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Topologically associating domains (TADs) have emerged as basic structural and functional units of genome organization and have been determined by many computational methods from Hi-C contact maps. However, the TADs obtained by different methods vary greatly, which makes the accurate determination of TADs a challenging issue and hinders subsequent biological analyses about their organization and functions. Obvious inconsistencies among the TADs identified by different methods indeed make the statistical and biological properties of TADs overly depend on the chosen method rather than on the data. To this end, we use the consensus structural information captured by these methods to define the TAD separation landscape for decoding the consensus domain organization of the 3D genome. We show that the TAD separation landscape could be used to compare domain boundaries across multiple cell types for discovering conserved and divergent topological structures, decipher three types of boundary regions with diverse biological features, and identify consensus TADs (ConsTADs). We illustrate that these analyses could deepen our understanding of the relationships between the topological domains and chromatin states, gene expression, and DNA replication timing.
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Montagem e Desmontagem da Cromatina , Cromatina , Consenso , Cromatina/genética , Genoma , CromossomosRESUMO
BACKGROUND: Hypertrophic cardiomyopathy (HCM) is the most prevalent monogenic heart disorder. However, the pathogenesis of HCM, especially its nongenetic mechanisms, remains largely unclear. Transcription factors are known to be involved in various biological processes including cell growth. We hypothesized that SP1 (specificity protein 1), the first purified TF in mammals, plays a role in the cardiomyocyte growth and cardiac hypertrophy of HCM. METHODS: Cardiac-specific conditional knockout of Sp1 mice were constructed to investigate the role of SP1 in the heart. The echocardiography, histochemical experiment, and transmission electron microscope were performed to analyze the cardiac phenotypes of cardiac-specific conditional knockout of Sp1 mice. RNA sequencing, chromatin immunoprecipitation sequencing, and adeno-associated virus experiments in vivo were performed to explore the downstream molecules of SP1. To examine the therapeutic effect of SP1 on HCM, an SP1 overexpression vector was constructed and injected into the mutant allele of Myh6 R404Q/+ (Myh6 c. 1211C>T) HCM mice. The human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) from a patient with HCM were used to detect the potential therapeutic effects of SP1 in human HCM. RESULTS: The cardiac-specific conditional knockout of Sp1 mice developed a typical HCM phenotype, displaying overt myocardial hypertrophy, interstitial fibrosis, and disordered myofilament. In addition, Sp1 knockdown dramatically increased the cell area of hiPSC-CMs and caused intracellular myofibrillar disorganization, which was similar to the hypertrophic cardiomyocytes of HCM. Mechanistically, Tuft1 was identified as the key target gene of SP1. The hypertrophic phenotypes induced by Sp1 knockdown in both hiPSC-CMs and mice could be rescued by TUFT1 (tuftelin 1) overexpression. Furthermore, SP1 overexpression suppressed the development of HCM in the mutant allele of Myh6 R404Q/+ mice and also reversed the hypertrophic phenotype of HCM hiPSC-CMs. CONCLUSIONS: Our study demonstrates that SP1 deficiency leads to HCM. SP1 overexpression exhibits significant therapeutic effects on both HCM mice and HCM hiPSC-CMs, suggesting that SP1 could be a potential intervention target for HCM.
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Cardiomiopatia Hipertrófica , Células-Tronco Pluripotentes Induzidas , Humanos , Camundongos , Animais , Células-Tronco Pluripotentes Induzidas/metabolismo , Cardiomiopatia Hipertrófica/metabolismo , Miofibrilas/metabolismo , Miócitos Cardíacos/metabolismo , Cardiomegalia/metabolismo , Fatores de Transcrição/metabolismo , MamíferosRESUMO
We investigated the metal-substituted catalytic activity of human cysteamine dioxygenase (ADO), an enzyme pivotal in regulating thiol metabolism and contributing to oxygen homeostasis. Our findings demonstrate the catalytic competence of cobalt(II)- and nickel(II)-substituted ADO in cysteamine oxygenation. Notably, Co(II)-ADO exhibited superiority over Ni(II)-ADO despite remaining significantly less active than the natural enzyme. Structural analyses through X-ray crystallography and cobalt K-edge excitation confirmed successful metal substitution with minimal structural perturbations. This provided a robust structural basis, supporting a conserved catalytic mechanism tailored to distinct metal centers. This finding challenges the proposed high-valent ferryl-based mechanism for thiol dioxygenases, suggesting a non-high-valent catalytic pathway in the native enzyme. Further investigation of the cysteamine-bound or a peptide mimic of N-terminus RGS5 bound Co(II)-ADO binary complex revealed the metal center's high-spin (S = 3/2) state. Upon reaction with O2, a kinetically and spectroscopically detectable intermediate emerged with a ground spin state of S = 1/2. This intermediate exhibits a characteristic 59Co hyperfine splitting (A = 67 MHz) structure in the EPR spectrum alongside UV-vis features, consistent with known low-spin Co(III)-superoxo complexes. This observation, unique for protein-bound thiolate-ligated cobalt centers in a protein, unveils the capacities for O2 activation in such metal environments. These findings provide valuable insights into the non-heme iron-dependent thiol dioxygenase mechanistic landscape, furthering our understanding of thiol metabolism regulation. The exploration of metal-substituted ADO sheds light on the intricate interplay between metal and catalytic activity in this essential enzyme.
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Cobalto , Dioxigenases , Cobalto/química , Cobalto/metabolismo , Dioxigenases/metabolismo , Dioxigenases/química , Humanos , Oxigênio/química , Oxigênio/metabolismo , Cristalografia por Raios X , Modelos Moleculares , Complexos de Coordenação/química , Complexos de Coordenação/metabolismoRESUMO
Understanding the impact of non-coding sequence variants on complex diseases is an essential problem. We present a novel ensemble learning framework-CASAVA, to predict genomic loci in terms of disease category-specific risk. Using disease-associated variants identified by GWAS as training data, and diverse sequencing-based genomics and epigenomics profiles as features, CASAVA provides risk prediction of 24 major categories of diseases throughout the human genome. Our studies showed that CASAVA scores at a genomic locus provide a reasonable prediction of the disease-specific and disease category-specific risk prediction for non-coding variants located within the locus. Taking MHC2TA and immune system diseases as an example, we demonstrate the potential of CASAVA in revealing variant-disease associations. A website (http://zhanglabtools.org/CASAVA) has been built to facilitate easily access to CASAVA scores.
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Estudo de Associação Genômica Ampla , Polimorfismo de Nucleotídeo Único , Genoma Humano , Genômica , Humanos , Aprendizado de MáquinaRESUMO
Pasteurella multocida is a zoonotic pathogen causing serious diseases in humans and animals. Here, we report P. multocida from wildlife on China's Qinghai-Tibet plateau with a novel capsular serotype, forming a single branch on the core-genome phylogenetic tree: four strains isolated from dead Himalayan marmot (Marmota himalayana) and one genome assembled from metagenomic sequencing of a dead Woolly hare (Lepus oiostolus). Four of the strains were identified as subspecies multocida and one was septica. The mouse model showed that the challenge strain killed mice within 24 h at an infectious dose of less than 300 bacteria. The short disease course is comparable to septicemic plague: the host has died before more severe pathological changes could take place. Though pathological changes were relatively mild, cytokine storm was obvious with a significant rise of IL-12p70, IL-6, TNF-αand IL-10 (P < 0.05). Our findings suggested P. multocida is a lethal pathogen for wildlife on Qinghai-Tibet plateau, in addition to Yersinia pestis. Individuals residing within the M. himalayana plague focus are at risk for P. multocida infection, and public health warnings are necessitated.
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Pasteurella multocida , Peste , Animais , Humanos , Camundongos , Tibet , Marmota/microbiologia , Pasteurella multocida/genética , Filogenia , Sorogrupo , China , Peste/microbiologia , Animais SelvagensRESUMO
Surveillance for animal plague was conducted in the Marmota himalayana plague focus of the Qinghai-Tibet Plateau from 2020 to 2023. A 22.89% positive rate of serum F1 antibody was detected in live-caught marmots, alongside a 43.40% incidence of Yersinia pestis isolation from marmot carcasses. Marmot carcasses infected with plague exhibited a significantly higher spleen-somatic index (P < 0.05). Twenty-one Y. pestis-specific phages were isolated, among which one Y. pestis lytic phage (AKS2022HT87GU_phi) was isolated from the bone marrow of a marmot carcass (no. AKS2022HT87) and was found to be symbiotic with Y. pestis. Microscopy revealed the coexistence of lysed and non-lysed colonies of Y. pestis AKS2022HT87. Genome-wide analysis showed that certain strains of the Y. pestis AKS2022HT87 carried phage DNA fragments consistent with phage AKS2022HT87GU_phi. The rare symbiotic relationship between a lytic phage and Y. pestis observed in vitro was highlighted in this study, laying the basis for further exploring the relationship between Y. pestis and its bacteriophages.IMPORTANCEBacteriophages and host bacteria commonly coexist in vivo or in soil environments through complex and interdependent microbial interactions. However, recapitulating this symbiotic state remains challenging in vitro due to limited medium nutrients. In this work, the natural symbiosis between Yersinia pestis and specific phages has been discovered in a Marmota himalayana specimen. Epidemiological analysis presented the characteristics of the Y. pestis and specific phages in the area with a strong plague epidemic. Crucially, comparative genomics has been conducted to analyze the genetic changes in both the Y. pestis and phages over different periods, revealing the dynamic and evolving nature of their symbiosis. These are the critical steps to study the mechanism of the symbiosis.
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BACKGROUND: Fungal skin diseases are common skin diseases with a heterogeneous distribution worldwide. OBJECTIVES: This study aimed to analyse the spatiotemporal trends in the burden of fungal skin diseases at global, regional, and national levels from 1990 to 2021. METHODS: Based on the data obtained from the Global Burden of Disease Study (GBD) 2021, we described the incident cases, prevalent cases, number of disability-adjusted life years (DALYs), and corresponding age-standardised rates (ASRs) for fungal skin diseases in 1990 and 2021 by sex, age, socio-demographic index (SDI), 21 GBD regions, and 204 countries and territories. We used Joinpoint regression analysis to assess the temporal trends in burden of fungal skin diseases during 1990 to 2021. Spearman's rank test was used to analyse the relationship between disease burden and potential factors. RESULTS: From 1990 to 2021, the incident cases, prevalent cases, and DALYs for fungal skin diseases worldwide increased by 67.93%, 67.73%, and 66.77%, respectively. Globally, the age-standardised incidence rate (ASIR), age-standardised prevalence rate (ASPR), and age-standardised DALYs rate (ASDR) for fungal skin diseases in 2021 were 21668.40 per 100,000 population (95% UI: 19601.19-23729.17), 7789.55 per 100,000 population (95% UI: 7059.28-8583.54), and 43.39 per 100,000 population (95% UI: 17.79-89.10), respectively. Between 1990 and 2021, the ASIR, ASPR, and ASDR for fungal skin diseases have modestly increased, with AAPC of 11.71% (95% confidence interval [CI]: 11.03%-12.39%), 19.24% (95% CI: 18.12%-20.36%), and 20.25% (95% CI: 19.33%-21.18%), respectively. Males experienced a higher burden of fungal skin diseases than females. The incident cases, prevalent cases, and DALYs for fungal skin diseases were highest at the age of 5-9, while the ASRs were highest among the elderly. At national level, the highest ASRs were observed in Nigeria, Ethiopia, and Mali. Overall, SDI was negatively correlated with the ASRs, whereas Global Land-Ocean Temperature Index (GLOTI) was remarkably positively correlated with the burden of fungal skin diseases. CONCLUSIONS: Between 1990 and 2021, the global burden of fungal skin diseases has increased, causing a high disease burden worldwide, particularly in underdeveloped regions and among vulnerable population such as children and the elderly. With global warming and aging of the population, the burden of fungal skin diseases may continue to increase in the future. Targeted and specific measures should be taken to address these disparities and the ongoing burden of fungal skin diseases.
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Dermatomicoses , Carga Global da Doença , Saúde Global , Humanos , Masculino , Feminino , Adulto , Dermatomicoses/epidemiologia , Pessoa de Meia-Idade , Prevalência , Incidência , Adulto Jovem , Saúde Global/estatística & dados numéricos , Adolescente , Idoso , Anos de Vida Ajustados por Deficiência , Pré-Escolar , Criança , Lactente , Recém-Nascido , Idoso de 80 Anos ou mais , Efeitos Psicossociais da DoençaRESUMO
BACKGROUND: Pulmonary fibrosis (PF) is a progressive fibrosing interstitial pneumonia that leads to respiratory failure and other complications, which is ultimately fatal. Mesenchymal stem cells (MSCs) transplant is a promising strategy to solve this problem, while the procurement of MSCs from the patient for autotransplant remains a challenge. METHODS: Here, we presented olfactory mucosa mesenchymal stem cells (OM-MSCs) from mouse turbinate and determined the preventing efficacy of allotransplant for PF. We demonstrated the antiinflammation and immunomodulatory effects of OM-MSCs. Flow cytometric analysis was used to verify the effect of OM-MSCs on monocyte-derived macrophage populations in the lung. RESULTS: Administration of OM-MSCs reduces inflammation, attenuates the matrix metallopeptidase 13 (MMP13) expression level and restores the bleomycin (BLM)-induced pulmonary fibrosis by assessing the architecture of lung, collagen type I; (COL1A1), actin alpha 2, smooth muscle, aorta (ACTA2/α-SMA) and hydroxyproline. This therapeutic effect of OM-MSCs was related to the increase in the ratio of nonclassical monocytes to proinflammatory monocytes in the lung. CONCLUSIONS: This study suggests that transplant of OM-MSCs represents an effective and safe treatment for PF.
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Células-Tronco Mesenquimais , Fibrose Pulmonar , Humanos , Camundongos , Animais , Fibrose Pulmonar/induzido quimicamente , Fibrose Pulmonar/terapia , Fibrose Pulmonar/metabolismo , Inflamação/metabolismo , Células-Tronco Mesenquimais/metabolismo , Imunomodulação , Mucosa Olfatória/metabolismoRESUMO
STUDY DESIGN: Animal studies OBJECTIVES: To evaluate the therapeutic effect of olfactory mucosa mesenchymal stem cell (OM-MSCs) transplantation in mice with spinal cord injury (SCI) and to explore the mechanism by which OM-MSCs inhibit neuroinflammation and improve SCI. SETTING: Xiangya Hospital, Central South University; Affiliated Hospital of Guangdong Medical University. METHODS: Mice (C57BL/6, female, 6-week-old) were randomly divided into sham, SCI, and SCI + OM-MSC groups. The SCI mouse model was generated using Allen's method. OM-MSCs were immediately delivered to the lateral ventricle after SCI using stereotaxic brain injections. One day prior to injury and on days 1, 5, 7, 14, 21, and 28 post-injury, the Basso Mouse Scale and Rivlin inclined plate tests were performed. Inflammation and microglial polarization were evaluated using histological staining, immunofluorescence, and qRT-PCR. RESULTS: OM-MSCs originating from the neuroectoderm have great potential in the management of SCI owing to their immunomodulatory effects. OM-MSCs administration improved motor function, alleviated inflammation, promoted the transformation of the M1 phenotype of microglia into the M2 phenotype, facilitated axonal regeneration, and relieved spinal cord injury in SCI mice. CONCLUSIONS: OM-MSCs reduced the level of inflammation in the spinal cord tissue, protected neurons, and repaired spinal cord injury by regulating the M1/M2 polarization of microglia.
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Transplante de Células-Tronco Mesenquimais , Camundongos Endogâmicos C57BL , Microglia , Mucosa Olfatória , Traumatismos da Medula Espinal , Animais , Traumatismos da Medula Espinal/terapia , Traumatismos da Medula Espinal/patologia , Transplante de Células-Tronco Mesenquimais/métodos , Mucosa Olfatória/citologia , Microglia/fisiologia , Camundongos , Feminino , Modelos Animais de Doenças , Células-Tronco Mesenquimais/fisiologia , Recuperação de Função Fisiológica/fisiologia , Polaridade Celular/fisiologiaRESUMO
The current concept of facial unit reconstruction has evolved from simple coverage of defects to the reconstruction of the 3-dimensional structure and delicate features. The reshaping of the middle third of the face, including the nose and cheek, remains a challenge for plastic surgeons due to its complex structure and the dynamic relationship between each part. In this article, the authors describe a clinical report of extensive facial burns with skin lesions in the middle third of the face. The 30-year-old female patient sustained burns throughout the full thickness of the skin burns on the entire nose and left cheek with hypertrophic scar. The authors performed an expanded cervical-facial flap and tube flap of the upper extremity to reconstruct the entire nasal and cheek region. The patient underwent 8 stages of the operation successively resulting in a satisfactory level of appearance and function.
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Queimaduras , Procedimentos de Cirurgia Plástica , Feminino , Humanos , Adulto , Retalhos Cirúrgicos/cirurgia , Transplante de Pele/métodos , Nariz/cirurgia , Queimaduras/complicações , Queimaduras/cirurgiaRESUMO
Thyroid cancer is a highly differentiated and poorly malignant tumor. Interfering with glycolysis has become an effective means of controlling cancer progression and autophagy is negatively correlated with glycolysis. Aldo-keto reductase family 1 member C3 (AKR1C3) has been demonstrated to be highly expressed in thyroid cancer tissue and the higher AKR1C3 expression predicted the worse prognosis. We aimed to explore whether AKR1C3 could affect thyroid cancer progression by regulating autophagy-dependent glycolysis. AKR1C3 expression in thyroid cancer cells was detected by western blot. Then, AKR1C3 was knocked down by transfection with short hairpin RNA specific to AKR1C3 in the absence or presence of 3-methyladenine (3-MA) or PMA treatment. Cell cycle and apoptosis was detected by flow cytometry. Immunofluorescence staining was used to analyze LC3B expression. Extracellular acidification, glucose uptake and lactic acid secretion were detected. To evaluate the tumorigenicity of AKR1C3 insufficiency on thyroid cancer in vivo, TPC-1 cells with AKR1C3 knockdown were injected subcutaneously into nude mice. Then, cyclinD1 and Ki67 expression in tumorous tissues was measured by immunohistochemical analysis. Apoptosis was assessed by terminal-deoxynucleoitidyl transferase mediated nick end labeling staining. Additionally, the expression of proteins related to cell cycle, apoptosis, glycolysis, autophagy, and extracellular signal-regulated kinase (ERK) signaling in cells and tumor tissues was assessed by western blot. Highly expressed AKR1C3 was observed in thyroid cancer cells. AKR1C3 knockdown induced cell cycle arrest and apoptosis of TPC-1 cells. Besides, autophagy was activated and glycolysis was inhibited following AKR1C3 silencing, and 3-MA treatment restored the impacts of AKR1C3 silencing on glycolysis. The further experiments revealed that AKR1C3 insufficiency inhibited ERK signaling and PMA application reversed AKR1C3 silencing-induced autophagy in TPC-1 cells. The in vivo results suggested that AKR1C3 knockdown inhibited the development of subcutaneous TPC-1 tumors in nude mice and inactivated the ERK signaling. Collectively, AKR1C3 silencing inhibited autophagy-dependent glycolysis in thyroid cancer by inactivating ERK signaling.
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MAP Quinases Reguladas por Sinal Extracelular , Neoplasias da Glândula Tireoide , Animais , Camundongos , Membro C3 da Família 1 de alfa-Ceto Redutase , Autofagia , Glicólise , Camundongos Nus , Neoplasias da Glândula Tireoide/genética , HumanosRESUMO
COVID-19 continues to spread around the world. This is mainly because new variants of the SARS-CoV-2 virus emerge due to genomic mutations, evade the immune system and result in the effectiveness of current therapeutics being reduced. We previously established a series of detection platforms, comprising computational docking analysis, S-protein-based ELISA, pseudovirus entry, and 3CL protease activity assays, which allow us to screen a large library of phytochemicals from natural products and to determine their potential in blocking the entry of SARS-CoV-2. In this new screen, rutaecarpine (an alkaloid from Evodia rutaecarpa) was identified as exhibiting anti-SARS-CoV-2 activity. Therefore, we conducted multiple rounds of structure-activity-relationship (SAR) studies around this phytochemical and generated several rutaecarpine analogs that were subjected to in vitro evaluations. Among these derivatives, RU-75 and RU-184 displayed remarkable inhibitory activity when tested in the 3CL protease assay, S-protein-based ELISA, and pseudovirus entry assay (for both wild-type and omicron variants), and they attenuated the inflammatory response induced by SARS-CoV-2. Interestingly, RU-75 and RU-184 both appeared to be more potent than rutaecarpine itself, and this suggests that they might be considered as lead candidates for future pharmacological elaboration.
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Antivirais , Desenho de Fármacos , Alcaloides Indólicos , Simulação de Acoplamento Molecular , Quinazolinas , SARS-CoV-2 , Alcaloides Indólicos/farmacologia , Alcaloides Indólicos/química , SARS-CoV-2/efeitos dos fármacos , Quinazolinas/farmacologia , Quinazolinas/química , Humanos , Antivirais/farmacologia , Antivirais/química , Relação Estrutura-Atividade , Tratamento Farmacológico da COVID-19 , Proteases 3C de Coronavírus/antagonistas & inibidores , Proteases 3C de Coronavírus/metabolismo , Proteases 3C de Coronavírus/química , Internalização do Vírus/efeitos dos fármacos , QuinazolinonasRESUMO
BACKGROUND: Malnutrition is prevalent among elderly cancer patients. This study aims to develop a predictive model for malnutrition in hospitalized elderly cancer patients. METHODS: Data from January 2022 to January 2023 on cancer patients aged 60+ were collected, involving 22 variables. Key variables were identified using the LASSO (Least Absolute Shrinkage and Selection Operator) method, and nine machine learning models were tested. SHAP was used to interpret the XGBoost model. Malnutrition prevalence was assessed. RESULTS: Among 450 participants, 46.4 % were malnourished. Key predictors identified were ADL (Activities of Daily Living), ALB (Albumin), BMI (Body Mass Index) and age. XGBoost had the highest AUC of 0.945, accuracy of 0.872, and sensitivity of 0.968. Higher ADL and age increased malnutrition risk, while lower ALB and BMI reduced it. CONCLUSIONS: The XGBoost model is highly effective in detecting malnutrition in elderly cancer patients, enabling early and rapid nutritional assessments.
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Hospitalização , Aprendizado de Máquina , Desnutrição , Neoplasias , Avaliação Nutricional , Humanos , Desnutrição/diagnóstico , Desnutrição/epidemiologia , Neoplasias/complicações , Idoso , Masculino , Feminino , Índice de Massa Corporal , Atividades Cotidianas , Avaliação Geriátrica/métodos , Prevalência , Idoso de 80 Anos ou maisRESUMO
n-propanol is an important pharmaceutical and pesticide intermediate. To produce n-propanol by electrochemical reduction of CO2 is a promising way, but is largely restricted by the very low selectivity and activity. How to promote the coupling of *C1 and *C2 intermediates to form the *C3 intermediate for n-propanol formation is challenging. Here, we propose the construction of bicontinuous structure of Cu2O/Cu electrocatalyst, which consists of ultra-small Cu2O nanodomains, Cu nanodomains and large amounts of grain boundaries between Cu2O and Cu nanodomains. The n-propanol current density is as high as 101.6â mA cm-2 at the applied potential of -1.1â V vs. reversible hydrogen electrode in flow cell, with the Faradaic efficiency up to 12.1 %. Moreover, the catalyst keeps relatively stable during electrochemical CO2 reduction process. Experimental studies and theoretical calculations reveal that the bicontinuous structure of Cu2O/Cu can facilitate the *CO formation, *CO-*CO coupling and *CO-*OCCO coupling for the final generation of n-propanol.
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MOTIVATION: Gene regulatory networks (GRNs) arise from the intricate interactions between transcription factors (TFs) and their target genes during the growth and development of organisms. The inference of GRNs can unveil the underlying gene interactions in living systems and facilitate the investigation of the relationship between gene expression patterns and phenotypic traits. Although several machine-learning models have been proposed for inferring GRNs from single-cell RNA sequencing (scRNA-seq) data, some of these models, such as Boolean and tree-based networks, suffer from sensitivity to noise and may encounter difficulties in handling the high noise and dimensionality of actual scRNA-seq data, as well as the sparse nature of gene regulation relationships. Thus, inferring large-scale information from GRNs remains a formidable challenge. RESULTS: This study proposes a multilevel, multi-structure framework called a pseudo-Siamese GRN (PSGRN) for inferring large-scale GRNs from time-series expression datasets. Based on the pseudo-Siamese network, we applied a gated recurrent unit to capture the time features of each TF and target matrix and learn the spatial features of the matrices after merging by applying the DenseNet framework. Finally, we applied a sigmoid function to evaluate interactions. We constructed two maize sub-datasets, including gene expression levels and GRNs, using existing open-source maize multi-omics data and compared them to other GRN inference methods, including GENIE3, GRNBoost2, nonlinear ordinary differential equations, CNNC, and DGRNS. Our results show that PSGRN outperforms state-of-the-art methods. This study proposed a new framework: a PSGRN that allows GRNs to be inferred from scRNA-seq data, elucidating the temporal and spatial features of TFs and their target genes. The results show the model's robustness and generalization, laying a theoretical foundation for maize genotype-phenotype associations with implications for breeding work.
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Redes Reguladoras de Genes , Melhoramento Vegetal , Regulação da Expressão Gênica , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , AlgoritmosRESUMO
Selective oxidation of benzylic C-H to benzylic alcohols is a well-known challenge in the chemical community since benzylic C-H is more prone to be overoxidized to benzylic ketones. In this work, we report the highly selective electro-oxidation of benzylic C-H to benzylic alcohols in an undivided cell in ionic liquid-based solution. As an example, the selectivity toward xanthydrol could be as high as 95.7% at complete conversion of xanthene, a typical benzylic C-H compound, on gram-scale in imidazolium bromide/H2O/DMF. Mechanism investigation reveals that the imidazolium radical generated in situ participants in a proton-coupled electron transfer process and low-barrier hydrogen bonds stabilize the reaction intermediates, together steering the redox equilibrium, favoring benzylic alcohols over benzylic ketones.
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BACKGROUND AND AIMS: Globally, NAFLD is one of the most common liver disorders, with an estimated prevalence rate of more than 30% in men and 15% in women and an even higher prevalence in people with type 2 diabetes mellitus. Optimal pharmacologic therapeutic approaches for NAFLD are an urgent necessity. APPROACH AND RESULTS: In this study, we showed that compared with healthy controls, hepatic ACSL4 levels in patients with NAFLD were found to be elevated. Suppression of ACSL4 expression promoted mitochondrial respiration, thereby enhancing the capacity of hepatocytes to mediate ß-oxidation of fatty acids and to minimize lipid accumulation by up-regulating peroxisome proliferator-activated receptor coactivator-1 alpha. Moreover, we found that abemaciclib is a potent and selective ACSL4 inhibitor, and low dose of abemaciclib significantly ameliorated most of the NAFLD symptoms in multiple NAFLD mice models. CONCLUSIONS: Therefore, inhibition of ACSL4 is a potential alternative therapeutic approach for NAFLD.
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Aminopiridinas/uso terapêutico , Benzimidazóis/uso terapêutico , Coenzima A Ligases/antagonistas & inibidores , Hepatopatia Gordurosa não Alcoólica/tratamento farmacológico , Aminopiridinas/farmacologia , Animais , Benzimidazóis/farmacologia , Biópsia , Coenzima A Ligases/análise , Coenzima A Ligases/metabolismo , Dieta Hiperlipídica/efeitos adversos , Modelos Animais de Doenças , Ácidos Graxos/metabolismo , Técnicas de Silenciamento de Genes , Células Hep G2 , Humanos , Fígado/efeitos dos fármacos , Fígado/enzimologia , Fígado/patologia , Camundongos , Camundongos Knockout , Hepatopatia Gordurosa não Alcoólica/etiologia , Hepatopatia Gordurosa não Alcoólica/patologia , Oxirredução/efeitos dos fármacosRESUMO
BACKGROUND: The aetiologies of large-to-giant congenital melanocytic naevi (LGCMN) remain ambiguous. A previous study discovered signatures associated with deficient mismatch repair (dMMR) in patients with LGCMN. However, a screening diagnostic immunohistochemistry (IHC) panel of dMMR in patients with LGCMN has not been performed to date. OBJECTIVES: To identify the MMR status and aetiologies of LGCMN. METHODS: A total of 110 patients with CMN, including 30 giant CMN, 30 large CMN, 30 medium CMN and 20 small CMN, underwent diagnostic IHC (for MSH6, MSH2, PMS2 and MLH1) screening of dMMR. The control group comprised normal skin samples from 20 healthy people. MMR proteins with little effect (MSH3 and PMS1) on the MMR system were stained in all samples. The surgical procedures conducted on each patient were noted because they might alter the behaviour of CMN and confound the results. Binary logistic regression analyses were performed between the phenotypic data and MMR status to identify associations. Whole-exome sequencing was performed on the main naevi, satellite naevi and normal skin tissues of four patients to detect variants. Mutational signature analyses were conducted to explore the aetiologies of LGCMN. RESULTS: dMMR was detected in 37% (11 of 30) of giant, 23% (7 of 30) of large and 7% (2 of 30) of medium CMNs, but were not identified in small CMNs or normal skin tissues. Moreover, multiple LGCMNs had a much higher dMMR rate than did single LGCMNs. The regression analyses showed that MMR status was significantly associated with CMN size and the presence of satellites, but was not correlated with age, sex, location, satellite diversity or tissue expansion. Notably, the pattern of protein loss in LGCMN mainly consisted of PMS2 loss. Mutational signature analyses detected dMMR-related signatures in patients with LGCMN. Additionally, rare deleterious germline mutations in DNA repair genes were detected in LGCMN, mainly in MSH6, ATM, RAD50, BRCA1 and ERCC8. These germline mutations were single-patient variants with unknown significance. CONCLUSIONS: dMMR is one of the aetiologies underlying LGCMN, particularly in patients with giant main lesions and multiple satellite lesions. Further studies are necessary to investigate the role of the DNA repair system, particularly MMR, in LGCMN.
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Nevo Pigmentado , Neoplasias Cutâneas , Humanos , Reparo de Erro de Pareamento de DNA , Endonuclease PMS2 de Reparo de Erro de Pareamento/genética , Endonuclease PMS2 de Reparo de Erro de Pareamento/metabolismo , Proteínas de Ligação a DNA/genética , Fatores de Transcrição/genética , Enzimas Reparadoras do DNA/genética , Enzimas Reparadoras do DNA/metabolismoRESUMO
Blue phase liquid crystals (BPLCs) have significant potential in the field of liquid crystal displays (LCDs) and are proposed as potential next-generation of LCDs candidates. However, BPLCs do not emit light directly and need an extra backlight device. As a result, the blue phase liquid crystal display retains the disadvantages of low brightness and low energy efficiency, which remarkably limit its application. Recently, as a kind of novel fluorescent carbon nanomaterials, carbon dots (CDs) have captured considerable attention because of their excellent optical properties. Here, CDs were directly synthesized by a simple solvothermal method and introduced into BPLCs. By combining the excellent optical properties of CDs with the blue phase liquid crystal system, the photoluminescent blue phase liquid crystals (CDs-BPLCs) with self-photoluminescence are prepared. Meanwhile, the stability of BPLCs can be improved by CDs. Such CDs-BPLCs have enormous potential in the development of novel energy-saving display devices.
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BACKGROUND: The objective of the present study was to investigate whether associations exist between inflammatory biomarkers and all-cause mortality and cardiovascular disease (CVD) mortality in women with postmenopausal osteoporosis (PMOP) or osteopenia. METHODS: In this retrospective cohort study, data were obtained from the National Health and Nutrition Examination Survey database from the years 2007 to 2010, 2013 to 2014, and 2017 to 2018. The inflammatory biomarkers including neutrophil/lymphocyte ratio (NLR), platelet/lymphocyte ratio (PLR), monocyte/lymphocyte ratio (MLR), neutrophil × platelet/lymphocyte (SII), neutrophil × monocyte/lymphocyte (SIRI), and neutrophil × monocyte × platelet/lymphocyte ratio (AISI) were calculated. RESULTS: A total of 2,834 women were included, with a median survival of 113.51 (3.15) months. During follow-up, 602 women died of all-cause mortality and 185 women died of CVD. NLR, MLR, SIRI, and AISI were significantly associated with all-cause mortality in postmenopausal women with osteoporosis or osteopenia. NLR, MLR, SIRI, and AISI were related to CVD mortality in postmenopausal women with osteoporosis or osteopenia (All P < 0.05). Based on the results of the subgroup analysis, AISI, SIRI, and MLR were associated with all-cause mortality and CVD mortality in postmenopausal women with PMOP or osteopenia who had a history of CVD and diabetes. AISI, SII, MLR, and NLR were associated with all-cause mortality and CVD mortality in PMOP or osteopenia women with a body mass index (BMI) > 25 kg/m2. PLR was associated with all-cause mortality in PMOP or osteopenia women aged ≥ 65 years. CONCLUSION: Inflammatory biomarkers were correlated with mortality risk in the PMOP or osteopenia population. This finding may be helpful for the prognosis management of PMOP or osteopenia in postmenopausal women.