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Zheng SL, Hu C, Huang SL, Xiao XY, Luo L. [Status of occupational exposure limits of air toxic substances in the GESTIS Substances Database]. ZHONGHUA LAO DONG WEI SHENG ZHI YE BING ZA ZHI = ZHONGHUA LAODONG WEISHENG ZHIYEBING ZAZHI = CHINESE JOURNAL OF INDUSTRIAL HYGIENE AND OCCUPATIONAL DISEASES 2024; 42:417-425. [PMID: 38964905 DOI: 10.3760/cma.j.cn121094-20230307-00069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 07/06/2024]
Abstract
Objective: In order to understand the current situation of air toxic substances without occupational exposure limits (OELs) in the workplace in the Germany GESTIS Substance Database, and to provide an effective reference for formulating OELs of corresponding toxic substances and improving health standards. Methods: From March 2022 to May 2023, based on the standard of GBZ 2.1-2019 Occupational Exposure Limits for Hazardous Agents in the Workplace-Part 1: Chemical Hazardous Agents, air toxic substances without OELs in the standard of GBZ/T 300.1-2017 Determination of Toxic Substances in Workplace Air-Part 1: General Principles were screened out, then corresponding OELs in other countrie/regions were queried through the Germany GESTIS Substance Database. Results: Among the 333 kinds (classes) of air toxic substances in 160 parts of GBZ/T 300.1-2017 standard, 48 kinds (classes) of air toxic substances were screened out and had not yet been formulated OELs in GBZ 2.1-2019 standard. By querying the Germany GESTIS Substance Database, it was found that among the 48 kinds (classes) of air toxic substances, 35 kinds (classes) of air toxic substances had both 8-hour occupational exposure limit and short-term occupational exposure limit, 4 kinds (classes) of air toxic substances had 8-hour occupational exposure limit but no short-term occupational exposure limit, 9 kinds (classes) of air toxic substances hadn't been retrieved any OELs. In addition, standard test methods of 7 kinds of air toxic substances hadn't been published in the present, including trimethylchlorosilane, trimethylbenzenes, cumene, chloroethane, chloropropane, dibromoethane and acetophenone. Conclusion: In the process of formulating or revising the standards of GBZ 2.1-2019 and GBZ/T 300, the latest published OELs in the Germany GESTIS Substance Database could be used as a reference basis.
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Wu Z, Li S, Luo L, Ding P. HKFGCN: A novel multiple kernel fusion framework on graph convolutional network to predict microbe-drug associations. Comput Biol Chem 2024; 110:108041. [PMID: 38471354 DOI: 10.1016/j.compbiolchem.2024.108041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 12/29/2023] [Accepted: 02/27/2024] [Indexed: 03/14/2024]
Abstract
Accumulating clinical studies have consistently demonstrated that the microbes in the human body closely interact with the human host, actively participating in the regulation of drug effectiveness. Identifying the associations between microbes and drugs can facilitate the development of drug discovery, and microbes have become a new target in antimicrobial drug development. However, the discovery of microbe-drug associations relies on clinical or biological experiments, which are not only time-consuming but also financially burdensome. Thus, the utilization of computational methods to predict microbe-drug associations holds promise for reducing costs and enhancing the efficiency of biological experiments. Here, we introduce a new computational method, called HKFGCN (Heterogeneous information Kernel Fusion Graph Convolution Network), to predict the microbe-drug associations. Instead of extracting feature from a single network in previous studies, HKFGCN separately extracts topological information features from different networks, and further refines them by generating Gaussian kernel features. HKFGCN consists of three main steps. Firstly, we constructed two similarity networks and a microbe-drug association network based on numerous biological data. Second, we employed two types of encoders to extract features from these networks. Next, Gaussian kernel features were obtained from the drug and microbe features at each layer. Finally, we reconstructed the bipartite microbe-drug graph based on the learned representations. Experimental results demonstrate the excellent performance of the HKFGCN model across different datasets using the cross-validation scheme. Additionally, we conduced case studies on human immunodeficiency virus, and the results were corroborated by existing literatures. The prediction model's code is available at https://github.com/roll-of-bubble/HKFGCN.
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Mubarik S, Luo L, Naeem S, Mubarak R, Iqbal M, Hak E, Yu C. Epidemiology and demographic patterns of cardiovascular diseases and neoplasms deaths in Western Europe: a 1990-2019 analysis. Public Health 2024; 231:187-197. [PMID: 38703493 DOI: 10.1016/j.puhe.2024.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/25/2024] [Accepted: 04/03/2024] [Indexed: 05/06/2024]
Abstract
OBJECTIVES Cardiovascular diseases (CVDs) and neoplasms have been considered as public health concerns worldwide. This study aimed to estimate the epidemiological patterns of death burden on CVDs and neoplasms and its attributable risk factors in Western Europe from 1990 to 2019 to discuss the potential causes of the disparities. STUDY DESIGN AND METHODS We collected data on CVDs and neoplasms deaths in 24 Western European countries from the Global Burden of Disease Study. We analyzed patterns by age, sex, country, and associated risk factors. The results include percentages of total deaths, age-standardized death rates per 100,000 population, and uncertainty intervals (UIs). Time trends were assessed using annual percent change. RESULTS In 2019, CVDs and neoplasms accounted for 33.54% and 30.15% of Western Europe's total deaths, with age-standardized death rates of 128.05 (95% UI: 135.37, 113.02) and 137.51 (95% UI: 142.54, 128.01) per 100,000. Over 1990-2019, CVDs rates decreased by 54.97%, and neoplasms rates decreased by 19.54%. Top CVDs subtypes were ischemic heart disease and stroke; top cancers for neoplasms were lung and colorectal. Highest CVD death burdens were in Finland, Greece, Austria; neoplasm burdens in Monaco, San Marino, Andorra. The major risk factors were metabolic (CVDs) and behavioral (neoplasms). Gender differences revealed higher CVDs death burden in males, while neoplasms burden varied by risk factors and age groups. CONCLUSION In 2019, CVDs and neoplasms posed significant health risks in Western Europe, with variations in death burdens and risk factors across genders, age groups, and countries. Future interventions should target vulnerable groups to lessen the impact of CVDs and neoplasms in the region.
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Luo L, Wang Z, Wang X, Gao J, Zheng A, Duan X. Fluorine-18 prostate-specific membrane antigen-1007-avid indeterminate bone lesions in prostate cancer: clinical and PET/CT features to predict outcomes and prognosis. Clin Radiol 2024; 79:346-353. [PMID: 38216370 DOI: 10.1016/j.crad.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/29/2023] [Accepted: 12/11/2023] [Indexed: 01/14/2024]
Abstract
AIM To determine clinical and fluorine-18 prostate-specific membrane antigen-1007 (18F-PSMA-1007) integrated positron-emission tomography (PET)/computed tomography (CT) features that could be used to interpret indeterminate bone lesions (IBLs) and assess the prognosis of prostate cancer (PCa) in patients with IBLs. MATERIALS AND METHODS Consecutive patients who underwent PSMA PET/CT were analysed retrospectively. IBLs were identified as benign or malignant based on follow-up imaging and clinical management. Lesion- and patient-based assessments were performed to define features predictive of bone lesion results and determine clinical risk. Patients' prognosis was analysed based on clinical characteristics, including prostate-specific antigen (PSA) and alkaline phosphatase (ALP), respectively. RESULTS A total of 105 patients (mean age ± SD, 72.1 ± 8 years) were evaluated and 158 IBLs were identified. Fifty-three (33.5%), 36 (22.8%), and 69 (43.7%) IBLs were benign, malignant, and equivocal, respectively. Variables including location, maximum standard uptake value (SUVmax), and lymph node metastases (LNM) were related to the benignancy or malignancy of IBLs (p=0.046, p<0.001 and p<0.001, respectively). Regression analysis indicated that LNM, SUVmax, and location of IBLs could be predictors of lesion interpretation (p<0.001, p=0.002 and p=0.035). Patients with benign IBLs experienced the most considerable decreases in PSA and ALP levels. CONCLUSIONS LNM, SUVmax, and location may contribute to IBL interpretation. A rapid decrease in PSA and ALP levels might suggest a better prognosis for patients with benign IBLs.
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Huang C, Luo L, Mootz M, Shang J, Man P, Su L, Perakis IE, Yao YX, Wu A, Wang J. Extreme terahertz magnon multiplication induced by resonant magnetic pulse pairs. Nat Commun 2024; 15:3214. [PMID: 38615025 PMCID: PMC11016094 DOI: 10.1038/s41467-024-47471-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/26/2024] [Indexed: 04/15/2024] Open
Abstract
Nonlinear interactions of spin-waves and their quanta, magnons, have emerged as prominent candidates for interference-based technology, ranging from quantum transduction to antiferromagnetic spintronics. Yet magnon multiplication in the terahertz (THz) spectral region represents a major challenge. Intense, resonant magnetic fields from THz pulse-pairs with controllable phases and amplitudes enable high order THz magnon multiplication, distinct from non-resonant nonlinearities such as the high harmonic generation by below-band gap electric fields. Here, we demonstrate exceptionally high-order THz nonlinear magnonics. It manifests as 7th-order spin-wave-mixing and 6th harmonic magnon generation in an antiferromagnetic orthoferrite. We use THz two-dimensional coherent spectroscopy to achieve high-sensitivity detection of nonlinear magnon interactions up to six-magnon quanta in strongly-driven many-magnon correlated states. The high-order magnon multiplication, supported by classical and quantum spin simulations, elucidates the significance of four-fold magnetic anisotropy and Dzyaloshinskii-Moriya symmetry breaking. Moreover, our results shed light on the potential quantum fluctuation properties inherent in nonlinear magnons.
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Luo Y, Shan W, Peng L, Luo L, Ding P, Liang W. A computational framework for predicting novel drug indications using graph convolutional network with contrastive learning. IEEE J Biomed Health Inform 2024; PP:1-10. [PMID: 38607707 DOI: 10.1109/jbhi.2024.3387937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2024]
Abstract
Inferring potential drug indications plays a vital role in the drug discovery process. It can be time-consuming and costly to discover novel drug indications through biological experiments. Recently, graph learning-based methods have gained popularity for this task. These methods typically treat the prediction task as a binary classification problem, focusing on modeling associations between drugs and diseases within a graph. However, labeled data for drug indication prediction is often limited and expensive to acquire. Contrastive learning addresses this challenge by aligning similar drug-disease pairs and separating dissimilar pairs in the embedding space. Thus, we developed a model called DrIGCL for drug indication prediction, which utilizes graph convolutional networks and contrastive learning. DrIGCL incorporates drug structure, disease comorbidities, and known drug indications to extract representations of drugs and diseases. By combining contrastive and classification losses, DrIGCL predicts drug indications effectively. In multiple runs of hold-out validation experiments, DrIGCL consistently outperformed existing computational methods for drug indication prediction, particularly in terms of top-k. Furthermore, our ablation study has demonstrated a significant improvement in the predictive capabilities of our model when utilizing contrastive learning. Finally, we validated the practical usefulness of DrIGCL by examining the predicted novel indications of Aspirin. The prediction model's code is available at https://github.com/yuxunluo9/DrIGCL.
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Dong XY, Zou YX, Lyu FF, Yang WH, Zhang HL, Niu YH, Wang HJ, Guo R, Wang X, Li L, Lin ZH, Luo L, Lu DL, Lu Q, Liu HM, Chen LN. [A multicenter study on respiratory pathogen detection with Mycoplasma pneumoniae pneumonia in children]. ZHONGHUA ER KE ZA ZHI = CHINESE JOURNAL OF PEDIATRICS 2024; 62:310-316. [PMID: 38527500 DOI: 10.3760/cma.j.cn112140-20240117-00054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Objective: To analyze the status of respiratory pathogen detection and the clinical features in children with Mycoplasma pneumoniae pneumonia (MPP). Methods: A prospective, multicenter study was conducted to collect clinical data, including medical history, laboratory examinations and multiplex PCR tests of children diagnosed with MPP from 4 hospitals in China between November 15th and December 20th, 2023. The multiplex PCR results and clinical characteristics of MPP children in different regions were analyzed. The children were divided into severe and mild groups according to the severity of the disease. Patients in the severe group were further divided into Mycoplasma pneumoniae (MP) alone and Multi-pathogen co-detection groups based on whether other pathogens were detected besides MP, to analyze the influence of respiratory pathogen co-detection rate on the severity of the disease. Mann-Whitney rank sum test and Chi-square test were used to compare data between independent groups. Results: A total of 298 children, 136 males and 162 females, were enrolled in this study, including 204 children in the severe group with an onset age of 7.0 (6.0, 8.0) years, and 94 children in the mild group with an onset age of 6.5 (4.0, 7.8) years. The level of C-reactive protein, D-dimer, lactic dehydrogenase (LDH) were significantly higher (10.0 (5.0, 18.0) vs. 5.0 (5.0, 7.5) mg/L, 0.6 (0.4, 1.1) vs. 0.5 (0.3, 0.6) mg/L, 337 (286, 431) vs. 314 (271, 393) U/L, Z=2.02, 2.50, 3.05, all P<0.05), and the length of hospitalization was significantly longer in the severe group compared with those in mild group (6.0 (6.0, 7.0) vs. 5.0 (4.0, 6.0) d, Z=4.37, P<0.05). The time from onset to admission in severe MPP children was significantly shorter than that in mild MPP children (6.0 (5.0, 9.5) vs. 9.0 (7.0, 13.0) d, Z=2.23, P=0.026). All patients completed the multiplex PCR test, with 142 cases (47.7%) MPP children detected with 21 pathogens including adenovirus 25 cases (8.4%), human coronavirus 23 cases (7.7%), rhinovirus 21 cases (7.0%), Streptococcus pneumoniae 21 cases (7.0%), influenza A virus 18 cases (6.0%). The pathogens with the highest detection rates in Tianjin, Shanghai, Wenzhou and Chengdu were Staphylococcus aureus at 10.7% (8/75), adenovirus at 13.0% (10/77), adenovirus at 15.3% (9/59), and both rhinovirus and Haemophilus influenzae at 11.5% (10/87) each. The multi-pathogen co-detection rate in severe MPP children was significantly higher than that in mild MPP group (52.9% (108/204) vs. 36.2% (34/94), χ²=10.62,P=0.005). Among severe MPP children, there are 89 cases in the multi-pathogen co-detection group and 73 cases in the simple MPP group. The levels of LDH, D-dimer and neutrophil counts in the multi-pathogen co-detection group were significantly higher than those in the simple MPP group (348 (284, 422) vs. 307 (270, 358) U/L, 0.8 (0.5, 1.5) vs. 0.6 (0.4, 1.0) mg/L, 4.99 (3.66, 6.89)×109 vs. 4.06 (2.91, 5.65)×109/L, Z=5.17, 4.99, 6.11, all P<0.05). Conclusions: The co-detection rate of respiratory pathogens, LDH and D-dimer in children with severe MPP were higher than those with mild MPP. Among severe MPP children the stress response of children in co-detection group was more serious than that of children with simple MPP.
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Luo L, Luo X. Diagnosis and treatment of right ventricular metastasis from esophageal squamous cell carcinoma: An unusual case report and a literature review. Medicine (Baltimore) 2023; 102:e36404. [PMID: 38065909 PMCID: PMC10713161 DOI: 10.1097/md.0000000000036404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 11/10/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Right ventricular metastasis from esophageal squamous cell carcinoma is very rare and only seen in few case reports. Patients with cardiac metastasis have a poor prognosis with a median survival period of 4 weeks due to the lack of standardized and effective treatment guidelines. Therefore, we aimed to clarify the feature and treatment of cardiac metastasis through literature review and reporting of an unusual case. CASE We reported a case of a 67 years-old man diagnosed as right ventricular metastasis from esophageal squamous cell with the help of echocardiography and pathological biopsy. Moreover, the patient survival period reached an astonishing 6 months, which far exceeded 4 weeks reported in previous literature. METHODS We searched for relevant literature in the past decade on PUBMED and summarized the content of the literature to better clarify cardiac metastasis. CONCLUSION Cardiac metastatic likely to occur in the elderly and in the right side of heart which related to hemodynamics. Surgical resection of metastatic tumors is the main treatment method, but patients usually die during the perioperative period due to its complexity and difficulty. Meanwhile, we have proposed some potentially effective treatment measures.
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Zhong Y, Shen C, Xi X, Luo Y, Ding P, Luo L. Multitask joint learning with graph autoencoders for predicting potential MiRNA-drug associations. Artif Intell Med 2023; 145:102665. [PMID: 37925217 DOI: 10.1016/j.artmed.2023.102665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 06/14/2023] [Accepted: 09/14/2023] [Indexed: 11/06/2023]
Abstract
The occurrence of many diseases is associated with miRNA abnormalities. Predicting potential drug-miRNA associations is of great importance for both disease treatment and new drug discovery. Most computation-based approaches learn one task at a time, ignoring the information contained in other tasks in the same domain. Multitask learning can effectively enhance the prediction performance of a single task by extending the valid information of related tasks. In this paper, we presented a multitask joint learning framework (MTJL) with a graph autoencoder for predicting the associations between drugs and miRNAs. First, we combined multiple pieces of information to construct a high-quality similarity network of both drugs and miRNAs and then used a graph autoencoder (GAE) to learn their embedding representations separately. Second, to further improve the embedding quality of drugs, we added an auxiliary task to classify drugs using the learned representations. Finally, the embedding representations of drugs and miRNAs were linearly transformed to obtain the predictive association scores between them. A comparison with other state-of-the-art models shows that MTJL has the best prediction performance, and ablation experiments show that the auxiliary task can enhance the embedding quality and improve the robustness of the model. In addition, we show that MTJL has high utility in predicting potential associations between drugs and miRNAs by conducting two case studies.
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Shan W, Shen C, Luo L, Ding P. Multi-task learning for predicting synergistic drug combinations based on auto-encoding multi-relational graphs. iScience 2023; 26:108020. [PMID: 37854693 PMCID: PMC10579440 DOI: 10.1016/j.isci.2023.108020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/26/2023] [Accepted: 09/19/2023] [Indexed: 10/20/2023] Open
Abstract
Combinatorial drug therapy is a promising approach for treating complex diseases by combining drugs with synergistic effects. However, predicting effective drug combinations is challenging due to the complexity of biological systems and the limited understanding of pathophysiological mechanisms and drug targets. In this paper, we proposed a computational framework called VGAETF (Variational Graph Autoencoder Tensor Decomposition), which leveraged multi-relational graph to model complex relationships between entities in biological systems and predicted disease-related synergistic drug combinations in an end-to-end manner. In the computational experiments, VGAETF achieved high performances (AUROC [the area under receiver operating characteristic] = 0.9767, AUPR [the area under precision-recall] = 0.9660), outperforming other compared methods. Moreover, case studies further demonstrated the effectiveness of VGAETF in identifying potential disease-related synergistic drug combinations.
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Chen T, Zheng B, Yang P, Zhang Z, Su Y, Chen Y, Luo L, Luo D, Lin Y, Xie R, Zeng L. The Incidence and Prognosis Value of Perineural Invasion in Rectal Carcinoma: From Meta-Analyses and Real-World Clinical Pathological Features. Clin Oncol (R Coll Radiol) 2023; 35:e611-e621. [PMID: 37263883 DOI: 10.1016/j.clon.2023.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 04/13/2023] [Accepted: 05/16/2023] [Indexed: 06/03/2023]
Abstract
AIMS Perineural invasion (PNI) is a special type of metastasis of several cancers and has been reported as being a factor for poor prognosis in colorectal carcinoma. However, investigations of PNI in only rectal cancer and a comprehensive analysis combining meta-analyses with real-world case studies remain lacking. MATERIALS AND METHODS First, articles from 2000 to 2020 concerning the relationship between PNI and rectal cancer prognoses and clinical features were meta-analysed. Subsequently, we carried out a retrospective analysis of 312 rectal cancer cases that underwent radical surgery in the real world. The incidence of PNI and the relationship between PNI and prognosis, as well as clinicopathological factors, were investigated. RESULTS The incidence of PNI was 23.09% and 33.01% in the meta-analysis and clinical cases, respectively. PNI occurred as early as stage I (2.94%). Moreover, neoadjuvant therapy significantly reduced the PNI-positive rate (20.34% versus 26.54%). Both meta-analysis and real-world clinical case studies suggested that PNI-positive patients had poorer prognoses than PNI-negative patients. We established an effective risk model consisting of T stage, differentiation and lymphovascular invasion to predict PNI in rectal cancer. CONCLUSION PNI is a poor prognostic factor for rectal cancer and could occur even in stage I. Additionally, neoadjuvant therapy could sufficiently reduce the PNI-positive rate. T stage, lymphovascular invasion and differentiation grade were independent risk factors for PNI and the risk model that included these factors could predict the probability of PNI.
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Yang L, Luo L, Zhang YT, Shi DD, Ci ZG, Xiao BS, Yang SQ. [Clinical implications of thrombolytic therapy for patients with acute intermediate-high risk pulmonary embolism in Tibet plateau, China]. ZHONGHUA JIE HE HE HU XI ZA ZHI = ZHONGHUA JIEHE HE HUXI ZAZHI = CHINESE JOURNAL OF TUBERCULOSIS AND RESPIRATORY DISEASES 2023; 46:924-929. [PMID: 37670647 DOI: 10.3760/cma.j.cn112147-20230413-00172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
At present, clinical studies and case reports of systemic thrombolytic therapy for patients with acute pulmonary embolism in Tibet Plateau are very rare. There is little understanding of the risk factors, clinical characteristics, and thrombolytic therapy for patients with acute pulmonary embolism at intermediate-high risk in Tibet Plateau. In this paper, we reported the data of 4 patients with acute intermediate-high risk pulmonary embolism treated with thrombolytic therapy in Lhasa People's Hospital. The demographic characteristics, clinical manifestations, treatment, and outcomes were analyzed. We summarized the clinical features and raised scientific issues. We aimed to provide basic data to improve the standardized diagnosis and treatment of acute pulmonary embolism in plateau, and to point out the direction of future clinical research in this field.
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Shui J, Luo L, Xiang YG, Shi GM, Wu JL, Pan JH. [Analysis of biofilm-forming ability and drug resistance for Hypervirulent Klebsiella pneumoniae]. ZHONGHUA YU FANG YI XUE ZA ZHI [CHINESE JOURNAL OF PREVENTIVE MEDICINE] 2023; 57:1452-1457. [PMID: 37743308 DOI: 10.3760/cma.j.cn112150-20220929-00938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Investigate the biofilm-forming ability and drug resistance of Hypervirulent Klebsiella pneumoniae (HvKP) to provide scientific basis for the treatment of HvKP-infection. A total of 96 Klebsiella pneumoniae strains isolated from clinical infection specimens in Changsha Central Hospital from January to December in 2021 were retrospectively collected, and the clinical data of patients were collected. The string test preliminarily distinguished between HvKP and classic Klebsiella pneumoniae (CKP). The biofilm-forming ability of clinical strains of Klebsiella pneumoniae (KP) was determined by microplate method. The Vitek 2 Compact automatic microbial identification/drug sensitivity analysis system was used for bacterial identification and drug sensitivity test. The clinical data of patients, biofilm forming ability and drug resistance in the HvKP group and those in the CKP group were compared and analyzed. The results showed that a total of 20 strains of HvKP were isolated from 96 non-repetitive KP, and the detection rate was 20.8%. HvKP mainly come from respiratory specimens, up to 75.0%.The prevalence of hepatobiliary diseases and the infection rate of multiple sites in patients with HvKP infection were higher than those in patients with CKP infection, and the difference was statistically significant(χ2=5.184,7.488;P=0.023,0.006).There was no significant difference between the two groups in terms of gender, age, ICU admission, hypertension, diabetes, coronary heart disease, lung disease, urinary system disease, central nervous system disease and laboratory test indexes (all P>0.05).17 (85.0%) strains of HvKP can form biofilm, including 2 strains with weak biofilm-forming ability (10.0%), 10 strains with moderate biofilm-forming ability (50.0%) and 5 strains with strong biofilm-forming ability (25.0%). Among the 76 CKP, 71 (93.4%) could form biofilm, including 13 (17.1%) with weak biofilm-forming ability, 30(39.5%) with moderate biofilm-forming ability and 28 (36.8%) with strong biofilm-forming ability. There was no significant difference in biofilm-forming ability between HvKP and CKP (χ2=1.470,P=0.225).The overall resistance rate of HvKP was not high, but a multi-resistant HvKP resistant to carbapenems was found. The detection rate of multi-resistant HvKP (5.0%) was lower than that of multi-resistant CKP (28.9%), and the difference was statistically significant (χ2=4.984, P=0.026).The resistance rate of HvKP to piperacillin/tazobactam, aztreonam, ciprofloxacin, levofloxacin, ceftazidime, cefepime, tobramycin, minocycline, doxycycline, and compound sulfamethoxazole was lower than that of CKP, and the difference was statistically significant (all P<0.05). In conclusion, most of hypervirulent Klebsiella pneumoniae can form biofilm in this study, but the difference of biofilm-forming ability is not obvious compared with classic Klebsiella pneumoniae. HvKP maintains high sensitivity to commonly used antibacterial drugs, but the drug resistance monitoring of the bacteria cannot be ignored.
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Chen C, Luo L, Zheng C, Ding P, Liu H, Luo H. Self-prediction of relations in GO facilitates its quality auditing. J Biomed Inform 2023; 144:104441. [PMID: 37437682 DOI: 10.1016/j.jbi.2023.104441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 06/29/2023] [Accepted: 07/05/2023] [Indexed: 07/14/2023]
Abstract
As applications of the gene ontology (GO) increase rapidly in the biomedical field, quality auditing of it is becoming more and more important. Existing auditing methods are mostly based on rules, observed patterns or hypotheses. In this study, we propose a machine-learning-based framework for GO to audit itself: we first predict the IS-A relations among concepts in GO, then use differences between predicted results and existing relations to uncover potential errors. Specifically, we transfer the taxonomy of GO 2020 January release into a dataset with concept pairs as items and relations between them as labels(pairs with no direct IS-A relation are labeled as ndrs). To fully obtain the representation of each pair, we integrate the embeddings for the concept name, concept definition, as well as concept node in a substring-based topological graph. We divide the dataset into 10 parts, and rotate over all the parts by choosing one part as the testing set and the remaining as the training set each time. After 10 rotations, the prediction model predicted 4,640 existing IS-A pairs as ndrs. In the GO 2022 March release, 340 of these predictions were validated, demonstrating significance with a p-value of 1.60e-46 when compared to the results of randomly selected pairs. On the other hand, the model predicted 2,840 out of 17,079 selected ndrs in GO to be IS-A's relations. After deleting those that caused redundancies and circles, 924 predicted IS-A's relations remained. Among 200 pairs randomly selected, 30 were validated as missing IS-A's by domain experts. In conclusion, this study investigates a novel way of auditing biomedical ontologies by predicting the relations in it, which was shown to be useful for discovering potential errors.
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Wang X, Luo L, Wang Y, An Z. Effect of Platelet Function Testing Guidance on Clinical Outcomes for Patients with Intracranial Aneurysms Undergoing Endovascular Treatment. AJNR Am J Neuroradiol 2023; 44:928-933. [PMID: 37414457 PMCID: PMC10411848 DOI: 10.3174/ajnr.a7923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/01/2023] [Indexed: 07/08/2023]
Abstract
BACKGROUND Platelet function testing has been proposed to better adjust individualized antiplatelet treatment for patients undergoing endovascular treatment for intracranial aneurysms. Its clinical significance needs to be comprehensively evaluated. PURPOSE Our aim was to evaluate the impact of platelet function testing-guided versus standard antiplatelet treatment in patients receiving endovascular treatment for intracranial aneurysms. DATA SOURCES PubMed, EMBASE, and the Cochrane Library of clinical trials were searched from inception until March 2023. STUDY SELECTION Eleven studies comprising 6199 patients were included. DATA ANALYSIS ORs with 95% CIs were calculated using random effects models. DATA SYNTHESIS The platelet function testing-guided group was associated with a decreased rate of symptomatic thromboembolic events (OR = 0.57; 95% CI, 0.42-0.76; I2 = 26%). No significant difference was found in asymptomatic thromboembolic events (OR = 1.07; 95% CI, 0.39-2.94; I2 = 48%), hemorrhagic events (OR = 0.71; 95% CI, 0.42-1.19; I2 = 34%), intracranial hemorrhagic events (OR = 0.61; 95% CI, 0.03-10.79; I2 = 62%), morbidity (OR = 0.53; 95% CI, 0.05-5.72; I2 = 86%), and mortality (OR = 1.96; 95% CI, 0.64-5.97; I2 = 0%) between the 2 groups. Subgroup analysis suggested that platelet function testing-guided therapy may contribute to fewer symptomatic thromboembolic events in patients who received stent-assisted coiling (OR = 0.43; 95% CI, 0.18-1.02; I2 = 43%) or a combination of stent-assisted and flow-diverter stent placement (OR = 0.61; 95% CI, 0.36-1.02; I2 = 0%) or who changed from clopidogrel to other thienopyridines (OR = 0.64; 95% CI, 0.40-1.02; I2 = 18%), though the difference did not reach statistical significance. LIMITATIONS Heterogeneous endovascular treatment methods and adjusted antiplatelet regimens were limitations. CONCLUSIONS Platelet function testing-guided antiplatelet strategy significantly reduced the incidence of symptomatic thromboembolic events without any increase in the hemorrhagic events for patients undergoing endovascular treatment for intracranial aneurysms.
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Kuang TY, Yin SQ, Dai WH, Luo L, Chen T, Liang XH, Wang RX, Liang HP, Zhu JY. [Effects of enhancing the expression of aryl hydrocarbon receptor in post-traumatic mice macrophages on the inflammatory cytokine level and bactericidal ability]. ZHONGHUA SHAO SHANG YU CHUANG MIAN XIU FU ZA ZHI 2023; 39:633-640. [PMID: 37805692 DOI: 10.3760/cma.j.cn501225-20230210-00040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 10/09/2023]
Abstract
Objective: To explore the expression pattern of aryl hydrocarbon receptor (AhR) in mice peritoneal macrophages (PMs) after major trauma and analyze the effects of enhanced AhR expression on the inflammatory cytokine level and bactericidal ability after trauma. Methods: The experimental study method was used. Forty 6-8-week-old male C57BL/6J mice (the same mouse age, sex, and strain below) were divided into control group, post trauma hour (PTH) 2 group, PTH 6 group, and PTH 12 group according to the random number table (the same grouping method below), with 10 mice in each group. Mice in the latter 3 groups were constructed as severe trauma model with fracture+blood loss, while mice in control group were left untreated. The primary PMs (the same cells below) were extracted from the mice in control group, PTH 2 group, PTH 6 group, and PTH 12 group when uninjured or at PTH 2, 6, and 12, respectively. Then the protein and mRNA expressions of AhR were detected by Western blotting and real-time fluorescence quantitative reverse transcription polymerase chain reaction, respectively, and the gene expressions of AhR signaling pathway related molecules were analyzed by transcriptome sequencing. Twenty mice were divided into control group and PTH 6 group, with 10 mice in each group, and the PMs were extracted. The level of ubiquitin of AhR was detected by immunoprecipitation. Twelve mice were divided into dimethyl sulfoxide (DMSO) alone group, PTH 6+DMSO group, MG-132 alone group, and PTH 6+MG-132 group, with 3 mice in each group. After the corresponding treatment, PMs were extracted, and the protein expression of AhR was detected by Western blotting. Twenty mice were constructed as PTH 6 model. Then, the PMs were extracted and divided into empty negative control adenovirus (Ad-NC) group and AhR overexpression adenovirus (Ad-AhR) group. The protein expression of AhR was detected by Western blotting at 36 h after some PMs were transfected with the corresponding adenovirus. The rest cells in Ad-NC group were divided into Ad-NC alone group and Ad-NC+endotoxin/lipopolysaccharide (LPS) group, and the rest cells in Ad-AhR group were divided into Ad-AhR alone group and Ad-AhR+LPS group. The expressions of interleukin-6 (IL-6) and tumor necrosis factor α (TNF-α) in the cell supernatant were detected by enzyme-linked immunosorbent assay at 12 h after the corresponding treatment (n=6). Twenty mice were obtained to extract PMs. The cells were divided into control+Ad-NC group, PTH 6+Ad-NC group, control+Ad-AhR group, and PTH 6+Ad-AhR group, and the intracellular bacterial load was detected by plate spread method after the corresponding treatment (n=6). Data were statistically analyzed with one-way analysis of variance, least significant difference test, analysis of variance for factorial design, and independent sample t test. Results: Compared with 1.16±0.28 of control group, the protein expressions of AhR in PMs in PTH 2 group (0.59±0.14), PTH 6 group (0.72±0.16), and PTH 12 group (0.71±0.17) were all significantly decreased (P<0.05). The overall comparison of the difference of AhR mRNA expression in PMs among control group, PTH 2 group, PTH 6 group, and PTH 12 group showed no statistical significance (P>0.05). The AhR signaling pathway related molecules included AhR, AhR inhibitor, cytochrome P450 family member 1b1, cytochrome P450 family member 11a1, heat shock protein 90, aryl hydrocarbon receptor-interaction protein, and heat shock protein 70 interaction protein. The heat shock protein 90 expression of PMs in PTH 2 group was higher than that in control group, while the expressions of other molecules did not change significantly after trauma. Compared with that in control group, the level of ubiquitin of AhR in PMs in PTH 6 group was increased. Compared with that in DMSO alone group, the protein expression of AhR in PMs in PTH 6+DMSO group was decreased, while that in PMs in MG-132 alone group had no significant change. Compared with that in PTH 6+DMSO group, the protein expression of AhR in PMs in PTH 6+MG-132 group was up-regulated. At transfection hour 36, compared with that in Ad-NC group, the protein expression of AhR in PMs in Ad-AhR group was increased. At treatment hour 12, compared with those in Ad-NC+LPS group, the expressions of IL-6 and TNF-α in PM supernatant of Ad-AhR+LPS group were significantly decreased (with t values of 4.80 and 3.82, respectively, P<0.05). The number of intracellular bacteria of 1×106 PMs in control+Ad-NC group, PTH 6+Ad-NC group, control+Ad-AhR group, and PTH 6+Ad-AhR group was (3.0±1.8), (41.8±10.2), (1.8±1.2), and (24.2±6.3) colony forming unit, respectively. Compared with that in PTH 6+Ad-NC group, the number of intracellular bacteria of PMs in PTH 6+Ad-AhR group was significantly decreased (t=3.61, P<0.05). Conclusions: Ubiquitin degradation of AhR in PMs of mice after major trauma results in decreased protein expression of AhR. Increasing the expression of AhR in post-traumatic macrophages can reduce the expressions of LPS-induced inflammatory cytokines IL-6 and TNF-α, and improve the bactericidal ability of macrophages after trauma.
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Luo L, Luo LZ, Lu ZB, Xiao YB. [Efficacy of high-frequency electrotome combined with balloon dilatation and cryotherapy through electronic bronchoscope in the management of lumen occlusion type of tracheobronchial tuberculosis]. ZHONGHUA JIE HE HE HU XI ZA ZHI = ZHONGHUA JIEHE HE HUXI ZAZHI = CHINESE JOURNAL OF TUBERCULOSIS AND RESPIRATORY DISEASES 2023; 46:587-591. [PMID: 37278173 DOI: 10.3760/cma.j.cn112147-20220928-00786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The lumen-occlusion type of tracheobronchial tuberculosis is the most severe type of tracheobronchial stenosis of tuberculosis, often leading to atelectasis or even lung damage in patients. Some patients require surgical resection of the diseased airways and lungs, which can seriously affect their quality of life and even be life-threatening. In order to improve the treatment ability of bronchoscopy physicians for lumen occlusion type of tracheobronchial tuberculosis, this article retrospectively analyzed 30 cases of tracheobronchial tuberculosis with lumen occlusion in Hunan Chest Hospital, and summarized the experience of achieving better results by high-frequency electrotome combined with balloon dilatation and cryotherapy.
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Luo H, Li Y, Liu H, Ding P, Yu Y, Luo L. SENet: A deep learning framework for discriminating super- and typical enhancers by sequence information. Comput Biol Chem 2023; 105:107905. [PMID: 37348298 DOI: 10.1016/j.compbiolchem.2023.107905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 05/08/2023] [Accepted: 06/09/2023] [Indexed: 06/24/2023]
Abstract
Super-enhancers are large domains on the genome where multiple short typical enhancers within a specific genomic distance are stitched together. Typically, they are cell type-specific and responsible for defining cell identity and regulating gene transcription. Numerous studies have demonstrated that super-enhancers are enriched for trait-associated variants, and mutations in super-enhancers are possibly related to known diseases. Recently, several machine learning-based methods have been used to distinguish super-enhancers from typical enhancers by using high-throughput data from various experimental methods. The acquisition of such experimental data is usually costly and time-consuming. In this paper, we innovatively proposed SENet, a groundbreaking method based on a deep neural network model, for discriminating between the two categories solely utilizing sequence information. SENet employs dna2vec feature embedding, convolution for local feature extraction, attention pooling for refined feature retention, and Transformer for contextual information extraction. Experiments demonstrate that SENet outperforms all current state-of-the-art computational methods and shows satisfactory performance in cross-species validation. Our method pioneers the distinction between super-enhancers and typical ones using only sequence information. The source code and datasets are stored in https://github.com/lhy0322/SENet.
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Luo L, Jiao Y, Yang P, Li Y, Huang WY, Ke XY, Zou DH, Jing HM. [Efficacy and prognostic factors of allogeneic hematopoietic stem cell transplantation treatment for T lymphoblastic leukemia/lymphoma]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2023; 44:388-394. [PMID: 37550188 PMCID: PMC10440623 DOI: 10.3760/cma.j.issn.0253-2727.2023.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Indexed: 08/09/2023]
Abstract
Objective: To analyze the efficacy and prognostic factors of allogeneic hematopoietic stem cell transplantation (allo-HSCT) for treating T lymphoblastic leukemia/lymphoma (T-ALL/LBL) . Methods: This study retrospectively evaluated 119 adolescent and adult patients with T-ALL/LBL from January 2006 to January 2020 at Peking University Third Hospital and Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences. Patients were divided into chemotherapy-only, chemotherapy followed by allo-HSCT, and chemotherapy followed by autologous hematopoietic stem cell transplantation (auto-HSCT) groups according to the consolidation regimen, and the 5-year overall survival (OS) and progression-free survival (PFS) rates of each group were compared. Results: Among 113 patients with effective follow-up, 96 (84.9%) patients achieved overall response (ORR), with 79 (69.9%) having complete response (CR) and 17 (15.0%) having partial response (PR), until July 2022. The analysis of the 96 ORR population revealed that patients without transplantation demonstrated poorer outcomes compared with the allo-HSCT group (5-year OS: 11.4% vs 55.6%, P=0.001; 5-year PFS: 8.9% vs 54.2%, P<0.001). No difference was found in 5-year OS and 5-year PFS between the allo-HSCT and auto-HSCT groups (P=0.271, P=0.197). The same results were achieved in the CR population. Allo-HSCT got better 5-year OS (37.5% vs 0) for the 17 PR cases (P=0.064). Different donor sources did not affect 5-year OS, with sibling of 61.1% vs hap-haploidentical of 63.6% vs unrelated donor of 50.0% (P>0.05). No significant difference was found in the treatment response in the early T-cell precursor acute lymphoblastic leukemia/lymphoma (ETP) and non-ETP populations. The ETP group demonstrated lower 5-year OS compared with the non-ETP group in the chemotherapy alone group (0 vs 12.6%, P=0.045), whereas no significant difference was found between the ETP and non-ETP groups in the allo-HSCT group (75.0% vs 62.9%, P=0.852). Multivariate analysis revealed that high serum lactate dehydrogenase level, without transplantation, and no CR after chemotherapy induction were independently associated with inferior outcomes (P<0.05) . Conclusion: Allo-HSCT could be an effective consolidation therapy for adult and adolescent patients with T-ALL/LBL. Different donor sources did not affect survival. Allo-HSCT may overcome the adverse influence of ETP-ALL/LBL on OS.
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Yan Y, Zhu M, Cao X, Xu G, Shen W, Li F, Zhang J, Luo L, Zhang X, Zhang D, Liu T. Thalamocortical Circuit Controls Neuropathic Pain via Up-regulation of HCN2 in the Ventral Posterolateral Thalamus. Neurosci Bull 2023; 39:774-792. [PMID: 36538279 PMCID: PMC10169982 DOI: 10.1007/s12264-022-00989-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 09/07/2022] [Indexed: 12/24/2022] Open
Abstract
The thalamocortical (TC) circuit is closely associated with pain processing. The hyperpolarization-activated cyclic nucleotide-gated (HCN) 2 channel is predominantly expressed in the ventral posterolateral thalamus (VPL) that has been shown to mediate neuropathic pain. However, the role of VPL HCN2 in modulating TC circuit activity is largely unknown. Here, by using optogenetics, neuronal tracing, electrophysiological recordings, and virus knockdown strategies, we showed that the activation of VPL TC neurons potentiates excitatory synaptic transmission to the hindlimb region of the primary somatosensory cortex (S1HL) as well as mechanical hypersensitivity following spared nerve injury (SNI)-induced neuropathic pain in mice. Either pharmacological blockade or virus knockdown of HCN2 (shRNA-Hcn2) in the VPL was sufficient to alleviate SNI-induced hyperalgesia. Moreover, shRNA-Hcn2 decreased the excitability of TC neurons and synaptic transmission of the VPL-S1HL circuit. Together, our studies provide a novel mechanism by which HCN2 enhances the excitability of the TC circuit to facilitate neuropathic pain.
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Wang F, Zhang YT, Su F, Huang CP, Luo L. [Determination of methylmercury in urine by direct mercury analyzer]. ZHONGHUA LAO DONG WEI SHENG ZHI YE BING ZA ZHI = ZHONGHUA LAODONG WEISHENG ZHIYEBING ZAZHI = CHINESE JOURNAL OF INDUSTRIAL HYGIENE AND OCCUPATIONAL DISEASES 2023; 41:304-306. [PMID: 37248187 DOI: 10.3760/cma.j.cn121094-20211110-00556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Objective: To develop asolvent extraction-direct mercury analyzer method for determination of methylmercury in urine. Methods: After the urinehydrolyzesd by hydrobromic acid, methylmercury was extracted by tolueneand reverse-extracted from L-cysteine solution, it was then detectedbydirect mercuryanalyzer. Results: The linear range was 0.2-50.0 μg/L, and the related coefficient was 0.9999. The relative standard deviations (RSD) within the group were 5.04%-6.64%, and the RSD between the group were 5.65%-8.11 %. The average recovery efficiencies were 85.4%-95.5%. The detection limitation was 0.0482 μg/L and the quantification concentrations was 0.1607 μg/L. Conclusion: The method, which has low detection limit, high sensitivity, easy to operate, is stability for the determination of methylmercury in urine.
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Ge J, Guo X, Zhao W, Zhang R, Bian Q, Luo L, Linlin X, Yao X. EVALUATION OF PRE-ABLATION NLR AND LMR AS PREDICTORS OF DISTANT METASTASES IN PATIENTS WITH DIFFERENTIATED THYROID CANCER. ACTA ENDOCRINOLOGICA (BUCHAREST, ROMANIA : 2005) 2023; 19:215-220. [PMID: 37908873 PMCID: PMC10614579 DOI: 10.4183/aeb.2023.215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Objective This research aim was to evaluates the role of the pre-ablation neutrophil-to-lymphocyte ratio (NLR) and lymphocyte-to-monocyte ratio (LMR) as predictors of distant metastases in patients with differentiated thyroid cancer (DTC). Methods A retrospective analysis was given to 140 patients with DTC who received 131I remnant ablation after surgery. The patients were divided into two groups based on the existence of distant metastasis. Results The two groups showed no significant difference in age, gender, WBCs, neutrophils, monocytes, eosinophils, basophils and whether the tumor was multifocal. In the univariate analysis, significant differences were found in tumor size (p=0.021), lymphocyte (p=0.012), NLR (p=0.027), and LMR (p=0.007). According to the ROC curves, NLR had an AUC of 0.612 ± 0.097 with a cut-off value of 1.845, sensitivity of 60.0%, and specificity of 66.2% (p=0.027). LMR had an AUC of 0.638 ± 0.095 with a cut-off value of 4.630, sensitivity of 84.6%, and specificity of 35.4% (p=0.007). In the multivariate analysis, larger tumor size (OR=5.246, 95% CI 1.269-10.907, p=0.009) and higher NLR (OR=2.087, 95% CI 0.977-4.459, p=0.034) were statistically significant for distant metastases. Conclusion This research reveals that pre-ablation NLR and tumor size are significantly statistically correlated with distant metastases in patients with DTC.
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Luo H, Shan W, Chen C, Ding P, Luo L. Improving language model of human genome for DNA-protein binding prediction based on task-specific pre-training. Interdiscip Sci 2023; 15:32-43. [PMID: 36136096 DOI: 10.1007/s12539-022-00537-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 08/30/2022] [Accepted: 09/07/2022] [Indexed: 11/27/2022]
Abstract
The DNA-protein binding plays a pivotal role in regulating gene expression and evolution, and computational identification of DNA-protein has drawn more and more attention in bioinformatics. Recently, variants of BERT are also used to capture the semantic information of DNA sequences for predicting DNA-protein bindings. In this study, we leverage a task-specific pre-training strategy on BERT using large-scale multi-source DNA-protein binding data and present TFBert. TFBert treats DNA sequences as natural sentences and k-mer nucleotides as words. It can effectively extract upstream and downstream nucleotide context information by pre-training the 690 unlabeled ChIP-seq datasets. Experiments show that the pre-trained model can achieve promising performance on every single dataset in the 690 ChIP-seq datasets after simple fine tuning, especially on small datasets. The average AUC is 94.7%, outperforming existing popular methods. In conclusion, this study provides a variant of BERT based on pre-training and achieved state-of-the-art results in predicting DNA-protein bindings. We believe that TFBert can provide insights into other biological sequence classification problems.
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Luo L, Yao XB, Zheng SJ, Yang WL. [A family study of the compound heterozygous mutation of the UGT1A1 gene causing Crigler-Najjar syndrome type II]. ZHONGHUA GAN ZANG BING ZA ZHI = ZHONGHUA GANZANGBING ZAZHI = CHINESE JOURNAL OF HEPATOLOGY 2023; 31:168-173. [PMID: 37137832 DOI: 10.3760/cma.j.cn501113-20211124-00580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Objective: To investigate the family gene features in Crigler-Najjar syndrome (CNS) type II. Methods: The UGT1A1 gene and related bilirubin metabolism genes were comprehensively analysed in a CNS-II family (3 CNS-II, 1 Gilbert syndrome, and 8 normal subjects). The genetics basis of CNS-II were investigated from the perspective of family analysis. Results: In three cases, compound heterozygous mutations at three sites of the UGT1A1 gene (c.-3279T > G, c.211G > A and c.1456T > G) caused CNS-II. Gilbert syndrome and CNS-II were not significantly associated with distribution or diversity loci. Conclusion: The compound heterozygous pathogenic mutations (c.-3279T > G, c.211G > A, and c.1456T > G) at three loci of the UGT1A1 gene may be the feature of the newly discovered CNS-II family genes based on the CNS-II family study.
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Zhou L, Luo L, Ying DM, Xiang JG, Xiong X, Gao CY, Sun QL, Chen ZQ. [Observation on the clinical outcomes of continued pregnancy following cesarean scar pregnancy in 55 women]. ZHONGHUA FU CHAN KE ZA ZHI 2023; 58:37-43. [PMID: 36720613 DOI: 10.3760/cma.j.cn112141-20220817-00515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Objective: To observe the clinical outcomes of continued pregnancy in pregnant women with cesarean scar pregnancy (CSP). Methods: A retrospective analysis was performed on the pregnancy outcomes of 55 pregnant women who were diagnosed with CSP at the Second Affiliated Hospital of Army Medical University during the first trimester of pregnancy from August 1st, 2018 to October 31st, 2021 and strongly requested to continue the pregnancy. Results: Of the 55 pregnant women, 15 terminated the pregnancy in the first trimester, 1 underwent hysterotomy at 23 weeks of gestation due to cervical dilation, and 39 (71%, 39/55) continued pregnancy to the third trimester achieving live births via cesarean section. The gestational age of the 39 pregnant women delivered by cesarean section was 35+6 weeks (range: 28+5-39+2 weeks), of whom 7 cases at 28+5-33+6 weeks, 20 cases at 34-36+6 weeks, and 12 cases at 37-39+2 weeks. The results of pathological examination were normal placenta in 3 cases (8%, 3/39), placenta creta in 4 cases (10%, 4/39), placenta increta in 9 cases (23%, 9/39) and placenta percreta in 23 cases (59%, 23/39). Among the 36 pregnant women who were pathologically confirmed as placenta accreta spectrum disorders (PAS) after surgery, the last prenatal ultrasonography showed placenta previa in 27 cases (75%, 27/36) and not observed placenta previa in 9 cases. The median intraoperative blood loss, autologous blood transfusion, and allogeneic suspended red blood cell infusion of 39 pregnant women during cesarean section were 1 000 ml (300-3 500 ml), 300 ml (0-2 000 ml) and 400 ml (0-2 400 ml), respectively. The uterine preservation rate was 100% (39/39), and only 1 case received cystostomy due to intracystic hemorrhage. The birth weight of the newborn was 2 580 g (1 350-3 800 g), and 1 case of mild asphyxia. Conclusions: Pregnant women with CSP who continue pregnancy under close monitoring after adequate ultrasound evaluation and doctor-patient communication could achieve better maternal and infant outcomes, but pregnant women with CSP are highly likely to continue pregnancy and develop into PAS. Effective hemostasis means and multidisciplinary team cooperation are needed in perinatal period for ensuring maternal and fetal safety.
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