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1.
World J Hepatol ; 16(3): 477-489, 2024 Mar 27.
Artigo em Inglês | MEDLINE | ID: mdl-38577540

RESUMO

BACKGROUND: The neutrophil-to-lymphocyte ratio (NLR) is commonly utilized as a prognostic indicator in end-stage liver disease (ESLD), encompassing conditions like liver failure and decompensated cirrhosis. Nevertheless, some studies have contested the prognostic value of NLR in ESLD. AIM: To investigate the ability of NLR to predict ESLD. METHODS: Databases, such as Embase, PubMed, Web of Science, Cochrane Library, China National Knowledge Infrastructure, Weipu, and Wanfang, were comprehensively searched to identify studies published before October 2022 assessing the prognostic ability of NLR to predict mortality in patients with ESLD. Effect sizes were calculated using comprehensive meta-analysis software and SATAT 15.1. RESULTS: A total of thirty studies involving patients with end-stage liver disease (ESLD) were included in the evaluation. Among the pooled results of eight studies, it was observed that the Neutrophil-to-Lymphocyte Ratio (NLR) was significantly higher in non-survivors compared to survivors (random-effects model: standardized mean difference = 1.02, 95% confidence interval = 0.67-1.37). Additionally, twenty-seven studies examined the associations between NLR and mortality in ESLD patients, reporting either hazard ratios (HR) or odds ratios (OR). The combined findings indicated a link between NLR and ESLD mortality (random-effects model; univariate HR = 1.07, 95%CI = 1.05-1.09; multivariate HR = 1.07, 95%CI = 1.07-1.09; univariate OR = 1.29, 95%CI = 1.18-1.39; multivariate OR = 1.29, 95%CI = 1.09-1.49). Furthermore, subgroup and meta-regression analyses revealed regional variations in the impact of NLR on ESLD mortality, with Asian studies demonstrating a more pronounced effect. CONCLUSION: Increased NLR in patients with ESLD is associated with a higher risk of mortality, particularly in Asian patients. NLR is a useful prognostic biomarker in patients with ESLD.

2.
Int J Clin Pharm ; 2024 Apr 03.
Artigo em Inglês | MEDLINE | ID: mdl-38570474

RESUMO

BACKGROUND: An increasing number of systematic reviews (SRs) have evaluated the diagnostic values of next-generation sequencing (NGS) in infectious diseases (IDs). AIM: This umbrella analysis aimed to assess the potential risk of bias in existing SRs and to summarize the published diagnostic values of NGS in different IDs. METHOD: We searched PubMed, Embase, and the Cochrane Library until September 2023 for SRs assessing the diagnostic validity of NGS for IDs. Two investigators independently determined review eligibility, extracted data, and evaluated reporting quality, risk of bias, methodological quality, and evidence certainty in the included SRs. RESULTS: Eleven SRs were analyzed. Most SRs exhibited a moderate level of reporting quality, while a serious risk of bias was observed in all SRs. The diagnostic performance of NGS in detecting pneumocystis pneumonia and periprosthetic/prosthetic joint infection was notably robust, showing excellent sensitivity (pneumocystis pneumonia: 0.96, 95% CI 0.90-0.99, very low certainty; periprosthetic/prosthetic joint infection: 0.93, 95% CI 0.83-0.97, very low certainty) and specificity (pneumocystis pneumonia: 0.96, 95% CI 0.92-0.98, very low certainty; periprosthetic/prosthetic joint infection: 0.95, 95% CI 0.92-0.97, very low certainty). NGS exhibited high specificity for central nervous system infection, bacterial meningoencephalitis, and tuberculous meningitis. The sensitivity to these infectious diseases was moderate. NGS demonstrated moderate sensitivity and specificity for multiple infections and pulmonary infections. CONCLUSION: This umbrella analysis indicates that NGS is a promising technique for diagnosing pneumocystis pneumonia and periprosthetic/prosthetic joint infection with excellent sensitivity and specificity. More high-quality original research and SRs are needed to verify the current findings.

3.
Adv Sci (Weinh) ; : e2308438, 2024 Apr 06.
Artigo em Inglês | MEDLINE | ID: mdl-38582099

RESUMO

Intratumor heterogeneity (ITH) of bladder cancer (BLCA) contributes to therapy resistance and immune evasion affecting clinical prognosis. The molecular and cellular mechanisms contributing to BLCA ITH generation remain elusive. It is found that a TM4SF1-positive cancer subpopulation (TPCS) can generate ITH in BLCA, evidenced by integrative single cell atlas analysis. Extensive profiling of the epigenome and transcriptome of all stages of BLCA revealed their evolutionary trajectories. Distinct ancestor cells gave rise to low-grade noninvasive and high-grade invasive BLCA. Epigenome reprograming led to transcriptional heterogeneity in BLCA. During early oncogenesis, epithelial-to-mesenchymal transition generated TPCS. TPCS has stem-cell-like properties and exhibited transcriptional plasticity, priming the development of transcriptionally heterogeneous descendent cell lineages. Moreover, TPCS prevalence in tumor is associated with advanced stage cancer and poor prognosis. The results of this study suggested that bladder cancer interacts with its environment by acquiring a stem cell-like epigenomic landscape, which might generate ITH without additional genetic diversification.

4.
BMC Genom Data ; 25(1): 24, 2024 Mar 04.
Artigo em Inglês | MEDLINE | ID: mdl-38438998

RESUMO

OBJECTIVES: Brasenia is a monotypic genus in the family of Cabombaceae. The only species, B. schreberi, is a macrophyte distributed worldwide. Because it requires good water quality, it is endangered in China and other countries due to the deterioration of aquatic habitats. The young leaves and stems of B. schreberi are covered by thick mucilage, which has high medical value. As an allelopathic aquatic plant, it can also be used in the management of aquatic weeds. Here, we present its assembled and annotated genome to help shed light on medial and allelopathic substrates and facilitate their conservation. DATA DESCRIPTION: Genomic DNA and RNA extracted from B. schreberi leaf tissues were used for whole genome and RNA sequencing using a Nanopore and/or MGI sequencer. The assembly was 1,055,148,839 bp in length, with 92 contigs and an N50 of 22,379,495 bp. The repetitive elements in the assembly were 555,442,205 bp. A completeness assessment of the assembly with BUSCO and compleasm indicated 88.4 and 90.9% completeness in the Eudicots database and 95.4 and 96.6% completeness in the Embryphyta database. Gene annotation revealed 67,747 genes that coded for 73,344 proteins.


Assuntos
Plantas Daninhas , Sementes , Alelopatia , China , Bases de Dados Factuais
5.
Front Pharmacol ; 15: 1162883, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38549665

RESUMO

Background: In clinical practice, antibiotics and/or inhaled or oral hormone preparations are the first line of treatment for chronic pharyngitis. However, this therapeutic regimen is not satisfactory enough. At present, medicinal plants as dietary supplements or functional foods are widely recognized for the treatment and prevention of different diseases. Purpose: This study aimed to evaluate the efficacy of the botanical lozenge made from several medicinal plant extracts in the treatment of chronic pharyngitis and its effects on patients' illness perception and adherence to treatment. Methods: Patients with chronic pharyngitis were randomly assigned to the experimental group (n = 52) or the control group (n = 51). Patients were given botanical lozenges prepared from the extracts of medicinal plants such as Siraitia grosvenorii (Swingle) C. Jeffrey ex A.M.Lu and Zhi Y. Zhang [Cucurbitaceae; Siraitiae fructus], Lonicera japonica Thunb [Caprifoliaceae; Lonicerae japonicae flos], Platycodon grandiflorus (Jacq.) A. DC [Campanulaceae; Platycodon radix], and Glycyrrhiza uralensis Fisch. ex DC [Fabaceae; Glycyrrhizae radix et rhizoma] or placebos made of starch for 15 days. The improvement of pharyngeal symptoms and signs, illness perception, and adherence to treatment were evaluated at the end of the intervention. Results: The total score of pharyngeal symptoms of patients in the experimental group (3.33 ± 2.33) was significantly lower than that in the control group (5.20 ± 2.93) (p < 0.01). In comparison to the control group (3.43 ± 1.43), the total pharyngeal signs score of patients in the experimental group (2.69 ± 1.59) was considerably lower (p < 0.01). The improvement rates of pharyngeal itching, dry throat, pharyngeal foreign body sensation, aggravation due to excessive speaking, and congestion of pharyngeal mucosa in the experimental group were 73.81%, 67.50%, 67.57%, 65.22% and 44%, respectively, which were significantly higher than those in the control group (p < 0.05). In addition, patients taking botanical lozenges had better illness perception and adherence to treatment than those taking placebos (p < 0.05). Patients with low adherence to treatment showed less personal control, concerns, and understanding of chronic pharyngitis (p < 0.05). Conclusion: Botanical lozenges not only aided patients in recovering from chronic pharyngitis but also improved their positive perceptions of the disease, which helped them adhere to their treatment regimen. Clinical Trial Registration: [https://www.chictr.org.cn/], identifier [ChiCTR2200062139].

6.
J Zhejiang Univ Sci B ; 25(3): 197-211, 2024 Mar 15.
Artigo em Inglês, Chinês | MEDLINE | ID: mdl-38453635

RESUMO

Osteoarthritis (OA), characterized by cartilage degeneration, synovial inflammation, and subchondral bone remodeling, is among the most common musculoskeletal disorders globally in people over 60 years of age. The initiation and progression of OA involves the abnormal metabolism of chondrocytes as an important pathogenic process. Cartilage degeneration features mitochondrial dysfunction as one of the important causative factors of abnormal chondrocyte metabolism. Therefore, maintaining mitochondrial homeostasis is an important strategy to mitigate OA. Mitophagy is a vital process for autophagosomes to target, engulf, and remove damaged and dysfunctional mitochondria, thereby maintaining mitochondrial homeostasis. Cumulative studies have revealed a strong association between mitophagy and OA, suggesting that the regulation of mitophagy may be a novel therapeutic direction for OA. By reviewing the literature on mitophagy and OA published in recent years, this paper elaborates the potential mechanism of mitophagy regulating OA, thus providing a theoretical basis for studies related to mitophagy to develop new treatment options for OA.


Assuntos
Cartilagem Articular , Osteoartrite , Humanos , Pessoa de Meia-Idade , Idoso , Mitofagia , Inflamação/metabolismo , Condrócitos , Cartilagem Articular/metabolismo , Cartilagem Articular/patologia
7.
J Zhejiang Univ Sci B ; 25(3): 212-232, 2024 Mar 15.
Artigo em Inglês, Chinês | MEDLINE | ID: mdl-38453636

RESUMO

The endoplasmic reticulum is a key site for protein production and quality control. More than one-third of proteins are synthesized and folded into the correct three-dimensional conformation in the endoplasmic reticulum. However, during protein folding, unfolded and/or misfolded proteins are prone to occur, which may lead to endoplasmic reticulum stress. Organisms can monitor the quality of the proteins produced by endoplasmic reticulum quality control (ERQC) and endoplasmic reticulum-associated degradation (ERAD), which maintain endoplasmic reticulum protein homeostasis by degrading abnormally folded proteins. The underlying mechanisms of protein folding and ERAD in mammals have not yet been fully explored. Therefore, this paper reviews the process and function of protein folding and ERAD in mammalian cells, in order to help clinicians better understand the mechanism of ERAD and to provide a scientific reference for the treatment of diseases caused by abnormal ERAD.


Assuntos
Degradação Associada com o Retículo Endoplasmático , Dobramento de Proteína , Animais , Proteínas , Estresse do Retículo Endoplasmático , Mamíferos/metabolismo
8.
Planta ; 259(4): 83, 2024 Mar 05.
Artigo em Inglês | MEDLINE | ID: mdl-38441675

RESUMO

MAIN CONCLUSION: WOX family gene WOX2 is highly expressed during seed development, which functions redundantly with WOX1 and WOX4 to positively regulate seed germination. WOX (WUSCHEL-related homeobox) is a family of transcription factors in plants. They play essential roles in the regulation of plant growth and development, but their function in seed germination is not well understood. In this report, we show that WOX1, WOX2, and WOX4 are close homologues in Arabidopsis. WOX2 has a redundant function with WOX1 and WOX4, respectively, in seed germination. WOX2 is highly expressed during seed development, from the globular embryonic stage to mature dry seeds, and its expression is decreased after germination. Loss of function single mutant wox2, and double mutants wox1 wox2 and wox2 wox4-1 show decreased germination speed. WOX2 and WOX4 are essential for hypocotyl-radicle zone elongation during germination, potentially by promoting the expression of cell wall-related genes. We also found that WOX2 and WOX4 regulate germination through the gibberellin (GA) pathway. These results suggest that WOX2 and WOX4 integrate the GA pathway and downstream cell wall-related genes during germination.


Assuntos
Proteínas de Arabidopsis , Arabidopsis , Arabidopsis/genética , Proteínas de Arabidopsis/genética , Parede Celular , Germinação/genética , Giberelinas , Proteínas de Homeodomínio/genética , Sementes/genética
9.
Biochim Biophys Acta Mol Basis Dis ; 1870(5): 167137, 2024 Mar 23.
Artigo em Inglês | MEDLINE | ID: mdl-38527593

RESUMO

BACKGROUND: Postoperative Cognitive Dysfunction (POCD) has attracted increased attention, but its precise mechanism remains to be explored. This study aimed to figure out whether HDAC6 could regulate NLRP3-induced pyroptosis by modulating the functions of HSP70 and HSP90 in microglia to participate in postoperative cognitive dysfunction in aged mice. METHODS: Animal models of postoperative cognitive dysfunction in aged mice were established by splenectomy under sevoflurane anesthesia. Morris water maze was used to examine the cognitive function and motor ability. Sixteen-months-old C57BL/6 male mice were randomly divided into six groups: control group (C group), sham surgery group (SA group), splenectomy group (S group), splenectomy + HDAC6 inhibitor ACY-1215 group (ACY group), splenectomy + HDAC6 inhibitor ACY-1215 + HSP70 inhibitor Apoptozole group (AP group), splenectomy + solvent control group (SC group). The serum and hippocampus of mice were taken after mice were executed. The protein levels of HDAC6, HSP90, HSP70, NLRP3, GSDMD-N, cleaved-Caspase-1 (P20), IL-1ß were detected by western blotting. Serum IL-1ß, IL-6 and S100ß were measured using ELISA assay, and cell localization of HDAC6 was detected by immunofluorescence. In vitro experiments, BV2 cells were used to validate whether this mechanism worked in microglia. The protein levels of HDAC6, HSP90, HSP70, NLRP3, GSDMD-N, P20, IL-1ß were detected by western blotting and the content of IL-1ß in the supernatant was measured using ELISA assay. The degree of acetylation of HSP90, the interaction of HSP70, HSP90 and NLRP3 were analyzed by coimmunoprecipitation assay. RESULTS: Splenectomy under sevoflurane anesthesia in aged mice could prolong the escape latency, reduce the number of crossing platforms, increase the expression of HDAC6 and activate the NLRP3 inflammasome to induce pyroptosis in hippocampus microglia. Using ACY-1215 could reduce the activation of NLRP3 inflammasome, the pyroptosis of microglia and the degree of spatial memory impairment. Apoptozole could inhibit the binding of HSP70 to NLRP3, reduce the degradation of NLRP3 and reverse the protective effect of HDAC6 inhibitors. The results acquired in vitro experiments closely resembled those in vivo, LPS stimulation led to the pyroptosis of BV2 microglia cells and the release of IL-1ß due to the activation of the NLRP3 inflammasome, ACY-1215 showed the anti-inflammatory effect and Apoptozole exerted the opposite effect. CONCLUSIONS: Our findings suggest that hippocampal HDAC6 promotes POCD by regulating NLRP3-induced microglia pyroptosis via HSP90/HSP70 in aged mice.

10.
Cell Oncol (Dordr) ; 2024 Mar 27.
Artigo em Inglês | MEDLINE | ID: mdl-38536650

RESUMO

OBJECTIVES: Previously, Interferon-induced Protein with Tetratricopeptide Repeats 1 (IFIT1) has been shown to promote cancer development. Here, we aimed to explore the role of IFIT1 in the development and progression of pancreatic cancer, including the underlying mechanisms. METHODS: We explored IFIT1 expression in pancreatic cancer samples using The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets. Cell Counting Kit-8 (CCK8), colony formation, scratch wound-healing and Transwell assays were performed to assess the proliferation, migration and invasion abilities of pancreatic cancer cells. Gene Set Enrichment Analysis (GSEA) and Western blotting were performed to assess the regulatory effect of IFIT1 on the Wnt/ß-catenin pathway. RESULTS: We found that upregulation of IFIT1 expression is common in pancreatic cancer and is negatively associated with overall patient survival. Knockdown of IFIT1 expression led to decreased proliferation, migration and invasion of pancreatic cancer cells. We also found that IFIT1 could regulate Wnt/ß-catenin signaling, and that a Wnt/ß-catenin agonist could reverse this effect. In addition, we found that IFIT1 can promote epithelial-mesenchymal transition (EMT) of pancreatic cancer cells. CONCLUSIONS: Our data indicate that IFIT1 increases pancreatic cancer cell proliferation, migration and invasion by activating the Wnt/ß-catenin pathway. In addition, we found that EMT could be regulated by IFIT1. IFIT1 may serve as a potential therapeutic target for pancreatic cancer.

11.
BMC Med Res Methodol ; 24(1): 65, 2024 Mar 11.
Artigo em Inglês | MEDLINE | ID: mdl-38468223

RESUMO

BACKGROUND: The Core Outcome Measures in Effectiveness Trials (COMET) working group proposed core outcome sets (COS) to address the heterogeneity in outcome measures in clinical studies. According to the recommendations of COMET, performing systematic reviews (SRs) usually was the first step for COS development. However, the SRs that serve as a basis for COS are not specifically appraised by organizations such as COMET regarding their quality. Here, we investigated the status of SRs related to development of COS and evaluated their methodological quality. METHODS: We conducted a search on PubMed to identify SRs related to COS development published from inception to May 2022. We qualitatively summarized the disease included in SR topics, and the studies included in the SRs. We evaluated the methodological quality of the SRs using AMSTAR 2.0 and compared the overall quality of SRs with and without protocols using the Mann-Whitney U test. RESULTS: We included 175 SRs from 23 different countries or regions, and they mainly focused on five diseases: musculoskeletal system or connective tissue disease (n = 19, 10.86%), injury, poisoning, or certain other consequences of external causes (n = 18, 10.29%), digestive system disease (n = 16, 9.14%), nervous system disease (n = 15, 8.57%), and genitourinary system disease (n = 15, 8.57%). Although 88.00% of SRs included randomized controlled trials (RCTs), only a few SRs (23.38%) employed appropriate tools to assess the risk of bias in RCTs. The assessment results on the basis of AMSTAR 2.0 indicated that most SRs (93.71%) were rated as ''critically low'' to ''low'' in terms of overall confidence. The overall confidence of SRs with protocols was significantly higher than that without protocols (P <.001). Compared to the SRs with protocols on Core Outcome Measures in Effectiveness Trials (COMET), SRs with protocols on PROSPERO were of better overall confidence (P = .017). CONCLUSION: The overall quality of published SRs regarding COS development was poor. Our findings emphasize the need for researchers to carefully select the disease topic and strictly adhere to the requirements of optimal methodology when conducting a SR for the establishment of a COS.


Assuntos
Avaliação de Resultados em Cuidados de Saúde , Projetos de Pesquisa , Humanos , Revisões Sistemáticas como Assunto , Viés
12.
ACS Appl Mater Interfaces ; 16(13): 16809-16819, 2024 Apr 03.
Artigo em Inglês | MEDLINE | ID: mdl-38502907

RESUMO

Polymers/polymer matrix composites possessing low dielectric constants (low-k polymer dielectrics) contribute to the advance of electronics, for instance, microprocessor chips, mobile phone antennas, and data communication terminals. However, the intrinsic long-chain structural characteristic results in poor thermal conductivities, which draw heat accumulation and undermine the outstanding low-k performance of polymers. Herein, multisource free-volume effects that combine two novel kinds of extra free volume with the known in-cage free volume of polyhedral oligomeric silsesquioxanes (POSSs) are discussed to reduce the capacity for dielectric constant reduction. The multisource free-volume effects of POSSs are associated with the thermal conductive network formed by the hexagonal boron nitride (BN) in the polymer matrix. The results show a decent balance between low-k performance (dielectric constant is 2.08 at 1 MHz and 1.98 at 10 GHz) and thermal conductivity (0.555 W m-1 K-1, 4.91 times the matrix). The results provide a new idea to maximize the free-volume effects of POSSs to optimize dielectric properties together with other desired performances for the dielectrics.

13.
Acta Biomater ; 178: 181-195, 2024 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-38447808

RESUMO

Valvular endothelial cells (VECs) derived from human induced pluripotent stem cells (hiPSCs) provide an unlimited cell source for tissue engineering heart valves (TEHVs); however, they are limited by their low differentiation efficiency and immature function. In our study, we applied unidirectional shear stress to promote hiPSCs differentiation into valvular endothelial-like cells (VELs). Compared to the static group, shear stress efficiently promoted the differentiation and functional maturation of hiPSC-VELs, as demonstrated by the efficiency of endothelial differentiation reaching 98.3% in the high shear stress group (45 dyn/cm2). Furthermore, we found that Piezo1 served as a crucial mechanosensor for the differentiation and maturation of VELs. Mechanistically, the activation of Piezo1 by shear stress resulted in the influx of calcium ions, which in turn initiated the Akt signaling pathway and promoted the differentiation of hiPSCs into mature VELs. Moreover, VELs cultured on decellularized heart valves (DHVs) exhibited a notable propensity for proliferation, robust adhesion properties, and antithrombotic characteristics, which were dependent on the activation of the Piezo1 channel. Overall, our study demonstrated that proper shear stress activated the Piezo1 channel to facilitate the differentiation and maturation of hiPSC-VELs via the Akt pathway, providing a potential cell source for regenerative medicine, drug screening, pathogenesis, and disease modeling. STATEMENT OF SIGNIFICANCE: This is the first research that systematically analyzes the effect of shear stress on valvular endothelial-like cells (VELs) derived from human induced pluripotent stem cells (hiPSCs). Mechanistically, unidirectional shear stress activates Piezo1, resulting in an elevation of calcium levels, which triggers the Akt signaling pathway and then facilitates the differentiation of functional maturation VELs. After exposure to shear stress, the VELs exhibited enhanced proliferation, robust adhesion capabilities, and antithrombotic characteristics while being cultured on decellularized heart valves. Thus, it is of interest to develop hiPSCs-VELs using shear stress and the Piezo1 channel provides insights into the functional maturation of valvular endothelial cells, thereby serving as a catalyst for potential applications in the development of therapeutic and tissue-engineered heart valves in the future.


Assuntos
Células-Tronco Pluripotentes Induzidas , Humanos , Células Endoteliais , Cálcio/metabolismo , Fibrinolíticos , Proteínas Proto-Oncogênicas c-akt/metabolismo , Diferenciação Celular/fisiologia , Endotélio
14.
Inorg Chem ; 63(14): 6173-6183, 2024 Apr 08.
Artigo em Inglês | MEDLINE | ID: mdl-38530927

RESUMO

Unfolding the solution coordination chemistry of high-valent transuranium elements with the "CHON"-type ligands is important to understand the fundamental chemistry of actinides and to design more efficient extractants for partitioning of transuranium elements in advanced nuclear fuel cycles. Here, the complexation of a hexavalent neptunyl ion (NpO22+ or Np(VI)) with oxydiacetic acid (ODA) has been systematically investigated in comparison with its amide analogues N,N-dimethyl-3-oxa-glutaramic acid (DMOGA) and N,N,N',N'-tetramethyl-3-oxa-glutaramide (TMOGA) both experimentally and computationally. The formation of both 1:1 and 1:2 complexes between Np(VI) and the three ligands was identified by spectrophotometry, and their stability constants were obtained and compared with those of hexavalent U(VI) and Pu(VI). The corresponding bonding nature is elucidated by using energy decomposition analysis (EDA), electrostatic potential (ESP), ELF contours, and natural orbitals for chemical valence (NOCV) methods, which shows that the Np-O bonds are essentially ionic in character and the unoccupied 6d orbitals of Np play a key role in enhancing the covalent interactions between Np(VI) and the three ligands.

15.
Nat Biotechnol ; 2024 Feb 23.
Artigo em Inglês | MEDLINE | ID: mdl-38396075

RESUMO

Many methods exist for determining protein structures from cryogenic electron microscopy maps, but this remains challenging for RNA structures. Here we developed EMRNA, a method for accurate, automated determination of full-length all-atom RNA structures from cryogenic electron microscopy maps. EMRNA integrates deep learning-based detection of nucleotides, three-dimensional backbone tracing and scoring with consideration of sequence and secondary structure information, and full-atom construction of the RNA structure. We validated EMRNA on 140 diverse RNA maps ranging from 37 to 423 nt at 2.0-6.0 Å resolutions, and compared EMRNA with auto-DRRAFTER, phenix.map_to_model and CryoREAD on a set of 71 cases. EMRNA achieves a median accuracy of 2.36 Å root mean square deviation and 0.86 TM-score for full-length RNA structures, compared with 6.66 Å and 0.58 for auto-DRRAFTER. EMRNA also obtains a high residue coverage and sequence match of 93.30% and 95.30% in the built models, compared with 58.20% and 42.20% for phenix.map_to_model and 56.45% and 52.3% for CryoREAD. EMRNA is fast and can build an RNA structure of 100 nt within 3 min.

16.
Environ Toxicol ; 39(5): 3055-3148, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38319140

RESUMO

BACKGROUND: This study aimed to type breast cancer in relation to reactive oxygen species (ROS), clinical indicators, single nucleotide variant (SNV) mutations, functional differences, immune infiltration, and predictive responses to immunotherapy or chemotherapy, and constructing a prognostic model. METHODS: We used uniCox analysis, ConsensusClusterPlus, and the proportion of ambiguous clustering (PAC) to analyze The Cancer Genome Atlas (TCGA) data to determine optimal groupings and obtain differentially expressed ROS-related genes. Clinical indicators were then combined with the classification results and the Chi-square test was used to assess differences. We further examined SNV mutations, and functional differences using gene set enrichment analysis (GSEA) analysis, the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, immune cell infiltration, and response to immunotherapy and chemotherapy. A prognostic model for breast cancer was constructed using these differentially expressed genes, immunotherapy or chemotherapy responses, and survival curves. RT-qPCR was used to detect the differences in the expression of LCE3D, CA1, PIRT and SMR3A in breast cancer cell lines and normal breast epithelial cell line. RESULTS: We identified two distinct tumor types with significant differences in ROS-related gene expression, clinical indicators, SNV mutations, functional pathways, and immune infiltration. The response to specific chemotherapy drugs and immunotherapy treatments also documented significant differences. The prognostic model constructed with 16 genes linked to survival could efficiently divide patients into high- and low-risk groups. The high-risk group showed a poorer prognosis, higher tumor purity, distinct immune microenvironment, and lower immunotherapy response. RT-qPCR results showed that LCE3D, CA1, PIRT and SMR3A are highly expressed in breast cancer. CONCLUSION: Our methodical examination presented an enhanced insight into the molecular and immunological heterogeneity of breast cancer. It can contribute to the understanding of prognosis and offer valuable insights for personalized treatment strategies. Further, the prognostic model can potentially serve as a powerful tool for risk stratification and therapeutic decision-making in clinical settings.

17.
Food Sci Nutr ; 12(2): 1119-1132, 2024 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-38370040

RESUMO

Functional constipation (FC) has a negative impact on patients' quality of life. We hypothesized that dietary supplementation with xylo-oligosaccharides (XOS) or fructo-oligosaccharides (FOS) would improve constipation symptoms by influencing the gut microbiota. A randomized double-blind controlled trial was conducted in FC patients. Patients were randomly divided into 6 groups and given a dietary supplement containing XOS at doses of 3, 5, or 10 g/day, FOS at doses of 10 and 20 g/day, or placebo at 5 g/day for one month. We compared improvements in gastrointestinal function after the intervention using the Bristol Stool Form Scale (BSFS), Cleveland Clinic Constipation Score (CCCS), and Quality of Life Scale for Patients with Constipation (PAC-QoL). 16S rRNA sequencing was used to assess changes in the structure of the gut microbiota. Changes in individual bacteria had significant effects in reducing gastrointestinal symptoms during the intervention, even though the flora structure remained unchanged from baseline. Compared to FOS, XOS enriched Bifidobacterium at a lower dose, and patients receiving XOS supplementation showed significant improvements in constipation symptoms without side effects such as diarrhea and flatulence.

18.
Beilstein J Nanotechnol ; 15: 168-179, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38352717

RESUMO

Modification of graphene oxide (GO) by vinyltriethoxysilane (VTES) was investigated to study the effect of silanized GO on radical graft copolymerization of GO onto deproteinized natural rubber (DPNR). The modified GO, GO-VTES (a and b), was characterized by X-ray diffraction (XRD), Fourier-transform infrared spectroscopy, contact angle, thermal gravimetric analysis, and scanning electron microscopy. The XRD results showed the appearance of an amorphous region of silica particles at a diffraction angle of 22°. The formation of silica was investigated by 29Si NMR, and it was found that the hydrolysis and condensation of VTES proceed more completely in basic conditions than in acidic conditions. The silica content of GO-VTES(b) was 43%, which is higher than that of GO-VTES(a) (8%). Morphology of silica was observed by SEM. The DPNR/GO-VTES nanocomposites prepared with the same amount of GO, GO-VTES(a), and GO-VTES(b) were characterized with tensile tests and dynamic mechanical tests. The stress at break of DPNR/GO-VTES(a) and DPNR/GO-VTES(b) was 5.2 MPa and 4.3 MPa, respectively, which were lower than that of DPNR/GO. However, it exhibited higher stress at small strains and higher storage modulus than DPNR/GO.

19.
Circulation ; 2024 Feb 15.
Artigo em Inglês | MEDLINE | ID: mdl-38357822

RESUMO

BACKGROUND: A main obstacle in current valvular heart disease research is the lack of high-quality homogeneous functional heart valve cells. Human induced pluripotent stem cells (hiPSCs)-derived heart valve cells may help with this dilemma. However, there are no well-established protocols to induce hiPSCs to differentiate into functional heart valve cells, and the networks that mediate the differentiation have not been fully elucidated. METHODS: To generate heart valve cells from hiPSCs, we sequentially activated the Wnt, BMP4, VEGF (vascular endothelial growth factor), and NFATc1 signaling pathways using CHIR-99021, BMP4, VEGF-165, and forskolin, respectively. The transcriptional and functional similarity of hiPSC-derived heart valve cells compared with primary heart valve cells were characterized. Longitudinal single-cell RNA sequencing was used to uncover the trajectory, switch genes, pathways, and transcription factors of the differentiation. RESULTS: An efficient protocol was developed to induce hiPSCs to differentiate into functional hiPSC-derived valve endothelial-like cells and hiPSC-derived valve interstitial-like cells. After 6-day differentiation and CD144 magnetic bead sorting, ≈70% CD144+ cells and 30% CD144- cells were obtained. On the basis of single-cell RNA sequencing data, the CD144+ cells and CD144- cells were found to be highly similar to primary heart valve endothelial cells and primary heart valve interstitial cells in gene expression profile. Furthermore, CD144+ cells had the typical function of primary heart valve endothelial cells, including tube formation, uptake of low-density lipoprotein, generation of endothelial nitric oxide synthase, and response to shear stress. Meanwhile, CD144- cells could secret collagen and matrix metalloproteinases, and differentiate into osteogenic or adipogenic lineages like primary heart valve interstitial cells. Therefore, we identified CD144+ cells and CD144- cells as hiPSC-derived valve endothelial-like cells and hiPSC-derived valve interstitial-like cells, respectively. Using single-cell RNA sequencing analysis, we demonstrated that the trajectory of heart valve cell differentiation was consistent with embryonic valve development. We identified the main switch genes (NOTCH1, HEY1, and MEF2C), signaling pathways (TGF-ß, Wnt, and NOTCH), and transcription factors (MSX1, SP5, and MECOM) that mediated the differentiation. Finally, we found that hiPSC-derived valve interstitial-like cells might derive from hiPSC-derived valve endothelial-like cells undergoing endocardial-mesenchymal transition. CONCLUSIONS: In summary, this is the first study to report an efficient strategy to generate functional hiPSC-derived valve endothelial-like cells and hiPSC-derived valve interstitial-like cells from hiPSCs, as well as to elucidate the differentiation trajectory and transcriptional dynamics of hiPSCs differentiated into heart valve cells.

20.
Phys Chem Chem Phys ; 26(4): 3008-3019, 2024 Jan 24.
Artigo em Inglês | MEDLINE | ID: mdl-38179673

RESUMO

Rhenium sulfide (ReS2) has emerged as a promising two-dimensional material, demonstrating broad-spectrum visible absorption properties that make it highly relevant for diverse optoelectronic applications. Manipulating and optimizing the pathway of photogenerated carriers play a pivotal role in enhancing the efficiency of charge separation and transfer in novel semiconductor composites. This study focuses on the strategic construction of a semiconductor heterostructure by synthesizing ZnO on vacancy-containing ReS2 (VRe-ReS2) through chemical bonding processes. The ingeniously engineered built-in electric field within the heterostructure effectively suppresses the recombination of photogenerated electron-hole pairs. A direct and well-established interfacial connection between VRe-ReS2 and ZnO is achieved through a robust Zn-S bond. This distinctive bond configuration leads to enhanced nonlinear optical conversion efficiency, attributed to shortened carrier migration distances and accelerated charge transfer rates. Furthermore, theoretical calculations unveil the superior chemical interactions between Re vacancies and sulfide moieties, facilitating the formation of Zn-S bonds. The photoluminescence (PL) intensity is increased by the formation of VRe-ReS2 and ZnO heterostructure and the PL quantum yield of VRe-ReS2 is improved. The intricate impact of the Zn-S bond on the nonlinear absorption behavior of the VRe-ReS2@ZnO heterostructure is systematically investigated using femtosecond Z-scan techniques. The charge transfer from ZnO to ReS2 defect levels induces a transition from saturable absorption to reverse saturable absorption in the VRe-ReS2@ZnO heterostructure. Transient absorption measurements further confirm the presence of the Zn-S bond between the interfaces, as evidenced by the prolonged relaxation time (τ3) in the VRe-ReS2@ZnO heterostructure. This study offers valuable insights into the rational construction of heterojunctions through tailored interfacial bonding and surface/interface charge transfer pathways. These endeavors facilitate the modulation of electron transfer dynamics, ultimately yielding superior nonlinear optical conversion efficiency and effective charge regulation in optoelectronic functional materials.

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