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101.
Allet N Barrillat N Baussant T Boiteau C Botti P Bougueleret L Budin N Canet D Carraud S Chiappe D Christmann N Colinge J Cusin I Dafflon N Depresle B Fasso I Frauchiger P Gaertner H Gleizes A Gonzalez-Couto E Jeandenans C Karmime A Kowall T Lagache S Mahé E Masselot A Mattou H Moniatte M Niknejad A Paolini M Perret F Pinaud N Ranno F Raimondi S Reffas S Regamey PO Rey PA Rodriguez-Tomé P Rose K Rossellat G Saudrais C Schmidt C Villain M Zwahlen C 《Proteomics》2004,4(8):2333-2351
We present an integrated proteomics platform designed for performing differential analyses. Since reproducible results are essential for comparative studies, we explain how we improved reproducibility at every step of our laboratory processes, e.g. by taking advantage of the powerful laboratory information management system we developed. The differential capacity of our platform is validated by detecting known markers in a real sample and by a spiking experiment. We introduce an innovative two-dimensional (2-D) plot for displaying identification results combined with chromatographic data. This 2-D plot is very convenient for detecting differential proteins. We also adapt standard multivariate statistical techniques to show that peptide identification scores can be used for reliable and sensitive differential studies. The interest of the protein separation approach we generally apply is justified by numerous statistics, complemented by a comparison with a simple shotgun analysis performed on a small volume sample. By introducing an automatic integration step after mass spectrometry data identification, we are able to search numerous databases systematically, including the human genome and expressed sequence tags. Finally, we explain how rigorous data processing can be combined with the work of human experts to set high quality standards, and hence obtain reliable (false positive < 0.35%) and nonredundant protein identifications. 相似文献
102.
Nicolas Guigue Samuel Lardeux Alexandre Alanio Samia Hamane Marc Tabouret Stéphane Bretagne 《PloS one》2015,10(4)
Background
The Platelia Aspergillus Ag assay (Bio-Rad) is designed for detecting Aspergillus galactomannan (GM) and is widely used for diagnosing invasive aspergillosis but is hampered by variable occurrences of unreproducible positive results. Frequency and origin of these unreproducible results have not been formally studied.Methods
Different technicians simultaneously performed four tests on 550 consecutive sera from adult patients (Test#1-Test#2 for extraction#1 and Test#3-Test#4 for extraction#2). The samples were classified as confirmed negative [all tests with GM optical density index (GM-ODI) <0.5], confirmed positive (all tests with GM-ODI ≥0.5), extraction unreproducible positive (Test#1 and Test#2 ODIs ≥0.5, and Test#3 and Test#4 GM-ODIs <0.5, or conversely), and ELISA unreproducible positive (only one test with GM-ODI ≥0.5). The samples with positive and negative GM-ODIs within the assay coefficient of variation values were classified as non-conclusive. Four similar additional tests were performed after ≤72h storage at 4°C and a new GM test after 8 months at -20°C.Results
Five-hundred-twenty sera (94.5%) were confirmed negative, 15 (2.7%) confirmed positive, 4 (0.7%) extraction unreproducible positive, 6 (1.1%) ELISA unreproducible positive, and 5 (0.9%) non-conclusive. Upon retesting, the unreproducible positive results turned negative except for one which turned non-conclusive. The confirmed positive and non-conclusive had similar GM-ODIs (p>0.4) upon retesting after storage ≤72h at 4°C (n = 20) or eight months at -20°C (n = 17).Conclusions
Operational unreproducible positives represent 33% of the GM-positive results and a second sample evaluation appears mandatory to avoid useless investigations or treatments. When operational artifacts are excluded, GM remains stable at standard storage conditions. 相似文献103.
Many swarm optimization algorithms have been introduced since the early 60’s, Evolutionary Programming to the most recent, Grey Wolf Optimization. All of these algorithms have demonstrated their potential to solve many optimization problems. This paper provides an in-depth survey of well-known optimization algorithms. Selected algorithms are briefly explained and compared with each other comprehensively through experiments conducted using thirty well-known benchmark functions. Their advantages and disadvantages are also discussed. A number of statistical tests are then carried out to determine the significant performances. The results indicate the overall advantage of Differential Evolution (DE) and is closely followed by Particle Swarm Optimization (PSO), compared with other considered approaches. 相似文献
104.
Heejung Shim Daniel I. Chasman Joshua D. Smith Samia Mora Paul M. Ridker Deborah A. Nickerson Ronald M. Krauss Matthew Stephens 《PloS one》2015,10(4)
We conducted a genome-wide association analysis of 7 subfractions of low density lipoproteins (LDLs) and 3 subfractions of intermediate density lipoproteins (IDLs) measured by gradient gel electrophoresis, and their response to statin treatment, in 1868 individuals of European ancestry from the Pharmacogenomics and Risk of Cardiovascular Disease study. Our analyses identified four previously-implicated loci (SORT1, APOE, LPA, and CETP) as containing variants that are very strongly associated with lipoprotein subfractions (log10Bayes Factor > 15). Subsequent conditional analyses suggest that three of these (APOE, LPA and CETP) likely harbor multiple independently associated SNPs. Further, while different variants typically showed different characteristic patterns of association with combinations of subfractions, the two SNPs in CETP show strikingly similar patterns - both in our original data and in a replication cohort - consistent with a common underlying molecular mechanism. Notably, the CETP variants are very strongly associated with LDL subfractions, despite showing no association with total LDLs in our study, illustrating the potential value of the more detailed phenotypic measurements. In contrast with these strong subfraction associations, genetic association analysis of subfraction response to statins showed much weaker signals (none exceeding log10Bayes Factor of 6). However, two SNPs (in APOE and LPA) previously-reported to be associated with LDL statin response do show some modest evidence for association in our data, and the subfraction response proles at the LPA SNP are consistent with the LPA association, with response likely being due primarily to resistance of Lp(a) particles to statin therapy. An additional important feature of our analysis is that, unlike most previous analyses of multiple related phenotypes, we analyzed the subfractions jointly, rather than one at a time. Comparisons of our multivariate analyses with standard univariate analyses demonstrate that multivariate analyses can substantially increase power to detect associations. Software implementing our multivariate analysis methods is available at http://stephenslab.uchicago.edu/software.html. 相似文献
105.
Haseeb Ahmad Khan Abdullah Saleh Alhomida Halima Al Madani Samia Hasan Sobki 《Metabolomics : Official journal of the Metabolomic Society》2013,9(4):828-838
Earlier studies have suggested an important role of carnitine pathway in cardiovascular pathology. However, the redistribution of carnitine and acylcarnitine pools, as a result of altered carnitine metabolism, is not clearly known in patients with acute myocardial infarction (AMI). We compared the carnitine and acylcarnitine profiles of 65 AMI patients, including 26 ST-elevated myocardial infarction (STEMI) and 39 non-ST-elevated myocardial infarction (NSTEMI), 28 patients with chest pain and 154 normal controls. The levels of carnitine and acylcarnitines in the blood spots were determined using LC-MS/MS. Total and free carnitine levels were significantly higher in all the patient groups in the following order: STEMI > NSTEMI > chest pain. The levels of short- and medium-chain acylcarnitines were significantly higher in patient groups. Among the long-chain acylcarnitines, C14:2 and C16:1 levels were significantly increased in STEMI and NSTEMI. The ratio of free carnitine to short-chain or medium-chain acylcarnitines was significantly decreased in STEMI, NSTEMI and chest pain patients however a significant increase was observed in the ratio of carnitine to long-chain acylcarnitines in all the patient groups as compared to normal controls. In conclusion, alterations in carnitine and acylcarnitine levels in the blood of AMI patients indicate the possibility of impaired carnitine homeostasis in ischemic myocardium. The clinical implications of these findings for the risk screening or diagnosis and prognosis of AMI require additional follow-up studies on large number of patients. We also suggest that a dual-marker strategy using carnitine (longer plasma half-life) in combination with troponin (shorter plasma half-life) could be a more promising biomarker strategy in risk stratification of patients. 相似文献
106.
Simone R.S. Conde Rosimar N.M. Feitosa Felipe Bonfim Freitas Renata B. Hermes Samia Demachki Marialva T.F. Araújo Manoel C.P. Soares Ricardo Ishak Antonio C.R. Vallinoto 《Cytokine》2013,61(3):940-944
ObjectiveThe present paper investigated possible correlations between the clinical presentation of hepatitis B and the TNF-α ?308G/A, IFN-γ +874A/T, TGF-beta1 ?509C/T, and IL-10 ?1081A/G polymorphisms and associated serum levels of these cytokines.MethodsFifty-three hepatitis patients were selected and divided into two groups: A – inactive (n = 30) and B – chronic hepatitis/cirrhosis (n = 23). The control group consisted of 100 subjects who were positive for anti-HBc and anti-HBs. The serum concentrations of the cytokines were determined by immunoenzymatic assays. The polymorphisms of the cytokines genes were assessed by PCR and PCR-SSP.ResultsThe mean serum levels of IFN-γ of the control group were significantly higher than those of groups A and B, whereas the mean levels TGF-beta1 were significantly higher in groups A and B in comparison with the control. In the case of IL-10, the mean serum level recorded in the control group was significantly higher than that of group B. The TNF-α ?308AG genotype was considerably more frequent in group B (43.3%) than the control (14.4%).ConclusionHigher serum levels of IFN-γ and TGF-beta1 were associated with chronic hepatitis B, and lower serum levels of IL-10 were found in patients with the active disease. Furthermore the presence of allele A of the TNF-α ?308 polymorphism suggest a risk of the progressive disease. 相似文献
107.
Background/Objective
Bladder cancer is the commonest type of malignant tumors as a result of schistosomaisis which is a major healthy problem in many subtropical developing countries. The aim of this study is to comparatively elucidate the underlying biochemical tumor markers in schistosomal bladder cancer versus non-schistosomal bladder cancer when compared to normal healthy ones. 相似文献108.
Kilpeläinen TO Qi L Brage S Sharp SJ Sonestedt E Demerath E Ahmad T Mora S Kaakinen M Sandholt CH Holzapfel C Autenrieth CS Hyppönen E Cauchi S He M Kutalik Z Kumari M Stančáková A Meidtner K Balkau B Tan JT Mangino M Timpson NJ Song Y Zillikens MC Jablonski KA Garcia ME Johansson S Bragg-Gresham JL Wu Y van Vliet-Ostaptchouk JV Onland-Moret NC Zimmermann E Rivera NV Tanaka T Stringham HM Silbernagel G Kanoni S Feitosa MF Snitker S Ruiz JR Metter J Larrad MT Atalay M Hakanen M Amin N 《PLoS medicine》2011,8(11):e1001116
Background
The FTO gene harbors the strongest known susceptibility locus for obesity. While many individual studies have suggested that physical activity (PA) may attenuate the effect of FTO on obesity risk, other studies have not been able to confirm this interaction. To confirm or refute unambiguously whether PA attenuates the association of FTO with obesity risk, we meta-analyzed data from 45 studies of adults (n = 218,166) and nine studies of children and adolescents (n = 19,268).Methods and Findings
All studies identified to have data on the FTO rs9939609 variant (or any proxy [r 2>0.8]) and PA were invited to participate, regardless of ethnicity or age of the participants. PA was standardized by categorizing it into a dichotomous variable (physically inactive versus active) in each study. Overall, 25% of adults and 13% of children were categorized as inactive. Interaction analyses were performed within each study by including the FTO×PA interaction term in an additive model, adjusting for age and sex. Subsequently, random effects meta-analysis was used to pool the interaction terms. In adults, the minor (A−) allele of rs9939609 increased the odds of obesity by 1.23-fold/allele (95% CI 1.20–1.26), but PA attenuated this effect (p interaction = 0.001). More specifically, the minor allele of rs9939609 increased the odds of obesity less in the physically active group (odds ratio = 1.22/allele, 95% CI 1.19–1.25) than in the inactive group (odds ratio = 1.30/allele, 95% CI 1.24–1.36). No such interaction was found in children and adolescents.Conclusions
The association of the FTO risk allele with the odds of obesity is attenuated by 27% in physically active adults, highlighting the importance of PA in particular in those genetically predisposed to obesity. Please see later in the article for the Editors'' Summary 相似文献109.
110.
The primexine matrix is finely granulo-fibrillar up to callose digestion; it becomes distinctly fibrillar at the free microspore stage. The columellae and the tectum are initiated at the middle tetrad stage, the foot layer and the endexine are initiated when the callose wall digestion begins. The columellae are initiated by the deposition of spiral elements around a clear central zone. This hollow aspect of columella disappears when thickening. The foot layer and the endexine are built by the expansion of plasmalemma derived components. The foot layer appears first at the poles, then at the interapertural levels and at last at the apertures while the endexine appears first at the mesoapertures, then it spreads laterally towards the interapertural levels and, at last, at the poles. The gemmae are formed at the free microspore stage over all the tectum. The thickening of the exine takes place essentially during the free microspore stage and continues during the vacuolate microspore one. Apertures are entirely formed before the complete digestion of the callose wall. The ectoapertures are determined by the lacking of the columellae; the sites of the pericolpal cavities and the mesoapertures result from the plasmalemma retraction even before the setting up of the foot layer and the endexine by which they will be delimited respectively afterwards. The endoapertures are determined by the lacking of compact endexine at their level, and merge into a continuous equatorial belt. 相似文献