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Search Results: 1 - 10 of 1878 matches for " Bertrand Perroud "
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Consequences of Normalizing Transcriptomic and Genomic Libraries of Plant Genomes Using a Duplex-Specific Nuclease and Tetramethylammonium Chloride
Marta Matvienko, Alexander Kozik, Lutz Froenicke, Dean Lavelle, Belinda Martineau, Bertrand Perroud, Richard Michelmore
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0055913
Abstract: Several applications of high throughput genome and transcriptome sequencing would benefit from a reduction of the high-copy-number sequences in the libraries being sequenced and analyzed, particularly when applied to species with large genomes. We adapted and analyzed the consequences of a method that utilizes a thermostable duplex-specific nuclease for reducing the high-copy components in transcriptomic and genomic libraries prior to sequencing. This reduces the time, cost, and computational effort of obtaining informative transcriptomic and genomic sequence data for both fully sequenced and non-sequenced genomes. It also reduces contamination from organellar DNA in preparations of nuclear DNA. Hybridization in the presence of 3 M tetramethylammonium chloride (TMAC), which equalizes the rates of hybridization of GC and AT nucleotide pairs, reduced the bias against sequences with high GC content. Consequences of this method on the reduction of high-copy and enrichment of low-copy sequences are reported for Arabidopsis and lettuce.
In vivo multiplex quantitative analysis of 3 forms of alpha melanocyte stimulating hormone in pituitary of prolyl endopeptidase deficient mice
Bertrand Perroud, Rudy J Alvarado, Glenda M Espinal, Alex R Morado, Brett S Phinney, Craig H Warden
Molecular Brain , 2009, DOI: 10.1186/1756-6606-2-14
Abstract: Using Multiple Reaction Monitoring (MRM), we analyzed peptide transitions to quantify three different forms of α-MSH. Transitions were first confirmed using standard peptides. Samples were then analyzed by mass spectrometry using a triple quadrupole mass spectrometer, after elution from a reverse phase C18 column by a gradient of acetonitrile.We first demonstrate in vitro that PREP digests biological active alpha melanocyte stimulating hormone (α-MSH1–13), by cleaving the terminal amidated valine and releasing a truncated alpha melanocyte stimulating hormone (α-MSH1–12) product – the 12 residues α-MSH form. We then use the technique in vivo to analyze the MRM transitions of the three different forms of α-MSH: the deacetylated α-MSH1–13, the acetylated α-MSH1–13 and the truncated form α-MSH1–12. For this experiment, we used a mouse model (PREP-GT) in which the serine protease, prolyl endopeptidase, is deficient due to a genetrap insertion. Here we report that the ratio between acetylated α-MSH1–13 and α-MSH1–12 is significantly increased (P-value = 0.015, N = 6) in the pituitaries of PREP-GT mice when compared to wild type littermates. In addition no significant changes were revealed in the relative level of α-MSH1–13 versus the deacetylated α-MSH1–13. These results combined with the demonstration that PREP digests α-MSH1–13 in vitro, strongly suggest that α-MSH1–13 is an in vivo substrate of PREP.The multiplex targeted quantitative peptidomics technique we present in this study will be decidedly useful to monitor several neuropeptide enzymatic reactions in vivo under varying conditions.In vitro reactions have been broadly applied to study the characteristics of enzymatic reactions. However results from in vitro experiments may not reflect true biologic reactions. The enzymatic reactions revealed in vitro may not even have the possibility of occurring in vivo because of substrate availability due to of space, timing or other restrictions. Therefore it is critical to
Pathway analysis of kidney cancer using proteomics and metabolic profiling
Bertrand Perroud, Jinoo Lee, Nelly Valkova, Amy Dhirapong, Pei-Yin Lin, Oliver Fiehn, Dietmar Kültz, Robert H Weiss
Molecular Cancer , 2006, DOI: 10.1186/1476-4598-5-64
Abstract: Using 2-dimensional electrophoresis and mass spectrometric analysis, we identified 31 proteins which were differentially expressed with a high degree of significance in ccRCC as compared to adjacent non-malignant tissue, and we confirmed some of these by immunoblotting, immunohistochemistry, and comparison to published transcriptomic data. When evaluated by several pathway and biological process analysis programs, these proteins are demonstrated to be involved with a high degree of confidence (p values < 2.0 E-05) in glycolysis, propanoate metabolism, pyruvate metabolism, urea cycle and arginine/proline metabolism, as well as in the non-metabolic p53 and FAS pathways. In a pilot study using random urine samples from both ccRCC and control patients, we performed metabolic profiling and found that only sorbitol, a component of an alternative glycolysis pathway, is significantly elevated at 5.4-fold in RCC patients as compared to controls.Extensive pathway and network analysis allowed for the discovery of highly significant pathways from a set of clear cell RCC samples. Knowledge of activation of these processes will lead to novel assays identifying their proteomic and/or metabolomic signatures in biofluids of patient at high risk for this disease; we provide pilot data for such a urinary bioassay. Furthermore, we demonstrate how the knowledge of networks, processes, and pathways altered in kidney cancer may be used to influence the choice of optimal therapy.While accounting for only 3% of cancer incidence and mortality in the US, kidney cancer (renal cell carcinoma; RCC) is the sixth leading cause of cancer death in the US. Early diagnosis of kidney-localized RCC is associated with a quite favorable prognosis (89%), but patients who have this disease often present with few signs, symptoms, or laboratory abnormalities and are frequently (~30%) diagnosed at the metastatic stage when the prospects for cure are dismal (9%)[1]. The incidence of RCC in the US, as well as it
Pharmacometabolomic Signature of Ataxia SCA1 Mouse Model and Lithium Effects
Bertrand Perroud, Paymaan Jafar-Nejad, William R. Wikoff, Jennifer R. Gatchel, Lu Wang, Dinesh K. Barupal, Juan Crespo-Barreto, Oliver Fiehn, Huda Y. Zoghbi, Rima Kaddurah-Daouk
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0070610
Abstract: We have shown that lithium treatment improves motor coordination in a spinocerebellar ataxia type 1 (SCA1) disease mouse model (Sca1154Q/+). To learn more about disease pathogenesis and molecular contributions to the neuroprotective effects of lithium, we investigated metabolomic profiles of cerebellar tissue and plasma from SCA1-model treated and untreated mice. Metabolomic analyses of wild-type and Sca1154Q/+ mice, with and without lithium treatment, were performed using gas chromatography time-of-flight mass spectrometry and BinBase mass spectral annotations. We detected 416 metabolites, of which 130 were identified. We observed specific metabolic perturbations in Sca1154Q/+ mice and major effects of lithium on metabolism, centrally and peripherally. Compared to wild-type, Sca1154Q/+ cerebella metabolic profile revealed changes in glucose, lipids, and metabolites of the tricarboxylic acid cycle and purines. Fewer metabolic differences were noted in Sca1154Q/+ mouse plasma versus wild-type. In both genotypes, the major lithium responses in cerebellum involved energy metabolism, purines, unsaturated free fatty acids, and aromatic and sulphur-containing amino acids. The largest metabolic difference with lithium was a 10-fold increase in ascorbate levels in wild-type cerebella (p<0.002), with lower threonate levels, a major ascorbate catabolite. In contrast, Sca1154Q/+ mice that received lithium showed no elevated cerebellar ascorbate levels. Our data emphasize that lithium regulates a variety of metabolic pathways, including purine, oxidative stress and energy production pathways. The purine metabolite level, reduced in the Sca1154Q/+ mice and restored upon lithium treatment, might relate to lithium neuroprotective properties.
Rela??es entre a Autistic Behavior Checklist (ABC) e o perfil funcional da comunica??o no espectro autístico
Fernandes, Fernanda Dreux Miranda;Miilher, Liliane Perroud;
Pró-Fono Revista de Atualiza??o Científica , 2008, DOI: 10.1590/S0104-56872008000200007
Abstract: backgroud: language and communication disorders are proposed as one of the three fundamental criteria for the description or diagnosis of pervasive developmental disorders (pdd), along with social disabilities and a narrow focus of interest. this way, the determination of simple procedures that can be used by health and education professionals to identify the persons that need specialized services is essential. the autistic behavior checklist (abc) is being used in several studies because it allows simple application and may be based on filmed behavior samples, interviews with parents or therapists. its' results, on the other side, had been tested for a few decades and been shown reliable. aim: the general aim of this study is to verify the possibility that the assessment of the relation between communicative profile and the abc score contributes to the diagnostic process of persons with disorders of the autistic spectrum. method: subjects were 117 children and adolescents with ages between 2 and 16 years attending language therapy. results: were statistically analyzed and indicated that there are negative correlations between the abc scores and communicative interaction and complexity. the small amount of correlations between language sub-scale and the other data suggest that there is a dissociation of the description provided by the abc and the criteria proposed by the dsm-iv and the icd-10 to the diagnosis of autism. conclusion: the search for objective criteria to determine subgroups of the autistic spectrum remains a challenge.
Habilidades pragmáticas, vocabulares e gramaticais em crian?as com transtornos do espectro autístico
Miilher, Liliane Perroud;Fernandes, Fernanda Dreux Miranda;
Pró-Fono Revista de Atualiza??o Científica , 2009, DOI: 10.1590/S0104-56872009000400008
Abstract: background: development of grammatical, functional and lexical aspects in the language of children with autism spectrum disorders. aim: to analyze the development of grammatical, functional and lexical aspects in three different moments: initial assessment, after six and twelve months of language therapy. method: participants of this study were ten boys with ages between 2:7 and 11:2 years, with psychiatric diagnosis within the autistic spectrum. video recorded samples of a 30 minutes patient-therapist interaction were recorded in three different moments (therapy onset, after six and twelve months of therapy) for each subject. the first 15 minutes of each sample was transcribed for the analysis of the functional communicative profile. grammatical and lexical aspects were analyzed through the transcription of 100 speech segments of each sample. all data were longitudinally compared within and between areas. results: there were significant associations between the studied variables but no statistically significant differences along the studied period of language therapy. conclusion: there are associations between grammatical and pragmatic performances.
Análise das fun??es comunicativas expressas por terapeutas e pacientes do espectro autístico
Miilher, Liliane Perroud;Fernandes, Fernanda Dreux Miranda;
Pró-Fono Revista de Atualiza??o Científica , 2006, DOI: 10.1590/S0104-56872006000300003
Abstract: abstract background: communicative functions used by language therapists and patients. aim: to analyze the communicative functions used by language therapists and patients of the autistic spectrum. method: the communicative functions expressed by six therapists in interaction with six patients each were analyzed, constituting 36 profiles of communicative functions expressed by the dyad therapist-patient. all therapists were part of a training program in childhood psychiatric disorders and the patients were diagnosed within the autistic spectrum. data were gathered using the transcriptions of a videotaped therapy session and these were analyzed according to the criteria suggested by fernandes (2000). the communicative functions were divided in two different ways: interpersonal and non-interpersonal, and instrumental, regulatory, interactive, personal, heuristic and imaginative. results: the comparison between the functions used by the language therapists and the patients indicated a statistically significant difference in use of the following functions: request of social routine, request of information, request of action, comment, recognition of other, exclamation, non-focused, exploratory, exhibition, play and reactive. there was also a statistically significant difference between the use of interpersonal, non-interpersonal, regulatory, interactive, personal and heuristic communicative functions. conclusion: the functional communicative profile of language therapists is different from the one presented by their patients when comparing each communicative function and when the communicative functions are grouped (interpersonal and non-interpersonal, and instrumental, regulatory, interactive, personal, heuristic and imaginative). therapists use communicative functions to fill in the communicative space and to make requests. this finding agrees with the findings of previous studies.
Minimum Penalized Hellinger Distance for Model Selection in Small Samples  [PDF]
Papa Ngom, Bertrand Ntep
Open Journal of Statistics (OJS) , 2012, DOI: 10.4236/ojs.2012.24045
Abstract: In statistical modeling area, the Akaike information criterion AIC, is a widely known and extensively used tool for model choice. The φ-divergence test statistic is a recently developed tool for statistical model selection. The popularity of the divergence criterion is however tempered by their known lack of robustness in small sample. In this paper the penalized minimum Hellinger distance type statistics are considered and some properties are established. The limit laws of the estimates and test statistics are given under both the null and the alternative hypotheses, and approximations of the power functions are deduced. A model selection criterion relative to these divergence measures are developed for parametric inference. Our interest is in the problem to testing for choosing between two models using some informational type statistics, when independent sample are drawn from a discrete population. Here, we discuss the asymptotic properties and the performance of new procedure tests and investigate their small sample behavior.
Relativistic Gauge Invariant Wave Equation of the Electron-Neutrino  [PDF]
Claude Daviau, Jacques Bertrand
Journal of Modern Physics (JMP) , 2014, DOI: 10.4236/jmp.2014.511102

With the right and the left waves of an electron, plus the left wave of its neutrino, we write the tensorial densities coming from all associations of these three spinors. We recover the wave equation of the electro-weak theory. A new non linear mass term comes out. The wave equation is form invariant, then relativistic invariant, and it is gauge invariant under the U(1)×SU(2), Lie group of electro-weak interactions. The invariant form of the wave equation has the Lagrangian density as real scalar part. One of the real equations equivalent to the invariant form is the law of conservation of the total current.

A Wave Equation including Leptons and Quarks for the Standard Model of Quantum Physics in Clifford Algebra  [PDF]
Claude Daviau, Jacques Bertrand
Journal of Modern Physics (JMP) , 2014, DOI: 10.4236/jmp.2014.518210

A wave equation with mass term is studied for all fermionic particles and antiparticles of the first generation: electron and its neutrino, positron and antineutrino, quarks u and d with three states of color and antiquarks \"\" and \"\". This wave equation is form invariant under the \"\" group generalizing the relativistic invariance. It is gauge invariant under the U(1)×SU(2)×SU(3) group of the standard model of quantum physics. The wave is a function of space and time with value in the Clifford algebra Cl1,5. Then many features of the standard model, charge conjugation, color, left waves, and Lagrangian formalism, are obtained in the frame of the first quantization.

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