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1.
Sci Total Environ ; 813: 151920, 2022 Mar 20.
Article in English | MEDLINE | ID: mdl-34838555

ABSTRACT

In this study, data-driven deep learning methods were applied in order to model and predict the treatment of real municipal wastewater using anaerobic membrane bioreactors (AnMBRs). Based on the one-year operating data of two AnMBRs, six parameters related to the experimental conditions (temperature of reactor, temperature of environment, temperature of influent, influent pH, influent COD, and flux) and eight parameters for wastewater treatment evaluation (effluent pH, effluent COD, COD removal efficiency, biogas composition (CH4, N2, and CO2), biogas production rate, and oxidation-reduction potential) were selected to establish the data sets. Three deep learning network structures were proposed to analyze and reproduce the relationship between the input parameters and output evaluation parameters. The statistical analysis showed that deep learning closely agrees with the AnMBR experimental results. The prediction accuracy rate of the proposed densely connected convolutional network (DenseNet) can reach up to 97.44%, and the single calculation time can be reduced to within 1 s, suggesting the high performance of AnMBR treatment prediction with deep learning methods.


Subject(s)
Deep Learning , Wastewater , Anaerobiosis , Bioreactors , Membranes, Artificial , Waste Disposal, Fluid
2.
Immunogenetics ; 69(6): 391-400, 2017 06.
Article in English | MEDLINE | ID: mdl-28451741

ABSTRACT

RAG1 and RAG2 are essential subunits of the V(D)J recombinase required for the generation of the variability of antibodies and T cell receptors in jawed vertebrates. It was demonstrated that the amphioxus homologue of RAG1-RAG2 is encoded in an active transposon, belonging to the transposase DDE superfamily. The data provided support the possibility that the RAG transposon has been active through the deuterostome evolution and is still active in several lineages. The RAG transposon corresponds to several families present in deuterostomes. RAG1-RAG2 V(D)J recombinase evolved from one of them, partially due to the new ability of the transposon to interact with the cellular reparation machinery. Considering the fact that the RAG transposon survived millions of years in many different lineages, in multiple copies, and that DDE transposases evolved their association with proteins involved in repair mechanisms, we propose that the apparition of V(D)J recombination machinery could be a predictable genetic event.


Subject(s)
DNA Transposable Elements , DNA-Binding Proteins/genetics , Evolution, Molecular , Homeodomain Proteins/genetics , Recombination, Genetic , Animals , Base Sequence , DNA-Binding Proteins/metabolism , Homeodomain Proteins/metabolism , Multigene Family , Phylogeny , V(D)J Recombination , Vertebrates/genetics
3.
Int J Antimicrob Agents ; 48(3): 286-91, 2016 Sep.
Article in English | MEDLINE | ID: mdl-27444117

ABSTRACT

Pneumonia is a leading cause of death in medical intensive care units (MICUs). Delayed or inappropriate antibiotic therapy largely increases morbidity and mortality. Multidrug-resistant (MDR) micro-organisms are major reasons for inappropriate antibiotic use. Currently there is no good antibiotic decision-making tool designed for critically ill patients. The objective of this study was to develop a convenient MDR prediction scoring system for patients admitted to MICUs with pneumonia. A retrospective cohort study was conducted using databases and chart reviews of pneumonia patients admitted to a 30-bed MICU from 2012 to 2013. Forward logistic regression was applied to identify independent MDR risk factors for prediction tool development. A total of 283 pneumonia episodes from 263 patients with positive cultures from blood or respiratory secretions were recruited, of which 154 (54.4%) were MDR episodes. Long-term ventilation (OR = 11.09; P = 0.026), residence in a long-term care facility (OR = 2.50; P = 0.005), MDR infection/colonisation during the preceding 90 days (OR = 2.08; P = 0.041), current hospitalisation ≥2 days (OR = 1.98; P = 0.019) and stroke (OR = 1.81; P = 0.035) were identified as independent predictors for MDR pneumonia. The area under the ROC curve of this prediction tool was much higher than that of ATS/IDSA classification (0.69 vs. 0.54; P <0.001). The prediction accuracy of this tool with risk score ≥1 for MDR infections was 63.7%. This simple five-item, one-step scoring tool for critically ill patients admitted to the MICU could help physicians provide timely appropriate empirical antibiotics.


Subject(s)
Anti-Bacterial Agents/administration & dosage , Decision Support Techniques , Drug Resistance, Multiple, Bacterial , Pneumonia/diagnosis , Pneumonia/drug therapy , Adult , Aged , Aged, 80 and over , Female , Humans , Intensive Care Units , Male , Middle Aged , Pneumonia/microbiology , Retrospective Studies , Risk Factors , Young Adult
4.
J Oral Pathol Med ; 45(2): 89-95, 2016 Feb.
Article in English | MEDLINE | ID: mdl-26211876

ABSTRACT

BACKGROUND: OCT4, SOX2, and NANOG are major transcription factors related to stem cell self-renewal and differentiation. The aim of this study was to examine the association of OCT4, SOX2, and NANOG expression levels with the development and prognosis of patients with oral squamous cell carcinoma (OSCC). MATERIALS AND METHODS: Expression levels of OCT4, SOX2, and NANOG were evaluated by immunohistochemistry with tissue microarray slides of 436 OSCC, 362 corresponding tumor-adjacent normal (CTAN) tissues, and 71 normal uvula epithelium tissues. The clinicopathologic and follow-up data of the OSCC patients were recorded. RESULTS: OCT4 expression was significantly higher in normal and CTAN tissues than in tumor tissue (both P < 0.001). SOX2 expression in CTAN tissue was significantly higher than that in normal (P = 0.021) and tumor tissues (P < 0.001). However, NANOG expression was significantly higher in CTAN (P = 0.014) and tumor tissues (P = 0.009) than in normal tissue. Higher OCT4 and SOX2 expressions were associated with earlier AJCC stage (P = 0.002 and P < 0.001), small tumor size (P = 0.017 and P = 0.001), and the absence of lymph node metastasis (P = 0.015 and P = 0.025). Higher levels of SOX2 expression were associated with better disease-specific survival (P = 0.002) even after adjustment for clinicopathologic factors. DISCUSSION: OCT4 and SOX2 are biomarkers of tumorigenesis and early stage OSCC. SOX2 is an independent prognostic factor for OSCC.


Subject(s)
Biomarkers, Tumor , Carcinoma, Squamous Cell/metabolism , Disease Progression , Mouth Neoplasms/metabolism , Nanog Homeobox Protein/biosynthesis , Octamer Transcription Factor-3/biosynthesis , SOXB1 Transcription Factors/biosynthesis , Adult , Aged , Aged, 80 and over , Biomarkers, Tumor/biosynthesis , Biomarkers, Tumor/genetics , Carcinogenesis/genetics , Carcinogenesis/pathology , Carcinoma, Squamous Cell/genetics , Carcinoma, Squamous Cell/pathology , Female , Humans , Lymphatic Metastasis/pathology , Male , Middle Aged , Mouth Neoplasms/genetics , Mouth Neoplasms/pathology , Nanog Homeobox Protein/genetics , Nanog Homeobox Protein/metabolism , Neoplastic Stem Cells/pathology , Octamer Transcription Factor-3/genetics , Octamer Transcription Factor-3/metabolism , Prognosis , SOXB1 Transcription Factors/genetics , SOXB1 Transcription Factors/metabolism , Transcription Factors/metabolism , Young Adult
5.
Breast Cancer Res Treat ; 153(1): 219-34, 2015 Aug.
Article in English | MEDLINE | ID: mdl-26253945

ABSTRACT

DNA methylation at the 5 position of cytosine (5 mC) is an epigenetic hallmark in cancer. The 5 mC can be converted to 5-hydroxymethylcytosine (5 hmC) through a ten-eleven-translocation (TET). We investigated the impact of 5 mC, 5 hmC, TET1, and TET2 on tumorigenesis and prognosis of breast cancer. Immunohistochemistry was used to assess the levels of 5 mC, 5 hmC, TET1, and TET2 in the corresponding tumor adjacent normal (n = 309), ductal carcinoma in situ (DCIS, n = 120), and invasive ductal carcinoma (IDC, n = 309) tissues for 309 breast ductal carcinoma patients. 5 mC, 5 hmC, TET1-n, and TET2-n were significantly decreased during DCIS and IDC progression. In IDC, the decrease of 5 hmC was correlated with the cytoplasmic mislocalization of TET1 (p < 0.001) as well as poor disease-specific survival (DSS) (adjusted hazard ratio [AHR] 1.95, p = 0.003) and disease-free survival (DFS) (AHR 1.91, p = 0.006). The combined decrease of 5 mC and 5 hmC was correlated with worse DSS (AHR 2.19, p = 0.008) and DFS (AHR 1.99, p = 0.036). Stratification analysis revealed that the low level of 5 mC was associated with poor DSS (AHR 1.89, p = 0.044) and DFS (AHR 2.02, p = 0.035) for the ER/PR-positive subtype. Conversely, the low level of 5 hmC was associated with worse DSS (AHR 2.77, p = 0.002) and DFS (AHR 2.69, p = 0.006) for the ER/PR-negative subtype. The decreases of 5 mC, 5 hmC, TET1-n, and TET2-n were biomarkers of tumor development. The global reduction of 5 hmC was a poor prognostic factor for IDC, especially for ER/PR-negative subtype.


Subject(s)
Breast Neoplasms/genetics , Breast Neoplasms/mortality , Cytosine/analogs & derivatives , DNA Methylation , 5-Methylcytosine/analogs & derivatives , Adult , Aged , Breast Neoplasms/epidemiology , Breast Neoplasms/pathology , Cytosine/metabolism , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Dioxygenases , Female , Gene Expression , Humans , Immunohistochemistry , Middle Aged , Mixed Function Oxygenases , Neoplasm Grading , Neoplasm Staging , Prognosis , Protein Transport , Proto-Oncogene Proteins/genetics , Proto-Oncogene Proteins/metabolism , Receptors, Estrogen/deficiency , Receptors, Progesterone/deficiency , Risk Factors , Survival Analysis , Young Adult
6.
Yi Chuan ; 32(1): 67-72, 2010 Jan.
Article in Chinese | MEDLINE | ID: mdl-20085888

ABSTRACT

As one of the closest living invertebrate relatives of vertebrates, amphioxus (subphylum Cephalochordata) occupies a key position in animal evolution and is becoming the best available proxy and model animal for studying the last common ancestor of all chordates, especially vertebrates. As long-term continuous culturing of amphioxus in laboratory became reliable, for pushing this animal to be a more successful model system, whole-genome sequencing of one or more species derived from this branch will be another urgent issue needed to address. In the present study, we described the construction and characterization of a bacterial artificial chromosome (BAC) library, using a single individual of Chinese amphioxus (Branchiostoma belcheri). High quality genomic DNA extracted from the spermary was partially digested with EcoRand EcoRmethylase. Desirable DNA fragments were isolated by pulsed field gel electrophoresis (PFGE), ligated to linearized and phosphorylased carrier pCC1BAC, and then transformed to Escherichia coli EPI300. The constructed library consists of 44 706 clones with the average insert fragment size around 80 kb as estimated by PFGE. The representation of the library is about 9 equivalents to the amhioxus genome. These results indicate that the BAC library will be useful for functional genomic studies and facilitate the whole-genome sequencing of Chinese amphioxus.


Subject(s)
Chordata/genetics , Chromosomes, Artificial, Bacterial/genetics , Genomic Library , Animals , Cloning, Molecular , Male
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