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ERI1 is a 3'-to-5' exoribonuclease involved in RNA metabolic pathways including 5.8S rRNA processing and turnover of histone mRNAs. Its biological and medical significance remain unclear. Here, we uncover a phenotypic dichotomy associated with bi-allelic ERI1 variants by reporting eight affected individuals from seven unrelated families. A severe spondyloepimetaphyseal dysplasia (SEMD) was identified in five affected individuals with missense variants but not in those with bi-allelic null variants, who showed mild intellectual disability and digital anomalies. The ERI1 missense variants cause a loss of the exoribonuclease activity, leading to defective trimming of the 5.8S rRNA 3' end and a decreased degradation of replication-dependent histone mRNAs. Affected-individual-derived induced pluripotent stem cells (iPSCs) showed impaired in vitro chondrogenesis with downregulation of genes regulating skeletal patterning. Our study establishes an entity previously unreported in OMIM and provides a model showing a more severe effect of missense alleles than null alleles within recessive genotypes, suggesting a key role of ERI1-mediated RNA metabolism in human skeletal patterning and chondrogenesis.
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Exorribonucleasas , Histonas , Humanos , Exorribonucleasas/genética , Histonas/genética , Mutación Missense/genética , ARN Ribosómico 5.8S , ARN , ARN Mensajero/genéticaRESUMEN
We present m6ACali, a novel machine-learning framework aimed at enhancing the accuracy of N6-methyladenosine (m6A) epitranscriptome profiling by reducing the impact of non-specific antibody enrichment in MeRIP-Seq. The calibration model serves as a genomic feature-based classifier that refines the identification of m6A sites, distinguishing those genuinely present from those that can be detected in in-vitro transcribed (IVT) control experiments. We find that m6ACali effectively identifies non-specific binding peaks reported by exomePeak2 and MACS2 in novel MeRIP-Seq datasets without the need for paired IVT controls. The model interpretation revealed that off-target antibody binding sites commonly occur at short exons and short mRNAs, originating from high read coverage regions that share the motif sequence with true m6A sites. We also reveal that the ML strategy can efficiently adjust differentially methylated peaks and other antibody-dependent, base-resolution m6A detection techniques. As a result, m6ACali offers a promising method for the universal enhancement of m6A profiles generated by MeRIP-Seq experiments, elevating the benchmark for omics-level m6A data integration.
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Adenosina , Aprendizaje Automático , Análisis de Secuencia de ARN , Humanos , Adenosina/análogos & derivados , Calibración , Metilación , ARN Mensajero/genética , ARN Mensajero/metabolismo , Análisis de Secuencia de ARN/métodos , TranscriptomaRESUMEN
N 6-Methyladenosine (m6A) is one of the most abundant internal chemical modifications on eukaryote mRNA and is involved in numerous essential molecular functions and biological processes. To facilitate the study of this important post-transcriptional modification, we present here m6A-Atlas v2.0, an updated version of m6A-Atlas. It was expanded to include a total of 797 091 reliable m6A sites from 13 high-resolution technologies and two single-cell m6A profiles. Additionally, three methods (exomePeaks2, MACS2 and TRESS) were used to identify >16 million m6A enrichment peaks from 2712 MeRIP-seq experiments covering 651 conditions in 42 species. Quality control results of MeRIP-seq samples were also provided to help users to select reliable peaks. We also estimated the condition-specific quantitative m6A profiles (i.e. differential methylation) under 172 experimental conditions for 19 species. Further, to provide insights into potential functional circuitry, the m6A epitranscriptomics were annotated with various genomic features, interactions with RNA-binding proteins and microRNA, potentially linked splicing events and single nucleotide polymorphisms. The collected m6A sites and their functional annotations can be freely queried and downloaded via a user-friendly graphical interface at: http://rnamd.org/m6a.
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Bases de Datos Genéticas , Metilación de ARN , ARN Mensajero , Transcriptoma , Empalme del ARN , ARN Mensajero/química , ARN Mensajero/metabolismo , Procesamiento Postranscripcional del ARNRESUMEN
With advanced technologies to map RNA modifications, our understanding of them has been revolutionized, and they are seen to be far more widespread and important than previously thought. Current next-generation sequencing (NGS)-based modification profiling methods are blind to RNA modifications and thus require selective chemical treatment or antibody immunoprecipitation methods for particular modification types. They also face the problem of short read length, isoform ambiguities, biases and artifacts. Direct RNA sequencing (DRS) technologies, commercialized by Oxford Nanopore Technologies (ONT), enable the direct interrogation of any given modification present in individual transcripts and promise to address the limitations of previous NGS-based methods. Here, we present the first ONT-based database of quantitative RNA modification profiles, DirectRMDB, which includes 16 types of modification and a total of 904,712 modification sites in 25 species identified from 39 independent studies. In addition to standard functions adopted by existing databases, such as gene annotations and post-transcriptional association analysis, we provide a fresh view of RNA modifications, which enables exploration of the epitranscriptome in an isoform-specific manner. The DirectRMDB database is freely available at: http://www.rnamd.org/directRMDB/.
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Secuenciación de Nucleótidos de Alto Rendimiento , Procesamiento Postranscripcional del ARN , Análisis de Secuencia de ARN , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Anotación de Secuencia Molecular , Isoformas de Proteínas , ARN/genética , Análisis de Secuencia de ARN/métodos , Bases de Datos de Ácidos NucleicosRESUMEN
Recent advances in epitranscriptomics have unveiled functional associations between RNA modifications (RMs) and multiple human diseases, but distinguishing the functional or disease-related single nucleotide variants (SNVs) from the majority of 'silent' variants remains a major challenge. We previously developed the RMDisease database for unveiling the association between genetic variants and RMs concerning human disease pathogenesis. In this work, we present RMDisease v2.0, an updated database with expanded coverage. Using deep learning models and from 873 819 experimentally validated RM sites, we identified a total of 1 366 252 RM-associated variants that may affect (add or remove an RM site) 16 different types of RNA modifications (m6A, m5C, m1A, m5U, Ψ, m6Am, m7G, A-to-I, ac4C, Am, Cm, Um, Gm, hm5C, D and f5C) in 20 organisms (human, mouse, rat, zebrafish, maize, fruit fly, yeast, fission yeast, Arabidopsis, rice, chicken, goat, sheep, pig, cow, rhesus monkey, tomato, chimpanzee, green monkey and SARS-CoV-2). Among them, 14 749 disease- and 2441 trait-associated genetic variants may function via the perturbation of epitranscriptomic markers. RMDisease v2.0 should serve as a useful resource for studying the genetic drivers of phenotypes that lie within the epitranscriptome layer circuitry, and is freely accessible at: www.rnamd.org/rmdisease2.
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Bases de Datos Factuales , Procesamiento Postranscripcional del ARN , Animales , Humanos , Fenotipo , SARS-CoV-2/genética , SARS-CoV-2/metabolismo , EpigenómicaRESUMEN
Anomalous pulmonary venous return (APVR) is a potentially lethal congenital heart disease. Elucidating the genetic etiology is crucial for understanding its pathogenesis and improving clinical practice, whereas its genetic basis remains largely unknown because of complex genetic etiology. We thus performed whole-exome sequencing for 144 APVR patients and 1636 healthy controls and report a comprehensive atlas of APVR-related rare genetic variants. Novel singleton, loss-of-function and deleterious missense variants (DVars) were enriched in patients, particularly for genes highly expressed in the developing human heart at the critical time point for pulmonary veins draining into the left atrium. Notably, PLXND1, encoding a receptor for semaphorins, represents a strong candidate gene of APVR (adjusted P = 1.1e-03, odds ratio: 10.9-69.3), accounting for 4.17% of APVR. We further validated this finding in an independent cohort consisting of 82 case-control pairs. In these two cohorts, eight DVars were identified in different patients, which convergently disrupt the GTPase-activating protein-related domain of PLXND1. All variant carriers displayed strikingly similar clinical features, in that all anomalous drainage of pulmonary vein(s) occurred on the right side and incorrectly connected to the right atrium, which may represent a novel subtype of APVR for molecular diagnosis. Studies in Plxnd1 knockout mice further revealed the effects of PLXND1 deficiency on severe heart and lung defects and cellular abnormalities related to APVR such as abnormal migration and vascular formation of vascular endothelial cells. These findings indicate the important role of PLXND1 in APVR pathogenesis, providing novel insights into the genetic etiology and molecular subtyping for APVR.
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Cardiopatías Congénitas , Venas Pulmonares , Síndrome de Cimitarra , Animales , Células Endoteliales , Atrios Cardíacos , Cardiopatías Congénitas/genética , Humanos , Péptidos y Proteínas de Señalización Intracelular , Glicoproteínas de Membrana , Ratones , Venas Pulmonares/anomalías , Síndrome de Cimitarra/genéticaRESUMEN
Vitamin D deficiency is a risk factor for developing multiple sclerosis. The PrevANZ trial was conducted to determine if vitamin D3 supplementation can prevent recurrent disease activity in people with a first demyelinating event. As a sub-study of this trial, we investigated the effect of supplementation on peripheral immune cell gene expression. Participants were randomized to 1000, 5000 or 10,000 international units daily of vitamin D3 or placebo. Peripheral blood was collected at baseline and 12 weeks and sent for ribonucleic acid sequencing. Datasets from 55 participants were included. Gene expression was modulated by high dose supplementation. Antigen presentation and viral response pathways were upregulated. Oxidative phosphorylation and immune signaling pathways, including tumor necrosis factor-alpha and interleukin-17 signaling, were downregulated. Overall, vitamin D3 supplementation for 12 weeks modulated the peripheral immune cell transcriptome with induction of anti-inflammatory gene expression profiles. Our results support a dose-dependent effect of vitamin D3 supplementation on immune gene expression.
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Colecalciferol , Deficiencia de Vitamina D , Humanos , Colecalciferol/farmacología , Suplementos Dietéticos , Método Doble Ciego , Factores de Riesgo , Transcriptoma , Deficiencia de Vitamina D/tratamiento farmacológico , Deficiencia de Vitamina D/genéticaRESUMEN
PURPOSE: Based on randomized clinical trials, this meta-analysis evaluated the efficacy and safety of intent-to-cure or prophylactic hyperthermic intraperitoneal chemotherapy (HIPEC) for the treatment of gastric cancer. METHODS: PubMed, Cochrane Library, Medline, and Embase databases were all systemically searched from 2004 to 2023. The quality of the study was assessed by using the Cochrane risk of bias method. The certainty of the evidence was determined by using the GRADE evaluation. RESULTS: In this study, 12 articles with a total of 1181 patients were analyzed based on the inclusion criteria. The findings revealed that HIPEC had a higher survival rate (risk ratio [RR] 0.60; 95% confidence interval [CI] [0.43, 0.86], P = 0.005, RR 0.82; 95% CI [0.70, 0.97], P = 0.02, RR 0.83; 95% CI [0.71, 0.96], P < 0.01, and RR 0.63 [0.54, 0.73], P < 0.00001) after 1, 2, 3, and 5 years compared with the control group. The RR was statistically significant for 1, 2, 3, and 5 years. Furthermore, the observed overall recurrence rate for the HIPEC group was lower than control group and statistically significant (RR 0.59; 95% CI [0.50, 0.68], P < 0.0001). Higher disease-free survival rate (RR 1.42; 95% CI [1.07, 1.89], P < 0.01) was observed in the HIPEC group and statistically significant. CONCLUSIONS: Gastric cancer patients treated with HIPEC have shown promising outcomes with regard to survival, recurrence, disease-free survival, and adverse reactions. However, multicenter trials with larger sample sizes consisting of different ethnicities is suggested.
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The development of diabetes mellitus (DM) is generally accompanied by erectile dysfunction (ED) and pulmonary arterial hypertension (PAH), which increases the use of combination drug therapy and the risk of drug-drug interactions. Saxagliptin for the treatment of DM, sildenafil for the treatment of ED and PAH, and macitentan for the treatment of PAH are all substrates of CYP3A4, which indicates their potential involvement in drug-drug interactions. Therefore, we investigated potential pharmacokinetic interactions between saxagliptin and sildenafil/macitentan. We investigated this speculation both in vitro and in vivo, and explored the underlying mechanism using in vitro hepatic metabolic models and molecular docking assays. The results showed that sildenafil substantially inhibited the metabolism of saxagliptin by occupying the catalytic site of CYP3A4 in a competitive manner, leading to the alterations in the pharmacokinetic properties of saxagliptin in terms of increased maximum plasma concentration (Cmax), area under the plasma concentration-time curve from time 0 to 24 h (AUC(0-t)), area under the plasma concentration-time curve from time 0 extrapolated to infinite time (AUC(0-∞)), decreased clearance rate (CLz/F), and prolonged terminal half-life (t1/2). In contrast, a slight inhibition was observed in saxagliptin metabolism when concomitantly used with macitentan, as no pharmacokinetic parameters were altered, except for CLz/F. Thus, dosage adjustment of saxagliptin may be required in combination with sildenafil to achieve safe therapeutic plasma concentrations and reduce the risk of potential toxicity, but it is not necessary for co-administration with macitentan.
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Adamantano , Dipéptidos , Interacciones Farmacológicas , Pirimidinas , Citrato de Sildenafil , Sulfonamidas , Citrato de Sildenafil/farmacocinética , Citrato de Sildenafil/farmacología , Sulfonamidas/farmacocinética , Sulfonamidas/farmacología , Dipéptidos/farmacocinética , Dipéptidos/farmacología , Pirimidinas/farmacocinética , Pirimidinas/farmacología , Humanos , Adamantano/análogos & derivados , Adamantano/farmacocinética , Adamantano/farmacología , Masculino , Animales , Citocromo P-450 CYP3A/metabolismo , Simulación del Acoplamiento Molecular , Microsomas Hepáticos/metabolismo , Microsomas Hepáticos/efectos de los fármacos , Inhibidores de la Dipeptidil-Peptidasa IV/farmacocinética , Inhibidores de la Dipeptidil-Peptidasa IV/farmacologíaRESUMEN
BACKGROUND: Ongoing controversy exists regarding optimal management of disease modifying therapy (DMT) in older people with multiple sclerosis (pwMS). There is concern that the lower relapse rate, combined with a higher risk of DMT-related infections and side effects, may alter the risk-benefit balance in older pwMS. Given the lack of pwMS above age 60 in randomised controlled trials, the comparative efficacy of high-efficacy DMTs such as ocrelizumab has not been shown in older pwMS. We aimed to evaluate the comparative effectiveness of ocrelizumab, a high-efficacy DMT, versus interferon/glatiramer acetate (IFN/GA) in pwMS over the age of 60. METHODS: Using data from MSBase registry, this multicentre cohort study included pwMS above 60 who switched to or started on ocrelizumab or IFN/GA. We analysed relapse and disability outcomes after balancing covariates using an inverse probability treatment weighting (IPTW) method. Propensity scores were obtained based on age, country, disease duration, sex, baseline Expanded Disability Status Scale, prior relapses (all-time, 12 months and 24 months) and prior DMT exposure (overall number and high-efficacy DMTs). After weighting, all covariates were balanced. Primary outcomes were time to first relapse and annualised relapse rate (ARR). Secondary outcomes were 6-month confirmed disability progression (CDP) and confirmed disability improvement (CDI). RESULTS: A total of 248 participants received ocrelizumab, while 427 received IFN/GA. The IPTW-weighted ARR for ocrelizumab was 0.01 and 0.08 for IFN/GA. The IPTW-weighted ARR ratio was 0.15 (95% CI 0.06 to 0.33, p<0.001) for ocrelizumab compared with IFN/GA. On IPTW-weighted Cox regression models, HR for time to first relapse was 0.13 (95% CI 0.05 to 0.26, p<0.001). The hazard of first relapse was significantly reduced in ocrelizumab users after 5 months compared with IFN/GA users. However, the two groups did not differ in CDP or CDI over 3.57 years. CONCLUSION: In older pwMS, ocrelizumab effectively reduced relapses compared with IFN/GA. Overall relapse activity was low. This study adds valuable real-world data for informed DMT decision making with older pwMS. Our study also confirms that there is a treatment benefit in older people with MS, given the existence of a clear differential treatment effect between ocrelizumab and IFN/GA in the over 60 age group.
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Anticuerpos Monoclonales Humanizados , Acetato de Glatiramer , Humanos , Acetato de Glatiramer/uso terapéutico , Masculino , Femenino , Anticuerpos Monoclonales Humanizados/uso terapéutico , Anticuerpos Monoclonales Humanizados/efectos adversos , Persona de Mediana Edad , Anciano , Factores Inmunológicos/uso terapéutico , Factores Inmunológicos/efectos adversos , Esclerosis Múltiple/tratamiento farmacológico , Resultado del Tratamiento , Estudios de Cohortes , Interferones/uso terapéutico , Interferones/efectos adversos , Recurrencia , Sistema de RegistrosRESUMEN
BACKGROUND: Neuromyelitis optica spectrum disorder (NMOSD) can be categorised into aquaporin-4 antibody (AQP4-IgG) NMOSD or seronegative NMOSD. While our knowledge of AQP4-IgG NMOSD has evolved significantly in the past decade, seronegative NMOSD remains less understood. This study aimed to evaluate the predictors of relapses and treatment responses in AQP4-IgG NMOSD and seronegative NMOSD. METHODS: This was a multicentre, international, retrospective cohort study using the MSBase registry. Recurrent relapse risk was assessed using an Andersen-Gill model and risk of first relapse was evaluated using a Cox proportional hazards model. Covariates that putatively influence relapse risk included demographic factors, clinical characteristics and immunosuppressive therapies; the latter was assessed as a time-varying covariate. RESULTS: A total of 398 patients (246 AQP4-IgG NMOSD and 152 seronegative NMOSD) were included. The AQP4-IgG NMOSD and seronegative NMOSD patients did not significantly differ by age at disease onset, ethnicity or annualised relapse rate. Both low-efficacy and high-efficacy immunosuppressive therapies were associated with significant reductions in recurrent relapse risk, with notably greater protection conferred by high-efficacy therapies in both AQP4-IgG NMOSD (HR 0.27, 95% CI 0.15 to 0.49, p<0.001) and seronegative NMOSD (HR 0.21, 95% CI 0.08 to 0.51, p<0.001). Longer disease duration (HR 0.97, 95% CI 0.95 to 0.99, p<0.001) and male sex (HR 0.52, 95% CI 0.34 to 0.84, p=0.007) were additional protective variables in reducing the recurrent relapse risk for the AQP4-IgG NMOSD group. CONCLUSION: Although further studies are needed to improve our understanding of seronegative NMOSD, our findings underscore the importance of aggressive treatment with high-efficacy immunotherapies in both NMOSD subtypes, regardless of serostatus.
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BACKGROUND: Obsessive-compulsive disorder (OCD) is a classic disorder on the compulsivity spectrum, with diverse comorbidities. In the current study, we sought to understand OCD from a dimensional perspective by identifying multimodal neuroimaging patterns correlated with multiple phenotypic characteristics within the striatum-based circuits known to be affected by OCD. METHODS: Neuroimaging measurements of local functional and structural features and clinical information were collected from 110 subjects, including 51 patients with OCD and 59 healthy control subjects. Linked independent component analysis (LICA) and correlation analysis were applied to identify associations between local neuroimaging patterns across modalities (including gray matter volume, white matter integrity, and spontaneous functional activity) and clinical factors. RESULTS: LICA identified eight multimodal neuroimaging patterns related to phenotypic variations, including three related to symptoms and diagnosis. One imaging pattern (IC9) that included both the amplitude of low-frequency fluctuation measure of spontaneous functional activity and white matter integrity measures correlated negatively with OCD diagnosis and diagnostic scales. Two imaging patterns (IC10 and IC27) correlated with compulsion symptoms: IC10 included primarily anatomical measures and IC27 included primarily functional measures. In addition, we identified imaging patterns associated with age, gender, and emotional expression across subjects. CONCLUSIONS: We established that data fusion techniques can identify local multimodal neuroimaging patterns associated with OCD phenotypes. The results inform our understanding of the neurobiological underpinnings of compulsive behaviors and OCD diagnosis.
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Imagen por Resonancia Magnética , Trastorno Obsesivo Compulsivo , Humanos , Imagen por Resonancia Magnética/métodos , Corteza Cerebral , Neuroimagen , Trastorno Obsesivo Compulsivo/diagnóstico por imagen , Conducta Compulsiva/diagnóstico por imagen , EncéfaloRESUMEN
Artificial photosynthesis for high-value hydrogen peroxide (H2O2) through a two-electron reduction reaction is a green and sustainable strategy. However, the development of highly active H2O2 photocatalysts is impeded by severe carrier recombination, ineffective active sites, and low surface reaction efficiency. We developed a dual optimization strategy to load dense Ni nanoparticles onto ultrathin porous graphitic carbon nitride (Ni-UPGCN). In the absence and presence of sacrificial agents, Ni-UPGCN achieved H2O2 production rates of 169 and 4116 µmol g-1 h-1 with AQY (apparent quantum efficiency) at 420 nm of 3.14% and 17.71%. Forming a Schottky junction, the surface-modified Ni nanoparticles broaden the light absorption boundary and facilitate charge separation, which act as active sites, promoting O2 adsorption and reducing the formation energy of *OOH (reaction intermediate). This results in a substantial improvement in both H2O2 generation activity and selectivity. The Schottky junction of dual modulation strategy provides novel insights into the advancement of highly effective photocatalytic agents for the photosynthesis of H2O2.
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Cucurbit[n]urils (Q[n]s or CB[n]s), as a classical of artificial organic macrocyclic hosts, were found to have excellent advantages in the fabricating of tunable and smart organic luminescent materials in aqueous media and the solid state with high emitting efficiency under the rigid pumpkin-shaped structure-derived macrocyclic-confinement effect in recent years. This review aims to give a systematically up-to-date overview of the Q[n]-based supramolecular organic luminescent emissions from the confined spaces triggered host-guest complexes, including the assembly fashions and the mechanisms of the macrocycle-based luminescent complexes, as well as their applications. Finally, challenges and outlook are provided. Since this class of Q[n]-based supramolecular organic luminescent emissions, which have essentially derived from the cavity-dependent confinement effect and the resulting assembly fashions, emerged only a few years ago, we hope this review will provide valuable information for the further development of macrocycle-based light-emitting materials and other related research fields.
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Compuestos Macrocíclicos , Compuestos Heterocíclicos con 2 Anillos , Imidazolidinas , Luminiscencia , AguaRESUMEN
Chlorinated volatile organic compounds come from a wide range of sources and are highly toxic, posing a serious threat to biological health and the environment. Herein, a high-efficiency and energy-saving photothermal synergistic catalytic oxidation method was developed for the removal of 1,2-dichloroethane (1,2-DCE). Compared to traditional thermocatalysis, the 1,2-DCE conversion over Ru-U6S in photothermal synergistic catalysis at 340 °C increased by approximately 44% not only reducing energy consumption but also avoiding the instability of MOF structure caused by high reaction temperature. The excellent photothermal catalytic oxidation activity was derived from the synergistic effect of photo- and thermocatalysis. Ru-U6S demonstrated excellent 1,2-DCE adsorption capacity and stronger light utilization and could produce more reactive oxygen species (â¢OH and â¢O2-) after light illumination, which participated in the oxidation reaction, promoting the release of the active site of the catalyst. The results of H2O-TPD and NH3-DRIFTS exhibited that the use of S-containing ligands in the synthesis process increased the hydroxyl groups and Brønsted acid sites, significantly improved the selectivity of CO2 and HCl in the oxidation process, and reduced the release of chlorine-containing byproducts. This work provides a high-efficiency and energy-saving strategy for removing chlorinated volatile organic compounds and increasing the selectivity of ideal products directly with MOFs directly.
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Previous studies found that prolonged musical training can promote language processing, but few studies have examined whether and how musical training affects the processing of accentuation in spoken language. In this study, a vocabulary detection task was conducted, with Chinese single sentences as materials, to investigate how musicians and non-musicians process corrective accent and information accent in the sentence-middle and sentence-final positions. In the sentence-middle position, results of the cluster-based permutation t-tests showed significant differences in the 574-714 ms time window for the control group. In the sentence-final position, the cluster-based permutation t-tests revealed significant differences in the 612-810 ms time window for the music group and in the 616-812 ms time window for the control group. These significant positive effects were induced by the processing of information accent relative to that of corrective accent. These results suggest that both groups were able to distinguish corrective accent from information accent, but they processed the two accent types differently in the sentence-middle position. These findings show that musical training has a cross-domain effect on spoken language processing and that the accent position also affects its processing.
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Música , Percepción del Habla , Humanos , Lenguaje , Potenciales Evocados , VocabularioRESUMEN
As the most pervasive epigenetic mark present on mRNA and lncRNA, N6-methyladenosine (m6A) RNA methylation regulates all stages of RNA life in various biological processes and disease mechanisms. Computational methods for deciphering RNA modification have achieved great success in recent years; nevertheless, their potential remains underexploited. One reason for this is that existing models usually consider only the sequence of transcripts, ignoring the various regions (or geography) of transcripts such as 3'UTR and intron, where the epigenetic mark forms and functions. Here, we developed three simple yet powerful encoding schemes for transcripts to capture the submolecular geographic information of RNA, which is largely independent from sequences. We show that m6A prediction models based on geographic information alone can achieve comparable performances to classic sequence-based methods. Importantly, geographic information substantially enhances the accuracy of sequence-based models, enables isoform- and tissue-specific prediction of m6A sites, and improves m6A signal detection from direct RNA sequencing data. The geographic encoding schemes we developed have exhibited strong interpretability, and are applicable to not only m6A but also N1-methyladenosine (m1A), and can serve as a general and effective complement to the widely used sequence encoding schemes in deep learning applications concerning RNA transcripts.
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Aprendizaje Profundo , ARN Largo no Codificante , Regiones no Traducidas 3' , Metilación , Isoformas de Proteínas/genética , ARN/genética , ARN/metabolismo , ARN Mensajero/genéticaRESUMEN
5-Methylcytosine (m5C) is one of the most prevalent covalent modifications on RNA. It is known to regulate a broad variety of RNA functions, including nuclear export, RNA stability and translation. Here, we present m5C-Atlas, a database for comprehensive collection and annotation of RNA 5-methylcytosine. The database contains 166 540 m5C sites in 13 species identified from 5 base-resolution epitranscriptome profiling technologies. Moreover, condition-specific methylation levels are quantified from 351 RNA bisulfite sequencing samples gathered from 22 different studies via an integrative pipeline. The database also presents several novel features, such as the evolutionary conservation of a m5C locus, its association with SNPs, and any relevance to RNA secondary structure. All m5C-atlas data are accessible through a user-friendly interface, in which the m5C epitranscriptomes can be freely explored, shared, and annotated with putative post-transcriptional mechanisms (e.g. RBP intermolecular interaction with RNA, microRNA interaction and splicing sites). Together, these resources offer unprecedented opportunities for exploring m5C epitranscriptomes. The m5C-Atlas database is freely accessible at https://www.xjtlu.edu.cn/biologicalsciences/m5c-atlas.
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Bases de Datos Genéticas , Epigenoma/genética , Programas Informáticos , Transcriptoma/genética , 5-Metilcitosina/química , 5-Metilcitosina/metabolismo , Humanos , MicroARNs/genética , Polimorfismo de Nucleótido Simple/genética , Procesamiento Postranscripcional del ARN/genética , Análisis de Secuencia de ARNRESUMEN
To investigate the associations of fundamental movement skill (FMS) proficiency with family factors, including socioeconomic status (SES) and caregiver characteristics, by sex in young children in China. Participants included 1,207 Chinese children aged 3-6 years in this cross-sectional study. Children's FMS, consisting of locomotor skills and object control (OC) skills, were assessed. Information on family SES and caregiver characteristics was reported by the parents. Sex differences in outcomes and the associations of FMS with family factors by sex were examined using SPSS 26.0. Boys scored significantly higher than girls in terms of overall FMS and OC skills (both p < 0.01). There were significant and negative associations between children's FMS and parental education level and parental body mass index (BMI), which varied by sex. Boys who were regularly cared for by parents had higher FMS and OC skill scores than did those who were primarily looked after by grandparents (both p < 0.01). This complex interplay between sex and family factors (i.e. parental education level, parental BMI, and the identity of primary caregiver) on FMS proficiency in young children underscores the urgent need for developing sex-tailored, family-involved, and socio-culturally adapted interventions to enhance FMS proficiency at the preschool stage.
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Índice de Masa Corporal , Destreza Motora , Humanos , Masculino , Femenino , Destreza Motora/fisiología , Estudios Transversales , Preescolar , Factores Sexuales , Niño , China , Escolaridad , Clase Social , Padres , Cuidadores , Movimiento/fisiologíaRESUMEN
Bi3+ doped Ti/Sb-SnO2/PbO2 electrode materials were fabricated by electrodeposition to improve their electrochemical performance in zinc electrowinning. The surface morphology, chemical composition, and hydrophilicity of the as-prepared electrodes were characterized using scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy (EDS), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), and contact angle. An electrochemical measurement and an accelerated lifetime experiment were also conducted to investigate the electrocatalytic performance and stability of the electrodes. The results show that the Bi3+ modification electrode has an important effect on the coating morphology, the crystal structure, the surface hydrophilicity, the electrocatalytic activity, and the stability. The electrode prepared from the solution containing 2 mmol·L-1 Bi(NO3)3 (marked as the Ti/Sb-SnO2/2Bi-PbO2 electrode) exhibits the best hydrophilicity performance (θ = 21.6°) and the longest service life (1196 h). During the electrochemical characterization analysis, the Ti/Sb-SnO2/2Bi-PbO2 electrode showed the highest oxygen evolution activity, which can be attributed to it having the highest electroactive surface (qT* = 21.20 C·cm-2) and the best charge-transfer efficiency. The DFT calculation demonstrated that the doping of Bi3+ leads to a decrease in the OER reaction barrier and an increase in the DOS of the electrode, which further enhances the catalytic activity and the conductivity of the electrode. Moreover, the simulated zinc electrowinning experiment demonstrated that the Ti/Sb-SnO2/2Bi-PbO2 electrode consumes less energy than other electrodes. Therefore, it is expected that the Bi3+ modified electrode will become a very promising electrode material for zinc electrowinning in the future.