Abolished frameshifting for predicted structure-stabilizing SARS-CoV-2 mutants: Implications to alternative conformations and their statistical structural analyses.

The SARS-CoV-2 frameshifting element (FSE) has been intensely studied and explored as a therapeutic target for coronavirus diseases including COVID-19. Besides the intriguing virology, this small RNA is known to adopt many length-dependent conformations, as verified by multiple experimental and computational approaches. However, the role these alternative conformations play in the frameshifting mechanism and how to quantify this structural abundance has been an ongoing challenge. Here, we show by DMS and dual-luciferase functional assays that previously predicted FSE mutants (using the RAG graph theory approach) suppress structural transitions and abolish frameshifting. Furthermore, correlated mutation analysis of DMS data by three programs (DREEM, DRACO, and DANCE-MaP) reveals important differences in their estimation of specific RNA conformations, suggesting caution in the interpretation of such complex conformational landscapes. Overall, the abolished frameshifting in three different mutants confirms that all alternative conformations play a role in the pathways of ribosomal transition.

Evolution of coronavirus frameshifting elements: Competing stem networks explain conservation and variability.

The frameshifting RNA element (FSE) in coronaviruses (CoVs) regulates the programmed -1 ribosomal frameshift (-1 PRF) mechanism common to many viruses. The FSE is of particular interest as a promising drug candidate. Its associated pseudoknot or stem loop structure is thought to play a large role in frameshifting and thus viral protein production. To investigate the FSE structural evolution, we use our graph theory-based methods for representing RNA secondary structures in the RNA-As-Graphs (RAG) framework to calculate conformational landscapes of viral FSEs with increasing sequence lengths for representative 10 Alpha and 13 Beta-CoVs. By following length-dependent conformational changes, we show that FSE sequences encode many possible competing stems which in turn favor certain FSE topologies, including a variety of pseudoknots, stem loops, and junctions. We explain alternative competing stems and topological FSE changes by recurring patterns of mutations. At the same time, FSE topology robustness can be understood by shifted stems within different sequence contexts and base pair coevolution. We further propose that the topology changes reflected by length-dependent conformations contribute to tuning the frameshifting efficiency. Our work provides tools to analyze virus sequence/structure correlations, explains how sequence and FSE structure have evolved for CoVs, and provides insights into potential mutations for therapeutic applications against a broad spectrum of CoV FSEs by targeting key sequence/structural transitions.

Which Specific Exercise Models Are Most Effective on Global Cognition in Patients with Cognitive Impairment? A Network Meta-Analysis.

(1) Introduction: Physical exercise interventions can impart significant cognitive benefits to older adults suffering from cognitive impairment (CI). However, the efficacy of these interventions can vary widely, depending on the type, intensity, duration and frequency of exercise. (2) Aim: To systematically review the efficacy of exercise therapy on global cognition in patients with CI using a network meta-analysis (NMA). (3) Methods: The PubMed, Embase, Sport Discus (EBSCO) and Cochrane Library databases were electronically searched to collect randomized controlled trials (RCTs) on exercise for patients with CI from inception to 7 August 2022. Two reviewers independently screened the literature, extracted data, and assessed the risk of bias of the included studies. The NMA was performed using the consistency model. (4) Results: A total of 29 RCTs comprising 2458 CI patients were included. The effects of different types of exercise on patients with CI were ranked as follows: multicomponent exercise (SMD = 0.84, 95% CI 0.31 to 1.36, p = 0.002), short duration (≤45 min) (SMD = 0.83, 95% CI 0.18 to 1.19, p = 0.001), vigorous intensity (SMD = 0.77, 95% CI 0.18 to 1.36, p = 0.011) and high frequency (5-7 times/week) (SMD = 1.28, 95% CI 0.41 to 2.14, p = 0.004). (5) Conclusion: These results suggested that multicomponent, short-duration, high-intensity, and high-frequency exercise may be the most effective type of exercise in improving global cognition in CI patients. However, more RCTs based on direct comparison of the effects of different exercise interventions are needed. (6) NMA registration identifier: CRD42022354978.

Evolutionarily distinct and sperm-specific supersized chromatin loops are marked by Helitron transposons in Xenopus tropicalis.

Transposable elements (TEs) are abundant in metazoan genomes and have multifaceted effects on host fitness. However, the mechanisms underlying the functions of TEs are still not fully understood. Here, we combine Hi-C, ATAC-seq, and ChIP-seq assays to report the existence of multimegabase supersized loop (SSL) clusters in the Xenopus tropicalis sperm. We show that SSL anchors are inaccessible and devoid of the architectural protein CTCF, RNA polymerase II, and modified histones. Nearly all SSL anchors are marked by Helitrons, a class II DNA transposon. Molecular dynamics simulations indicate that SSL clusters are likely formed via a molecular agent-mediated chromatin condensation process. However, only slightly more SSL anchor-associated genes are expressed at late embryo development stages, suggesting that SSL anchors might only function in sperm. Our work shows an evolutionarily distinct and sperm-specific genome structure marked by a subset of Helitrons, whose establishment and function remain to be explored.

Computational Modeling of RNA Aptamers: Structure Prediction of the Apo State.

RNA aptamers are single-stranded oligonucleotides that bind to specific molecular targets with high affinity and specificity. To design aptamers for new applications, it is critical to understand the ligand binding mechanism in terms of the structure and dynamics of the ligand-bound and apo states. The problem is that most of the NMR or X-ray crystal structures available for RNA aptamers are for ligand-bound states. Available apo state structures, mostly characterized by crystallization under nonphysiological conditions or probed by low resolution techniques, might fail to represent the diverse structural variations of the apo state in solution. Here, we develop an approach to obtain a representative ensemble of apo structures that are based on in silico RNA 3D structure prediction and in vitro experiments that characterize base stacking. Using the neomycin-B aptamer as a case study, an ensemble of structures for the aptamer in the apo (unbound) state are validated and then used to investigate the ligand-binding mechanism for the aptamer in complex with neomycin-B.

Influence of the Urban Built Environment on Physical and Mental Health of the Elderly under the Background of Big Data.

With the advent of the information technology revolution and the Internet era, information technology is gradually occupying an important position and becoming an important strategic factor in economic development. As an emerging technology that has been developing continuously in recent years, big data is becoming an important industry to improve the innovation and development of the urban economy. Like AI technology, cloud computing, and the Internet, big data has become an important application technology for economic growth and economic efficiency improvement in today's world. It is an effective means of progress and development in a region and an important strategic resource. As a new technology, big data has attracted more and more attention from all walks of life. Many companies have turned their attention to developing big data for economic benefits. "Enjoy your old age" is the yearning of every old man and his family. In recent years, the national level has been committed to "creating an urban built environment for the elderly to achieve healthy aging." From the perspective of promoting the physical and mental health of the elderly, this paper analyzes the impact of the urban built environment on the physical and mental health of the elderly based on the needs of the elderly and puts forward countermeasures and suggestions based on the current status and existing problems of the urban built environment for the elderly. Based on the combined data analysis method and technology in big data, this paper conducted a field questionnaire survey on a total of 4,000 elderly people in urban and rural areas by means of the questionnaire survey. It is found that the existing problems of the built environment in the old cities include scattered content, one-sided understanding, and rigid design. According to the problems, the solutions of building consensus, paying attention to planning, combining urban characteristics, and the joint efforts of all sectors of society are put forward. And programming tools are used to combine formulas and analyze related data in detail. The analysis results show that the physical and mental health index of the elderly is highly correlated with factors such as changes in the consensus degree of the urban built environment, urban built environment planning, urban built environment policy support, and multiparty efforts in the urban built environment. Changes show a positive change.

Length-dependent motions of SARS-CoV-2 frameshifting RNA pseudoknot and alternative conformations suggest avenues for frameshifting suppression.

The SARS-CoV-2 frameshifting element (FSE), a highly conserved mRNA region required for correct translation of viral polyproteins, defines an excellent therapeutic target against Covid-19. As discovered by our prior graph-theory analysis with SHAPE experiments, the FSE adopts a heterogeneous, length-dependent conformational landscape consisting of an assumed 3-stem H-type pseudoknot (graph motif 3_6), and two alternative motifs (3_3 and 3_5). Here, for the first time, we build and simulate, by microsecond molecular dynamics, 30 models for all three motifs plus motif-stabilizing mutants at different lengths. Our 3_6 pseudoknot systems, which agree with experimental structures, reveal interconvertible L and linear conformations likely related to ribosomal pausing and frameshifting. The 3_6 mutant inhibits this transformation and could hamper frameshifting. Our 3_3 systems exhibit length-dependent stem interactions that point to a potential transition pathway connecting the three motifs during ribosomal elongation. Together, our observations provide new insights into frameshifting mechanisms and anti-viral strategies.

Length-dependent motions of SARS-CoV-2 frameshifting RNA pseudoknot and alternative conformations suggest avenues for frameshifting suppression.

Conserved SARS-CoV-2 RNA regions of critical biological functions define excellent targets for anti-viral therapeutics against Covid-19 variants. One such region is the frameshifting element (FSE), responsible for correct translation of viral polyproteins. Here, we analyze molecular-dynamics motions of three FSE conformations, discovered by graph-theory analysis, and associated mutants designed by graph-based inverse folding: two distinct 3-stem H-type pseudoknots and a 3-way junction. We find that the prevalent H-type pseudoknot in literature adopts ring-like conformations, which in combination with 5' end threading could promote ribosomal pausing. An inherent shape switch from "L" to linear that may help trigger the frameshifting is suppressed in our designed mutant. The alternative conformation trajectories suggest a stable intermediate structure with mixed stem interactions of all three conformations, pointing to a possible transition pathway during ribosomal translation. These observations provide new insights into anti-viral strategies and frameshifting mechanisms.

Adjusting COVID-19 Seroprevalence Survey Results to Account for Test Sensitivity and Specificity.

Population-based seroprevalence surveys can provide useful estimates of the number of individuals previously infected with serious acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and still susceptible, as well as contribute to better estimates of the case-fatality rate and other measures of coronavirus disease 2019 (COVID-19) severity. No serological test is 100% accurate, however, and the standard correction that epidemiologists use to adjust estimates relies on estimates of the test sensitivity and specificity often based on small validation studies. We have developed a fully Bayesian approach to adjust observed prevalence estimates for sensitivity and specificity. Application to a seroprevalence survey conducted in New York State in 2020 demonstrates that this approach results in more realistic-and narrower-credible intervals than the standard sensitivity analysis using confidence interval endpoints. In addition, the model permits incorporating data on the geographical distribution of reported case counts to create informative priors on the cumulative incidence to produce estimates and credible intervals for smaller geographic areas than often can be precisely estimated with seroprevalence surveys.

To Knot or Not to Knot: Multiple Conformations of the SARS-CoV-2 Frameshifting RNA Element.

The SARS-CoV-2 frameshifting RNA element (FSE) is an excellent target for therapeutic intervention against Covid-19. This small gene element employs a shifting mechanism to pause and backtrack the ribosome during translation between Open Reading Frames 1a and 1b, which code for viral polyproteins. Any interference with this process has a profound effect on viral replication and propagation. Pinpointing the structures adapted by the FSE and associated structural transformations involved in frameshifting has been a challenge. Using our graph-theory-based modeling tools for representing RNA secondary structures, "RAG" (RNA-As-Graphs), and chemical structure probing experiments, we show that the 3-stem H-type pseudoknot (3_6 dual graph), long assumed to be the dominant structure, has a viable alternative, an HL-type 3-stem pseudoknot (3_3) for longer constructs. In addition, an unknotted 3-way junction RNA (3_5) emerges as a minor conformation. These three conformations share Stems 1 and 3, while the different Stem 2 may be involved in a conformational switch and possibly associations with the ribosome during translation. For full-length genomes, a stem-loop motif (2_2) may compete with these forms. These structural and mechanistic insights advance our understanding of the SARS-CoV-2 frameshifting process and concomitant virus life cycle, and point to three avenues of therapeutic intervention.

Meta-Analysis of Clinical Efficacy and Safety of Tripterygium wilfordii Polyglycosides Tablets in the Treatment of Chronic Kidney Disease.

OBJECTIVE: Tripterygium wilfordii polyglycosides tablet (TGt) is an oral preparation extracted from plant Tripterygium wilfordii. It has the effects of anti-inflammation and inhibition of cellular and humoral immunity. However, many reports of adverse reactions caused by TGt have limited its application. In this paper, the clinical efficacy and safety of TGt in the treatment of chronic kidney disease (CKD) were verified by data mining and analysis, so as to provide theoretical data support for the application and development of TGt. METHODS: A computer search of the following databases was conducted: PubMed, Web of Science, CBM, VIP, Wanfang Data, and CNKI. The search time limit is from the establishment of the database to September 2020. We searched for clinical randomized controlled trials of TGt in the treatment of CKD. The main types of CKD involved are nephrotic syndrome (NS), primary nephrotic syndrome (PNS), refractory nephrotic syndrome (RNS), and IgA nephropathy (IgAN). RevMan 5.2 and Stata 12.0 software were used to evaluate the literature quality and analyze the data. Finally, GRADEpro software was used to evaluate the quality of evidence. RESULTS: According to the inclusion and exclusion criteria, 75 articles with a total of 6418 subjects were included. The results of the meta-analysis showed that TGt could reduce 24-hour urinary protein, increase serum albumin, improve clinical efficacy, and reduce disease recurrence rate in patients (P < 0.05) with CKD compared with adrenocortical hormones or immunosuppressants. TGt could significantly reduce the level of serum creatinine (Scr) in patients with CKD (P < 0.05), but it was not significant in reducing the level of blood urea nitrogen (P > 0.05). In terms of safety evaluation, in patients with CKD, it could significantly reduce the incidence of gastrointestinal adverse reactions and neurogenic dizziness and headache (P < 0.05). However, in terms of adverse reactions such as liver injury, respiratory infection, and leukopenia, TGt was as harmful as corticosteroids or immunosuppressants (P < 0.05). The quality of the evidence was evaluated with GRADEpro software, and the results showed that TGt was strongly recommended for the treatment of CKD. CONCLUSION: TGt has certain efficacy in the treatment of CKD and has fewer side effects in certain types of diseases. The effect of TGt combined with other drugs is better than that of single use. This paper also has some limitations. Due to the limited number of the included studies, with all being from China, there may be methodological differences. Therefore, more high-quality literature data from different countries are needed.

To knot or not to knot: Multiple conformations of the SARS-CoV-2 frameshifting RNA element.

The SARS-CoV-2 frameshifting RNA element (FSE) is an excellent target for therapeutic intervention against Covid-19. This small gene element employs a shifting mechanism to pause and backtrack the ribosome during translation between Open Reading Frames 1a and 1b, which code for viral polyproteins. Any interference with this process has profound effect on viral replication and propagation. Pinpointing the structures adapted by the FSE and associated structural transformations involved in frameshifting has been a challenge. Using our graph-theory-based modeling tools for representing RNA secondary structures, "RAG" (RNA-As-Graphs), and chemical structure probing experiments, we show that the 3-stem H-type pseudoknot (3_6 dual graph), long assumed to be the dominant structure has a viable alternative, an HL-type 3-stem pseudoknot (3_3) for longer constructs. In addition, an unknotted 3-way junction RNA (3_5) emerges as a minor conformation. These three conformations share Stems 1 and 3, while the different Stem 2 may be involved in a conformational switch and possibly associations with the ribosome during translation. For full-length genomes, a stem-loop motif (2_2) may compete with these forms. These structural and mechanistic insights advance our understanding of the SARS-CoV-2 frameshifting process and concomitant virus life cycle, and point to three avenues of therapeutic intervention.

Structure-altering mutations of the SARS-CoV-2 frameshifting RNA element.

With the rapid rate of COVID-19 infections and deaths, treatments and cures besides hand washing, social distancing, masks, isolation, and quarantines are urgently needed. The treatments and vaccines rely on the basic biophysics of the complex viral apparatus. Although proteins are serving as main drug and vaccine targets, therapeutic approaches targeting the 30,000 nucleotide RNA viral genome form important complementary approaches. Indeed, the high conservation of the viral genome, its close evolutionary relationship to other viruses, and the rise of gene editing and RNA-based vaccines all argue for a focus on the RNA agent itself. One of the key steps in the viral replication cycle inside host cells is the ribosomal frameshifting required for translation of overlapping open reading frames. The RNA frameshifting element (FSE), one of three highly conserved regions of coronaviruses, is believed to include a pseudoknot considered essential for this ribosomal switching. In this work, we apply our graph-theory-based framework for representing RNA secondary structures, "RAG (or RNA-As-Graphs)," to alter key structural features of the FSE of the SARS-CoV-2 virus. Specifically, using RAG machinery of genetic algorithms for inverse folding adapted for RNA structures with pseudoknots, we computationally predict minimal mutations that destroy a structurally important stem and/or the pseudoknot of the FSE, potentially dismantling the virus against translation of the polyproteins. Our microsecond molecular dynamics simulations of mutant structures indicate relatively stable secondary structures. These findings not only advance our computational design of RNAs containing pseudoknots, they pinpoint key residues of the SARS-CoV-2 virus as targets for antiviral drugs and gene editing approaches.

Meta-Analysis of Randomized Controlled Trials of Xueshuantong Injection in Prevention of Deep Venous Thrombosis of Lower Extremity after Orthopedic Surgery.

OBJECTIVE: To systematically evaluate the clinical efficacy of Xueshuantong injection (Panax notoginseng saponins) in preventing deep venous thrombosis (DVT) of lower extremity after orthopedic surgery. METHODS: The randomized controlled trials (RCTs) of Xueshuantong injection in prevention of lower extremity DVT after orthopedic surgery were retrieved from CNKI, Wanfang database, VIP, PubMed, and Cochrane Library by August 2020. Revman5.2 was used to analyze the results. RESULTS: A total of 20 articles including 2336 patients were included. The results of meta-analysis showed that the incidence of DVT in the experimental group was lower than that in the control group; after operation, the D-dimer (Ddimer), thrombin time (APTT), and prothrombin time (PT) in the experimental group were significantly improved compared with those in the control group, and the difference between the two groups was statistically significant. CONCLUSION: Xueshuantong injection can effectively prevent the formation of lower extremity DVT after orthopedic surgery and antagonize the postoperative hypercoagulable state of blood, which has high clinical value.

Sampling Performance of Multiple Independent Molecular Dynamics Simulations of an RNA Aptamer.

Using multiple independent simulations instead of one long simulation has been shown to improve the sampling performance attained with the molecular dynamics (MD) simulation method. However, it is generally not known how long each independent simulation should be, how many independent simulations should be used, or to what extent either of these factors affects the overall sampling performance achieved for a given system. The goal of the present study was to assess the sampling performance of multiple independent MD simulations, where each independent simulation begins from a different initial molecular conformation. For this purpose, we used an RNA aptamer that is 25 nucleotides long as a case study. The initial conformations of the aptamer are derived from six de novo predicted 3D structures. Each of the six de novo predicted structures is energy minimized in solution and equilibrated with MD simulations at high temperature. Ten conformations from these six high-temperature equilibration runs are selected as initial conformations for further simulations at ambient temperature. In total, we conducted 60 independent MD simulations, each with a duration of 100 ns, to study the conformation and dynamics of the aptamer. For each group of 10 independent simulations that originated from a particular de novo predicted structure, we evaluated the potential energy distribution of the RNA and used recurrence quantification analysis to examine the sampling of RNA conformational transitions. To assess the impact of starting from different de novo predicted structures, we computed the density of structure projection on principal components to compare the regions sampled by the different groups of ten independent simulations. The recurrence rate and dependence of initial conformation among the groups were also compared. We stress the necessity of using different initial configurations as simulation starting points by showing long simulations from different initial structures suffer from being trapped in different states. Finally, we summarized the sampling efficiency for the complete set of 60 independent simulations and determined regions of under-sampling on the potential energy landscape. The results suggest that conducting multiple independent simulations using a diverse set of de novo predicted structures is a promising approach to achieve sufficient sampling. This approach avoids undesirable outcomes, such as the problem of the RNA aptamer being trapped in a local minimum. For others wishing to conduct multiple independent simulations, the analysis protocol presented in this study is a guide for examining overall sampling and determining if more simulations are necessary for sufficient sampling.

Computed tomography (CT) imaging evaluation of integrated traditional Chinese medicine cooperative therapy in treating acute cerebral infarction: A randomized controlled trial.

INTRODUCTION: Acute cerebral infarction is a clinically common cerebrovascular disease. Acute cerebral infarction is characterized by sudden onset, dangerous illness, high risk of death, and disability. Computed tomography perfusion imaging can detect abnormal brain tissue perfusion 30 minutes after the onset of cerebral ischemia, providing the earliest and most valuable information for clinical diagnosis and treatment. In recent years, the effect of traditional Chinese medicine on acute cerebral infarction has been remarkable. METHODS/DESIGN: This study plan randomly divided eligible acute cerebral infarction patients into two groups. Patients in the control group will be treated with conventional Western medicine; patients in the intervention group will be treated with traditional Chinese medicine cooperative therapy on the basis of conventional Western medicine. The curative effects will be selected before treatment, 2 weeks after treatment, and 3 months follow-up. The changes in CT imaging evaluation, NIHSS score, and BI index of the two groups of patients will be observed. DISCUSSION: We aim to provide higher evidence-based medical evidence for traditional Chinese medicine treatment of acute cerebral infarction. And clarify the application value of computed tomography perfusion imaging in the diagnosis and efficacy evaluation of acute cerebral infarction. TRIAL REGISTRATION: ClinicalTrials.gov, ChiCTR2000030230, Registered on 03 March 2020.

Effects of Different Processed Products of Polygonum multiflorum on the Liver.

OBJECTIVE: Based on in vitro and in vivo experimental studies, the changes of the main components of Polygonum multiflorum and different processed products and their effects on hepatotoxicity were investigated. METHODS: The components of different processed products of Polygonum multiflorum and different processed products and their effects on hepatotoxicity were investigated. RESULTS: With the extension of processing time, the contents of various chemical components in Polygonum multiflorum and different processed products and their effects on hepatotoxicity were investigated. Polygonum multiflorum and different processed products and their effects on hepatotoxicity were investigated. Polygonum multiflorum and different processed products and their effects on hepatotoxicity were investigated. Polygonum multiflorum and different processed products and their effects on hepatotoxicity were investigated. CONCLUSION: The content of the main components in Radix Polygonum multiflorum can be affected by processing time; stilbene glycoside may be the main component leading to liver injury. The degree of liver injury caused by Radix Polygonum multiflorum is negatively correlated with processing time.Polygonum multiflorum and different processed products and their effects on hepatotoxicity were investigated. Polygonum multiflorum and different processed products and their effects on hepatotoxicity were investigated.

Common Secondary and Tertiary Structural Features of Aptamer-Ligand Interaction Shared by RNA Aptamers with Different Primary Sequences.

Aptamer selection can yield many oligonucleotides with different sequences and affinities for the target molecule. Here, we have combined computational and experimental approaches to understand if aptamers with different sequences but the same molecular target share structural and dynamical features. NEO1A, with a known NMR-solved structure, displays a flexible loop that interacts differently with individual aminoglycosides, its ligand affinities and specificities are responsive to ionic strength, and it possesses an adenosine in the loop that is critical for high-affinity ligand binding. NEO2A was obtained from the same selection and, although they are only 43% identical in overall sequence, NEO1A and NEO2A share similar loop sequences. Experimental analysis by 1D NMR and 2-aminopurine reporters combined with molecular dynamics modeling revealed similar structural and dynamical characteristics in both aptamers. These results are consistent with the hypothesis that the target ligand drives aptamer structure and also selects relevant dynamical characteristics for high-affinity aptamer-ligand interaction. Furthermore, they suggest that it might be possible to "migrate" structural and dynamical features between aptamer group members with different primary sequences but with the same target ligand.

Structural stability and elastic and electronic properties of rhenium borides: first principle investigations.

The structural stability and elastic and electronic properties of rhenium borides with different boron concentration are calculated systemically by means of first principle total energy calculations. The total energy calculations reveal that the WC-type structure is more energetically favorable for ReB and that the Re(2)P-type structure is more preferred for Re(2)B. The formation enthalpy of these borides have been studied by the solid synthesis routes. The calculated elastic properties indicate that Re(2)B(3), ReB, and Re(2)B phases are also potential hard materials. Although valence-electron density was often employed to evaluate elastic properties of materials, our calculations indicate that the bulk elastic properties of these borides are not direct correlation with their valence-electron density. The analysis of electronic structure, charge density distribution, and Mulliken overlap population provides further understanding of the elastic and superconductivity properties of these borides.