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Chen YM, Lin P, He JQ, He Y, Li XL. Combination of the Manifold Dimensionality Reduction Methods with Least Squares Support vector machines for Classifying the Species of Sorghum Seeds. Sci Rep 2016; 6:19917. [PMID: 26817580 PMCID: PMC4730150 DOI: 10.1038/srep19917] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 12/21/2015] [Indexed: 11/09/2022] Open
Abstract
This study was carried out for rapid and noninvasive determination of the class of sorghum species by using the manifold dimensionality reduction (MDR) method and the nonlinear regression method of least squares support vector machines (LS-SVM) combing with the mid-infrared spectroscopy (MIRS) techniques. The methods of Durbin and Run test of augmented partial residual plot (APaRP) were performed to diagnose the nonlinearity of the raw spectral data. The nonlinear MDR methods of isometric feature mapping (ISOMAP), local linear embedding, laplacian eigenmaps and local tangent space alignment, as well as the linear MDR methods of principle component analysis and metric multidimensional scaling were employed to extract the feature variables. The extracted characteristic variables were utilized as the input of LS-SVM and established the relationship between the spectra and the target attributes. The mean average precision (MAP) scores and prediction accuracy were respectively used to evaluate the performance of models. The prediction results showed that the ISOMAP-LS-SVM model obtained the best classification performance, where the MAP scores and prediction accuracy were 0.947 and 92.86%, respectively. It can be concluded that the ISOMAP-LS-SVM model combined with the MIRS technique has the potential of classifying the species of sorghum in a reasonable accuracy.
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Min M, Lin P, Lee M, Ho Shon I, Lin M, Forstner D, Tieu MT, Chicco A, Bray V, Fowler A. Prognostic Value of 2-[(18)F] Fluoro-2-deoxy-D-glucose Positron Emission Tomography-Computed Tomography Scan Carried out During and After Radiation Therapy for Head and Neck Cancer Using Visual Therapy Response Interpretation Criteria. Clin Oncol (R Coll Radiol) 2016; 28:393-401. [PMID: 26782837 DOI: 10.1016/j.clon.2015.12.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Revised: 12/02/2015] [Accepted: 12/08/2015] [Indexed: 10/25/2022]
Abstract
AIMS To evaluate the prognostic utility of 2-[(18)F] fluoro-2-deoxy-d-glucose positron emission tomography-computed tomography (FDG PET-CT) carried out in the third week (iPET) and after completion (pPET) of definitive radiation therapy in patients with mucosal primary head and neck squamous cell carcinoma (MPHNSCC) and to investigate the optimal visual grading criteria for therapy response assessment. MATERIALS AND METHODS Sixty-nine consecutive patients with newly diagnosed MPHNSCC treated with radical radiation therapy with or without systemic therapy underwent staging. PET-CT, iPET and pPET were included. All PET-CT images were reviewed by using a visual grading system to assess metabolic response for primary tumour: 0 = similar to adjacent background blood pool activity; 1 = more than background but < mediastinal blood pool; 2 ≥ mediastinal blood pool and < liver; 3 ≥ liver; and 4 ≥ brain. The results were correlated with locoregional recurrence-free survival (LRFS), disease-free survival (DFS) and overall survival, using Kaplan-Meier analysis. RESULTS The median follow-up was 28 months (range 6-62), the median age was 61 years (range 39-81) and AJCC 7th edition clinical stage II, III and IV were six, 18 and 45 patients, respectively. The optimal threshold for non-complete metabolic response (non-CMR) was defined as focal uptake ≥ liver (grade 3) for iPET and focal uptake ≥ mediastinum (grade 2) for pPET. The 2 year Kaplan-Meier LRFS, DFS and overall survival estimates for primary CMR and non-CMR in iPET were 89.8% versus 71.5% (P = 0.062), 80.1% versus 65.3% (P = 0.132), 79.1% versus 72.1% (P = 0.328) and in pPET 86.2% versus 44.6% (P = 0.0005), 77.6% versus 41.2% (P = 0.006), 81.2% versus 40.6% (P = 0.01), respectively. The negative predictive value (NPV) for LRFS for patients achieving both primary and nodal CMR in iPET was 100%. No locoregional failure was observed in patients with both primary and nodal iPET CMR (P = 0.038), whereas those with nodal iPET CMR had no regional failure (P = 0.033). However, the positive predictive values (PPV) for LRFS and DFS for iPET and pPET were found to be poor: 30% and 36% for iPET and 35% and 39% for pPET, respectively. CONCLUSION Standardised criteria using visual assessment are feasible. The metabolic response using visual assessment with standardised interpretation criteria of iPET and pPET can be useful predictors of tumour control. Dose de-escalation can be considered on the basis of a high NPV for iPET. However, the PPV of iPET is poor, indicating that additional discriminative tools are needed.
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Zheng Y, Zhao Y, Yue L, Lin P, Liu Y, Xian J, Zhou G, Wang D. Pilot study of DNA methylation in the pathogenesis of chronic rhinosinusitis with nasal polyps. Rhinology 2015. [DOI: 10.4193/rhin14.086] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Lin P, Stoakes E, Scott A, Sam S, Chicco A. Clinical Impact of Fluorodeoxyglucose Positron Emission Tomography-Computed Tomography Carried Out for Non-Medicare Eligible Indications in Australia: A Prospective Study. Clin Oncol (R Coll Radiol) 2015; 27:753-4. [PMID: 26345249 DOI: 10.1016/j.clon.2015.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Revised: 08/13/2015] [Accepted: 08/19/2015] [Indexed: 10/23/2022]
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Wang X, Wang F, Jing Y, Wang Y, Lin P, Yang L. Application of Orthogonal Design to Optimize Extraction of Polysaccharide from <i>Cynomorium songaricum</i> Rupr (Cynomoriaceae). TROP J PHARM RES 2015. [DOI: 10.4314/tjpr.v14i7.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Zhao H, Wang J, Jiang Y, Cheng Y, Lin P, Zhu H, Han G, Yi L, Zhang S, Guo L, Cheng S. Typing of Canine Parvovirus Strains Circulating in North-East China. Transbound Emerg Dis 2015; 64:495-503. [DOI: 10.1111/tbed.12390] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Indexed: 11/30/2022]
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Emery P, Kavanaugh A, Bao Y, Betts K, Macalalad A, Lin P, Galebach P, Garg V. FRI0129 Assessing the Economic Impact of Comprehensive Disease Control on Total Direct Medical Expenditures for Rheumatoid Arthritis. Ann Rheum Dis 2015. [DOI: 10.1136/annrheumdis-2015-eular.5157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Wang W, Cortes JE, Lin P, Khoury JD, Ai D, Tang Z, Tang G, Jorgensen JL, Medeiros LJ, Hu S. Impact of trisomy 8 on treatment response and survival of patients with chronic myelogenous leukemia in the era of tyrosine kinase inhibitors. Leukemia 2015; 29:2263-6. [PMID: 25931274 DOI: 10.1038/leu.2015.96] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Wei FX, Hu XF, Xu B, Zhang MH, Li SY, Sun QY, Lin P. Ammonia concentration and relative humidity in poultry houses affect the immune response of broilers. GENETICS AND MOLECULAR RESEARCH 2015; 14:3160-9. [PMID: 25966081 DOI: 10.4238/2015.april.10.27] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
To investigate the effect of ammonia (NH3) and humidity on the immune response of broilers, broilers were exposed to 30 or 70 mg/kg atmospheric NH3 for 21 days. Additionally, birds were exposed to 35, 60, and 85% relative humidity (RH). The relative weights of lymphoid organs, serum total protein, serum globulin, serum albumin, serum lysozyme, proliferation index of peripheral blood lymphocytes, and splenic cytokine gene expression were determined. Exposure to 70 mg/kg NH3 decreased the relative weight of the spleen during the experimental period, serum lysozyme concentration in the first and second weeks, and serum globulin concentration in the third week. The proliferation of peripheral blood lymphocytes was reduced. High levels of NH3 caused increase in IL-1β gene expression in the experimental period and IL-4 gene expression in the first week. Birds exposed to 85% RH had lower thymus and bursa of Fabricius weights in the third week and serum lysozyme concentration in the first week; IL-1β and IL-4 expressions were higher in the second and third weeks and first and second weeks, respectively, than in birds exposed to 60% RH. IL-4 expression was lower during the first week, and IL-1β expression was higher during the second week with 35% RH than with 60% RH. In conclusion, high NH3 level in the poultry house suppressed the immune response of broiler chickens. Neither high nor low RH benefited the immune response of broilers. Furthermore, there was an interactive effect between NH3 and RH on the immune response of broilers.
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Huang B, Lu J, Lin P, Chen C. PO-0981: Optimizing the planning parameters to obtain the lowest monitor units in lung stereotactic body radiation therapy. Radiother Oncol 2015. [DOI: 10.1016/s0167-8140(15)40973-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Min M, Lin P, Lee M, Ho Shon I, Lin M, Forstner D, Bray V, Chicco A, Tieu M, Fowler A. PO-118: Prognostic role of FDG-PET metabolic parameters during radiotherapy for head and neck squamous cell carcinoma. Radiother Oncol 2015. [DOI: 10.1016/s0167-8140(15)34878-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Ma G, Zhang X, Ma Q, Rong T, Long H, Lin P, Fu J, Zhang L. A novel multivariate scoring system for determining the prognosis of lymph node-negative esophageal squamous cell carcinoma following surgical therapy: an observational study. Eur J Surg Oncol 2015; 41:541-7. [PMID: 25659876 DOI: 10.1016/j.ejso.2015.01.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 12/06/2014] [Accepted: 01/15/2015] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Identifying patients with esophageal squamous cell carcinoma (ESCC) with negative prognostic factors, which have an extremely low survival rate, has been problematic. METHODS We retrospectively collected clinical data for 648 patients with lymph node-negative ESCC who were treated at the Sun Yat-Sen University Cancer Center from 1990 to 2005. Survival difference was compared using Kaplan-Meier analysis and multivariate Cox regression analysis. RESULTS We identified advancing age, smoking history, alcohol consumption history, decreased forced expiratory volume in 1 s (FEV1), surgical procedure, tumor location, number of resected lymph nodes, poor tumor differentiation, and surgical stage as independent prognostic risk factors. Furthermore, based on the results of multivariate analysis, we constructed a novel scoring system that included the factors of age, smoking history, alcohol consumption history, number of resected lymph nodes, tumor differentiation, and surgical stage. Risk score (RS) was computed with the scoring system, and patients were divided into Class A (RS: 0-5) and Class B (RS: 6-10). P < 0.001 indicated statistical significance. A significant difference (p < 0.001) demonstrated that Class B was strongly related to a low survival rate and poor prognosis. CONCLUSION We developed a new simple flexible scoring system of high prognostic significance, which has the potential to guide postoperative therapeutic strategies and follow-up frequency and to provide better prognostic information for patients and their families.
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Yang Y, Wu J, Ma J, Lin P. Chemical Composition and Antimicrobial Activity of the Essential Oil from Artemisia carvifolia Leaves. Chem Nat Compd 2015. [DOI: 10.1007/s10600-015-1229-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Sidhu P, Lin P, Son H, Rosenfeld D, Lin M. Testicular fluorine-18 fludeoxyglucose uptake on positron emission tomography CT in patients with lymphoma: clinical significance and management impact. Br J Radiol 2014; 87:20140472. [PMID: 25333503 DOI: 10.1259/bjr.20140472] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
OBJECTIVE This is the first case series examining the role of fluorine-18 fludeoxyglucose ((18)F-FDG) positron emission tomography-CT (PET-CT) in the diagnosis of lymphoma, and its impact on the clinical management of patients with secondary testicular involvement. This study explores the clinical significance of abnormal testicular uptake, maximum standardized uptake values and the diagnostic value of the CT component in PET-CT scans of these patients. METHODS The case notes and PET scans of 12 patients with diagnosis of lymphoma that were reported to have abnormal (18)F-FDG uptake in the testes were examined. Case notes were reviewed for the underlying diagnosis, indication for the scan and its effect on the management decision. RESULTS 12 patients demonstrated abnormal (18)F-FDG uptake on the PET-CT scans (mean age, 63 years; range, 37-82 years). Seven patients were diagnosed with testicular lymphoma. Six out of the seven (86%) patients received additional intrathecal chemotherapy in addition to their systemic chemotherapy, and one patient had testicular radiotherapy. CONCLUSION This study establishes the importance of identifying and reporting abnormal (18)F-FDG uptake in the testes on PET-CT in patients with lymphoma. (18)F-FDG PET-CT is superior to conventional imaging in identifying testicular lymphoma and has significant management impact. It also emphasizes the importance of incorporating the testes as part of the scan coverage. ADVANCES IN KNOWLEDGE The appearances of testicular lymphoma on (18)F-FDG PET-CT can be variable and abnormal testicular uptake warrants further investigations and confirmation. FDG PET-CT is an important tool and can be used in addition to conventional imaging in the identification of testicular lymphoma.
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Cristea M, Rivkin S, Lim D, Chung V, Chao J, Wakabayashi M, Paz B, Han E, Lin P, Leong L, Hakim A, Frankel P, Synold T, Carroll M, Openshaw H, Prakash N, Dellinger T, Park M, Morgan R. Phase I Trial of Intraperitoneal Nab-Paclitaxel in the Treatment of Advanced Malignancies Primarily Confined to the Peritoneal Cavity. Ann Oncol 2014. [DOI: 10.1093/annonc/mdu331.37] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Huang B, Lu J, Lin P, Chen J, Kuang Y, Chen C. Optimizing Dose Delivery Strategies in Stereotactic Body Radiation Therapy of Early-Stage Non-Small Cell Lung Cancer With RapidArc and Flattering Filter–Free Beams. Int J Radiat Oncol Biol Phys 2014. [DOI: 10.1016/j.ijrobp.2014.05.2665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Huang B, Fang Z, Huang Y, Lin P, Chen Z. A dosimetric analysis of volumetric-modulated arc radiotherapy with jaw width restriction vs 7 field intensity-modulated radiotherapy for definitive treatment of cervical cancer. Br J Radiol 2014; 87:20140183. [PMID: 24834477 PMCID: PMC4075592 DOI: 10.1259/bjr.20140183] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 05/03/2014] [Accepted: 05/14/2014] [Indexed: 02/05/2023] Open
Abstract
OBJECTIVE Radiation therapy treatment planning was performed to compare the dosimetric difference between volumetric-modulated arc radiotherapy (RapidArc™ v. 10; Varian® Medical Systems, Palo Alto, CA) and 7-field intensity-modulated radiotherapy (7f-IMRT) in the definitive treatment of cervical cancer. METHODS 13 patients with cervical cancer were enrolled in this study. Planning target volume (PTV) 50 and PTV60 were prescribed at a dose of 50 and 60 Gy in 28 fractions, respectively. The dose to the PTV60 was delivered as a simultaneous integrated boost to the pelvic lymph nodes. Owing to the mechanical limitation of the multileaf collimator in which the maximum displacement was limited to 15 cm, two types of RapidArc with different jaw width restrictions (15 and 20-23 cm) were investigated to evaluate their dosimetric differences. The RapidArc plan type with dosimetric superiority was then compared against the 7f-IMRT on the target coverage, sparing of the organs at risk (OARs), monitor units, treatment time and delivery accuracy to determine whether RapidArc is beneficial for the treatment of cervical cancer. RESULTS The 15-cm jaw width restriction had better performance compared with the restrictions that were longer than 15 cm in the sparing of the OARs. The 15-cm RapidArc spared the OARs, that is, the bladder, rectum, small intestine, femoral heads and bones, and improved treatment efficiency compared with 7f-IMRT. Both techniques delivered a high quality-assurance passing rate (>90%) according to the Γ3mm,3% criterion. CONCLUSION RapidArc with a 15-cm jaw width restriction spares the OARs and improves treatment efficiency in cervical cancer compared with 7f-IMRT. ADVANCES IN KNOWLEDGE This study describes the dosimetric superiority of RapidArc with a 15-cm jaw width restriction and explores the feasibility of using RapidArc for the definitive treatment of cervical cancer.
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Lin P, Chen YM, He Y, Hu GW, Fu XL, Gu CL. Study on Nonlinear Multivariate Methods Combined with the Visible Near-Infrared Spectroscopy (Vis/NIRS) Technique for Detecting the Protein Content of Cheese. FOOD BIOPROCESS TECH 2014. [DOI: 10.1007/s11947-014-1341-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Huang B, Lu J, Lin P, Chen J, Kuang Y, Chen C. TH-C-12A-02: Comparison of Two RapidArc Delivery Strategies in Stereotactic Body Radiotherapy of Stage I and II Peripheral Lung Tumors with Unflattened Beams. Med Phys 2014. [DOI: 10.1118/1.4889639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Jaso JM, Wang SA, Jorgensen JL, Lin P. Multi-color flow cytometric immunophenotyping for detection of minimal residual disease in AML: past, present and future. Bone Marrow Transplant 2014; 49:1129-38. [PMID: 24842529 DOI: 10.1038/bmt.2014.99] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 03/15/2014] [Accepted: 03/21/2014] [Indexed: 01/15/2023]
Abstract
Current chemotherapeutic regimens achieve CR in a large percentage of patients with AML. However, relapse after CR remains a significant problem. The presence of leukemic cells at levels too low to be detected by conventional microscopy, termed minimal residual disease (MRD), has been associated with an increased risk of relapse and shortened survival. Detection of MRD requires the use of highly sensitive ancillary techniques. Multi-color flow cytometric immunophenotyping is a sensitive method for quick and accurate detection of MRD. Use of this method in patient management may result in lower rates of relapse and improved survival, and is an effective means of assessing novel therapeutic agents. This method can be used in the vast majority of patients with AML, regardless of the immunophenotypic, cytogenetic and molecular genetic abnormalities present. Unfortunately, conflicting data regarding optimum methods of measurement and reporting, as well as the expertize required to interpret results have limited broad application of this technique. We provide a broad overview of this technique, including its advantages and limitations, and discuss the methods employed at our institution. We also review several possible areas of future investigation.
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Guo J, Lin P, Zhao X, Zhang J, Wei X, Wang Q, Wang C. Etazolate abrogates the lipopolysaccharide (LPS)-induced downregulation of the cAMP/pCREB/BDNF signaling, neuroinflammatory response and depressive-like behavior in mice. Neuroscience 2014; 263:1-14. [PMID: 24434771 DOI: 10.1016/j.neuroscience.2014.01.008] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2013] [Revised: 01/05/2014] [Accepted: 01/06/2014] [Indexed: 12/16/2022]
Abstract
Increasing evidence has indicated that immune challenge by bacterial lipopolysaccharide (LPS) induces depressive-like behavior, neuroinflammatory response and upregulates phosphodiesterase-4 (PDE4), an enzyme that specifically hydrolyzes cyclic adenosine monophosphate (cAMP). However, whether the potential PDE4 inhibitor etazolate prevents the LPS-induced depressive-like behavior remains unclear. Here using a model of depression induced by the repeated administration of LPS during 16days, and then investigated the influence of LPS on the expression of PDE4, interleukin-1β (IL-1β) and antidepressant action of etazolate in mice through forced swimming, novelty suppressed feeding, sucrose preference and open-field tests. Our results showed that etazolate pretreatment facilitated the recovery from weight loss and prevented the depressive-like behavior induced by repeated LPS administration. Moreover, the antidepressant action of etazolate was paralleled by significantly reducing the expression levels of PDE4A, PDE4B, PDE4D and IL-1β and up-regulating the cAMP/phosphorylated cAMP response-element binding protein (pCREB)/brain-derived neurotrophic factor (BDNF) signaling in the hippocampus and prefrontal cortex of mice. These results indicate that the effects of etazolate on the depressive-like behavior induced by repeated LPS treatment may partially depend on the inhibition of PDE4 subtypes, the activation of the cAMP/pCREB/BDNF signaling and the anti-inflammatory responses in the hippocampus and prefrontal cortex.
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Zhou CF, Lin P, Yao XH, Wang KL, Chang J, Han XJ. Selection of reference genes for quantitative real-time PCR in six oil-tea camellia based on RNA-seq. Mol Biol 2013. [DOI: 10.1134/s0026893313060198] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Zhou CF, Lin P, Yao XH, Wang KL, Chang J, Han XJ. [Selection of reference genes for quantitative real-time PCR in six oil-tea camellia based on RNA]. Mol Biol (Mosk) 2013; 47:959-975. [PMID: 25509858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
qRT-PCR is becoming a routine tool in molecular biology to study gene expression. It is nec- essary to find stable reference genes when performing qRT-PCR. The expression of genes cloned in oil-tea camellia currently can't be accurately analyzed because of a lack of suitable reference genes. We collected different tissues (including roots, stems, leaves, flowers and seeds) from six oil-tea camellia species to determine stable reference genes. Five novel and ten traditional reference gene sequences were selected from the RNA-seq database of Camellia oleifera C. Abel seeds and specific PCR primers were designed for each. Cycle threshold (Ct) data were obtained from each reaction for all samples. Three different software tools, geNorm, NormFinder and BestKeeper were applied to calculate the expression stability of the candidate reference genes according to the Ct values. The results were similar between analyzed by the three software packages, and indicated that the traditional gene TUBa-3, AC17a and the novel gene CESA were relatively stable in all species and tissues. However, no genes were sufficiently stable across all species and tissues, thus the optimal number of reference genes required for accurate normalization varied from two to six. Finally, the relative expression ofsqualene synthase (SQS) and squalene epoxidase (SQE) genes related to important ingredients squalene and tea saponin in oil-tea camellia seeds were compared by using stable to less stable reference genes. The comparison results validated the selection of reference genes in the current study. In summary, different optimal numbers of suitable reference genes were found for the different tissues of six oil-tea camellia species.
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Todor D, Barani I, Lin P, Anscher M, Axente M, Hagan M. Towards a Meaningful Prescription for Focal Treatments in Prostate Brachytherapy. Int J Radiat Oncol Biol Phys 2013. [DOI: 10.1016/j.ijrobp.2013.06.1001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Meng YQ, Cao X, Wen ZS, Liu QW, Tan ZH, Duan H, Ma GW, Lin P. Preoperative level of serum amyloid A is superior to C-reactive protein in the prognosis of esophageal squamous cell carcinoma. Dis Esophagus 2013; 27:670-7. [PMID: 24033446 DOI: 10.1111/dote.12128] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Preoperative elevations in the levels of serum amyloid A (SAA) or C-reactive protein (CRP) have been reported to be prognostic indicators in several malignancies. The aim of this study is to evaluate the serum levels of SAA and CRP in the prognosis of esophageal squamous cell carcinoma (ESCC). In total, 252 patients with ESCC who had undergone surgery with curative-intent were retrospectively recruited. The specificity, sensitivity, and prognostic value of SAA or CRP levels were measured as the area under the receiver operating characteristic (ROC) curve (AUC). The clinical value of SAA and CRP levels as prognostic indicators was evaluated using Cox's proportional hazards model. The 1-, 3-, and 5-year overall survival (OS) rates for the entire cohort of patients with ESCC were 71.0%, 61.0%, and 43.0%, respectively. The correlation between the levels of SAA and CRP was significant (r(2) = 0. 685, P < 0.001). The ROC analysis showed that the levels of CRP were associated with a significantly lower overall accuracy than were the SAA levels (AUC, 0.615 vs. 0.880; P < 0.001). For the complete cohort, the median OS was 52.0 months longer in patients with low preoperative serum levels of SAA (72.0 months) compared with patients who had high SAA levels (20.0 months, P < 0.001). The median OS among patients with low CRP levels was also longer compared with the patients who had high CRP levels (72.0 vs. 51.0 months, respectively; P < 0.001). Subgroup analyses showed that the preoperative elevated levels of SAA could find significant differences in OS for stage I, stage II, and stage III (P < 0.001, P = 0.001, and P < 0.001, respectively), whereas the increased levels of CRP could only find a difference in OS for stage II cancers. After a multivariate analysis, preoperative elevated level of SAA was found to be an independently and significant prognostic factor (P < 0.001). Our study indicates that the preoperative levels of SAA and CRP can act as prognostic factors, and that elevated levels of these proteins are associated with negative effects on the survival of patients with ESCC. SAA showed a higher prognostic value than CRP in both cohort and subgroup analysis.
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