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Objective: To compare serum levels of pepsinogen I (PGI), pepsinogen II (PGII), and gastrin-17 (G-17) among patients with gastritis, gastric ulcer, and gastric cancer, and to assess the effectiveness of these biomarkers individually and in combination for screening gastric cancer. Methods: Serum levels of PGI, PGII, and G-17 were measured using enzyme-linked immunosorbent assay (ELISA) in 50 patients with gastric cancer, 60 with chronic gastritis, and 60 with gastric ulcer from February 2020 to June 2021. The diagnostic value of these biomarkers was analyzed through sensitivity, specificity, and ROC curve assessments. Results: Serum PGI levels were significantly lower in patients with advanced gastric cancer compared to those with early gastric cancer (P < .05), while PGII and G-17 levels were significantly higher in advanced-stage patients (P < .05). The combined ROC curve analysis of PGI, PGII, and G-17 yielded an area under the curve (AUC) of 0.933, indicating higher diagnostic accuracy than any of the markers alone. Statistically significant differences were noted between the combined and individual tests (Z = 2.376, P < .05). Patients with PGI levels lower than 17.21 ng/ml had a worse prognosis compared to those with higher levels. Similarly, patients with PGII levels greater than 74.65 ng/ml and G-17 levels greater than 17.03 pmol/L had poorer prognoses. Additionally, higher G-17 levels were associated with significantly lower serum PGI levels. Conclusions: Patients with low expression of PGI have a poorer prognosis, and those with high expression of PGII and G-17 also have a poor prognosis. Combining the three indicators has clear value for the screening and prognostic evaluation of gastric cancer, making it worthy of clinical promotion and application.
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OBJECTIVE: This study aimed to predict the bronchopulmonary dysplasia (BPD) in preterm infants with a gestational age(GA) < 32 weeks utilizing clinical data, serum mediator complex subunit 1 (MED1), and serum peroxisome proliferator-activated receptor gamma coactivator-1alpha (PGC-1α). METHODS: This prospective observational study enrolled 70 preterm infants with GA < 32 weeks. The infants were categorized into two groups: non-BPD group(N = 35) and BPD group(N = 35), including 25 cases with mild BPD and 10 patients with moderate/severe subgroups. We performed multifactorial regression analysis to investigate the postnatal risk factors for BPD. Furthermore, we compared serum levels of biomarkers, including MED1 and PGC-1α, among infants with and without BPD at postnatal days 1, 7, 14, 28, and PMA 36 weeks. A logistic regression model was constructed to predict BPD's likelihood using clinical risk factors and serum biomarkers. RESULTS: Serum levels of MED1 on the first postnatal day, PGC-1α on the 1st, 7th, and 28th days, and PMA at 36 weeks were significantly lower in the BPD group than in the non-BPD group (P < 0.05). Furthermore, the predictive model for BPD was created by combing serum levels of MED1 and PGC-1α on postnatal day 1 along with clinical risk factors such as frequent apnea, mechanical ventilation time > 7 d, and time to reach total enteral nutrition. Our predictive model had a high predictive accuracy(C statistics of 0.989) . CONCLUSION: MED1and PGC-1α could potentially serve as valuable biomarkers, combined with clinical factors, to aid clinicians in the early diagnosis of BPD.
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Biomarcadores , Displasia Broncopulmonar , Recien Nacido Prematuro , Coactivador 1-alfa del Receptor Activado por Proliferadores de Peroxisomas gamma , Humanos , Displasia Broncopulmonar/sangre , Displasia Broncopulmonar/diagnóstico , Coactivador 1-alfa del Receptor Activado por Proliferadores de Peroxisomas gamma/sangre , Recién Nacido , Femenino , Masculino , Estudios Prospectivos , Recien Nacido Prematuro/sangre , Biomarcadores/sangre , Edad Gestacional , Factores de Riesgo , Valor Predictivo de las Pruebas , Modelos LogísticosRESUMEN
Necrotizing enterocolitis (NEC) is a leading cause of morbidity and mortality in premature infants with no specific treatments available. We aimed to identify the molecular mechanisms underlying NEC and investigate the therapeutic effects of Bacteroides fragilis on NEC. Clinical samples of infant feces, bile acid-targeted metabolomics, pathological staining, bioinformatics analysis, NEC rat model, and co-immunoprecipitation were used to explore the pathogenesis of NEC. Taxonomic characterization of the bile salt hydrolase (bsh) gene, enzyme activity assays, 16S rRNA sequencing, and organoids were used to explore the therapeutic effects of B. fragilis on NEC-related intestinal damage. Clinical samples, NEC rat models, and in vitro experiments revealed that total bile acid increased in the blood but decreased in feces. Moreover, the levels of FXR and other bile acid metabolism-related genes were abnormal, resulting in disordered bile acid metabolism in NEC. Taurochenodeoxycholic acid accelerated NEC pathogenesis and taurodeoxycholate alleviated NEC. B. fragilis displayed bsh genes and enzyme activity and alleviated intestinal damage by restoring gut microbiota dysbiosis and bile acid metabolism abnormalities by inhibiting the FXR-NLRP3 signaling pathway. Our results provide valuable insights into the therapeutic role of B. fragilis in NEC. Administering B. fragilis may substantially alleviate intestinal damage in NEC.
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Amidohidrolasas , Bacteroides fragilis , Ácidos y Sales Biliares , Enterocolitis Necrotizante , Microbioma Gastrointestinal , Proteína con Dominio Pirina 3 de la Familia NLR , Receptores Citoplasmáticos y Nucleares , Transducción de Señal , Enterocolitis Necrotizante/metabolismo , Enterocolitis Necrotizante/microbiología , Enterocolitis Necrotizante/tratamiento farmacológico , Animales , Proteína con Dominio Pirina 3 de la Familia NLR/metabolismo , Proteína con Dominio Pirina 3 de la Familia NLR/genética , Bacteroides fragilis/metabolismo , Bacteroides fragilis/genética , Transducción de Señal/efectos de los fármacos , Ácidos y Sales Biliares/metabolismo , Ratas , Receptores Citoplasmáticos y Nucleares/metabolismo , Receptores Citoplasmáticos y Nucleares/genética , Microbioma Gastrointestinal/efectos de los fármacos , Amidohidrolasas/metabolismo , Amidohidrolasas/genética , Humanos , Ratas Sprague-Dawley , Recién Nacido , Modelos Animales de Enfermedad , Masculino , Femenino , Probióticos/administración & dosificación , Probióticos/farmacología , Recien Nacido Prematuro , Disbiosis/microbiologíaRESUMEN
Complement factor H-related protein (CFHR) plays an important role in regulating complement activation and defensive responses. The function of CFHR2 (complement factor H related 2), a member of the CFHR family, in fish remains unclear. Here, we report the genetic relationship, expression characteristics and regulatory mechanism of cfhl5 (complement factor H like 5) gene, which encodes CFHR2 in Chinese tongue sole. We observed that the cfhl5 gene was widely expressed in several tissues, such as brain, heart and immune organs, and was most abundantly expressed in liver. After injection with Vibrio harveyi, the expression of cfhl5 was up-regulated significantly in liver, spleen and kidney at 12 or 24 hours post infection (hpi), suggesting an involvement of this gene in the acute immune response. Knockdown of cfhl5 in liver cells significantly up-regulated the expression of the pro-inflammatory cytokines tnf-α (tumor necrosis factor-alpha) and il1ß (interleukin-1beta), the immunomodulatory factor il10 (interleukin-10) and the lectin complement pathway gene masp1 (MBL-associated serine protease 1), and down-regulated the expression of complement components c3 (complement 3) and cfi (complement factor I). In our previous work, we found that cfhl5 gene was significantly higher methylated and lower expressed in the resistant family compared with the susceptible family. Therefore, we used dual-luciferase reporter system to determine the effect of DNA methylation on this gene and found that DNA methylation could inhibit the promoter activity to reduce its expression. These results demonstrated that the expression of cfhl5 is regulated by DNA methylation, and this gene might play an important role in the immune response by regulating the expression of cytokines and complement components genes in Chinese tongue sole.
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Enfermedades de los Peces , Proteínas de Peces , Peces Planos , Regulación de la Expresión Génica , Inmunidad Innata , Vibriosis , Vibrio , Animales , Vibrio/fisiología , Enfermedades de los Peces/inmunología , Vibriosis/inmunología , Vibriosis/veterinaria , Proteínas de Peces/genética , Proteínas de Peces/inmunología , Inmunidad Innata/genética , Peces Planos/inmunología , Peces Planos/genética , Regulación de la Expresión Génica/inmunología , Perfilación de la Expresión Génica/veterinaria , FilogeniaRESUMEN
BACKGROUND: Langerhans cell histiocytosis (LCH) is characterized by diabetes insipidus and is an uncommon occurrence. Pathological biopsies still have a certain degree of diagnostic probability. We present a case in which LCH initially affected the pituitary gland. This resulted in a misdiagnosis of chronic inflammation upon pathological examination. CASE SUMMARY: A 25-year-old female exhibited symptoms of diabetes insipidus. Magnetic resonance imaging revealed an enhanced foci in the pituitary gland. After surgical resection of the pituitary lesion, the pathological diagnosis was chronic inflammation. However, the patient later experienced bone destruction in the skull and lower limb bones. After the lower limb bone lesion was compared with the initial pituitary lesion, the final diagnosis was modified to LCH. The patient was treated with multiple chemotherapy courses. However, the patient's condition gradually worsened, and she eventually passed away at home. CONCLUSION: LCH should be considered when patients exhibit diabetes insipidus and absence of high signal intensity in the pituitary gland on sagittal T1-weighted image and abnormal enhancement in the pituitary region.
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BACKGROUND: Quantitative transport mapping (QTM) of blood velocity, based on the transport equation has been demonstrated higher accuracy and sensitivity of perfusion quantification than the traditional Kety's method-based cerebral blood flow (CBF). This study aimed to investigate the associations between QTM velocity and cognitive function in Alzheimer's disease (AD) using multiple post-labeling delay arterial spin labeling (ASL) MRI. METHODS: A total of 128 subjects (21 normal controls (NC), 80 patients with mild cognitive impairment (MCI), and 27 AD) were recruited prospectively. All participants underwent MRI examination and neuropsychological evaluation. QTM velocity and traditional CBF maps were computed from multiple delay ASL. Regional quantitative perfusion measurements were performed and compared to study group differences. We tested the hypothesis that cognition declines with reduced cerebral blood perfusion with consideration of age and gender effects. RESULTS: In cortical gray matter (GM) and the hippocampus, QTM velocity and CBF showed decreased values in the AD group compared to NC and MCI groups; QTM velocity, but not CBF, showed a significant difference between MCI and NC groups. QTM velocity and CBF showed values decreasing with age; QTM velocity, but not CBF, showed a significant gender difference between male and female. QTM velocity and CBF in the hippocampus were positively correlated with cognition, including global cognition, memory, executive function, and language function. CONCLUSION: This study demonstrated an increased sensitivity of QTM velocity as compared with the traditional Kety's method-based CBF. Specifically, we observed only in QTM velocity, reduced perfusion velocity in GM and the hippocampus in MCI compared with NC. Both QTM velocity and CBF demonstrated a reduction in AD vs. controls. Decreased QTM velocity and CBF in the hippocampus were correlated with poor cognitive measures. These findings suggest QTM velocity as potential biomarker for early AD blood perfusion alterations and it could provide an avenue for early intervention of AD.
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Enfermedad de Alzheimer , Circulación Cerebrovascular , Disfunción Cognitiva , Imagen por Resonancia Magnética , Marcadores de Spin , Humanos , Masculino , Femenino , Enfermedad de Alzheimer/diagnóstico por imagen , Enfermedad de Alzheimer/fisiopatología , Anciano , Circulación Cerebrovascular/fisiología , Disfunción Cognitiva/diagnóstico por imagen , Disfunción Cognitiva/fisiopatología , Imagen por Resonancia Magnética/métodos , Persona de Mediana Edad , Encéfalo/diagnóstico por imagen , Encéfalo/irrigación sanguínea , Pruebas Neuropsicológicas , Anciano de 80 o más Años , Estudios Prospectivos , Velocidad del Flujo Sanguíneo/fisiologíaRESUMEN
OBJECTIVES: Homopolymer (HP) sequencing is error-prone in next-generation sequencing (NGS) assays, and may induce false insertion/deletions and substitutions. This study aimed to evaluate the performance of dichromatic and tetrachromatic fluorogenic NGS platforms when sequencing homopolymeric regions. RESULTS: A HP-containing plasmid was constructed and diluted to serial frequencies (3%, 10%, 30%, 60%) to determine the performance of an MGISEQ-2000, MGISEQ-200, and NextSeq 2000 in HP sequencing. An evident negative correlation was observed between the detected frequencies of four nucleotide HPs and the HP length. Significantly decreased rates (P < 0.01) were found in all 8-mer HPs in all three NGS systems at all four expected frequencies, except in the NextSeq 2000 at 3%. With the application of a unique molecular identifier (UMI) pipeline, there were no differences between the detected frequencies of any HPs and the expected frequencies, except for poly-G 8-mers using the MGI 200 platform. UMIs improved the performance of all three NGS platforms in HP sequencing. CONCLUSIONS: We first constructed an HP-containing plasmid based on an EGFR gene backbone to evaluate the performance of NGS platforms when sequencing homopolymeric regions. A highly comparable performance was observed between the MGISEQ-2000 and NextSeq 2000, and introducing UMIs is a promising approach to improve the performance of NGS platforms in sequencing homopolymeric regions.
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Secuenciación de Nucleótidos de Alto Rendimiento , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Plásmidos/genética , Humanos , Análisis de Secuencia de ADN/métodosRESUMEN
ARPC1B encodes the protein known as actin-related protein 2/3 complex subunit 1 B (ARPC1B), which controls actin polymerization in the human body. Although ARPC1B has been linked to several human malignancies, its function in these cancers remains unclear. TCGA, GTEx, CCLE, Xena, CellMiner, TISIDB, and molecular signature databases were used to analyze ARPC1B expression in cancers. Visualization of data was primarily achieved using R language, version 4.0. Nineteen tumors exhibited high levels of ARPC1B expression, which were associated with different tumor stages and significantly affected the prognosis of various cancers. The level of ARPC1B expression substantially connected the narrative of ARPC1B expression with several TMB cancers and showed significant changes in MSI. Additionally, tolerance to numerous anticancer medications has been linked to high ARPC1B gene expression. Using Gene Set Variation Analysis/Gene Set Enrichment Analysisanalysis and concentrating on Rectum adenocarcinoma (READ), we thoroughly examined the molecular processes of the ARPC1B gene in pan-cancer. Using WGCNA, we examined the co-expression network of READ and ARPC1B. Meanwhile, ten specimens were selected for immunohistochemical examination, which showed high expression of ARPC1B in READ. Human pan-cancer samples show higher ARPC1B expression than healthy tissues. In many malignancies, particularly READ, ARPC1B overexpression is associated with immune cell infiltration and a poor prognosis. These results imply that the molecular biomarker ARPC1B may be used to assess the prognosis and immune infiltration of patients with READ.
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Background: Quantitative transport mapping (QTM) of blood velocity, based on the transport equation has been demonstrated higher accuracy and sensitivity of perfusion quantification than the traditional Kety's method-based blood flow (Kety flow). This study aimed to investigate the associations between QTM velocity and cognitive function in Alzheimer's disease (AD) using multiple post-labeling delay arterial spin labeling (ASL) MRI. Methods: A total of 128 subjects (21 normal controls (NC), 80 patients with mild cognitive impairment (MCI), and 27 AD) were recruited prospectively. All participants underwent MRI examination and neuropsychological evaluation. QTM velocity and traditional Kety flow maps were computed from multiple delay ASL. Regional quantitative perfusion measurements were performed and compared to study group differences. We tested the hypothesis that cognition declines with reduced cerebral blood flow with consideration of age and gender effects. Results: In cortical gray matter (GM) and the hippocampus, QTM velocity and Kety flow showed decreased values in AD group compared to NC and MCI groups; QTM velocity, but not Kety flow, showed a significant difference between MCI and NC groups. QTM velocity and Kety flow showed values decreasing with age; QTM velocity, but not Kety flow, showed a significant gender difference between male and female. QTM velocity and Kety flow in the hippocampus were positively correlated with cognition, including global cognition, memory, executive function, and language function. Conclusion: This study demonstrated an increased sensitivity of QTM velocity as compared with the traditional Kety flow. Specifically, we observed only in QTM velocity, reduced perfusion velocity in GM and the hippocampus in MCI compared with NC. Both QTM velocity and Kety flow demonstrated reduction in AD vs controls. Decreased QTM velocity and Kety flow in the hippocampus were correlated with cognitive measures. These findings suggest QTM velocity as an improved biomarker for early AD blood flow alterations.
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OBJECTIVE: To explore the risk factors affecting the survival and efficacy of patients with acute myeloid leukemia with myelodysplasia-related changes (AML-MRC) transformed from myelodysplastic syndrome (MDS). METHODS: The clinical data of 60 patients with AML-MRC transformed from MDS who hospitalized in The Third Affiliated Hospital of Soochow University from January 2010 to December 2021 were retrospectively analyzed. The demographic data and laboratory parameters, cytogenetic karyotypes, target genes of AML detected by next generation sequence, risk stratification, treatment regimen, therapeutic efficacy and survival outcome were documented. Rank sum test and Chi-square test or Fisher exact test were used to compare the survival and efficacy. The effects of clinical parameters, risk stratification and treatment regimens on the survival and efficacy of the AML-MRC patients were analyzed by univariate and multivariate analysis. RESULTS: The median overall survival (OS) of the AML-MRC patients was 4.5 months, the 1-year OS rate was 28.3%, and the complete remission (CR) rate after treatment was 33.3%. The univariate analysis showed that age≥60 years, leukocytosis, severe thrombocytopenia, poor-risk group and only accepted hypomethylating agents(HMAs) or supportive therapy were the risk factors affecting OS. COX multivariate analysis showed that thrombocytopenia ( HR=4.46), HMAs therapy (compared to transplantation, HR=10.47), supportive therapy (compared to transplantation, HR=25.80) and poor-risk group (compared to medium-risk group, HR=13.86) were independent hazard factors for median OS of patients with AML-MRC. The univariate analysis showed that the risk factors affecting 1-year OS in patients with AML-MRC were age≥60 years, thrombocytopenia, time of transformation from MDS to AML (TTA)≥3 months, fibrinogen-albumin ratio index (FARI)≥0.07, CONUT score≥5, poor-risk group and supportive therapy. Binary logistic regression analysis showed that the independent risk factors for 1-year OS in AML-MRC patients were age≥60 years ( HR=11.23), thrombocytopenia ( HR=8.71), FARI≥0.07 ( HR=5.19) and poor-risk group ( HR=14.00). The risk factors affecting CR of AML-MRC patients in univariate analysis were age≥60 years, thrombocytopenia, FARI≥0.1, CONUT score≥5, poor-risk group and supportive therapy, while binary logistic regression analysis showed that age≥60 years( HR=7.35), CONUT score≥5 ( HR=9.60), thrombocytopenia ( HR=12.05) and poor-risk group ( HR=32.5) were independent risk factors affecting CR of the patients. CONCLUSION: The OS of AML-MRC patients is poor, old age(≥60 years old), supportive therapy, HMA therapy, poor-risk, thrombocytopenia, FARI≥0.07 and CONUT score≥5 may be associated with poor prognosis.
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Leucemia Mieloide Aguda , Síndromes Mielodisplásicos , Humanos , Síndromes Mielodisplásicos/complicaciones , Pronóstico , Tasa de Supervivencia , Factores de Riesgo , Persona de Mediana Edad , Progresión de la Enfermedad , Trombocitopenia/etiología , Femenino , Inducción de Remisión , MasculinoRESUMEN
Globally, over 287 million tons of plastic are disposed in landfills, rivers, and oceans or are burned every year. The results are devastating to our ecosystems, wildlife and human health. One promising remedy is the yellow mealworm (Tenebrio molitor larvae), which has proved capable of degrading microplastics (MPs). This paper presents a new investigation into the biodegradation of aged polyethylene (PE) film and polystyrene (PS) foam by the Tenebrio molitor larvae. After a 35 - day feeding period, both pristine and aged MPs can be consumed by larvae. Even with some inhibitions in larvae growth due to the limited nutrient supply of aged MPs, when compared with pristine MPs, the aged MPs were depolymerized more efficiently in gut microbiota based on gel permeation chromatography (GPC) and Fourier transform infrared spectroscopy (FTIR) analysis. With the change in surface chemical properties, the metabolic intermediates of aged MPs contained more oxygen-containing functional groups and shortened long-chain alkane, which was confirmed by gas chromatography and mass spectrometry (GC-MS). High-throughput sequencing revealed that the richness and diversity of gut microbes were restricted in the MPs-fed group. Although MPs had a negative effect on the relative abundance of the two dominant bacteria Enterococcaceae and Lactobacillaceae, the aged MPs may promote the relative abundance of Enterobacteriaceae and Streptococcaceae. Redundancy analysis (RDA) further verified that the aged MPs are effectively biodegraded by yellow mealworm. This work provides new insights into insect-mediated mechanisms of aged MP degradation and promising strategies for MP sustainable and efficient solutions.
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Biodegradación Ambiental , Larva , Microplásticos , Polietileno , Poliestirenos , Tenebrio , Animales , Microplásticos/metabolismo , Tenebrio/metabolismo , Polietileno/metabolismo , Microbioma Gastrointestinal , Contaminantes Químicos del Agua/metabolismoRESUMEN
Cross-sample contamination is one of the major issues in next-generation sequencing (NGS)-based molecular assays. This type of contamination, even at very low levels, can significantly impact the results of an analysis, especially in the detection of somatic alterations in tumor samples. Several contamination identification tools have been developed and implemented as a crucial quality-control step in the routine NGS bioinformatic pipeline. However, no study has been published to comprehensively and systematically investigate, evaluate, and compare these computational methods in the cancer NGS analysis. In this study, we comprehensively investigated nine state-of-the-art computational methods for detecting cross-sample contamination. To explore their application in cancer NGS analysis, we further compared the performance of five representative tools by qualitative and quantitative analyses using in silico and simulated experimental NGS data. The results showed that Conpair achieved the best performance for identifying contamination and predicting the level of contamination in solid tumors NGS analysis. Moreover, based on Conpair, we developed a Python script, Contamination Source Predictor (ConSPr), to identify the source of contamination. We anticipate that this comprehensive survey and the proposed tool for predicting the source of contamination will assist researchers in selecting appropriate cross-contamination detection tools in cancer NGS analysis and inspire the development of computational methods for detecting sample cross-contamination and identifying its source in the future.
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Biología Computacional , Neoplasias , Humanos , Biología Computacional/métodos , Secuenciación de Nucleótidos de Alto Rendimiento , Neoplasias/diagnóstico , Neoplasias/genética , Control de CalidadRESUMEN
Background: Obesity and psychological factors were identified as risk factors for female infertility. The study investigated the correlation between WWI, depression, and secondary infertility, focusing on the potential mediating role of depression. Methods: According to the data from NHANES, this cross-sectional study used multiple regression analysis, subgroup analysis, and smooth curve fitting to explore the relationship between WWI, depression, and secondary infertility. The diagnostic ability of WWI was evaluated and compared to other obesity indicators using the ROC curve. The mediating effect test adopted the distribution of the product. Results: This study involved 2778 participants, including 381 (13.7%) women with secondary infertility. Results showed that higher WWI (OR = 1.31; 95% CI, 1.11-1.56) and depression scores (OR = 1.03; 95% CI, 1.01-1.06) were associated with secondary infertility. There was a positive correlation between WWI and secondary infertility (nonlinear p = 0.8272) and this association was still consistent in subgroups (all P for interaction> 0.05). Compared with other obesity indicators, WWI (AUC = 0.588) also shows good predictive performance for secondary infertility. Mediation analysis showed that depression mediated the relationship between 3.94% of WWI and secondary infertility, with a confidence interval of Za * Zb excluding 0. Conclusion: WWI exhibited a relatively good correlation in predicting secondary infertility than other obesity indicators, and depression may be a mediator between WWI and secondary infertility. Focusing on the potential mediating role of depression, the risk of secondary infertility due to obesity may be beneficially reduced in women.
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Infertilidad Femenina , Obesidad Mórbida , Femenino , Humanos , Masculino , Estudios Transversales , Depresión/complicaciones , Depresión/epidemiología , Encuestas Nutricionales , Infertilidad Femenina/complicaciones , Infertilidad Femenina/epidemiología , Obesidad/complicacionesRESUMEN
BACKGROUND: Hybridization capture-based targeted next generation sequencing (NGS) is gaining importance in routine cancer clinical practice. DNA library preparation is a fundamental step to produce high-quality sequencing data. Numerous unexpected, low variant allele frequency calls were observed in libraries using sonication fragmentation and enzymatic fragmentation. In this study, we investigated the characteristics of the artifact reads induced by sonication and enzymatic fragmentation. We also developed a bioinformatic algorithm to filter these sequencing errors. RESULTS: We used pairwise comparisons of somatic single nucleotide variants (SNVs) and insertions and deletions (indels) of the same tumor DNA samples prepared using both ultrasonic and enzymatic fragmentation protocols. Our analysis revealed that the number of artifact variants was significantly greater in the samples generated using enzymatic fragmentation than using sonication. Most of the artifacts derived from the sonication-treated libraries were chimeric artifact reads containing both cis- and trans-inverted repeat sequences of the genomic DNA. In contrast, chimeric artifact reads of endonuclease-treated libraries contained palindromic sequences with mismatched bases. Based on these distinctive features, we proposed a mechanistic hypothesis model, PDSM (pairing of partial single strands derived from a similar molecule), by which these sequencing errors derive from ultrasonication and enzymatic fragmentation library preparation. We developed a bioinformatic algorithm to generate a custom mutation "blacklist" in the BED region to reduce errors in downstream analyses. CONCLUSIONS: We first proposed a mechanistic hypothesis model (PDSM) of sequencing errors caused by specific structures of inverted repeat sequences and palindromic sequences in the natural genome. This new hypothesis predicts the existence of chimeric reads that could not be explained by previous models, and provides a new direction for further improving NGS analysis accuracy. A bioinformatic algorithm, ArtifactsFinder, was developed and used to reduce the sequencing errors in libraries produced using sonication and enzymatic fragmentation.
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Artefactos , Genoma Humano , Humanos , Biblioteca de Genes , Análisis de Secuencia de ADN/métodos , ADN de Neoplasias , Secuenciación de Nucleótidos de Alto Rendimiento/métodosRESUMEN
BACKGROUND: Understanding the trends of tuberculosis (TB) burden and its risk factors at the provincial level in the context of global End TB targets is crucial to identify the progress and challenges in TB control. We aimed to estimate the burden of TB and risk factors for death from 2006 to 2020 for the first time in Guizhou Province, China. METHODS: Data were collected from the national TB surveillance system. Four indicators of TB burden and their corresponding age-standardized rates (ASRs), including incidence (ASIR), prevalence (ASPR), mortality (ASMR) and disability-adjusted life years (DALYs) (ASDR), were estimated and stratified by year, age, gender and prefecture. Temporal trends of ASRs were presented by locally weighted regression, and the annual percentage change was calculated. The correlation between gross domestic product (GDP) per capita and ASRs was evaluated by Pearson correlation analysis. The associated risk factors for death in PTB patients were determined using logistic regression models. RESULTS: A total of 557,476 pulmonary TB (PTB) cases and 11,234 deaths were reported, including 2233 (19.9%) TB specific deaths and 9001 (80.1%) deaths from other causes. The 15-year average incidence, prevalence and mortality rates were 94.6, 102.6 and 2.1 per 100,000 population, respectively. The average DALY rate was 0.60 per 1000 population. The ASIR and ASPR have shown downward trends since 2012, with the largest percentage decrease in 2020 (ASIR: -29.8%; ASPR: -30.5%). The number in TB specific deaths consistently decreased during the study period (P<0.001), while the increase in deaths from other causes drove the overall upward trend in ASMR and ASDR. Four ASRs remained high in males and 5 prefectures. GDP per capita was negatively associated with the ASIR, ASPR and ASDR (P<0.05). Among PTB patients, men, patients with no fixed job, those with a low GDP level, patients with increasing age, those previously treated, those with severe symptoms, those transferred in and those receiving directly observed treatment were more likely to suffer death. CONCLUSION: Guizhou has made progress in reducing PTB cases and TB specific deaths over the last 15 years. Targeted interventions are needed to address these risk factors for death in PTB patients and high-risk areas.
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Tuberculosis Pulmonar , Tuberculosis , Masculino , Humanos , Factores de Riesgo , Tuberculosis/epidemiología , Tuberculosis Pulmonar/epidemiología , China/epidemiología , Años de Vida Ajustados por Discapacidad , Años de Vida Ajustados por Calidad de Vida , Carga Global de Enfermedades , Incidencia , Salud GlobalRESUMEN
Nasopharyngeal tuberculosis is a rare extrapulmonary tuberculosis caused by Mycobacterium tuberculosis invading the nasopharynx. Early clinical symptoms are atypical, making the condition easy to overlook and misdiagnosed. We retrospectively reviewed the case of a 37-year-old man who visited the clinic in March 2023, presenting with enlarged cervical lymph nodes persisting for over a year. Computed tomography and magnetic resonance imaging showed the nasopharynx wall was thickened, and cervical multiple enlarged lymph nodes were visible, presenting bead-like appearance. The enhanced scan revealed the lesion uneven enhancement. He was diagnosed with nasopharyngeal carcinoma with lymph node metastasis based on the images. However, the histopathological examination finally confirmed that the nasopharyngeal and neck mass were tuberculous granulomas. Nasopharyngeal tuberculosis is easily misdiagnosed and mistreated, and it is especially difficult to differentiate from nasopharyngeal carcinoma. When diagnosing and treating neck masses, clinicians should consider the possibility of nasopharyngeal tuberculosis in patients with chronic nasopharyngeal symptoms. Nasopharyngoscope biopsy and histopathological examination have great value in the diagnosis of nasopharyngeal tuberculosis.
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IgG4-related diseases (IgG4-RD) are a group of chronic progressive autoimmune diseases of unknown etiology that are increasingly recognized as an important pathophysiological basis for a variety of systemic diseases. It is thought to involve almost any organ of the body, but the involvement of the central nervous system is relatively rare. We report the case of a 56-year-old male patient admitted to the hospital d recurrent dizziness and nausea for more than 3 months. The preoperative imaging was misdiagnosed as a meningioma, with this lesion demonstrated localized inhomogeneous thickening of the meninges in the left parietal region on T2-weighted and T2 fat suppression sequences with localized nodular changes. The patient's final pathologic diagnosis was IgG4-associated sclerosing thick encephalitis. The diagnosis of IgG4-associated hypertrophic pontine meningitis is challenging. Clinically, IgG4-associated sclerosing diseases usually present as mass-like lesions, which can be easily misdiagnosed as neoplastic lesions due to their similar appearance. These fundamentally recognized autoimmune disorders respond well to corticosteroid therapy. Therefore, accurate detection of IgG4-related disease is critical to prevent patients from undergoing unnecessary surgery.
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Dry eye disease is a multifactorial dysfunction of the tear film and ocular surface, with etiology involving inflammation and oxidative stress on the ocular surface. Pterostilbene (PS) is a secondary metabolite extracted from plants, which possesses remarkable anti-inflammatory and antioxidant effects. However, its application is limited by light instability and very poor water solubility. We modified fat-soluble PS into a biparental pterostilbene-glutaric anhydride-arginine-glycine-aspartic acid (PS-GA-RGD) nanomedicine by prodrug ligation of functional peptides. The aim of this study was to explore the protective effect and potential mechanism of PS-GA-RGD on dry eye disease in vitro and in vivo. We demonstrated good long-term biocompatibility of PS-GA-RGD through rabbit eye stimulation test. Lipopolysaccharide (LPS) was used to induce murine macrophages RAW 264.7 to establish an inflammation and oxidative stress model. In this model, PS-GA-RGD effectively reduced the production of ROS and 8-OHdG, enhancing the expression of antioxidant factor Nrf2 and antioxidant enzyme heme oxygenase-1. In addition, the expression of NF-κB inflammatory pathway significantly increased in LPS-induced RAW 264.7 cells, while PS-GA-RGD could significantly reduce this pathway. Hypertonic saline was utilized to establish a hypertonic model of human corneal epithelial cells. PS-GA-RGD was found to significantly reduce the production of ROS and NLRP3 inflammasomes in this model, exhibiting superior efficacy compared to PS. Experimental dry eye animal models were co-induced with subcutaneous injection of scopolamine and an intelligently controlled environmental system. We demonstrated that PS-GA-RGD nano drugs can prevent and reduce corneal epithelial cell defects and apoptosis, protect conjunctival goblet cells, and have an excellent anti-inflammatory effect. Finally, we demonstrated that RGD sequence in PS-GA-RGD can enhance cellular uptake, corneal retention, and penetration, thereby increasing their bioavailability and efficacy by a cell uptake assay and rabbit corneal drug retention experiment. Overall, this study highlights the potential of PS-GA-RGD nanomedicines in the treatment of dry eyes.
Asunto(s)
Antioxidantes , Síndromes de Ojo Seco , Ratones , Humanos , Animales , Conejos , Antioxidantes/farmacología , Antioxidantes/uso terapéutico , Especies Reactivas de Oxígeno/metabolismo , Lipopolisacáridos , Síndromes de Ojo Seco/metabolismo , Inflamación/tratamiento farmacológico , Antiinflamatorios/uso terapéutico , Oligopéptidos/farmacología , Oligopéptidos/uso terapéutico , Modelos Animales de EnfermedadRESUMEN
BACKGROUND: Peri-implantitis is a polybacterial infection that can lead to the failure of dental implant rehabilitation. This study aimed to profile the microbiome of the peri-implant plaque and estimate the effect of periodontitis on it among 40 Chinese participants with dental implant prostheses and presenting with varying peri-implant and periodontal health states. METHODS: Submucosal plaque samples were collected from four distinct clinical categories based on both their implant and periodontal health status at sampling point. Clinical examinations of dental implant and remaining teeth were carried out. Metagenomic analysis was then performed. RESULTS: The microbiome of the peri-implantitis sites differed from that of healthy implant sites, both taxonomically and functionally. Moreover, the predominant species in peri-implantitis sites were slightly affected by the presence of periodontitis. T. forsythia, P. gingivalis, T. denticola, and P. endodontalis were consistently associated with peri-implantitis and inflammatory clinical parameters regardless of the presence of periodontitis. Prevotella spp. and P. endodontalis showed significant differences in the peri-implantitis cohorts under different periodontal conditions. The most distinguishing function between diseased and healthy implants is related to flagellar assembly, which plays an important role in epithelial cell invasion. CONCLUSIONS: The composition of the peri-implant microbiome varied in the diseased and healthy states of implants and is affected by individual periodontal conditions. Based on their correlations with clinical parameters, certain species are associated with disease and healthy implants. Flagellar assembly may play a vital role in the process of peri-implantitis.
Asunto(s)
Implantes Dentales , Placa Dental , Microbiota , Periimplantitis , Enfermedades Periodontales , Periodontitis , Humanos , Periimplantitis/microbiología , Implantes Dentales/microbiología , Estudios Transversales , Placa Dental/microbiologíaRESUMEN
Over the past decade, colorectal cancer has reported a higher incidence in younger adults and a lower mortality rate. Recently, the influence of the intestinal flora in the initiation, progression, and treatment of colorectal cancer has been extensively studied, as well as their positive therapeutic impact on inflammation and the cancer microenvironment. Historically, traditional Chinese medicine (TCM) has been widely used in the treatment of colorectal cancer via promoted cancer cell apoptosis, inhibited cancer metastasis, and reduced drug resistance and side effects. The present research is more on the effect of either herbal medicine or intestinal flora on colorectal cancer. The interactions between TCM and intestinal flora are bidirectional and the combined impacts of TCM and gut microbiota in the treatment of colon cancer should not be neglected. Therefore, this review discusses the role of intestinal bacteria in the progression and treatment of colorectal cancer by inhibiting carcinogenesis, participating in therapy, and assisting in healing. Then the complex anticolon cancer effects of different kinds of TCM monomers, TCM drug pairs, and traditional Chinese prescriptions embodied in apoptosis, metastasis, immune suppression, and drug resistance are summarized separately. In addition, the interaction between TCM and intestinal flora and the combined effect on cancer treatment were analyzed. This review provides a mechanistic reference for the application of TCM and intestinal flora in the clinical treatment of colorectal cancer and paves the way for the combined development and application of microbiome and TCM.