecules assist the ribose recognition in the RNA nucleotide preinsertion, and help Tyr(639) stacking to the end basepair in the case of a DNA nucleotide. It was also seen that a base-mismatched nucleotide at preinsertion directly grabs Tyr(639) for the active site stabilization. We also find that in a mutant polymerase Y639F the strong stabilization of residue 639 in the active site cannot establish upon the DNA nucleotide preinsertion. The finding explains the reduced differentiation between ribo- and deoxyribonucleotides that has been recorded experimentally for the mutant polymerase.

Aberrant increase of arachidonic acid (ARA) has long been implicated in the pathology of Alzheimer's disease (AD), while the underlying causal mechanism remains unclear. In this study, we revealed a link between ARA mobilization and microglial dysfunction in Aß pathology. Lipidomic analysis of primary microglia from AppNL-GF mice showed a marked increase in free ARA and lysophospholipids (LPLs) along with a decrease in ARA-containing phospholipids, suggesting increased ARA release from phospholipids (PLs). To manipulate ARA-containing PLs in microglia, we genetically deleted lysophosphatidylcholine acyltransferase 3 (Lpcat3), the main enzyme catalyzing the incorporation of ARA into PLs. Loss of microglial Lpcat3 reduced the levels of ARA-containing PLs, free ARA and LPLs, leading to a compensatory increase in monounsaturated fatty acid (MUFA)-containing PLs in both male and female AppNL-GF mice. Notably, the reduction of ARA in microglia significantly ameliorated oxidative stress and inflammatory responses while enhancing the phagocytosis of Aß plaques and promoting the compaction of Aß deposits. Mechanistically, scRNA seq suggested that LPCAT3 deficiency facilitates phagocytosis by facilitating de novo lipid synthesis while protecting microglia from oxidative damage. Collectively, our study reveals a novel mechanistic link between ARA mobilization and microglial dysfunction in AD. Lowering brain ARA levels through pharmacological or dietary interventions may be a potential therapeutic strategy to slow down AD progression. [ABSTRACT FROM AUTHOR]

Consensus tracking control problem of the multi-agent systems with both noise and disturbances is studied in this paper. A robust adaptive control scheme is designed according to Lyapunov stability theory. The main contribution of this paper is that the consensus is realized in multi-agent systems with both noise and external disturbances. Numerical simulations are carried out for the proposed scheme to demonstrate the effectiveness of the control strategy proposed in this paper. [ABSTRACT FROM AUTHOR]