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The SysteMHC Atlas v1.0 was the first public repository dedicated to mass spectrometry-based immunopeptidomics. Here we introduce a newly released version of the SysteMHC Atlas v2.0 (https://systemhc.sjtu.edu.cn), a comprehensive collection of 7190 MS files from 303 allotypes. We extended and optimized a computational pipeline that allows the identification of MHC-bound peptides carrying on unexpected post-translational modifications (PTMs), thereby resulting in 471K modified peptides identified over 60 distinct PTM types. In total, we identified approximately 1.0 million and 1.1 million unique peptides for MHC class I and class II immunopeptidomes, respectively, indicating a 6.8-fold increase and a 28-fold increase to those in v1.0. The SysteMHC Atlas v2.0 introduces several new features, including the inclusion of non-UniProt peptides, and the incorporation of several novel computational tools for FDR estimation, binding affinity prediction and motif deconvolution. Additionally, we enhanced the user interface, upgraded website framework, and provided external links to other resources related. Finally, we built and provided various spectral libraries as community resources for data mining and future immunopeptidomic and proteomic analysis. We believe that the SysteMHC Atlas v2.0 is a unique resource to provide key insights to the immunology and proteomics community and will accelerate the development of vaccines and immunotherapies.
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Bases de Dados de Proteínas , Peptídeos , Proteômica , Espectrometria de Massas , Peptídeos/química , Peptídeos/imunologia , Processamento de Proteína Pós-Traducional , Proteômica/métodos , Bases de Dados de Proteínas/normas , Internet , Humanos , AnimaisRESUMO
PURPOSE: The purpose of the study was to investigate the effect of spread through air spaces (STAS) on the postoperative prognosis of patients with multiple primary lung cancers staged from IA to IB based on tumor size. METHODS: Clinicopathological and follow-up data of 122 patients with multiple primary lung cancers diagnosed at stages IA-IB and surgically treated at the Department of Thoracic Surgery, Shenzhen people's Hospital from January 2019 to December 2021 were retrospectively analyzed. The study involved 42 males and 80 females. STAS status was used to divide them into two groups (87 cases in STAS (-) and 35 cases in STAS (+)). A logistic regression analysis, univariate and multivariate Cox regression analysis, and Kaplan-Meier curves (K-M) were used to determine how STAS affected recurrence-free survival (RFS) in patients. RESULTS: STAS (+) had a significantly higher recurrence rate than STAS (-). STAS was predicted by smoking history (P = 0.044), main tumor diameter (P = 0.02), and solid nodules on chest CT (P = 0.02). STAS incidence was not significantly different between lobectomy and sublobar resection groups (P = 0.17). Solid nodules on CT, tumor diameter, vascular invasion, pleural invasion, and STAS were significant predictors of recurrence in the univariate Cox regression analysis. Tumor diameter, pleural invasion and STAS were significant prognostic factors for recurrence in the multivariate Cox regression analysis. Furthermore, STAS (+) group was at greater risk of recurrence than STAS (-) group (34% vs. 0%, P < 0.05)ã. CONCLUSION: Stage IA-IB multiple primary lung cancer patients with STAS (+) had a higher recurrence rate and a shorter overall survival rate.
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Neoplasias Pulmonares , Neoplasias Primárias Múltiplas , Feminino , Masculino , Humanos , Neoplasias Pulmonares/cirurgia , Estudos Retrospectivos , Hospitais , Análise MultivariadaRESUMO
Efficient nitric oxide (NO) removal without nitrogen dioxide (NO2 ) emission is desired for the control of air pollution. Herein, a series of (Zr/Ti)UiO-66-NH2 with congenetic shell-core structure, denoted as Ti-UION, are rapidly synthesized by microwave-assisted post-synthetic modification for NO removal. The optimal Ti-UION (i.e., 2.5Ti-UION) exhibits the highest activity of 80.74% without NO2 emission with moisture, which is 21.65% greater than that of the UiO-66-NH2 . The NO removal efficiency of 2.5Ti-UION further increases to 95.92% without photocatalyst deactivation under an anhydrous condition. This is because selectively produced NO2 in photocatalysis is completely adsorbed into micropores, refreshing active sites for subsequent reaction. In addition, the enhanced photocatalytic activity after Ti substitution is due to the presence of Ti electron acceptor, the potential difference between the shell and core of Ti-UION crystal, and the high conductivity of TiO units. Additionally, the improved adsorption of gas molecules not only favors NO oxidation, but also avoids the emission of NO2 . This work provides a feasible strategy for rapid metal substitution in metal-organic frameworks and insights into enhanced NO photodegradation.
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The nasolabial folds (NLFs) may be shallowed with the use of nostril base augmentation. This study aimed to design and customize patient-specific implants (PSIs) with computer-aided design/computer-aided manufacturing (CAD/CAM) to correct NLF deepening caused by midfacial aging. The patient's head computed tomography data obtained and were used for reconstruction. The PSIs were customized by CAD/CAM techniques, which were implanted into a nasal base for shallow NLFs caused by midfacial aging. Preoperative and postoperative photos and a wrinkle severity rating scale were used to evaluate the changes in NLFs. Also, the global esthetic improvement scale was used to investigate the surgical satisfaction of patients. Eleven patients (22 NLFs) received PSIs in the nasal base (22 implants). The customized PSI matched well with premaxilla, reducing the difficulty of operation. After 3 to 12 months of follow-up, PSI was stable without foreign body reaction or inflammatory reaction. Postoperative wrinkle severity rating scale scores showed that NLF severity was reduced in all patients, with a significant esthetic improvement compared with preoperatively ( P < 0.01). The global esthetic improvement scale showed an extremely satisfied improved NLF in 27.27% of patients, much improved in 63.63%, and improved in 9.90% (2/22), and none reported change or poor NLF. Patient satisfaction with their midface appearance differed significantly before and after surgery ( P < 0.01). Individualized PSI designed with high precision and matching degree by CAD and prepared using CAM could be applied to overcome the limitations of noncustomized implants.
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Implantes Dentários , Envelhecimento da Pele , Humanos , Sulco Nasogeniano , Satisfação do Paciente , Envelhecimento , Ácido HialurônicoRESUMO
BACKGROUND: To assess preliminarily the effect of concentrated growth factor (CGF) for repair of nasal septal mucosal defect after rhinoplasty. METHODS: Ten women with mucosal defects of the nasal septum were enrolled from May 2017 to May 2018. Liquid and gel CGF was prepared from each patient's blood sample using a Medifuge system, including benchtop centrifuge. After debridement of the defect, the prepared liquid CGF was injected around the wound, and a membranous CGF film was applied to the surface. Vaseline gauze was used to pack the nostrils. All patients were treated with CGF at intervals from 3 to 5 days. RESULTS: After 3 to 12 treatments, all the patients achieved successful repair of the nasal septal mucosal defect, with good appearance and function. During a follow-up of 3 to 6 months, no recurrence was observed. CONCLUSION: CGF appeared to have great curative effect for patients with nasal septal mucosal defects after rhinoplasty. The procedure was easy to perform and should be considered worthwhile in clinical practice. LEVEL OF EVIDENCE IV: This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266.
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Rinoplastia , Feminino , Humanos , Peptídeos e Proteínas de Sinalização Intercelular , Septo Nasal/cirurgia , Plasma , Estudos Retrospectivos , Resultado do TratamentoRESUMO
An oval-shaped face is considered ideal in Chinese culture, which means not only narrow mid and low face but also appropriate proportion between them. Numerous surgical resections of the malar and mandibular angles began in the 1980s. The objective of this study was to investigate the facial proportion index before and after facial contour surgery. All 266 patients were subjected to L-shaped reduction malarplasty and reduction of mandibular angles with partial masseter muscle resection. All computed tomographic parameters (preoperative and 2 years postoperative) were conducted on facial morphometry to reveal the change of the facial proportion index of hard and soft tissue, respectively, such as the widest part of the mid face (WM), widest part of the lower face (WL), facial height (FH), WM/WL, WM/FH, and WL/FH. All patients were satisfied with the optimal outcome of the combined facial contour surgery. Morphometric analysis indicated that the ideal WM/WL ratio was 1.27 ± 0.1 (1.21 ± 0.09 preoperative) in hard tissue and 1.2 ± 0.12 (1.16 ± 0.12 preoperative) in soft tissue 2 years postoperatively. The combined facial contour surgery could acquire an ideal facial contour for Chinese patients. Furthermore, the relative proportion index can be referenced as the standard for preoperative design.
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Povo Asiático , Estética , Face/cirurgia , Mandíbula/cirurgia , Músculo Masseter/cirurgia , Procedimentos de Cirurgia Plástica , Zigoma/cirurgia , Adulto , Cefalometria , Face/diagnóstico por imagem , Feminino , Humanos , Imageamento Tridimensional , Masculino , Mandíbula/diagnóstico por imagem , Osteotomia Mandibular/métodos , Músculo Masseter/diagnóstico por imagem , Pessoa de Meia-Idade , Tomografia Computadorizada por Raios X , Adulto Jovem , Zigoma/diagnóstico por imagemRESUMO
INTRODUCTION: HA fillers may induce facial vascular embolism. The resulting tissue ischemia and necrosis are severe iatrogenic complications for which no effective treatments are available. OBJECTIVE: This single-center case series studied the use of liquid CGF in the management of facial tissue necrosis due to HA injection. METHODS: All 12 patients with facial tissue necrosis (2 mild, 3 moderate, 7 severe) were previously treated with hyaluronidase injection in outside hospitals. They received a routine injection of hyaluronidase (dose of 400-1500 U) at the site of ischemia immediately after admission to the authors' hospital, but CGF was also injected. CGF injection was repeated once weekly until wound healing. Efficacy was assessed at 4 weeks (mean, 24.08 days). RESULTS: No patient experienced wound expansion or aggravation or infection at the sites of necrosis. A complete healing rate of 91.67% was noted at the 4-week follow-up. No scarring was evident in patients with mild to moderate necrosis. Those with moderate necrosis exhibited varied degrees of scarring after recovery, and scarring was evident in those with severe necrosis. No severe adverse effects occurred. CONCLUSION: CGF promoted the healing of ischemic and necrotic tissue wounds induced by facial vascular embolism following injection of HA fillers. CGF should be considered as a nonsurgical treatment method for vascular embolism following HA filler injection.
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Preenchedores Dérmicos , Embolia , Humanos , Ácido Hialurônico/uso terapêutico , Preenchedores Dérmicos/efeitos adversos , Hialuronoglucosaminidase/uso terapêutico , Hialuronoglucosaminidase/efeitos adversos , Injeções Subcutâneas , Necrose/etiologia , Embolia/induzido quimicamente , Embolia/tratamento farmacológico , Isquemia/tratamento farmacológico , Isquemia/complicações , Peptídeos e Proteínas de Sinalização IntercelularRESUMO
Background: Until now, the relevance of the tanning response to sun exposure and skin diseases has incomplete and inconsistent epidemiological observations. In this case, it is valuable to find out the causality of tanning response to sun exposure and skin diseases, and take a step further toward developing effective therapies as well as prevention methods. Methods: We investigated the causal effect of tanning response to sun exposure on 10 major skin diseases that have been studied in recent large-scale genome-wide association studies (GWASs). Significant independent genetic variants from large-scale GWAS on ease of skin tanning (N = 453,065) are selected as the effective instrumental variables (IVs). For each skin disease, we extracted the summary statistics of those IVs (or their proxies) from the corresponding skin disease-GWAS as the valid IVs. Mendelian randomization (MR) was further performed to evaluate the causal association of ease of skin tanning with each of the skin diseases using different statistical methods, including inverse-variance weighted (IVW), the weighted median, and MR-Egger. Sensitivity analysis was also conducted to evaluate the effect of horizontal pleiotropy and heterogeneity. Results: We observe significant associations between six skin diseases with tanning response to sun exposure with adjusted p-value derived by IVW less than 0.05 and with nominal p value less than 0.05 at the same time derived by either MR-Egger or weighted median. The six skin diseases include actinic keratosis (IVW FDR = 1.71E-40, MR Egger p-value = 3.46E-22), seborrhoeic keratosis (IVW FDR = 2.97E-4, MR Egger p-value = 1.06E-3), blepharochalasis (IVW FDR = 1.30E-3, MR Egger p-value = 2.91E-4), seborrhoeic dermatitis (IVW FDR = 1.29E-2, MR Egger p-value = 1.23E-2), malignant melanoma of skin (IVW FDR = 2.95E-2, MR Egger p-value = 1.91E-2), and freckles (IVW FDR = 2.95E-2, weighted median p-value = 1.02E-3). Interestingly, we find increased trends of developing all of the six skin diseases with increased tanning response to sun exposure (beta values are positive using IVW, MR-egger, and weighted median methods). We also replicate the association on three skin diseases using an independent outcome GWAS cohort, including malignant melanoma of the skin (replication IVW p-value = 2.13E-39), actinic keratosis (replication IVW p-value = 4.64E-32), and seborrhoeic keratosis (replication IVW p-value = 1.79E-3). Conclusion: Our observation shows that the tanning response to sun exposure is positively correlated with the development of skin diseases in people of European descent by Mendelian randomization studies. But randomized controlled trials are still needed to add proof to our observations.
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BACKGROUND AND OBJECTIVE: The identification of carotid plaque, one of the most crucial tasks in stroke screening, is of great significance in the assessment of subclinical atherosclerosis and preventing the onset of stroke. However, traditional ultrasound examination is not prevalent or cost-effective for asymptomatic people, particularly low-income individuals in rural areas. Thus, it is necessary to develop an accurate and explainable model for early identification of the risk of plaque prevalence that can help in the primary prevention of stroke. METHODS: We developed an ensemble learning method to predict the occurrence of carotid plaques. A dataset comprising 1440 subjects (50% with plaques and 50% without plaques) and ten-fold cross-validation were utilized to evaluate the model performance. Four machine learning methods (extreme gradient boosting (XGBoost), gradient boosting decision tree, random forest, and support vector machine) were evaluated. Subsequently, the interpretability of the XGBoost model, which provided the best performance, was analyzed from three aspects: feature importance, feature effect on prediction model, and feature effect on prediction decision for a specific subject. RESULTS: The XGBoost algorithm provided the best performance (sensitivity: 0.8678, specificity: 0.8592, accuracy: 0.8632, F1 score: 0.8621, area under the curve: 0.8635) in carotid plaque prediction and also had excellent performance under missing data circumstances. Further, interpretability analysis showed that the decisions of the XGBoost model were highly congruent with clinical knowledge. CONCLUSION: The model results are superior to those of state-of-the-art methods. Thus, it is a promising carotid plaque prediction tool that could be used in the primary prevention of stroke.
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Placa Aterosclerótica , Acidente Vascular Cerebral , Artérias Carótidas/diagnóstico por imagem , Humanos , Aprendizado de Máquina , Placa Aterosclerótica/diagnóstico por imagem , Acidente Vascular Cerebral/diagnóstico por imagem , Máquina de Vetores de SuporteRESUMO
INTRODUCTION: This study aimed to analyze the effects of ultrasonic removal of fractured files from the middle third of root canals on the vertical root fracture resistance. METHODS: This study was an extension of a previous study assessing the effects of fractured file removal on dentinal microcracks. It included 18 bilaterally matched pairs of human mandibular incisors prepared and analyzed in the previous study. Briefly, 1 member of each pair was assigned to an ultrasonic or a control group. In the ultrasonic group, K-files were fractured in the middle third of canals followed by ultrasonic file removal and canal preparation. In the control group, the root canals were simply prepared. Micro-computed tomographic imaging was performed before and after treatment, and the cross-sectional root images were screened for microcracks. For the present study, 3-dimensional reconstruction was performed for volumetric assessments. The fracture resistance was measured using a universal testing machine. All data were statistically analyzed. RESULTS: Fracture loads were significantly smaller in the ultrasonic group (P < .05). The percentage increase in the canal volume significantly influenced the root fracture resistance (P < .05), whereas microcracks had no significant effect (P > .05). CONCLUSIONS: Ultrasonic removal of fractured instruments from the middle third of root canals lowers the vertical root fracture resistance, with increased dentin removal being the primary cause.