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1.
World J Gastroenterol ; 25(17): 2099-2109, 2019 May 07.
Artigo em Inglês | MEDLINE | ID: mdl-31114136

RESUMO

BACKGROUND: The methylated septin 9 (mSEPT9) assay was the first blood-based test approved by the United States Food and Drug Administration as a colorectal screening test. However, the diagnostic and prognostic role of preoperative mSEPT9 for colorectal cancer (CRC) in Chinese patients is still unknown. AIM: To improve the understanding of diagnostic and prognostic factors, serum mSEPT9 was detected in Chinese CRC patients. METHODS: A retrospective analysis of 354 cases, of which 300 had CRC and 54 were normal, was performed in China. Patients' characteristics, treatments, and laboratory data, including age, the date of surgery, Union for International Cancer Control (UICC) stages, distant metastasis (M), and so on, were collected. Methylation levels of SEPT9 were quantified by quantitative, methylation-specific polymerase chain reaction before surgery. In addition, the effects of mSEPT9 on the occurrence and prognosis of 330 CRC cases from The Cancer Genome Atlas (TCGA) database were evaluated using bioinformatics analyses. Potential prognostic factors for overall survival (OS) and progression-free survival (PFS) were evaluated by Kaplan-Meier univariate analysis. RESULTS: In Chinese CRC patients, positive mSEPT9 was strongly associated with advanced UICC stages, deeper invasion by the primary tumor, and more distant metastasis. Methylation levels of SEPT9 were stage-dependent and showed a stepwise increase in UICC stages (I-IV), primary tumor categories (T1-T4), regional node categories (N0-N2), and distant metastasis categories (M0-M1). The patients with positive mSEPT9 showed a tendency toward lower PFS. After analyzing TCGA clinical data, the high mSEPT9 group was found to be obviously correlated only with more distant metastasis. The patients with high mSEPT9 levels showed a tendency toward lower OS. Besides, nine meaningful mSEPT9 sites were found to provide guidance for the follow-up studies. CONCLUSION: MSEPT9 analysis may add valuable information to current tumor staging. Serum mSEPT9 in Chinese CRC patients appears to offer promising novel prognostic markers and might be considered for monitoring CRC recurrence.


Assuntos
Biomarcadores Tumorais/metabolismo , Neoplasias Colorretais/diagnóstico , Septinas/metabolismo , Adenoma/sangue , Adenoma/diagnóstico , Adenoma/cirurgia , Idoso , China , Neoplasias Colorretais/sangue , Neoplasias Colorretais/cirurgia , Biologia Computacional , Metilação de DNA , Detecção Precoce de Câncer , Feminino , Perfilação da Expressão Gênica , Humanos , Estimativa de Kaplan-Meier , Masculino , Pessoa de Meia-Idade , Estadiamento de Neoplasias , Período Pré-Operatório , Prognóstico , Estudos Retrospectivos
2.
J Clin Neurosci ; 37: 6-14, 2017 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-27816260

RESUMO

Several studies examined a possible link between multidrug resistance-associated protein 2 (ABCC2) gene variants and the risk of resistance to antiepileptic drugs (AEDs) in epilepsy, but the results were contradictory. In this study, a meta-analysis was conducted to assess the relevance of ABCC2 common variants (c.-24C>T, c.1249G>A, c.3972C>T) with the response risk of AEDs. We searched Embase, PubMed, the Cochrane Library and CNKI databases for case-control studies published through May 2016 that evaluated the role of ABCC2 gene variants in pharmacoresistance to AEDs. Odds ratios (ORs) and their 95% confidence intervals (CIs) were calculated to assess the strength of associations between the ABCC2 c.-24C>T, c.1249G>A and c.3972C>T variants and the risk of resistance to AEDs using an allele frequency model, dominant model and recessive model. Subgroup analyses were performed by ethnicity and the definition of drug-resistance. A total of 13 published studies involving 4300 patients (2261 patients with drug-resistant epilepsy and 2039 controls with drug-responsive epilepsy) met the selection criteria. We observed that the variant c.-24C>T was associated with a significantly increased risk of AED resistance (TT+CT vs CC: OR=1.24, 95%CI=1.06-1.46, p=0.009; TT vs CT+CC: OR=1.90, 95%CI=1.31-2.76, p=0.0008; T vs C: OR=1.27, 95%CI=1.11-1.46, p=0.0006). However, we identified no significant association of the ABCC2 c.1249G>A, c.3972C>T variants and haplotypes with the response to anticonvulsant drug in the overall population. In summary, these observations suggest that the ABCC2 c.-24C>T polymorphism is a likely risk factor for resistance to AEDs.


Assuntos
Anticonvulsivantes/uso terapêutico , Resistência a Medicamentos/genética , Epilepsia/tratamento farmacológico , Proteínas Associadas à Resistência a Múltiplos Medicamentos/genética , Polimorfismo de Nucleotídeo Único , Epilepsia/genética , Frequência do Gene , Predisposição Genética para Doença , Haplótipos , Humanos
3.
Oncol Lett ; 10(3): 1444-1446, 2015 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-26622687

RESUMO

Giant cystic pheochromocytomas (GPCCs) are rare adrenal tumors and the majority of them present as asymptomatic. As a result GPCCs often remain undiagnosed until surgery and therefore the surgical team face a greater challenge in perioperative management. The present study describes the case of a 36 year-old woman with an undiagnosed GPCC, which was successfully resected despite the occurrence of perioperative cardiovascular events, including hypertension, hypotension, ventricular arrhythmias, acute heart failure, acute myocardial infarction, and the patient was discharged home without any recurrence. It should be considered in retroperitoneal tumour of patients with nonspecific symptoms and given adequate treatment to promote the perioperative safety.

4.
Int J Clin Exp Pathol ; 7(7): 3836-44, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-25120760

RESUMO

HMGB1 is a necessary and critical mediator of acute lung injury and can act as a chemoattractant and anti-apoptosis factor in injury or repair in diseases. In this study we sought to determine whether HMGB1 is involved in the remodeling of pulmonary artery and investigate the mechanism. A rat model of pulmonary artery remodeling was successful induced with LPS infusion and the increasing of pulmonary arteries media was obviously inhibited in rats treated with thrice inject of HMGB1 neutralizing antibody. The percent of areas of tunica media to total artery wall was (0.53 ± 0.15), (0.81 ± 0.10) and (0.59 ± 0.11) in control, LPS and antibody group respectively (p<0.05). Meanwhile, treatment with HMGB1 neutralizing antibody not only decreased the level of HMGB1 mRNA and protein significantly, but inhibited the expression of PCAN and Bcl-2 as well. On the contrary, Bax, a gen which represented the apoptosis, revealed an absolutely reversed trend to Bcl-2 in pulmonary arteries. Experiments in vitro showed that HMGB1 could stimulate the proliferation of hPASMC in MTT test and increase the number of migrated cells in a concentration-dependent manner in chemotaxis assay using modified Boyden chambers. In conclusion, data from this study support the concept that HMGB1 is involved in the remodeling of pulmonary artery by enhancing proliferation and migration of smooth muscle cell. Inhibiting HMGB1 may be a new target to deal with the remodeling of pulmonary artery.


Assuntos
Proteína HMGB1/metabolismo , Miócitos de Músculo Liso/patologia , Artéria Pulmonar/patologia , Remodelação Vascular/fisiologia , Animais , Western Blotting , Linhagem Celular , Movimento Celular/fisiologia , Proliferação de Células/fisiologia , Modelos Animais de Doenças , Humanos , Imuno-Histoquímica , Marcação In Situ das Extremidades Cortadas , Masculino , Músculo Liso Vascular/metabolismo , Músculo Liso Vascular/patologia , Miócitos de Músculo Liso/metabolismo , Ratos , Ratos Wistar , Reação em Cadeia da Polimerase em Tempo Real
5.
Zhonghua Nei Ke Za Zhi ; 52(7): 562-6, 2013 Jul.
Artigo em Chinês | MEDLINE | ID: mdl-24266996

RESUMO

OBJECTIVE: To investigate the discrepancy of anorectal function in patients of Parkinson's disease (PD) with constipation and functional constipation (FC). METHODS: Fifteen consecutive male PD patients with constipation and 45 male FC patients were recruited for the study. All subjects underwent colonoscopy or barium enema in order to exclude organic colon diseases. Every patient underwent anorectal manometry and was categorized into subgroups of either dyssynergia defecation (F3a) or inadequate defecatory propulsion (F3b). RESULTS: The ages of PD with constipation and FC patients were (70 ± 11) and (68 ± 11) years old respectively. The rectal resting pressure in PD with constipation was higher than that in FC group without statistical significance [9.0(4.0, 15.0) mm Hg vs 6.0(3.0, 9.5) mm Hg, P = 0.082, 1 mm Hg = 0.133 kPa]. The anal resting pressure in PD group was not different from FC group [(51.2 ± 17.2) mm Hg vs (59.7 ± 20.4) mm Hg, P = 0.152]. During anal squeezing, the maximal contraction pressure and area under the squeeze curve in PD with constipation group were both significantly lower than FC patients [maximal contraction pressure: (136.9 ± 43.8) mm Hg vs (183.0 ± 62.1) mm Hg, P = 0.010; area under the squeeze curve: (823.5 ± 635.7) mm Hg·s vs (1392.4 ± 939.9) mm Hg·s, P = 0.033]. During forced defecation, both of the defecation rectal pressure and defecation anal pressure in PD with constipation group were significantly lower than that of FC patients [22.0(15.0, 30.0) vs 42.0(31.0, 55.0) mm Hg, P = 0.000; and (46.3 ± 23.3) vs (77.9 ± 35.1) mm Hg, P = 0.002]. The proportions of F3a subtype were 10/15 and 46.7% (21/45) in PD with constipation and FC patients respectively. There was no significant difference in the constituent ratio (P = 0.120). Initial rectal sensory volumes were (91.3 ± 56.9) ml and (67.2 ± 38.9) ml in PD with constipation and FC patients respectively. Even both volumes were higher than the normal controls, there was no significant difference between the two groups (P = 0.074). CONCLUSIONS: Both PD with constipation and FC patients have abnormal anorectal motility and sensation comparing to the FC group, the parameters of anal contraction and defecation are significantly lower, F3b is dominant, and rectal sensory threshold is higher in PD with constipation patients. These parameters could possibly characterize the anorectal manometry for PD with constipation patients, which is helpful to understand the pathogenesis of PD and differentiate from other diseases.


Assuntos
Canal Anal/fisiopatologia , Constipação Intestinal/fisiopatologia , Doença de Parkinson/fisiopatologia , Reto/fisiopatologia , Idoso , Idoso de 80 Anos ou mais , Constipação Intestinal/etiologia , Humanos , Masculino , Manometria , Pessoa de Meia-Idade , Doença de Parkinson/complicações
6.
BMC Gastroenterol ; 12: 157, 2012 Nov 07.
Artigo em Inglês | MEDLINE | ID: mdl-23134719

RESUMO

BACKGROUND: To compare the characteristics between 22-channel water-perfusion manometry (WPM) and solid-state manometry (SSM) with 36 sensors of the pressure measurements, as well as patients' discomfort indices in nose and pharynx, the preparation and operation time of the manometry. METHODS: 12 volunteers were included in the study. Each of the volunteers underwent esophageal manometry by both 22-channel water-perfusion catheter (WPC) and solid-state catheter (SSC) with 36 sensors in random order, and separated by 30 min. The subjects gave a VAS score soon after each test. Non-parametric tests were used to analyze the differences and Bland-Altman plots were used to assess the consistency of the two systems. RESULTS: During the wet swallows, there were significant differences between the two systems in three measurements of location of lower esophageal sphincter (LES) upper margin (Z = -2.11, P = 0.035), LES relax ratio (Z = -2.20, P = 0.028) and IRP4s (Z = -2.05, P = 0.041). During the jelly pocket swallows, LES relax ratio measurements of the two systems showed significant differences (Z = -2.805, P = 0.005). Further Bland-Altman plots analysis presented good agreement between the two systems measurements of location of LES upper margin, LES relax ratio and IRP4s. The discomfort indices of subjects' nasal sensation were higher when inserting the solid-state catheter [5(3.75-5)] than water-perfusion one (2.5(2-4)) (Z = -2.471, P = 0.013), as well as the discomfort indices of pharyngeal sensation (7.5(4.75-9) vs. 4.5(3.75-6.5)), (Z = -2.354, P = 0.019). The preparation time for WPC was 40(39-41) minutes, which was much longer than that for SSC 32.5(31.75-33) minutes, (Z = -3.087, P = 0.002). And the nurses reported it's much easier to insert WPC (Z = -3.126, P = 0.002). CONCLUSIONS: In conclusion, most pressure measurements were consistent between WPM and SSM. Patients tolerated better with WPC, while for operators, the SSC presented more convenient.


Assuntos
Esôfago , Manometria/instrumentação , Perfusão/instrumentação , Adolescente , Adulto , Idoso , Deglutição , Feminino , Humanos , Masculino , Manometria/métodos , Pessoa de Meia-Idade , Nariz , Medição da Dor , Faringe , Reprodutibilidade dos Testes , Adulto Jovem
7.
Zhonghua Yi Xue Za Zhi ; 91(18): 1228-32, 2011 May 17.
Artigo em Chinês | MEDLINE | ID: mdl-21756791

RESUMO

OBJECTIVE: To compare the diagnostic values of GerdQ questionnaire, 24-h pH monitoring and 24-h impedance-pH monitoring for gastroesophageal reflux disease (GERD) and to analyze the reflux patterns of Barrett's esophagus (BE), reflux esophagitis (RE) and non-erosive disease (NERD). METHODS: From June 1, 2009 to September 30, 2010, 205 GERD patients were included according to the Montreal consensus. All were surveyed by a GerdQ questionnaire and underwent 24-h impedance-pH monitoring. The diagnostic sensitivities of GerdQ, 24-h pH-DeM and 24-h IMP-pH were compared and the reflux pattern of BE, RE and NERD analyzed. RESULTS: A total of 205 GERD patients including 10 BE, 28 RE and 167 NERD were recruited. (1) The diagnostic rate of 24-h IMP-pH was 74.1%. It was significantly higher than that of GerdQ (51.7%) and 24-h pH-DeM (29.2%). (2) The diagnostic sensitivities of GerdQ and 24-h pH-DeM for BE and RE were higher than that for NERD. But there were no significant differences of 24-h IMP-pH for three types of GERD (70.0%, 82.1% and 73.1%). (3) There were positive correlations among the scores of GerdQ, pH-DeM scores and acid scores in IMP-pH (r = 0.242, P = 0.000; r = 0.182, P = 0.009 and r = 0.632, P = 0.000). (4) Added diagnostic values of IMP-pH were 58.5% and 74.5% respectively in patients who would have been missed by GerdQ and pH-DeM. (5) The detection rate and score of acid reflux in RE patients were higher than that of NERD [53.6% vs 23.4%, P < 0.05; 45.6 (35.0 - 67.5) vs 23.1 (9.3 - 35.0), P < 0.05]. But gas score and separate acid reflux were lower than that in NERD [17 (0 - 194) vs 30 (0 - 500), P < 0.05; 57.4% vs 28.6%, P < 0.05]. CONCLUSIONS: Acid reflux plays an important role in RE. The value of GerdQ and 24-h pH-DeM and 24-h IMP-pH monitoring were similar for the diagnosis of RE. Weak acid may be more important for BE and NERD patients than separate acid reflux. And 24-h IMP-pH monitoring has a distinct advantage in diagnosing these two types.


Assuntos
Esôfago de Barrett/diagnóstico , Monitoramento do pH Esofágico , Refluxo Gastroesofágico/diagnóstico , Adulto , Idoso , Esofagoscopia , Feminino , Humanos , Concentração de Íons de Hidrogênio , Masculino , Pessoa de Meia-Idade , Inquéritos e Questionários
8.
J Dig Dis ; 12(4): 279-85, 2011 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-21791022

RESUMO

OBJECTIVE: To investigate the intrinsic fluorescence spectrum of gastric juice as a diagnostic method for gastric cancer. METHODS: We collected gastric juice by gastroscopy in 1,870 patients from May 2001 to March 2006, of whom 202 were involved in a preliminary test, 162 in experimental optimization and 1,506 in clinical verification. The best dilution and pH value were chosen in the experimental optimization phase. Clinical verification was based on optimized samples. Intrinsic fluorescence spectra were measured in all samples with a fluorescence spectrophotometer using an excitation wavelength of 288 nm. RESULTS: The first peak of fluorescence intensity (P(1) FI) of the intrinsic fluorescence spectrum was significantly higher in gastric juice from patients with gastric cancer than from those with benign lesions. There was no significant difference in the P(1) FI differences between patients with benign and malignant lesions with samples diluted by 20-fold to 80-fold and from pH 9 to pH 11. Clinical verification in 1,506 patients showed that P(1) FI ≥ 76.5 was the optimal cut-off on the receiver operating characteristic curve for diagnosing gastric cancers: sensitivity was 83.2%, specificity 80.7% and accuracy 82.0%. CONCLUSIONS: P(1) FI of the intrinsic fluorescence at 288 nm is significantly higher in patients with gastric cancers than in individuals with benign lesions. As a clinical indicator of gastric cancer, its sensitivity, specificity and accuracy were high.


Assuntos
Suco Gástrico/fisiologia , Espectrometria de Fluorescência/métodos , Neoplasias Gástricas/diagnóstico , Neoplasias Gástricas/fisiopatologia , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Análise Custo-Benefício , Reações Falso-Negativas , Reações Falso-Positivas , Feminino , Humanos , Concentração de Íons de Hidrogênio , Masculino , Pessoa de Meia-Idade , Curva ROC , Estudos Retrospectivos , Sensibilidade e Especificidade , Adulto Jovem
9.
Artigo em Inglês | MEDLINE | ID: mdl-19157918

RESUMO

A case is reported of bilateral coronoid hyperplasia. The literature is reviewed concerning this condition's etiology, pathogenesis, clinical characteristics, diagnosis, and treatment. Jacob disease and coronoid elongation are both clinical features of coronoid hyperplasia. It is usually accompanied by restricted opening. The etiology and pathogenesis of coronoid hyperplasia are unclear. The condition can be diagnosed by panoramic radiographs and with 3-dimensional reconstructions from computerized tomography image data sets. Hyperplasia of the coronoid processes can be treated using an intraoral approach for coronoidectomy and dynamic laser physiotherapy after surgery. Although hyperplasia of the coronoid processes is uncommon in clinic, it can be found through careful examination and proper radiographic study. A 39-year-old female patient was referred for coronoid hyperplasia (Jacob disease on right and elongation on left). The histologic diagnosis for the right condylar condition was osteochondroma.


Assuntos
Côndilo Mandibular/patologia , Doenças Mandibulares/patologia , Neoplasias Mandibulares/patologia , Procedimentos Cirúrgicos Bucais/métodos , Osteocondroma/patologia , Adulto , Diagnóstico Diferencial , Feminino , Humanos , Hiperplasia , Mandíbula/cirurgia , Doenças Mandibulares/cirurgia , Neoplasias Mandibulares/cirurgia , Osteocondroma/cirurgia , Amplitude de Movimento Articular , Transtornos da Articulação Temporomandibular/diagnóstico
10.
J Theor Biol ; 232(1): 7-15, 2005 Jan 07.
Artigo em Inglês | MEDLINE | ID: mdl-15498588

RESUMO

Introduction of the concept of pseudo amino acid composition (PROTEINS: Structure, Function, and Genetics 43 (2001) 246; Erratum: ibid. 44 (2001) 60) has made it possible to incorporate a considerable amount of sequence-order effects by representing a protein sample in terms of a set of discrete numbers, and hence can significantly enhance the prediction quality of membrane protein type. As a continuous effort along such a line, the Supervised Locally Linear Embedding (SLLE) technique for nonlinear dimensionality reduction is introduced (Science 22 (2000) 2323). The advantage of using SLLE is that it can reduce the operational space by extracting the essential features from the high-dimensional pseudo amino acid composition space, and that the cluster-tolerant capacity can be increased accordingly. As a consequence by combining these two approaches, high success rates have been observed during the tests of self-consistency, jackknife and independent data set, respectively, by using the simplest nearest neighbour classifier. The current approach represents a new strategy to deal with the problems of protein attribute prediction, and hence may become a useful vehicle in the area of bioinformatics and proteomics.


Assuntos
Algoritmos , Aminoácidos/análise , Proteínas de Membrana/química , Sequência de Aminoácidos , Animais , Biologia Computacional/métodos , Análise de Sequência de Proteína/métodos
11.
Med Chem ; 1(1): 39-47, 2005 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-16789884

RESUMO

It has been observed by conducting an extensive analysis of the two-dimensional cellular automata images of known SARS-CoV genome sequences that the V-shaped cross-lines only exist in some special locations, and hence can be used as a fingerprint to identify the SARS sequences. Such a discovery can be used to rapidly and reliably diagnose SARS coronavirus for both basic research in laboratories and practical application in clinics.


Assuntos
Algoritmos , Processamento Eletrônico de Dados/métodos , Processamento Eletrônico de Dados/normas , Mapeamento de Nucleotídeos , RNA Viral , Vírus da SARS/genética , Biblioteca Genômica , Armazenamento e Recuperação da Informação , Modelos Teóricos , RNA Viral/química , RNA Viral/genética
12.
Zhonghua Yi Xue Za Zhi ; 85(45): 3210-5, 2005 Nov 30.
Artigo em Chinês | MEDLINE | ID: mdl-16405842

RESUMO

OBJECTIVE: To compare the differences in the psychological scale scoring among different subgroups reflux esophagitis (RE) and non-erosive reflux disease (NERD) and to explore the influence of mental factors on the pathogenesis of RE and NERD. METHODS: Two hundred and six patients with typical heartburn and acid regurgitation underwent endoscopy and esophageal pH monitoring and then were divided into 4 groups: RE+ group (n = 35, 24.3%) with RE and positive pH monitoring results, RH- group (n = 15, 30.0%) with RE and negative pH monitoring results, NERD+ group (n = 77, 40%), with NERD and positive pH monitoring results, and NERD- group (n = 79, 50.6%) with NERD and negative pH monitoring results that was re-divided into 2 subgroups according to the symptom index (SI): NERD-SI+ group (n = 18, 22.8%) with positive symptom index and NERD-SI- group (n = 61, 77.2%) with negative SI. The demographic data and body mass index (BMI) were investigated. The psychological questionnaires: Symptom Checklist 90 (SCL-90), and Hospital Anxiety and Depression Scale (HAD) were used. RESULTS: (1) Male patients were dominant in the RE group and RE+ subgroup, while female patients were dominant in the NERD group and NERD+ subgroup. The values of BMI of the RE group and RE+ subgroup were significantly higher than those of the NERD group and NERD+ subgroup. (2) The abnormal pH monitoring rate of the RE group was 70.0%, significantly higher than that of the NERD group (49.4%). The average DeMeester's score of the RE group was 39.3 (96.5), significantly higher than that of the NERD group 13.8 (33.6). The average DeMeester's score of the RE+ group was 68.1 (95.2), significantly higher than that of the NERD+ group 40.1 (64.4). (3) 44.6% (29/65) of the patients presented depression and 36.9% (24/65) had anxiety, most of them were in mild or moderate degree. The scores of most items of each mental scale were significantly higher in the NERD- patients than in the NERD+ patients, especially in the NERD-SI- subgroup. CONCLUSION: The symptoms of RE+ and NERD+ patients are associated with esophageal acid exposure and the acid reflux in the RE patients is much severer than that in the NERD patients. Anxiety and depression are related to the symptoms of patients without objective evidence of esophageal mucosal injury and acid reflux (NERD-), especially in the symptom index negative subgroup. Visceral hypersensitivity and stress play an important role in the pathogenesis of gastroesophageal reflux.


Assuntos
Depressão/complicações , Refluxo Gastroesofágico/fisiopatologia , Adolescente , Adulto , Idoso , Ansiedade/complicações , Ansiedade/psicologia , Depressão/psicologia , Esofagite Péptica/etiologia , Esofagite Péptica/fisiopatologia , Esofagite Péptica/psicologia , Feminino , Refluxo Gastroesofágico/etiologia , Refluxo Gastroesofágico/psicologia , Humanos , Concentração de Íons de Hidrogênio , Masculino , Pessoa de Meia-Idade , Escalas de Graduação Psiquiátrica , Inquéritos e Questionários
13.
Protein Eng Des Sel ; 17(6): 509-16, 2004 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-15314209

RESUMO

Membrane proteins are generally classified into the following five types: (1) type I membrane proteins, (2) type II membrane proteins, (3) multipass transmembrane proteins, (4) lipid chain-anchored membrane proteins and (5) GPI-anchored membrane proteins. Prediction of membrane protein types has become one of the growing hot topics in bioinformatics. Currently, we are facing two critical challenges in this area: first, how to take into account the extremely complicated sequence-order effects, and second, how to deal with the highly uneven sizes of the subsets in a training dataset. In this paper, stimulated by the concept of using the pseudo-amino acid composition to incorporate the sequence-order effects, the spectral analysis technique is introduced to represent the statistical sample of a protein. Based on such a framework, the weighted support vector machine (SVM) algorithm is applied. The new approach has remarkable power in dealing with the bias caused by the situation when one subset in the training dataset contains many more samples than the other. The new method is particularly useful when our focus is aimed at proteins belonging to small subsets. The results obtained by the self-consistency test, jackknife test and independent dataset test are encouraging, indicating that the current approach may serve as a powerful complementary tool to other existing methods for predicting the types of membrane proteins.


Assuntos
Algoritmos , Aminoácidos/genética , Biologia Computacional/métodos , Proteínas de Membrana/classificação , Aminoácidos/química , Inteligência Artificial , Metodologias Computacionais , Bases de Dados de Proteínas , Proteínas de Membrana/química , Proteínas de Membrana/genética , Proteômica/métodos , Reprodutibilidade dos Testes
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