1.Constructing Support Vector Machine Ensembles for Cancer Classification Based on Proteomic Profiling
Mao YONG ; Zhou XIAO-BO ; Pi DAO-YING ; Sun YOU-XIAN
Genomics, Proteomics & Bioinformatics 2005;3(4):238-241
In this study, we present a constructive algorithm for training cooperative support vector machine ensembles (CSVMEs). CSVME combines ensemble architecture design with cooperative training for individual SVMs in ensembles. Unlike most previous studies on training ensembles, CSVME puts emphasis on both accuracy and collaboration among individual SVMs in an ensemble. A group of SVMs selected on the basis of recursive classifier elimination is used in CSVME, and the number of the individual SVMs selected to construct CSVME is determined by 10-fold cross-validation. This kind of SVME has been tested on two ovarian cancer datasets previously obtained by proteomic mass spectrometry. By combining several individual SVMs, the proposed method achieves better performance than the SVME of all base SVMs.
2.Community characters of Lophatherum gracile in Yongchuan district of Chongqing.
Fu-jun YIN ; Shu SHU ; Hua-rong ZHOU ; Xian-you QU ; Rui PAN ; Yi-quan ZHOU ; Wei SUN
China Journal of Chinese Materia Medica 2014;39(22):4277-4282
To understand Lophatherum gracile plant community's structural characteristics, a survey of community structure and species diversity was conducted through quadrat sampling in Yongchuan district of Chongqing. The results showed that there were 386 species vascular plants, belonging to 117 families and 229 genera. Based on habitat, community structure and species composition, L. gracile were found in three community types: Pinus massoniana community, banboo community, shurb community. Vertical structure was composed of three layers, including tree layer, shrub layer and herb layer. Species in shrub layer was the richness. P. massoniana is the only dominant species of the community, it can not regenerate naturally, the shrub layer has a greater effect on the community of L. gracile in the future. In addition, the banboo community and shurb community is not stable because of human's activity. Therefore, the community characters of L. gracile should be taken care of conservation when the resources are utilized.
China
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Ecosystem
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Pinus
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physiology
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Plants
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Poaceae
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physiology
4.An individualized approach combining local flaps with radiotherapy for the treatment of auricle keloid.
Xiao LONG ; Xiao-jun WANG ; You-bin WANG ; Wen-bo LI ; Xian-song SUN
Acta Academiae Medicinae Sinicae 2013;35(2):213-216
OBJECTIVETo investigate an individualized approach to the treatment of auricle keloid to maintain the normal appearance of external ear and meanwhile reduce the recurrence.
METHODSDifferent local flaps were performed according to the location of the keloid in our approach. The auricle was divided into different anatomical regions and all the patients received local postoperative radiotherapy.
RESULTSOf 68 patients with auricle keloid received the individualized approach, 3 cases suffered delayed healing due to partial flap necrosis. The remaining patients were followed up for 8-21 months(mean:11.5 months) . Recurrence occurred in one patient(1.47%) .
CONCLUSIONThe individualized approach combining local flaps with radiotherapy in treating auricle keloid can effectively maintain the normal ear appearance with low recurrence rate.
Adult ; Ear, External ; surgery ; Female ; Follow-Up Studies ; Humans ; Keloid ; radiotherapy ; surgery ; Male ; Radiotherapy, Adjuvant ; Recurrence ; Surgical Flaps ; Young Adult
5.Study on the protective effect of ursolic acid on alloxan-induced diabetic renal injury and its underlying mechanisms.
Min-You QI ; Jun-Jie YANG ; Bin ZHOU ; Ding-Yi PAN ; Xian SUN
Chinese Journal of Applied Physiology 2014;30(5):445-448
OBJECTIVETo investigate the effect of ursolic acid (UA) on the alloxan-induced kidney injury in diabetic mice and explored its possible mechanisms.
METHODSDiabetes mellitus was induced in male Kunming mice by an injection of alloxan (70 mg/kg, i.v.). After 72 hours, blood glucose levels were detected and mice with blood glucose levels over 13.9 mmol/L were considered as diabetic and selected for further experiment. Thirty mice were randomly divided into three groups: control, diabetic and diabetic + UA(35 mg/kg/d, i.g. continuously for 8 weeks). Blood glucose concentration, organ coefficient of kidney, blood urea nitrogen (BUN), creatinine (Cr) as well as renal tissue levels of superoxide dismutase (SOD), methane dicarboxylic aldehyde (MDA), tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6) were determined. Pathology of the renal tissue was measured by hematoxylin-eosin staining.
RESULTSCompared to the control group, blood glucose, organ coefficient of kidney, BUN and Cr increased significantly. In addition, SOD activities was reduced markedly and levels of MDA and inflammatory factors (TNF-α, IL-6) increased significantly. Renal cells from model group rats showed atrophy and disordered after HE staining and infiltration of inflammatory cells also appeared in renal tissue of the model group. These changes were significantly attenuated in the diabetic group treated with UA.
CONCLUSIONUA can significantly relieve renal damage in mice with diabetic nephropathy induced by alloxan, which might be related to decreased blood glucose level, antioxidation effect and inhibiting the production of inflammatory factors such as TNF-α and IL-6.
Alloxan ; adverse effects ; Animals ; Antioxidants ; metabolism ; Blood Glucose ; Blood Urea Nitrogen ; Creatinine ; metabolism ; Diabetes Mellitus, Experimental ; physiopathology ; Diabetic Nephropathies ; chemically induced ; drug therapy ; Interleukin-6 ; metabolism ; Kidney ; physiopathology ; Male ; Mice ; Superoxide Dismutase ; metabolism ; Triterpenes ; pharmacology ; Tumor Necrosis Factor-alpha ; metabolism
6.Serum growth hormone and prolactin levels in neonates with hypoxic-ischemic encephalopathy.
Guang-You ZHANG ; Xian-Mei LU ; Ruo-Peng SUN ; Shu-Zhen WANG
Chinese Journal of Contemporary Pediatrics 2006;8(6):450-452
OBJECTIVETo investigate the levels and roles of serum growth hormone (GH) and prolactin (PRL) in neonatal hypoxic-ischemic encephalopathy (HIE).
METHODSSerum GH and PRL levels were measured by radioimmunoassay in 54 neonates with HIE (20 mild, 19 moderate and 15 severe HIE) at the acute and convalescence stages. Twenty normal neonates were used as controls.
RESULTSSerum GH levels were significantly lower, but PRL levels were significantly higher in moderate and severe HIE neonates at the acute stage compared with those of controls and mild HIE neonates (P < 0.01). There were noticeable differences in serum levels of GH and PRL between the moderate and severe HIE cases (P < 0.01). During the convalescence stage, serum GH levels increased and PRL levels decreased in moderate and severe HIE neonates compared with those at the acute stage (P < 0.01); serum GH and PRL levels in each sub-group of HIE restored to the levels of controls. There was a closely negative correlation between GH and PRL levels at the acute stage of HIE (r = -0.8759, P < 0.01).
CONCLUSIONSGH and PRL might be involved in the pathophysiological process of HIE. The levels of GH and PRL closely relate to the severity of HIE at the acute stage.
Female ; Human Growth Hormone ; blood ; Humans ; Hypoxia-Ischemia, Brain ; blood ; Infant, Newborn ; Male ; Prolactin ; blood
7.Application of retrobulbar nerve block combined with general anesthesia in corneal transplantation
Aihua LAI ; Huang ZHANG ; Shan YOU ; Tao SUN ; Xian LIU ; Wentian ZHOU
Organ Transplantation 2019;10(5):578-
Objective To explore the application value of retrobulbar nerve block combined with general anesthesia in the penetrating keratoplasty (PKP). Methods A total of 100 recipients undergoing PKP from January 2017 to January 2019 were recruited in this study. All recipients were divided into the observation group (
8.Relationship between cortical watershed infarction and carotid artery stenosis and a follow-up and control study on prognosis after stent insertion
Fu-Qiang GUO ; Wen-Bin WU ; Tian ZHANG ; Neng-Wei YU ; Xiang-Rong SUN ; You-Song YANG ; Hong-Bin SUN ; Jun XIAO ; Ling-Lin DONG ; Xian-Rong ZENG ; Hong-Yuan DAI
Chinese Journal of Neuromedicine 2008;7(9):935-938
Objective To investigate the relationship between cortical watershed infarction and carotid artery stenosis and evaluate the stent insertion operation.Methods After 23 cortical watershed infarction patients diagnosed by CT or MRI received DSA detection,we performed stent insertion operationon 11 patients according to their requirements,and conservative treatment on the remaining 12 patients.All the patients underwent follow up for 6-12 months post-operatively.Results Among the 23 cortical watershed infarction patients,22 Were detected with carotid artery stenosis.Statistical analysis showed that the degree of carotid artery stenosis was associated With the elinical svmDtoms and the volume of steal phenomenon(P<0.05);further,the artery stenosis improvement was over 90%with the stent inserted;conversely,dizziness and steal phenomenon disappeared.The post procedure follow-up,ranging 6-12 months,showed that the patients with stent insertion got less new symptoms,steal phenomenon and artery stenosis,compared with the patients with conservation treatment(P<0.05).Conclusion Cortical watershed infarction is associated with carotid artery stenosis.The stent insertion iS useful for the treatment ofcarotid artery stenosis and prevention of cortical watershed infarction.
9.Feasibility of whole body diffusion weighted imaging in detecting bone metastasis on 3.0T MR scanner.
Xian XU ; Lin MA ; Jin-Shan ZHANG ; You-Quan CAI ; Bai-Xuan XU ; Liu-Quan CHEN ; Fei SUN ; Xing-Gao GUO
Chinese Medical Sciences Journal 2008;23(3):151-157
OBJECTIVETo evaluate the feasibility of whole body diffusion weighted imaging (DWI) in bone metastasis detection using bone scintigraphy as comparison.
METHODSForty-five patients with malignancy history were enrolled in our study. All the patients received the whole body DWI and bone scintigraphy scan within 1 week. The magnetic resonance (MR) examination was performed on 3.0T MR scanner using embedded body coil. The images were reviewed separately by two radiologists and two nuclear medicine physicians, who were blinded to the results of the other imaging modality. The sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of the two techniques for detecting bone metastasis were analyzed.
RESULTSA total of 181 metastatic lesions in 77 regions of 34 patients were detected by whole body DWI, and 167 metastatic lesions in 76 regions of 31 patients were identified by bone scintigraphy. The patient-based sensitivity and PPV of whole body DWI and bone scintigraphy were similar (89.5% vs. 81.6%, 97.1% vs. 91.2%), whereas, the patient-based specificity and NPV of whole body DWI were obviously higher than those of bone scintigraphy (85.7% vs. 57.1%, 60.0% vs. 36.4%). Ten regions negative in scintigraphy but positive in whole body DWI, mainly located in spine, pelvis, and femur; nine regions only detected by scintigraphy, mainly located in skull, sternum, clavicle, and scapula. The region-based sensitivity and specificity of whole body DWI were slightly higher than those of bone scintigraphy (89.5% vs. 88.4%, 95.6% vs. 87.6%).
CONCLUSIONWhole body DWI reveals excellent concordance with bone scintigraphy regarding detection of bone metastasis, and the two techniques are complementary for each other.
Aged ; Bone Neoplasms ; diagnosis ; pathology ; secondary ; Diffusion Magnetic Resonance Imaging ; instrumentation ; methods ; Female ; Humans ; Male ; Middle Aged ; Predictive Value of Tests ; Radionuclide Imaging ; Sensitivity and Specificity ; Whole Body Imaging ; instrumentation ; methods
10.Evaluation of sequest result filter-Xcorr and Unified Score.
Wei SUN ; Fu-xin LI ; You-he GAOL ; De-xian ZHENG
Chinese Medical Sciences Journal 2005;20(2):99-103
OBJECTIVETo estimate the effect of two simple filters, two or more positive peptide filter and Unified Score filter on the true positive rate of protein and peptide.
METHODSTwenty-two LC-MS/MS datasets were from 18 known protein mixture. Two or more positive peptide filter and Unified Score filter were applied to the 22 datasets. The filters effect was evaluated according to the true positive rate of protein and peptide for each filter.
RESULTSThe positive rates of protein and peptide from two or more peptide filter raised from 56.49% to 92.86%-99.12% (for protein) and from 90.67% to 97.74%-99.62% (for peptide), but many positive proteins were filtered out. The positive rates of protein and peptide from Unified Score (ThermoFinnigan value 2400) were only about 35.51% and 82.99%, but after adjusted the value (3900) according to the number of false positive peptide, those positive rate raised to 63.61% (for protein) and 91.97% (for peptide).
CONCLUSIONSTwo or more peptides requirement could significantly decrease false positive rate, but it also may filter out many true positive proteins especially low molecular weight and less abundant proteins. Unified Score may be a better filter than Xcorr and DeltaCn combination and the value of 3900 is found to be more suitable for this particular datasets.
Algorithms ; Animals ; Databases, Protein ; Mass Spectrometry ; methods ; Peptides ; chemistry ; Proteins ; chemistry ; Proteomics ; methods ; Sequence Analysis, Protein ; methods ; Software ; Statistics as Topic