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Bacteriophages are the viruses that infect bacterial cells. They are the most diverse biological entities on earth and play important roles in microbiome. According to the phage lifestyle, phages can be divided into the virulent phages and the temperate phages. Classifying virulent and temperate phages is crucial for further understanding of the phage-host interactions. Although there are several methods designed for phage lifestyle classification, they merely either consider sequence features or gene features, leading to low accuracy. A new computational method, DeePhafier, is proposed to improve classification performance on phage lifestyle. Built by several multilayer self-attention neural networks, a global self-attention neural network, and being combined by protein features of the Position Specific Scoring Matrix matrix, DeePhafier improves the classification accuracy and outperforms two benchmark methods. The accuracy of DeePhafier on five-fold cross-validation is as high as 87.54% for sequences with length >2000bp.
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Bacteriófagos , Redes Neurales de la Computación , Bacteriófagos/genética , Biología Computacional/métodos , Proteínas Virales/genética , Proteínas Virales/metabolismo , AlgoritmosRESUMEN
Viruses are the most abundant biological entities on earth and are important components of microbial communities. A metagenome contains all microorganisms from an environmental sample. Correctly identifying viruses from these mixed sequences is critical in viral analyses. It is common to identify long viral sequences, which has already been passed thought pipelines of assembly and binning. Existing deep learning-based methods divide these long sequences into short subsequences and identify them separately. This makes the relationships between them be omitted, leading to poor performance on identifying long viral sequences. In this paper, VirGrapher is proposed to improve the identification performance of long viral sequences by constructing relationships among short subsequences from long ones. VirGrapher see a long sequence as a graph and uses a Graph Convolutional Network (GCN) model to learn multilayer connections between nodes from sequences after a GCN-based node embedding model. VirGrapher achieves a better AUC value and accuracy on validation set, which is better than three benchmark methods.
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Metagenoma , Microbiota , Microbiota/genética , BenchmarkingRESUMEN
Juvenile myelomonocytic leukaemia (JMML) is a rare myeloproliferative neoplasm requiring haematopoietic stem cell transplantation (HSCT) for potential cure. Relapse poses a significant obstacle to JMML HSCT treatment, as the lack of effective minimal residual disease (MRD)-monitoring methods leads to delayed interventions. This retrospective study utilized the droplet digital PCR (ddPCR) technique, a highly sensitive nucleic acid detection and quantification technique, to monitor MRD in 32 JMML patients. The results demonstrated that ddPCR detected relapse manifestations earlier than traditional methods and uncovered molecular insights into JMML MRD dynamics. The findings emphasized a critical 1- to 3-month window post-HSCT for detecting molecular relapse, with 66.7% (8/12) of relapses occurring within this period. Slow MRD clearance post-HSCT was observed, as 65% (13/20) of non-relapse patients took over 6 months to achieve ddPCR-MRD negativity. Furthermore, bone marrow ddPCR-MRD levels at 1-month post-HSCT proved to be prognostically significant. Relapsed patients exhibited significantly elevated ddPCR-MRD levels at this time point (p = 0.026), with a cut-off of 0.465% effectively stratifying overall survival (p = 0.007), event-free survival (p = 0.035) and cumulative incidence of relapse (p = 0.035). In conclusion, this study underscored ddPCR's superiority in JMML MRD monitoring post-HSCT. It provided valuable insights into JMML MRD dynamics, offering guidance for the effective management of JMML.
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Trasplante de Células Madre Hematopoyéticas , Leucemia Mielomonocítica Juvenil , Neoplasia Residual , Reacción en Cadena de la Polimerasa , Humanos , Neoplasia Residual/diagnóstico , Masculino , Femenino , Reacción en Cadena de la Polimerasa/métodos , Leucemia Mielomonocítica Juvenil/terapia , Leucemia Mielomonocítica Juvenil/genética , Leucemia Mielomonocítica Juvenil/diagnóstico , Estudios Retrospectivos , Pronóstico , Preescolar , Lactante , NiñoRESUMEN
Idiopathic multicentric Castleman disease (iMCD) is subclassified into iMCD-thrombocytopenia, anasarca, reticulin fibrosis, renal dysfunction, organomegaly (TAFRO) and iMCD-not otherwise specified (NOS) according to the Castleman Disease Collaborative Network (CDCN) consensus criteria. With a deeper understanding of iMCD, a group of patients with iMCD-NOS characterised by polyclonal hypergammaglobulinaemia, plasmacytic/mixed-type lymph node histopathology and thrombocytosis has attracted attention. This group of patients has been previously described as having idiopathic plasmacytic lymphadenopathy (IPL). Whether these patients should be excluded from the current classification system lacks sufficient evidence. This retrospective analysis of 228 patients with iMCD-NOS identified 103 (45.2%) patients with iMCD-IPL. The clinical features and outcomes of patients with iMCD-IPL and iMCD-NOS without IPL were compared. Patients with iMCD-IPL showed a significantly higher inflammatory state but longer overall survival. No significant difference in overall survival was observed between severe and non-severe patients in the iMCD-IPL group according to the CDCN severity classification. Compared with lymphoma-like treatments, multiple myeloma-like and IL-6-blocking treatment approaches in the iMCD-IPL group resulted in significantly higher response rates and longer time to the next treatment. These findings highlight the particularities of iMCD-IPL and suggest that it should be considered a new subtype of iMCD-NOS.
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Enfermedad de Castleman , Linfadenopatía , Humanos , Enfermedad de Castleman/patología , Enfermedad de Castleman/mortalidad , Enfermedad de Castleman/clasificación , Enfermedad de Castleman/diagnóstico , Masculino , Femenino , Persona de Mediana Edad , Adulto , Estudios Retrospectivos , Anciano , Linfadenopatía/patología , Linfadenopatía/etiología , Células Plasmáticas/patologíaRESUMEN
Lipid metabolism diseases have become a tremendous risk worldwide, along with the development of productivity and particular attention to public health. It has been an urgent necessity to exploit reliable imaging strategies for lipids and thus to monitor fatty liver diseases. Herein, by converting the NIR-I signal to the NIR-II signal with IR1061 for the monitoring of lipid, the in vivo imaging of fatty liver disease was promoted on the contrast and visual effect. The main advantages of the imaging promotion in this work included a long emission wavelength, rapid response, and high signal-background-ratio (SBR) value. After promoting the NIR-I signal to NIR-II signal, IR1061 achieved higher SBR value and exhibited a dose-dependent fluorescence intensity at 1100 nm along with the increase of the EtOH proportion as well as steady and selective optical responses toward liposomes. IR1061 was further applied in the in vivo imaging of lipid in fatty liver diseases. In spite of the differences in body weight gain and TC level between healthy mice and fatty liver diseases two models, IR1061 achieved high-resolution imaging in the liver region to monitor the fatty liver disease status. This work might be informatic for the clinical diagnosis and therapeutical treatments of fatty liver diseases.
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Boratos , Metabolismo de los Lípidos , Hepatopatías , Piranos , Animales , Ratones , Imagen Óptica/métodos , Colorantes Fluorescentes , LípidosRESUMEN
BACKGROUND: This study was designed to compare the clinical and patient-reported outcomes (PROs) between the enhanced recovery after surgery (ERAS) protocol and conventional care in patients undergoing esophagectomy for cancer, which have not previously been compared. METHODS: This single-center retrospective study included prospective PRO data from August 2019 to June 2021. Clinical outcomes included perioperative complications and postoperative length of stay (PLOS). Patient-reported outcomes were assessed by using the European Organization for Research and Treatment of Cancer Quality of Life Questionnaire Core-30 (QLQ-C30) and esophagus-specific module (QLQ-OES18) preoperatively to 6 months postoperatively. Mixed-effects models were used to longitudinally compare quality of life (QOL) scores between the two modes. RESULTS: Patients undergoing conventional care and ERAS were analyzed (n = 348 and 109, respectively). The ERAS group had fewer overall complications, pneumonia, arrhythmia, and a shorter PLOS than the conventional group, and outperformed the conventional group in five functional QLQ-C30 domains and five symptom QLQ-OES18 domains, including less dysphagia (p < 0.0001), trouble talking (p = 0.0006), and better eating (p < 0.0001). These advantages persisted for 3 months postoperatively. For the cervical circular stapled anastomosis, the initial domains and duration of benefit were reduced in the ERAS group. CONCLUSIONS: The ERAS protocol has significant advantages over conventional care in terms of clinical outcomes, lowering postoperative symptom burden, and improving functional QOL in patients who have undergone esophagectomy. Selection of the optimal technique for cervical anastomosis is a key operative component of ERAS that maintains the symptom domains and duration of the advantages of PROs.
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Recuperación Mejorada Después de la Cirugía , Neoplasias Esofágicas , Esofagectomía , Medición de Resultados Informados por el Paciente , Complicaciones Posoperatorias , Calidad de Vida , Humanos , Esofagectomía/efectos adversos , Esofagectomía/métodos , Neoplasias Esofágicas/cirugía , Neoplasias Esofágicas/patología , Masculino , Femenino , Persona de Mediana Edad , Estudios Retrospectivos , Estudios de Seguimiento , Anciano , Estudios Prospectivos , Pronóstico , Tiempo de InternaciónRESUMEN
We present a light sheet fluorescence microscopy (LSFM) with active optical manipulation by using linear optical tweezers (LOTs). In this method, two coaxially transmitting laser beams of different wavelengths are shaped using cylindrical lenses to form a linear optical trapping perpendicular to the optical axis and an excitation light sheet (LS) parallel to the optical axis, respectively. Multiple large-sized polystyrene fluorescent microspheres are stably captured by LOTs, and their rotation angles around specific rotation axes are precisely controlled. During a sample rotation, the stationary excitation LS scans the sample to obtain fluorescence sectioning images of the sample at different angles.
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Refractory/relapsed idiopathic multicentric Castleman disease (R/R iMCD) has limited treatment options. With studies showing increased mTOR activation in iMCD patients, sirolimus becomes an attractive and promising therapy for R/R iMCD. Here we report the results of a retrospective study involving 26 R/R iMCD patients treated with sirolimus-containing regimen. The median age at sirolimus initiation was 40.5 years (23-60), with a median prior treatment line of 2 (1-5). 18 patients (69.2%) achieved symptomatic and biochemical response, with a median time to at least overall partial remission of 1.9 months (0.5-14.6). The median follow-up time from sirolimus initiation was 11.7 months (1.6-50.7) and the median time to next treatment (TTNT) was 46.2 months. No patients died at the end of follow-up. Most of the patients in the cohort are in ongoing responses and continue sirolimus therapy. Sirolimus is well tolerated with minor adverse effects. In conclusion, sirolimus is effective for R/R iMCD patients with good tolerance.
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Cerebral ischemia-reperfusion injury (I/RI) is one of the principal pathogenic factors in the poor prognosis of ischemic stroke, for which current therapeutic options to enhance neurological recovery are notably insufficient. Dental pulp stem cell-derived extracellular vesicles (DPSC-EVs) have promising prospects in stroke treatment and the specific underlying mechanisms have yet to be fully elucidated. The present study observed that DPSC-EVs ameliorated the degree of cerebral edema and infarct volume by reducing the apoptosis of neurons. Furthermore, the miRNA sequencing and functional enrichment analysis identified that miR-877-3p as a key component in DPSC-EVs, contributing to neuroprotection and anti-apoptotic effects. Following target prediction and dual-luciferase assay indicated that miR-877-3p interacted with Bcl-2-associated transcription factor (Bclaf1) to play a function. The miR-877-3p inhibitor or Bclaf1 overexpression reversed the neuroprotective effects of DPSC-EVs. The findings reveal a novel therapeutic pathway where miR-877-3p, transferred via DPSC-EVs, confers neuroprotection against cerebral I/RI, highlighting its potential in promoting neuronal survival and recovery post-ischemia.
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Apoptosis , Pulpa Dental , Vesículas Extracelulares , MicroARNs , Neuronas , Recuperación de la Función , Daño por Reperfusión , Transducción de Señal , Células Madre , MicroARNs/genética , MicroARNs/metabolismo , Animales , Vesículas Extracelulares/metabolismo , Vesículas Extracelulares/trasplante , Pulpa Dental/citología , Pulpa Dental/metabolismo , Daño por Reperfusión/metabolismo , Daño por Reperfusión/genética , Daño por Reperfusión/terapia , Neuronas/metabolismo , Neuronas/patología , Masculino , Células Madre/metabolismo , Proteína p53 Supresora de Tumor/metabolismo , Proteína p53 Supresora de Tumor/genética , Ratas Sprague-Dawley , Isquemia Encefálica/metabolismo , Isquemia Encefálica/genética , Ratones Endogámicos C57BL , Ratas , Células CultivadasRESUMEN
BACKGROUND: There is increasing interest in elucidating the relationship between adenoid hypertrophy (AH) and allergic rhinitis (AR). However, the impact of aeroallergen sensitization patterns on children with AH and AR remains unclear. METHODS: Patients aged 2-8 years (recruited from January 2019 to December 2022) with nasal symptoms were assessed for allergies, adenoid size, and respiratory viral infection history. The serum total immunoglobulin E (IgE) and specific IgE levels were measured, and flexible nasal endoscopy was performed. The relationship between AH, aeroallergen sensitization patterns, and lymphocyte subpopulations in adenoid samples was analyzed using flow cytometry. RESULTS: In total, 5281 children were enrolled (56.5% with AR; and 48.6% with AH). AH was more prevalent in children with AR. Compared to nonsensitized individuals, those polysensitized to molds had a higher prevalence of AH (adjusted OR 1.61, 95% CI 1.32-1.96) and a greater occurrence of two or more respiratory viral infections, particularly in adenoidectomy patients. The percentages and corrected absolute counts of regulatory T (Treg) cells, activated Tregs, class-switched memory B cells (CSMBs), natural killer (NK) T cells, and NK cell subpopulations were reduced in the adenoid tissues of children with both AH and AR (AH-AR) compared to AH-nAR children. Polysensitization in AH-AR children correlated with lower CSMB percentages. CONCLUSION: Polysensitivity to molds is associated with an increased risk of AH in children with AR. Fewer B cells, NK cells, and Treg cells with an effector/memory phenotype were detected in the adenoids of AR children, and these lower percentages of immune cells, particularly CSMBs, were closely linked to aeroallergen sensitization models and respiratory viral infection.
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Tonsila Faríngea , Hipertrofia , Inmunoglobulina E , Rinitis Alérgica , Humanos , Tonsila Faríngea/inmunología , Tonsila Faríngea/patología , Niño , Masculino , Femenino , Hipertrofia/inmunología , Preescolar , Rinitis Alérgica/inmunología , Rinitis Alérgica/epidemiología , Inmunoglobulina E/sangre , Fenotipo , Alérgenos/inmunología , Linfocitos T Reguladores/inmunología , Prevalencia , AdenoidectomíaRESUMEN
PURPOSE: Surgery for esophageal squamous cell carcinoma (ESCC) is characterized by a poor prognosis and high complication rate, resulting in a heavy symptom burden and poor health-related quality of life (QOL). We evaluated longitudinal patient-reported outcomes (PROs) to analyze the correlations between symptoms and QOL and their changing characteristics during postoperative rehabilitation. METHODS: We investigated patients with ESCC who underwent minimally invasive McKeown esophagectomy at Sichuan Cancer Hospital between April 2019 and December 2019. Longitudinal data of the clinical characteristics and PROs were collected. The MD Anderson Symptom Inventory and European Organization for Research and Treatment of Cancer (EORTC) QOL questionnaires were used to assess symptoms and QOL and compare the trajectories of PROs during the investigation. RESULTS: A total of 244 patients with ESCC were enrolled in this study. Regarding QOL, role and emotional functions returned to baseline at 1 month after surgery, and cognitive and social functions returned to baseline at 3 months after surgery. However, physical function and global QOL did not return to baseline at 1 year after surgery. At 7 days and 1, 3, 6, and 12 months after surgery, the main symptoms of the patients were negatively correlated with physical, role, emotional, cognitive, and social functions and the overall health status (P < 0.05). CONCLUSION: Patients with ESCC experience reduced health-related QOL and persisting symptoms after minimally invasive McKeown esophagectomy, but a recovery trend was observed within 1 month. The long-term QOL after esophagectomy is acceptable.
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Neoplasias Esofágicas , Carcinoma de Células Escamosas de Esófago , Humanos , Carcinoma de Células Escamosas de Esófago/cirugía , Carcinoma de Células Escamosas de Esófago/complicaciones , Calidad de Vida , Neoplasias Esofágicas/cirugía , Neoplasias Esofágicas/patología , Esofagectomía/efectos adversos , Examen Físico , Complicaciones Posoperatorias/etiología , Estudios Retrospectivos , Resultado del TratamientoRESUMEN
BACKGROUND: Subarachnoid hemorrhage (SAH) is a severe stroke subtype that lacks effective treatment. Exosomes derived from human dental pulp stem cells (DPSCs) are a promising acellular therapeutic strategy for neurological diseases. However, the therapeutic effects of DPSC-derived exosomes (DPSC-Exos) on SAH remain unknown. In this study, we investigated the therapeutic effects and mechanisms of action of DPSC-Exos in SAH. MATERIALS AND METHODS: SAH was established using 120 male Sprague-Dawley rats. One hour after SAH induction, DPSC-Exos were administered via tail vein injection. To investigate the effect of DPSC-Exos, SAH grading, short-term and long-term neurobehavioral assessments, brain water content, western blot (WB), immunofluorescence staining, Nissl staining, and HE staining were performed. The role of miR-197-3p/FOXO3 in regulating pyroptosis was demonstrated through miRNA sequencing, bioinformatics analysis, and rescue experiments. The SAH model in vitro was established by stimulating BV2 cells with hemoglobin (Hb) and the underlying mechanism of DPSC-Exos was investigated through WB and Hoechst/PI staining. RESULTS: The expressions of pro-inflammatory cytokines (IL-1ß, IL-6, and TNF-α) were increased after SAH. DPSC-Exos alleviated brain edema and neuroinflammation by inhibiting the expression of FOXO3 and reducing NLRP3 inflammasome activation, leading to improved neurobehavioral functions at 24 h after SAH. In vitro, the expression of the NLRP3 inflammasome components (NLRP3 and caspase1-p20), GSDMD-N, and IL-18 was inhibited in BV2 cells pretreated with DPSC-Exos. Importantly, DPSC-Exos overexpressing miR-197-3p had a more obvious protective effect than those from NC-transfected DPSCs, while those from DPSCs transfected with the miR-197-3p inhibitor had a weaker protective effect. Functional studies indicated that miR-197-3p bound to the 3'-untranslated region of FOXO3, inhibiting its transcription. Furthermore, the overexpression of FOXO3 reversed the protective effects of miR-197-3p. CONCLUSIONS: DPSC-Exos inhibited activation of the NLRP3 inflammasome and related cytokine release via the miR-197-3p/FOXO3 pathway, alleviated neuroinflammation, and inhibited microglial pyroptosis. These findings suggest that using DPSC-Exos is a promising therapeutic strategy for SAH.
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Pulpa Dental , Exosomas , Proteína Forkhead Box O3 , Células Madre Mesenquimatosas , MicroARNs , Microglía , Enfermedades Neuroinflamatorias , Piroptosis , Ratas Sprague-Dawley , Hemorragia Subaracnoidea , Animales , Exosomas/metabolismo , MicroARNs/metabolismo , MicroARNs/genética , Proteína Forkhead Box O3/metabolismo , Masculino , Células Madre Mesenquimatosas/metabolismo , Ratas , Pulpa Dental/citología , Pulpa Dental/metabolismo , Hemorragia Subaracnoidea/metabolismo , Hemorragia Subaracnoidea/terapia , Humanos , Enfermedades Neuroinflamatorias/metabolismo , Microglía/metabolismo , Proteína con Dominio Pirina 3 de la Familia NLR/metabolismo , Ratones , Modelos Animales de EnfermedadRESUMEN
Despite advancements in treatment modalities such as flow diverters, the optimal management of posterior communicating artery (PComA) aneurysms remains uncertain. While PComA aneurysms treated with the Pipeline Embolization Device (PED) has been reported, the characteristics and progression of incomplete occluded aneurysms remain unclear. Therefore, our study aims to investigate the occlusion status and recurrence rates of PComA aneurysms treated with PED. A retrospective review of consecutive PComA aneurysm patients treated with PED was conducted between January 2015 and December 2020. Only patients with radiological follow-up were included. PComA aneurysms were categorized into incomplete occlusion and complete occlusion group. The primary outcomes included the characteristics of incomplete occlusion at the follow-up angiography. Among 121 PComA aneurysms treated with PED at our institution, 80 aneurysms were eligible in our study. During the follow-up period, 19 (23.8%) aneurysms demonstrated incomplete occlusion. Notably, there were no instances of recurrence among the 80 followed-up cases. Baseline characteristics of patients and aneurysms were comparable between the groups with complete and incomplete occlusion. However, the incomplete occlusion group showed a lower rate of assisted coils embolization (21.2% vs. 55.7%, P = 0.017) and shorter median operative time (91.0 vs. 145.5 min, P = 0.039). Differences in functional outcomes, complications, and PComA occlusion status between the groups were not significant. Multivariate analysis revealed the use of coils was associated with lower odds of incomplete PComA aneurysm occlusion (OR 0.01, 95% CI 0.001-0.12; P = 0.001), while aneurysm size was associated with higher odds of incomplete occlusion (OR 1.25, 95% CI 1.10-1.46; P = 0.002). The treatment of PED for PComA aneurysm demonstrated favorable outcomes, with an acceptable rate of incomplete occlusion and no instances of recurrence observed. However, further research is needed to explore the optimal procedural strategy for large-sized PComA aneurysms.
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Embolización Terapéutica , Aneurisma Intracraneal , Recurrencia , Humanos , Aneurisma Intracraneal/terapia , Masculino , Embolización Terapéutica/métodos , Embolización Terapéutica/instrumentación , Femenino , Persona de Mediana Edad , Anciano , Estudios Retrospectivos , Resultado del Tratamiento , Adulto , Angiografía CerebralRESUMEN
OBJECTIVE: This study aims to investigate the quality consistency between traditional decoction (TD) of Amomum villosum and its dispensing granule decoction (DGD). Fifteen batches of TD and nine batches of dispensing granules (manufactured by A, B, and C) were prepared and evaluated for their consistency. METHODS: Firstly, The chemical similarity of TD and DGD was examined using GC and HPLC, coupled with hierarchical cluster analysis (HCA), criteria importance though intercrieria correlation(CRITIC) weighting method, and principal component analysis (PCA). Secondly, the gastrointestinal motility experiments in mice, along with the CRITIC weighting method, were employed to assess the bioequivalence of TD and DGD of Amomum villosum. Finally, the entropy weight technique-gray relative analysis(GRA) method was used to compare the quality of Amomum villosum decoctions. RESULTS: â The CRITIC weighting method indicated significantly higher scores for TD than DGD (p < 0.01). HCA and PCA results demonstrated a clear distinction between TD and DGD. â¡Gastrointestinal motility test results revealed no significant difference between TD and DGD in other indicators (p > 0.05).â¢Gray relative analysis results showed that the relative correlation of TD was more significant than that of DGD. CONCLUSION: The chemical composition of DGD and TD differed. The biological activity of DGD-A/B was consistent with that of TD, while the difference between DGD-C and TD was significant. A comprehensive evaluation showed that TD exhibited better quality than DGD. DGD manufacturers should optimize the preparation process to enhance product quality.
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Amomum , Medicamentos Herbarios Chinos , Animales , Ratones , Medicamentos Herbarios Chinos/química , Amomum/química , Equivalencia Terapéutica , Cromatografía Líquida de Alta Presión/métodos , Análisis de Componente PrincipalRESUMEN
OBJECTIVE: To explore the genetic etiology for a Chinese pedigree affected with Treacher-Collins syndrome (TCS) through whole exome sequencing (WES). METHODS: A TCS pedigree which was diagnosed at the Women and Children's Hospital Affiliated to Qingdao University on February 5, 2020 was selected as the study subject. Following collection of clinical data, WES was carried out. Candidate variant was validated through Sanger sequencing and bioinformatic analysis. RESULTS: The WES results showed that the proband has harbored a heterozygous c.3337C>T variant of the TCOF1 gene, and Sanger sequencing confirmed that his mother and brother also carried the same variant. Based on guidelines from the American College of Medical Genetics and Genomics (ACMG), the variant was predicted as pathogenic (PVS1+PM2_Supporting+PP4). CONCLUSION: The heterozygous c.3337C>T variant of the TCOF1 gene probably underlay the pathogenesis of TCS in this pedigree.
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Pueblo Asiatico , Disostosis Mandibulofacial , Niño , Femenino , Humanos , Masculino , Pueblo Asiatico/genética , China , Secuenciación del Exoma , Disostosis Mandibulofacial/genética , Madres , Proteínas Nucleares/genética , Linaje , Fosfoproteínas/genéticaRESUMEN
Juvenile myelomonocytic leukaemia (JMML) is an aggressive paediatric leukaemia characterized by mutations in five canonical RAS pathway genes, including the NF1 gene. JMML is driven by germline NF1 gene mutations, with additional somatic aberrations resulting in the NF1 biallelic inactivation, leading to disease progression. Germline mutations in the NF1 gene alone primarily cause benign neurofibromatosis type 1 (NF1) tumours rather than malignant JMML, yet the underlying mechanism remains unclear. Here, we demonstrate that with reduced NF1 gene dose, immune cells are promoted in anti-tumour immune response. Comparing the biological properties of JMML and NF1 patients, we found that not only JMML but also NF1 patients driven by NF1 mutations could increase monocytes generation. But monocytes cannot further malignant development in NF1 patients. Utilizing haematopoietic and macrophage differentiation from iPSCs, we revealed that NF1 mutations or knockout (KO) recapitulated the classical haematopoietic pathological features of JMML with reduced NF1 gene dose. NF1 mutations or KO promoted the proliferation and immune function of NK cells and iMacs derived from iPSCs. Moreover, NF1-mutated iNKs had a high capacity to kill NF1-KO iMacs. NF1-mutated or KO iNKs administration delayed leukaemia progression in a xenograft animal model. Our findings demonstrate that germline NF1 mutations alone cannot directly drive JMML development and suggest a potential cell immunotherapy for JMML patients.
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Leucemia Mielomonocítica Juvenil , Neurofibromatosis 1 , Animales , Humanos , Leucemia Mielomonocítica Juvenil/genética , Leucemia Mielomonocítica Juvenil/terapia , Leucemia Mielomonocítica Juvenil/metabolismo , Neurofibromina 1/genética , Genes de Neurofibromatosis 1 , Mutación de Línea Germinal , Neurofibromatosis 1/genética , Neurofibromatosis 1/terapia , Mutación , Inmunidad , Células Germinativas/metabolismo , Células Germinativas/patologíaRESUMEN
MOTIVATION: Viruses, the most abundant biological entities on earth, are important components of microbial communities, and as major human pathogens, they are responsible for human mortality and morbidity. The identification of viral sequences from metagenomes is critical for viral analysis. As massive quantities of short sequences are generated by next-generation sequencing, most methods utilize discrete and sparse one-hot vectors to encode nucleotide sequences, which are usually ineffective in viral identification. RESULTS: In this article, Virtifier, a deep learning-based viral identifier for sequences from metagenomic data is proposed. It includes a meaningful nucleotide sequence encoding method named Seq2Vec and a variant viral sequence predictor with an attention-based long short-term memory (LSTM) network. By utilizing a fully trained embedding matrix to encode codons, Seq2Vec can efficiently extract the relationships among those codons in a nucleotide sequence. Combined with an attention layer, the LSTM neural network can further analyze the codon relationships and sift the parts that contribute to the final features. Experimental results of three datasets have shown that Virtifier can accurately identify short viral sequences (<500 bp) from metagenomes, surpassing three widely used methods, VirFinder, DeepVirFinder and PPR-Meta. Meanwhile, a comparable performance was achieved by Virtifier at longer lengths (>5000 bp). AVAILABILITY AND IMPLEMENTATION: A Python implementation of Virtifier and the Python code developed for this study have been provided on Github https://github.com/crazyinter/Seq2Vec. The RefSeq genomes in this article are available in VirFinder at https://dx.doi.org/10.1186/s40168-017-0283-5. The CAMI Challenge Dataset 3 CAMI_high dataset in this article is available in CAMI at https://data.cami-challenge.org/participate. The real human gut metagenomes in this article are available at https://dx.doi.org/10.1101/gr.142315.112. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Aprendizaje Profundo , Microbiota , Humanos , Metagenoma , Programas Informáticos , Redes Neurales de la ComputaciónRESUMEN
BACKGROUND: Standard treatment for drug-susceptible tuberculosis (DS-TB) includes a multidrug regimen requiring at least 6 months of treatment, and this lengthy treatment easily leads to poor adherence. There is an urgent need to simplify and shorten treatment regimens to reduce interruption and adverse event rates, improve compliance, and reduce costs. METHODS: ORIENT is a multicenter, randomized controlled, open-label, phase II/III, non-inferiority trial involving DS-TB patients to evaluate the safety and efficacy of short-term regimens compared with the standardized six-month treatment regimen. In stage 1, corresponding to a phase II trial, a total of 400 patients are randomly divided into four arms, stratified by site and the presence of lung cavitation. Investigational arms include 3 short-term regimens with rifapentine 10 mg/kg, 15 mg/kg, and 20 mg/kg, while the control arm uses the standardized six-month treatment regimen. A combination of rifapentine, isoniazid, pyrazinamide, and moxifloxacin is administered for 17 or 26 weeks in rifapentine arms, while a 26-week regimen containing rifampicin, isoniazid, pyrazinamide, and ethambutol is applied in the control arm. After the safety and preliminary effectiveness analysis of patients in stage 1, the control arm and the investigational arm meeting the conditions will enter into stage 2, which is equivalent to a phase III trial and will be expanded to recruit DS-TB patients. If all investigational arms do not meet the safety conditions, stage 2 will be canceled. In stage 1, the primary safety endpoint is permanent regimen discontinuation at 8 weeks after the first dose. The primary efficacy endpoint is the proportion of favorable outcomes at 78 weeks after the first dose for both two stages. DISCUSSION: This trial will contribute to the optimal dose of rifapentine in the Chinese population and suggest the feasibility of the short-course treatment regimen containing high-dose rifapentine and moxifloxacin for DS-TB. TRIAL REGISTRATION: The trial has been registered on ClinicalTrials.gov on 28 May 2022 with the identifier NCT05401071.
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Rifampin , Tuberculosis , Humanos , Rifampin/efectos adversos , Isoniazida/efectos adversos , Pirazinamida , Moxifloxacino/uso terapéutico , Tuberculosis/tratamiento farmacológico , Ensayos Clínicos Controlados Aleatorios como Asunto , Estudios Multicéntricos como Asunto , Ensayos Clínicos Fase II como AsuntoRESUMEN
OBJECTIVE: The small intestinal bacterial overgrowth (SIBO) in acute pancreatitis correlates with the severity of the disease. However, corresponding studies on the microbial composition of the duodenal mucosa of patients are uncommon. METHODS: Duodenal mucosal biopsies were collected by gastroscopy from 16 patients with mild acute pancreatitis (the Ap group) and 16 healthy individuals (the control group) and subjected to histological studies as well as bacterial 16S rRNA gene sequencing. Caerulein and L-arginine were used to induce mild acute pancreatitis (MAP) and severe acute pancreatitis (SAP) in mice, respectively, and their pancreas and duodenum were collected for histological studies. RESULTS: H&E analysis displayed no significant pathological damage in the descending duodenum of patients with acute pancreatitis compared with that of the controls. Immunofluorescence and Real-time PCR revealed that the expressions of tight junction proteins (TJPs) in duodenal mucosa were decreased in acute pancreatitis. The results of the alpha diversity analysis revealed no significant difference between the two groups, while LEfSe and the random forest revealed a few differences, indicating that the descending duodenum mucosal microbiota changed slightly in patients with mild acute pancreatitis. We observed the pathological changes and the expression of TJPs in the duodenum in the three groups of mice and found that SAP mice had more severe pathological damage in the duodenum. Furthermore, the expression of TJPs in the duodenum was lower in the MAP and SAP groups of mice compared to control mice, but it was similar in both groups. CONCLUSION: Patients with mild acute pancreatitis had mild duodenal barrier dysfunction and slight changes in duodenal mucosal microbiota.
Asunto(s)
Microbiota , Pancreatitis , Humanos , Enfermedad Aguda , ARN Ribosómico 16S/genética , Pancreatitis/metabolismo , Duodeno/patología , Mucosa Intestinal/metabolismo , Proteínas de Uniones Estrechas/metabolismoRESUMEN
BACKGROUND: We aimed to assess the role of histogram analysis of DCE-MRI parameters for accurately distinguishing renal clear cell carcinoma from renal hamartoma with minimal fat. METHODS: Patients with renal tumors were enrolled from January 2013 to December 2015, including renal clear cell carcinoma (n = 39) and renal hamartoma (n = 10). Preoperative DCE-MR Imaging was performed, and whole-tumor regions of interest were drawn to obtain the corresponding histogram parameters, including skewness, kurtosis, frequency size, energy, quartile, etc. Histogram parameters differences between renal clear cell car-cinoma and renal hamartoma with minimal fat were compared. The diagnostic value of each significant parameter in predicting malignant tumors was determined. RESULTS: Histogram parameters of the DCE map contributed to differentiating the benign from malignant renal tumor groups. Histogram analysis of DCE maps could effectively present the heterogeneity of renal tumors and aid in differentiating benign and malignant tumors. ROC analysis results indicated that when frequency size = 1,732 was set as the threshold value, favorable diagnostic performance in predicting malignant tumors was achieved (AUC - 0.964; sensitivity - 84.6%; specificity - 100%), followed by skewness, Energy, Entropy, Uniformity, quartile 5, quartile 50, and kurtosis. CONCLUSIONS: Histogram analysis of DCE-MRI shows promise for differentiating benign and malignant renal tumors. Frequency size was the most significant parameter for predicting renal clear cell carcinoma.